From 6ab186ad85a78b8925c84a44e322b759901cd2be Mon Sep 17 00:00:00 2001 From: Jianfeng Li Date: Mon, 20 Apr 2020 12:00:07 +0800 Subject: [PATCH] rename annovarR to anor --- .vscode/tasks.json | 24 + ChangeLog | 2 +- DESCRIPTION | 10 +- Dockerfile | 6 +- Makefile | 2 +- NEWS.md | 4 +- R/annotation.R | 20 +- R/annotation.utils.R | 2 +- R/{annovarR.R => anor.R} | 20 +- R/auto.R | 40 +- R/build.R | 28 +- R/download.R | 8 +- R/external_function.R | 2 +- R/external_tools.R | 4 +- R/get.R | 26 +- R/utils.R | 2 +- README.md | 62 +- _pkgdown.yml | 12 +- annovarR.Rproj => anor.Rproj | 0 docs/404.html | 133 + docs/LICENSE-text.html | 135 + docs/apple-touch-icon-120x120.png | Bin 0 -> 15975 bytes docs/apple-touch-icon-152x152.png | Bin 0 -> 22281 bytes docs/apple-touch-icon-180x180.png | Bin 0 -> 27495 bytes docs/apple-touch-icon-60x60.png | Bin 0 -> 5353 bytes docs/apple-touch-icon-76x76.png | Bin 0 -> 8093 bytes docs/apple-touch-icon.png | Bin 0 -> 27495 bytes docs/articles/database_of_anor.html 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+ "tasks": [ + { + "label": "build", + "type": "shell", + "command": "make build" + }, + { + "label": "test", + "type": "shell", + "command": "make test", + "problemMatcher": [] + }, + { + "label": "pkgdown_build", + "type": "shell", + "command": "Rscript -e 'pkgdown::build_site()'", + "problemMatcher": [] + }, + ] +} \ No newline at end of file diff --git a/ChangeLog b/ChangeLog index ad6b6ee..245f8b8 100644 --- a/ChangeLog +++ b/ChangeLog @@ -74,7 +74,7 @@ 2018-02-26 Li Jianfeng - * initial annovarR shiny App (inst/extdata/tools/shiny) + * initial anor shiny App (inst/extdata/tools/shiny) 2018-01-19 Li Jianfeng diff --git a/DESCRIPTION b/DESCRIPTION index b8c871a..98e0f22 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,14 +1,14 @@ -Package: annovarR +Package: anor Type: Package Title: Integrated Framework to Annotate Genetic Variants Version: 1.3 Authors@R: person("Jianfeng", "Li", email = "lee_jianfeng@sjtu.edu.cn", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2349-208X")) Description: - The 'annovarR' package provides R functions as well as database resources which offer an integrated framework to annotate genetic variants from genome and transcriptome data. The wrapper functions of 'annovarR' unified the interface of many published annotation tools, such as 'VEP' (), 'ANNOVAR' (), 'vcfanno' () and 'AnnotationDbi' (). It also simplified the use of some of the external annotation tools in R. Besides, massive published genetic variants annotation databases were integrated into 'annovarR'. For example, 'annovarR' provides a newly RNA-seq allele frequency database, BRVar, which built from total 1,285 cases public B-progenitor acute lymphoblastic leukemia (B-ALL) transcriptome data. + The 'anor' package provides R functions as well as database resources which offer an integrated framework to annotate genetic variants from genome and transcriptome data. The wrapper functions of 'anor' unified the interface of many published annotation tools, such as 'VEP' (), 'ANNOVAR' (), 'vcfanno' () and 'AnnotationDbi' (). It also simplified the use of some of the external annotation tools in R. Besides, massive published genetic variants annotation databases were integrated into 'anor'. For example, 'anor' provides a newly RNA-seq allele frequency database, BRVar, which built from total 1,285 cases public B-progenitor acute lymphoblastic leukemia (B-ALL) transcriptome data. Depends: R (>= 3.3.0) -URL: https://github.com/JhuangLab/annovarR -BugReports: https://github.com/JhuangLab/annovarR/issues +URL: https://github.com/JhuangLab/anor +BugReports: https://github.com/JhuangLab/anor/issues License: MIT + file LICENSE Encoding: UTF-8 LazyData: true @@ -29,7 +29,7 @@ Imports: devtools, AnnotationDbi, liteq -RoxygenNote: 6.1.1 +RoxygenNote: 7.1.0 Suggests: testthat, knitr, rmarkdown, diff --git a/Dockerfile b/Dockerfile index b2a7981..3e7d304 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,10 +3,10 @@ FROM bioinstaller/ngsjs:latest ## This handle reaches Jianfeng MAINTAINER "Jianfeng Li" lee_jianfeng@openbiox.org -ADD . /tmp/annovarR +ADD . /tmp/anor Run runuser -s /bin/bash -l opencpu -c "Rscript -e 'pacman::p_load(maftools, clusterProfiler, CEMiTool, org.Hs.eg.db, DT)'" \ - && runuser -s /bin/bash -l opencpu -c "Rscript -e 'devtools::install(\"/tmp/annovarR\", dependences = T)'" \ - && rm -rf /tmp/annovarR \ + && runuser -s /bin/bash -l opencpu -c "Rscript -e 'devtools::install(\"/tmp/anor\", dependences = T)'" \ + && rm -rf /tmp/anor \ && rm -rf /var/lib/apt/lists/* \ && rm -rf /tmp/downloaded_packages/ /tmp/*.rds diff --git a/Makefile b/Makefile index 4b6006b..e58c0c1 100644 --- a/Makefile +++ b/Makefile @@ -2,7 +2,7 @@ PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION) PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION) PKGSRC := $(shell basename `pwd`) -all: doc build check_cran +all: doc build check doc: Rscript -e "devtools::document()" diff --git a/NEWS.md b/NEWS.md index 2a72b6f..8706cce 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,10 +1,10 @@ -# annovarR 1.1.0 +# anor 1.1.0 ## New features * Shiny app for maftools and gvmap -# annovarR 1.0.0 +# anor 1.0.0 ## New features diff --git a/R/annotation.R b/R/annotation.R index a4068c1..a801346 100644 --- a/R/annotation.R +++ b/R/annotation.R @@ -33,13 +33,13 @@ #' end <- c('10020', '10020', '10020') #' ref <- c('A', 'A', 'A') #' alt <- c('-', '-', '-') -#' database <- system.file('extdata', 'demo/hg19_avsnp147.txt', package = 'annovarR') +#' database <- system.file('extdata', 'demo/hg19_avsnp147.txt', package = 'anor') #' database.dir <- dirname(database) #' dat <- data.table(chr = chr, start = start, end = end, ref = ref, alt = alt) #' x <- annotation.cols.match(dat, 'avsnp147', database.dir = database.dir, #' return_col_names = 'avSNP147', db.type = 'txt') annotation.cols.match <- function(dat = data.table(), anno.name = "", buildver = "hg19", - database.dir = Sys.getenv("annovarR_DB_DIR", ""), db_col_order = 1:5, index_cols = c("chr", + database.dir = Sys.getenv("anor_DB_DIR", ""), db_col_order = 1:5, index_cols = c("chr", "start"), matched_cols = c("chr", "start", "end", "ref", "alt"), return_col_index = 6, return_col_names = "", return_col_names_profix = "", format_dat_fun = format.cols, dbname_fixed = NULL, table_name_fixed = NULL, setdb_fun = set.db, set_table_fun = set.table, @@ -108,7 +108,7 @@ annotation.cols.match <- function(dat = data.table(), anno.name = "", buildver = #' @export #' @examples #' library(data.table) -#' bed.file <- system.file('extdata', 'demo/example.bed', package = 'annovarR') +#' bed.file <- system.file('extdata', 'demo/example.bed', package = 'anor') #' bed.sqlite <- sprintf('%s/%s.sqlite', tempdir(), basename(bed.file)) #' connect.params <- list(dbname = bed.sqlite, table.name = 'bed') #' sqlite.build(bed.file, connect.params) @@ -122,7 +122,7 @@ annotation.cols.match <- function(dat = data.table(), anno.name = "", buildver = #' params = list(...);return(params[[1]])}) #' file.remove(bed.sqlite) annotation.region.match <- function(dat = data.table(), anno.name = "", buildver = "hg19", - database.dir = Sys.getenv("annovarR_DB_DIR", ""), db_col_order = 1:3, index_cols = c("chr", + database.dir = Sys.getenv("anor_DB_DIR", ""), db_col_order = 1:3, index_cols = c("chr", "start", "end"), full.matched_cols = "chr", inferior_col = "start", superior_col = "end", return_col_index = 4, return_col_names = "", return_col_names_profix = "", format_dat_fun = format.cols, dbname_fixed = NULL, table_name_fixed = NULL, setdb_fun = set.db, set_table_fun = set.table, @@ -184,7 +184,7 @@ annotation.region.match <- function(dat = data.table(), anno.name = "", buildver #' the names can be found on the http://annovar.openbioinformatics.org/en/latest/user-guide/download/ #' @param database.dir Dir of the databases #' @param db.type Setting the database type (sqlite or txt) -#' @param database.cfg Configuration file of annovarR databases infomation +#' @param database.cfg Configuration file of anor databases infomation #' @param func Function to anntate the dat data, default is to search the function in extdata/database.toml #' @param mysql.connect.params Connect MySQL database other parameters, #' e.g. list(host='11.11.11.1', port = '3306', user = '', password = '123456') @@ -199,14 +199,14 @@ annotation.region.match <- function(dat = data.table(), anno.name = "", buildver #' end <- c('10020', '10020', '10020') #' ref <- c('A', 'A', 'A') #' alt <- c('-', '-', '-') -#' database <- system.file('extdata', 'demo/hg19_avsnp147.txt', package = 'annovarR') +#' database <- system.file('extdata', 'demo/hg19_avsnp147.txt', package = 'anor') #' database.dir <- dirname(database) #' dat <- data.table(chr = chr, start = start, end = end, ref = ref, alt = alt) #' x <- annotation(dat, 'avsnp147', database.dir = database.dir, #' return_col_names = 'avSNP147', db.type = 'txt') annotation <- function(dat = data.table(), anno.name = "", buildver = "hg19", annovar.anno.names = "", - database.dir = Sys.getenv("annovarR_DB_DIR", ""), db.type = NULL, database.cfg = system.file("extdata", - "config/databases.toml", package = "annovarR"), func = NULL, mysql.connect.params = list(host = "", + database.dir = Sys.getenv("anor_DB_DIR", ""), db.type = NULL, database.cfg = system.file("extdata", + "config/databases.toml", package = "anor"), func = NULL, mysql.connect.params = list(host = "", dbname = "", table.name = "", user = "", password = ""), sqlite.connect.params = list(dbname = ""), ...) { if (length(anno.name) > 1) { @@ -244,7 +244,7 @@ annotation <- function(dat = data.table(), anno.name = "", buildver = "hg19", an #' end <- c('10020', '10020', '10020') #' ref <- c('A', 'A', 'A') #' alt <- c('-', '-', '-') -#' database <- system.file('extdata', 'demo/hg19_avsnp147.txt', package = 'annovarR') +#' database <- system.file('extdata', 'demo/hg19_avsnp147.txt', package = 'anor') #' database.dir <- dirname(database) #' dat <- data.table(chr = chr, start = start, end = end, ref = ref, alt = alt) #' x <- annotation.merge(dat = dat, anno.names = c('avsnp147'), @@ -262,7 +262,7 @@ annotation.merge <- function(anno.names, ...) { }) names(result.list.2) <- perl_annovar_names if (length(result.list.1) != 0) { - return(list(annovarR = as.data.table(result.list.1), annovar = result.list.2)) + return(list(anor = as.data.table(result.list.1), annovar = result.list.2)) } else { return(list(annovar = result.list.2)) } diff --git a/R/annotation.utils.R b/R/annotation.utils.R index b7ddf9b..f25ebac 100644 --- a/R/annotation.utils.R +++ b/R/annotation.utils.R @@ -1,6 +1,6 @@ # preprocess before to query with database before.query.steps <- function(dat = data.table(), anno.name = "", buildver = "hg19", - database.dir = Sys.getenv("annovarR_DB_DIR", ""), db_col_order = 1:5, index_cols = c("chr", + database.dir = Sys.getenv("anor_DB_DIR", ""), db_col_order = 1:5, index_cols = c("chr", "start"), matched_cols = c("chr", "start", "end", "ref", "alt"), format_dat_fun = format.cols, dbname_fixed = NULL, table_name_fixed = NULL, setdb_fun = set.db, set_table_fun = set.table, db.type = NULL, db.file.prefix = NULL, mysql.connect.params = list(), sqlite.connect.params = list(), diff --git a/R/annovarR.R b/R/anor.R similarity index 69% rename from R/annovarR.R rename to R/anor.R index 6956d5c..ac60cbb 100644 --- a/R/annovarR.R +++ b/R/anor.R @@ -1,12 +1,12 @@ -#' The 'annovarR' package provides R functions as well as database resources which offer an +#' The 'anor' package provides R functions as well as database resources which offer an #' integrated framework to annotate genetic variants from genome and transcriptome data. -#' The wrapper functions of 'annovarR' unified the interface of many published annotation tools, +#' The wrapper functions of 'anor' unified the interface of many published annotation tools, #' such as 'VEP' (\url{http://asia.ensembl.org/info/docs/tools/vep/index.html}), #' 'ANNOVAR' (\url{http://annovar.openbioinformatics.org/}), 'vcfanno' (\url{https://github.com/brentp/vcfanno}) #' and 'AnnotationDbi' (\url{http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.html}). #' It also simplified the use of some of the external annotation tools in R. -#' Besides, massive published genetic variants annotation databases were integrated into 'annovarR'. -#' For example, 'annovarR' provides a newly RNA-seq allele frequency database, BRVar, +#' Besides, massive published genetic variants annotation databases were integrated into 'anor'. +#' For example, 'anor' provides a newly RNA-seq allele frequency database, BRVar, #' which built from total 1,285 cases public B-progenitor acute lymphoblastic leukemia (B-ALL) transcriptome data. #' #' @author @@ -14,12 +14,12 @@ #' @seealso #' Useful links: #' -#' \url{https://github.com/JhuangLab/annovarR} +#' \url{https://github.com/JhuangLab/anor} #' -#' Report bugs at \url{https://github.com/JhuangLab/annovarR/issues} +#' Report bugs at \url{https://github.com/JhuangLab/anor/issues} #' #' @docType package -#' @name annovarR +#' @name anor #' @import stringr DBI data.table futile.logger configr BioInstaller glue liteq #' @importFrom stringi stri_rand_strings #' @importFrom utils packageVersion head installed.packages compareVersion install.packages @@ -35,9 +35,9 @@ NULL .onAttach <- function(libname, pkgname) { op <- options() - # msg <- sprintf('annovarR %s \n', packageVersion('annovarR')) msg <- - # sprintf('%s Documentation: ?annovarR, example(annovarR) and - # browseVignettes(\'annovarR\')', msg) packageStartupMessage(msg) + # msg <- sprintf('anor %s \n', packageVersion('anor')) msg <- + # sprintf('%s Documentation: ?anor, example(anor) and + # browseVignettes(\'anor\')', msg) packageStartupMessage(msg) Sys.setenv(R_TESTS = "") invisible() } diff --git a/R/auto.R b/R/auto.R index 1739c01..ade84b9 100644 --- a/R/auto.R +++ b/R/auto.R @@ -1,4 +1,4 @@ -#' Build annovarR database in sqlite (auto from extdata/config/database.toml) +#' Build anor database in sqlite (auto from extdata/config/database.toml) #' #' @param anno.name Annotation name, eg. avsnp138, avsnp147, 1000g2015aug_all #' @param buildver Genome version, hg19, hg38, mm10 and others @@ -8,7 +8,7 @@ #' default is FALSE #' @param index Index name in sqlite #' @param db.type Setting the database type (sqlite, txt or mysql) -#' @param database.cfg Configuration file of annovarR databases infomation +#' @param database.cfg Configuration file of anor databases infomation #' @param extra_fread_params Pass to \code{\link[ngstk]{batch_file}}, #' default is to get value from database.cfg #' @param sqlite.build.params Extra params pass to \code{\link{sqlite.build}} @@ -20,14 +20,14 @@ #' @export #' @examples #' i <- 'hg19_avsnp147' -#' database <- system.file('extdata', sprintf('demo/%s.txt', i), package = 'annovarR') +#' database <- system.file('extdata', sprintf('demo/%s.txt', i), package = 'anor') #' file.copy(database, sprintf('%s/%s.txt', tempdir(), i)) #' sqlite.auto.build('avsnp147', 'hg19', database.dir = tempdir(), verbose = TRUE) #' unlink(sprintf('%s/%s.txt', tempdir(), i)) #' unlink(sprintf('%s/%s.sqlite', tempdir(), i)) sqlite.auto.build <- function(anno.name = "", buildver = "hg19", database.dir = "/path/", overwrite = FALSE, append = FALSE, index = "chr_start_index", db.type = "sqlite", - database.cfg = system.file("extdata", "config/databases.toml", package = "annovarR"), + database.cfg = system.file("extdata", "config/databases.toml", package = "anor"), extra_fread_params = list(sep = "\t", header = TRUE, return_1L = FALSE), sqlite.build.params = list(fread.params = list(sep = "\t")), batch_lines = 1e+07, start_index = 1, new.colnames = NULL, verbose = TRUE) { info.msg(sprintf("Auto build database %s %s in %s", buildver, anno.name, database.dir), @@ -99,18 +99,18 @@ sqlite.auto.build <- function(anno.name = "", buildver = "hg19", database.dir = } } -#' Index annovarR database in sqlite (auto from extdata/config/database.toml) +#' Index anor database in sqlite (auto from extdata/config/database.toml) #' @param anno.name Annotation name, eg. avsnp138, avsnp147, 1000g2015aug_all #' @param buildver Genome version, hg19, hg38, mm10 and others #' @param database.dir Dir of the databases #' @param index Index name in sqlite #' @param db.type Setting the database type (sqlite, txt or mysql) -#' @param database.cfg Configuration file of annovarR databases infomation +#' @param database.cfg Configuration file of anor databases infomation #' @param verbose Logical indicating wheather print the extra log infomation #' @export #' @examples #' i <- 'hg19_avsnp147' -#' database <- system.file('extdata', sprintf('demo/%s.txt', i), package = 'annovarR') +#' database <- system.file('extdata', sprintf('demo/%s.txt', i), package = 'anor') #' file.copy(database, sprintf('%s/%s.txt', tempdir(), i)) #' sqlite.auto.build('avsnp147', 'hg19', database.dir = tempdir(), verbose = TRUE) #' sqlite.auto.index('avsnp147', 'hg19', database.dir = tempdir(), index = 'chr_start_index2', @@ -119,7 +119,7 @@ sqlite.auto.build <- function(anno.name = "", buildver = "hg19", database.dir = #' unlink(sprintf('%s/%s.sqlite', tempdir(), i)) sqlite.auto.index <- function(anno.name = "", buildver = "hg19", database.dir = "/path/", index = "chr_start_index", db.type = "sqlite", database.cfg = system.file("extdata", - "config/databases.toml", package = "annovarR"), verbose = TRUE) { + "config/databases.toml", package = "anor"), verbose = TRUE) { info.msg(sprintf("Auto build database %s %s in %s", buildver, anno.name, database.dir), verbose = verbose) auto.parameters <- c("need_cols", "db_col_order", "setdb_fun", "set_table_fun", @@ -160,7 +160,7 @@ sqlite.auto.index <- function(anno.name = "", buildver = "hg19", database.dir = } } -#' Build annovarR database in mysql (auto from extdata/config/database.toml) +#' Build anor database in mysql (auto from extdata/config/database.toml) #' #' @param anno.name Annotation name, eg. avsnp138, avsnp147, 1000g2015aug_all #' @param buildver Genome version, hg19, hg38, mm10 and others @@ -171,7 +171,7 @@ sqlite.auto.index <- function(anno.name = "", buildver = "hg19", database.dir = #' default is FALSE #' @param index Index name in sqlite #' @param db.type Setting the database type (sqlite, txt or mysql) -#' @param database.cfg Configuration file of annovarR databases infomation +#' @param database.cfg Configuration file of anor databases infomation #' @param extra_fread_params Pass to \code{\link[ngstk]{batch_file}}, #' default is to get value from database.cfg #' @param mysql.build.params Extra params pass to \code{\link{mysql.build}} @@ -183,17 +183,17 @@ sqlite.auto.index <- function(anno.name = "", buildver = "hg19", database.dir = #' @export #' @examples #' i <- 'hg19_avsnp147' -#' database <- system.file('extdata', sprintf('demo/%s.txt', i), package = 'annovarR') +#' database <- system.file('extdata', sprintf('demo/%s.txt', i), package = 'anor') #' file.copy(database, sprintf('%s/%s.txt', tempdir(), i)) #' \dontrun{ #' mysql.auto.build(anno.name = 'avsnp147', database.dir = tempdir(), #' mysql.connect.params = list(user = 'username', password = 'password', -#' host = 'localhost', port = 3306, dbname = 'annovarR')) +#' host = 'localhost', port = 3306, dbname = 'anor')) #' } mysql.auto.build <- function(anno.name = "", buildver = "hg19", database.dir = "/path/", mysql.connect.params = list(user = "", password = "", host = "localhost", port = "3306"), overwrite = FALSE, append = FALSE, index = "chr_start_index", db.type = "mysql", - database.cfg = system.file("extdata", "config/databases.toml", package = "annovarR"), + database.cfg = system.file("extdata", "config/databases.toml", package = "anor"), extra_fread_params = list(sep = "\t", header = TRUE, return_1L = FALSE), mysql.build.params = list(fread.params = list(sep = "\t")), batch_lines = 1e+07, start_index = 1, new.colnames = NULL, verbose = TRUE) { info.msg(sprintf("Auto build database %s %s in mysql database [host:%s, port:%s]", @@ -270,29 +270,29 @@ mysql.auto.build <- function(anno.name = "", buildver = "hg19", database.dir = " } } -#' Index annovarR database in mysql (auto from extdata/config/database.toml) +#' Index anor database in mysql (auto from extdata/config/database.toml) #' @param anno.name Annotation name, eg. avsnp138, avsnp147, 1000g2015aug_all #' @param buildver Genome version, hg19, hg38, mm10 and others #' @param database.dir Dir of the databases (mysql no need) #' @param mysql.connect.params Mysql parameters, [host, dbname, table.name, user, password etc.] #' @param index Index name in sqlite #' @param db.type Setting the database type (sqlite, txt or mysql) -#' @param database.cfg Configuration file of annovarR databases infomation +#' @param database.cfg Configuration file of anor databases infomation #' @param verbose Logical indicating wheather print the extra log infomation #' @export #' @examples #' i <- 'hg19_avsnp147' -#' database <- system.file('extdata', sprintf('demo/%s.txt', i), package = 'annovarR') +#' database <- system.file('extdata', sprintf('demo/%s.txt', i), package = 'anor') #' file.copy(database, sprintf('%s/%s.txt', tempdir(), i)) #' \dontrun{ #' mysql.auto.index(anno.name = 'avsnp147', database.dir = tempdir(), #' mysql.connect.params = list(user = 'username', password = 'password', -#' host = 'localhost', port = 3306, dbname = 'annovarR')) +#' host = 'localhost', port = 3306, dbname = 'anor')) #' } mysql.auto.index <- function(anno.name = "", buildver = "hg19", database.dir = "/path/", mysql.connect.params = list(user = "", password = "", host = "localhost", port = "3306"), index = "chr_start_index", db.type = "mysql", database.cfg = system.file("extdata", - "config/databases.toml", package = "annovarR"), verbose = TRUE) { + "config/databases.toml", package = "anor"), verbose = TRUE) { info.msg(sprintf("Auto index database %s %s in mysql database [host:%s, port:%s]", buildver, anno.name, mysql.connect.params$host, mysql.connect.params$port), verbose = verbose) @@ -336,7 +336,7 @@ mysql.auto.index <- function(anno.name = "", buildver = "hg19", database.dir = " } } -# Auto to annotation accodring the database.cfg annovarR supported anno.names +# Auto to annotation accodring the database.cfg anor supported anno.names annotation.auto <- function(dat = NULL, anno.name = NULL, return_col_names = NULL, return_col_names_profix = NULL, return_col_index = NULL, db_col_order = NULL, index_cols = NULL, matched_cols = NULL, full.matched_cols = NULL, inferior_col = NULL, @@ -391,7 +391,7 @@ annotation.auto <- function(dat = NULL, anno.name = NULL, return_col_names = NUL # A auto recognition function to get the annotation function from database.cfg get.annotation.func <- function(anno.name = "", database.cfg = system.file("extdata", - "config/databases.toml", package = "annovarR")) { + "config/databases.toml", package = "anor")) { all.supported.db <- get.annotation.names(database.cfg) if (!(anno.name %in% all.supported.db)) { stop(sprintf("%s not be supported.", anno.name)) diff --git a/R/build.R b/R/build.R index a2664b8..f3f97b9 100644 --- a/R/build.R +++ b/R/build.R @@ -1,4 +1,4 @@ -#' Build annovarR database in sqlite +#' Build anor database in sqlite #' #' @param filename Path of raw data, will be read by fread #' @param sqlite.connect.params Connect to sqlite database params [dbname, table.name] @@ -10,7 +10,7 @@ #' @param ... Other parameters be used in dbWriteTable #' @export #' @examples -#' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'annovarR') +#' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'anor') #' test.sqlite <- sprintf('%s/snp.test.sqlite', tempdir()) #' x <- sqlite.build(filename = test.dat, list(dbname = test.sqlite, #' table.name = 'snp_test')) @@ -64,7 +64,7 @@ sqlite.build <- function(filename = NULL, sqlite.connect.params = list(dbname = return(status) } -#' Generate search index of annovarR database table in sqlite +#' Generate search index of anor database table in sqlite #' #' @param sqlite.connect.params Connect to sqlite database params [dbname, table.name] #' @param index Index name in sqlite @@ -74,7 +74,7 @@ sqlite.build <- function(filename = NULL, sqlite.connect.params = list(dbname = #' @export #' @examples #' test.sqlite <- sprintf('%s/snp.test.sqlite', tempdir()) -#' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'annovarR') +#' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'anor') #' x <- sqlite.build(filename = test.dat, list(dbname = test.sqlite, #' table.name = 'snp_test')) #' x <- sqlite.index(list(dbname = test.sqlite, table.name = 'snp_test'), @@ -111,7 +111,7 @@ sqlite.index <- function(sqlite.connect.params = list(dbname = "", table.name = return(status) } -#' Drop search index of annovarR database table in sqlite +#' Drop search index of anor database table in sqlite #' #' @param sqlite.connect.params Connect to sqlite database params [dbname] #' @param index Index name in sqlite @@ -120,7 +120,7 @@ sqlite.index <- function(sqlite.connect.params = list(dbname = "", table.name = #' @export #' @examples #' test.sqlite <- sprintf('%s/snp.test.sqlite', tempdir()) -#' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'annovarR') +#' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'anor') #' x <- sqlite.build(filename = test.dat, list(dbname = test.sqlite, #' table.name = 'snp_test')) #' x <- sqlite.index(list(dbname = test.sqlite, table.name = 'snp_test'), @@ -157,7 +157,7 @@ drop.sqlite.index <- function(sqlite.connect.params = list(dbname = "", table.na } -#' Build annovarR database in mysql +#' Build anor database in mysql #' #' @param filename Path of raw data, will be read by fread #' @param mysql.connect.params Mysql parameters, [host, dbname, table.name, user, password etc.] @@ -168,7 +168,7 @@ drop.sqlite.index <- function(sqlite.connect.params = list(dbname = "", table.na #' @param ... Other parameters be used in dbWriteTable #' @export #' @examples -#' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'annovarR') +#' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'anor') #' \dontrun{ #' mysql.build(test.dat, list(host = 'host', dbname = 'db', #' table.name = 'table', user = 'user', password = 'password')) @@ -211,7 +211,7 @@ mysql.build <- function(filename = "", mysql.connect.params = list(host = "", db return(status) } -#' Generate search index of annovarR database table in mysql +#' Generate search index of anor database table in mysql #' #' @param mysql.connect.params Mysql parameters, [host, dbname, table.name, user, password etc.] #' @param index Index name in mysql @@ -220,7 +220,7 @@ mysql.build <- function(filename = "", mysql.connect.params = list(host = "", db #' @param ... Other parameters be used in dbSendQuery #' @export #' @examples -#' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'annovarR') +#' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'anor') #' \dontrun{ #' mysql.index(list(host = 'host', dbname = 'db', table.name = 'table', #' user = 'user', password = 'password'), index = 'index_name', cols = c('V1', 'V2')) @@ -257,7 +257,7 @@ mysql.index <- function(mysql.connect.params = list(host = "", dbname = "", tabl return(status) } -#' Drop search index of annovarR database table in mysql +#' Drop search index of anor database table in mysql #' #' @param mysql.connect.params Mysql parameters, [host, dbname, table.name, user, password etc.] #' @param index Index name in mysql @@ -265,7 +265,7 @@ mysql.index <- function(mysql.connect.params = list(host = "", dbname = "", tabl #' @param ... Other parameters be used in dbSendQuery #' @export #' @examples -#' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'annovarR') +#' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'anor') #' \dontrun{ #' drop.mysql.index(list(host = 'host', dbname = 'db', user = 'user', password = 'password'), #' index = 'index_name') @@ -316,7 +316,7 @@ drop.mysql.index <- function(mysql.connect.params = list(host = "", dbname = "", #' db <- tempfile() #' file.create(db) #' del(db, del.type = 'file') -#' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'annovarR') +#' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'anor') #' test.sqlite <- sprintf('%s/snp.test.sqlite', tempdir()) #' x <- sqlite.build(filename = test.dat, list(dbname = test.sqlite, #' table.name = 'snp_test')) @@ -375,7 +375,7 @@ del <- function(filename = "", sqlite.connect.params = list(), mysql.connect.par #' @param ... Other parameters be used in dbSendQuery #' @export #' @examples -#' sql.file <- system.file('extdata', 'demo/hg19_avsnp147.sqlite.sql', package = 'annovarR') +#' sql.file <- system.file('extdata', 'demo/hg19_avsnp147.sqlite.sql', package = 'anor') #' out.sqlite <- tempfile() #' sqlite <- Sys.which(c('sqlite3', 'sqlite')) #' sqlite <- sqlite[sqlite != ''][1] diff --git a/R/download.R b/R/download.R index 8b36545..873f9e5 100644 --- a/R/download.R +++ b/R/download.R @@ -1,4 +1,4 @@ -#' Download annovarR databases +#' Download anor databases #' #' @param download.name Download name, default is NULL and get value from database.cfg #' dependence_db @@ -6,7 +6,7 @@ #' @param version Version of download database, supported version can be get by #' download.database('db_annovar_avsnp', show.all.versions = TRUE) #' @param buildver Genome version, e.g hg19, hg38, mm10 -#' @param download.cfg Configuration file for download, most of annovarR database +#' @param download.cfg Configuration file for download, most of anor database #' resources can be found in system.file('extdata', #' 'config/db/db_annovar.toml', package = 'BioInstaller') #' @param show.all.versions Logical indicating wheather show all avaliable versions @@ -155,12 +155,12 @@ download.database <- function(download.name = NULL, database.dir = tempdir(), ve #' Use annotation name to get download.name that can be used #' to download the database use \code{download.database} #' @param anno.name Annotation name, eg. avsnp138, avsnp147, 1000g2015aug_all -#' @param database.cfg Configuration file of annovarR databases infomation +#' @param database.cfg Configuration file of anor databases infomation #' @export #' @examples #' get.download.name('avsnp147') get.download.name <- function(anno.name = "", database.cfg = system.file("extdata", - "config/databases.toml", package = "annovarR")) { + "config/databases.toml", package = "anor")) { download.name <- get.cfg.value.by.name(anno.name, database.cfg, key = "dependence_db") if (is.null(download.name) || is.na(download.name)) { download.name <- get.cfg.value.by.name(anno.name, database.cfg, key = "dependence_db", diff --git a/R/external_function.R b/R/external_function.R index 3a01588..6a86235 100644 --- a/R/external_function.R +++ b/R/external_function.R @@ -1,4 +1,4 @@ -# annovarR default function: setdb_fun, set_table_fun, format_db_tb_fun You can +# anor default function: setdb_fun, set_table_fun, format_db_tb_fun You can # re-write this R source file format.cols <- function(dat.input = "") { dat.input <- dat.input diff --git a/R/external_tools.R b/R/external_tools.R index de42056..556e9a6 100644 --- a/R/external_tools.R +++ b/R/external_tools.R @@ -234,7 +234,7 @@ vep <- function(vep = Sys.which("vep"), cache = TRUE, cache_version = 91, offlin #' #' @param vcfanno Executable file of vcfanno (Download from https://github.com/brentp/vcfanno/releases) #' @param vcfanno_database_cfg vcfanno required database configuration file -#' (Not the annovarR database.cfg) +#' (Not the anor database.cfg) #' @param base_path Optional base_path to prepend to annotation files in the config #' @param lua Optional path to a file containing custom javascript functions to be used as ops #' @param ends Annotate the start and end as well as the interval itself. @@ -249,7 +249,7 @@ vep <- function(vep = Sys.which("vep"), cache = TRUE, cache_version = 91, offlin #' vcfanno(debug = TRUE) vcfanno <- function(vcfanno = Sys.which(c("vcfanno", "vcfanno_osx", "vcfanno_linux64")), vcfanno_database_cfg = system.file("extdata", "demo/vcfanno_demo/conf.toml", - package = "annovarR"), base_path = "", lua = "", ends = FALSE, input.file = "input.vcf", + package = "anor"), base_path = "", lua = "", ends = FALSE, input.file = "input.vcf", out = "output.vcf", thread = 2, permissive_overlap = FALSE, debug = FALSE) { vcfanno <- vcfanno[vcfanno != ""][1] if (!file.exists(vcfanno) && !debug) { diff --git a/R/get.R b/R/get.R index 5e045fc..9916f22 100644 --- a/R/get.R +++ b/R/get.R @@ -8,7 +8,7 @@ #' @export #' @examples #' test.sqlite <- sprintf('%s/snp.test.sqlite', tempdir()) -#' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'annovarR') +#' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'anor') #' x <- sqlite.build(filename = test.dat, list(dbname = test.sqlite, #' table.name = 'snp_test')) #' sqlite.head(list(dbname = test.sqlite, table.name = 'snp_test')) @@ -48,29 +48,29 @@ mysql.head <- function(mysql.connect.params = list(host = "", dbname = "", table return(nlines) } -#' Get all annovarR supported databases +#' Get all anor supported databases #' -#' @param database.cfg Configuration file of annovarR databases infomation +#' @param database.cfg Configuration file of anor databases infomation #' @export #' @examples -#' cfg <- system.file('extdata', 'config/config.toml', package = 'annovarR') +#' cfg <- system.file('extdata', 'config/config.toml', package = 'anor') #' get.annotation.names(cfg) get.annotation.names <- function(database.cfg = system.file("extdata", "config/databases.toml", - package = "annovarR")) { + package = "anor")) { config <- configr::read.config(file = database.cfg, rcmd.parse = TRUE, glue.parse = TRUE) config <- config[names(config) != "Title"] return(unname(unlist(lapply(config, function(x) x["versions"])))) } -#' Get annovarR default databases type [sqlite, txt] +#' Get anor default databases type [sqlite, txt] #' #' @param anno.name Annotation name, eg. avsnp138, avsnp147, 1000g2015aug_all -#' @param database.cfg Configuration file of annovarR databases infomation +#' @param database.cfg Configuration file of anor databases infomation #' @export #' @examples #' get.annotation.dbtype('avsnp147') get.annotation.dbtype <- function(anno.name = "", database.cfg = system.file("extdata", - "config/databases.toml", package = "annovarR")) { + "config/databases.toml", package = "anor")) { dbtype <- tryCatch(get.cfg.value.by.name(name = anno.name, database.cfg = database.cfg, key = "default_dbtype"), error = function(e) { return("txt") @@ -86,15 +86,15 @@ get.annotation.dbtype <- function(anno.name = "", database.cfg = system.file("ex return(dbtype) } -#' Get annovarR annotation needed colnames according the anno.name +#' Get anor annotation needed colnames according the anno.name #' #' @param anno.name Annotation name, eg. avsnp138, avsnp147, 1000g2015aug_all -#' @param database.cfg Configuration file of annovarR databases infomation +#' @param database.cfg Configuration file of anor databases infomation #' @export #' @examples #' get.annotation.dbtype('avsnp147') get.annotation.needcols <- function(anno.name = "", database.cfg = system.file("extdata", - "config/databases.toml", package = "annovarR")) { + "config/databases.toml", package = "anor")) { need_cols <- get.cfg.value.by.name(anno.name, database.cfg, key = "need_cols", coincident = TRUE) return(need_cols) @@ -106,7 +106,7 @@ get.annotation.needcols <- function(anno.name = "", database.cfg = system.file(" #' @export #' @examples #' test.sqlite <- sprintf('%s/snp.test.sqlite', tempdir()) -#' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'annovarR') +#' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'anor') #' x <- sqlite.build(filename = test.dat, list(dbname = test.sqlite, #' table.name = 'snp_test')) #' sqlite.tb.colnames(list(dbname = test.sqlite, table.name = 'snp_test')) @@ -147,7 +147,7 @@ mysql.tb.colnames <- function(mysql.connect.params = list(host = "", dbname = "" #' @export #' @examples #' test.sqlite <- sprintf('%s/snp.test.sqlite', tempdir()) -#' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'annovarR') +#' test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'anor') #' params <- list(dbname = test.sqlite, #' table.name = 'snp_test') #' x <- sqlite.build(filename = test.dat, params) diff --git a/R/utils.R b/R/utils.R index 52a73fb..2a33f3f 100644 --- a/R/utils.R +++ b/R/utils.R @@ -48,7 +48,7 @@ disconnect.db <- function(database = "", db.type = "sqlite") { # level name of database.cfg, `key` is the key of first level name, `coincident` # decide wheather using one value to reprenst all of version get.cfg.value.by.name <- function(name = "", database.cfg = system.file("extdata", - "config/databases.toml", package = "annovarR"), key = "", coincident = FALSE, + "config/databases.toml", package = "anor"), key = "", coincident = FALSE, extra.list = list(), rcmd.parse = TRUE, glue.parse = TRUE) { config <- configr::read.config(database.cfg, extra.list = extra.list, rcmd.parse = rcmd.parse, glue.parse = glue.parse) diff --git a/README.md b/README.md index e5116a0..d91ad9f 100644 --- a/README.md +++ b/README.md @@ -1,37 +1,37 @@ -# annovarR +# anor [![Build -Status](https://img.shields.io/circleci/project/github/JhuangLab/annovarR/master.svg)](https://circleci.com/gh/JhuangLab/annovarR/tree/master) -[![CRAN](http://www.r-pkg.org/badges/version/annovarR)](https://cran.r-project.org/package=annovarR) [![Downloads](http://cranlogs.r-pkg.org/badges/annovarR?color=brightgreen)](http://www.r-pkg.org/pkg/annovarR) [![License](https://img.shields.io/badge/license-MIT-brightgreen.svg?style=flat)](https://en.wikipedia.org/wiki/MIT_License) [![codecov](https://codecov.io/github/JhuangLab/annovarR/branch/master/graphs/badge.svg)](https://codecov.io/github/JhuangLab/annovarR) +Status](https://img.shields.io/circleci/project/github/JhuangLab/anor/master.svg)](https://circleci.com/gh/JhuangLab/anor/tree/master) +[![CRAN](http://www.r-pkg.org/badges/version/anor)](https://cran.r-project.org/package=anor) [![Downloads](http://cranlogs.r-pkg.org/badges/anor?color=brightgreen)](http://www.r-pkg.org/pkg/anor) [![License](https://img.shields.io/badge/license-MIT-brightgreen.svg?style=flat)](https://en.wikipedia.org/wiki/MIT_License) [![codecov](https://codecov.io/github/JhuangLab/anor/branch/master/graphs/badge.svg)](https://codecov.io/github/JhuangLab/anor) ## Introduction -The [annovarR](https://life2cloud.com/tools/annovarR) package provides R functions as well as database resources which offer an integrated framework to annotate genetic variants from genome and transcriptome data. The wrapper functions of annovarR unified the interface of many published annotation tools, such as [VEP](http://asia.ensembl.org/info/docs/tools/vep/index.html), [ANNOVAR](http://annovar.openbioinformatics.org/), [vcfanno](https://github.com/brentp/vcfanno) and [AnnotationDbi](http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.html). +The [anor](https://life2cloud.com/tools/anor) package provides R functions as well as database resources which offer an integrated framework to annotate genetic variants from genome and transcriptome data. The wrapper functions of anor unified the interface of many published annotation tools, such as [VEP](http://asia.ensembl.org/info/docs/tools/vep/index.html), [ANNOVAR](http://annovar.openbioinformatics.org/), [vcfanno](https://github.com/brentp/vcfanno) and [AnnotationDbi](http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.html). -It also simplified the use of some of the external annotation tools in R. Besides, massive published genetic variants annotation databases were integrated into annovarR. +It also simplified the use of some of the external annotation tools in R. Besides, massive published genetic variants annotation databases were integrated into anor. -The main development motivation of annovarR is to increase the supported database and facilitate the variants annotation work. There are already too many tools and databases available and the usage is quite different. annovarR will integrate these annotation tools and get the merged annotation result in R. +The main development motivation of anor is to increase the supported database and facilitate the variants annotation work. There are already too many tools and databases available and the usage is quite different. anor will integrate these annotation tools and get the merged annotation result in R. - + -annovarR will not only provides annotation functions (both internal and external) but also hope to establish a shared annotation database resources. In fact, we have made some efforts in the relevant direction that massive scattered databases can easily to be download via using [BioInstaller](https://github.com/JhuangLab/BioInstaller) R package. +anor will not only provides annotation functions (both internal and external) but also hope to establish a shared annotation database resources. In fact, we have made some efforts in the relevant direction that massive scattered databases can easily to be download via using [BioInstaller](https://github.com/JhuangLab/BioInstaller) R package. Besides, we collected total 1,285 cases public B-progenitor acute lymphoblastic leukemia (B-ALL) transcriptome data from five different published datasets and built a novel large-scale transcript level sequencing variant database. [The Genome Analysis Toolkit (GATK)](https://software.broadinstitute.org/gatk/), [VarScan2](http://massgenomics.org/varscan) and [LoFreq](http://csb5.github.io/lofreq/) be used to call variants from the RNA-seq data (Database called BRVar). This work can help us to screen candidate systematic sequencing bias and evaluate variant calling trait from B-ALL RNA-seq. - + If you want to download the 1,285 RNA-seq variants frequency database, you need click [here](http://bioinfo.rjh.com.cn/labs/jhuang/contact.php) and send us a short application message (Whether it is for commercial use?). If the application is applied, we will reply you within 24 hours with a download required license code. ```r # Download BRVar database # You must input the applied license code -library(annovarR) +library(anor) download.database("db_annovar_brvar", "/path/annovar.dir", license = "licence_code") ``` ## Requirements -annovarR annotation system: +anor annotation system: - [R](https://cran.r-project.org/) >= 3.3.0 - [perl](http://strawberryperl.com/) @@ -56,13 +56,13 @@ vcfanno annotationo system ### Core softwares ``` r -# CRAN to install annovarR (The R package BioInstaller will be installed) +# CRAN to install anor (The R package BioInstaller will be installed) setRepositories(ind=1:2) -install.packages('annovarR') +install.packages('anor') -# Github to install annovarR (The R package BioInstaller will be installed) +# Github to install anor (The R package BioInstaller will be installed) # install.packages("devtools") -devtools::install_github("JhuangLab/annovarR") +devtools::install_github("JhuangLab/anor") # Set needed directory annovar.dir <- "/opt/bin/annovar" @@ -81,9 +81,9 @@ install.bioinfo('vcfanno', vcfanno.dir) ### Annotation Database ``` r -# Use download.database to download databases supported by annovarR and ANNOVAR +# Use download.database to download databases supported by anor and ANNOVAR # Some of examples as shown as below -library(annovarR) +library(anor) download.database('db_annovar_refgene', database.dir = database.dir, buildver = "hg19") download.database('db_ucsc_cytoband', database.dir = database.dir, buildver = "hg19") download.database('db_annovar_avsnp147', database.dir = database.dir, buildver = "hg19") @@ -91,7 +91,7 @@ download.database('db_annovar_avsnp147', database.dir = database.dir, buildver = download.database(c("db_annovar_refgene", "db_ucsc_cytoband"), database.dir = database.dir, buildver = "hg19") -# All annovarR supported big annotation database required SQLite format +# All anor supported big annotation database required SQLite format download.database('db_annovar_avsnp147_sqlite', database.dir = database.dir, buildver = "hg19") ``` @@ -105,10 +105,10 @@ download.database('db_annovar_avsnp147_sqlite', database.dir = database.dir, bui ## Basic Usage ```r -# View the vignettes in annovarR package -browseVignettes("annovarR") +# View the vignettes in anor package +browseVignettes("anor") -# Get all annovarR supported annotation name +# Get all anor supported annotation name get.annotation.names() # Get annotation name needed download.name and @@ -122,7 +122,7 @@ download.database(download.name = download.name, show.all.versions = TRUE) download.database(download.name = download.name, version = "avsnp147", buildver = "hg19", database.dir = database.dir) -# Annotate variants from avsnp147 database use annovarR +# Annotate variants from avsnp147 database use anor library(data.table) chr <- c("chr1", "chr2", "chr1") start <- c("10020", "10020", "10020") @@ -136,7 +136,7 @@ x <- annotation(dat = dat, anno.name = "avsnp147", database.dir = database.dir) x <- annotation.merge(dat = dat, anno.names = c("cosmic81", "avsnp147"), database.dir = database.dir) # Database configuration file -database.cfg <- system.file('extdata', 'config/databases.toml', package = "annovarR") +database.cfg <- system.file('extdata', 'config/databases.toml', package = "anor") # Get anno.name needed input cols get.annotation.needcols('avsnp147') @@ -155,9 +155,9 @@ x <- annotation(dat, anno.name = "perl_annovar_refGene", annovar.dir = annovar.d x <- annotation(input.file = tmpfn, anno.name = "perl_annovar_refGene", annovar.dir = annovar.dir, database.dir = database.dir) -# Annotate avinput format R data using annovarR and ANNOVAR +# Annotate avinput format R data using anor and ANNOVAR # It will return a list contatin two data.table object that -# one is annovarR annotation system and the another is ANNOVAR output +# one is anor annotation system and the another is ANNOVAR output x <-annotation.merge(dat = dat, anno.names = c('avsnp147', 'perl_annovar_refGene'), annovar.dir = annovar.dir, database.dir = database.dir) x <- annotation.merge(dat = dat, anno.names = c('avsnp147', '1000g2015aug_all', @@ -168,7 +168,7 @@ x <- annotation.merge(dat = dat, anno.names = c('avsnp147', '1000g2015aug_all', 'perl_annovar_merge'), annovar.anno.names = c('refGene', 'ensGene'), annovar.dir = annovar.dir, database.dir = database.dir) # Annotate VCF file using ANNOVAR -test.vcf.raw <- system.file("extdata", "demo/example.vcf", package = "annovarR") +test.vcf.raw <- system.file("extdata", "demo/example.vcf", package = "anor") test.vcf <- tempfile() file.copy(test.vcf.raw, test.vcf) x <- annotation(anno.name = "perl_annovar_ensGene", input.file = test.vcf, @@ -236,17 +236,9 @@ bioshiny_start ``` -## Docker - -You can use the annovarR in Docker. - -```bash -docker run -it -v /tmp/db:/tmp/db -v /tmp/input:/tmp/input -v /home/user/.annovarR:/home/opencpu/.annovarR -p 80:80 bioinstaller/annovarr -``` - ## How to contribute? -Please fork the [GitHub annovarR repository](https://github.com/JhuangLab/annovarR), modify it, and submit a pull request to us. +Please fork the [GitHub anor repository](https://github.com/JhuangLab/anor), modify it, and submit a pull request to us. ## Maintainer diff --git a/_pkgdown.yml b/_pkgdown.yml index e5eca58..5044d87 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -10,17 +10,17 @@ navbar: type: default left: - text: Get started - href: articles/introduction_to_annovarR.html + href: articles/introduction_to_anor.html - text: Reference href: reference/index.html - text: Articles menu: - - text: Database in annovarR - href: articles/database_in_annovarR.html - - text: Shiny app of annovarR - href: articles/shiny_of_annovarR.html + - text: Database in anor + href: articles/database_in_anor.html + - text: Shiny app of anor + href: articles/shiny_of_anor.html - text: News href: news/index.html right: - icon: fa-github fa-lg - href: https://github.com/JhuangLab/annovarR + href: https://github.com/JhuangLab/anor diff --git a/annovarR.Rproj b/anor.Rproj similarity index 100% rename from annovarR.Rproj rename to anor.Rproj diff --git a/docs/404.html b/docs/404.html new file mode 100644 index 0000000..a46a1d9 --- /dev/null +++ b/docs/404.html @@ -0,0 +1,133 @@ + + + + + + + + +Page not found (404) • anor + + + + + + + + + + + + + + + + + + + + + + + + +
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+ +
+
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zkRcsSOjDc}!w+%+Z{NBxqCNsWjBl0^cs_{*bquD@EZJI ze<440jEh32sPD73>w{*jY;kNIUFF4+kB)zPxRFZwY4c5Gj0vXu0TPl8#mH<)@B#o_NfUIRC&o_VRf^RoHi^-p~a8$ cr#b*@mx0Rb^rb{9<`r0KD%#4GFW-m%AGrQOQUCw| literal 0 HcmV?d00001 diff --git a/docs/articles/database_of_anor.html b/docs/articles/database_of_anor.html new file mode 100644 index 0000000..ae57e78 --- /dev/null +++ b/docs/articles/database_of_anor.html @@ -0,0 +1,180 @@ + + + + + + + +Database of anor • anor + + + + + + +

+
+ + + + +
+ + + + + + +
+
+
+

Database of anor

+

Jianfeng Li

+ +

2020-04-20

+ + Source: vignettes/database_of_anor.Rmd + + +
+ + + +
+

+Introduction

+

In this reference manual, we arranged the databases in anor and provide several meta information about the anor supported databases and other BioInstaller supported (download only) databases. Some of description or comments have been described in the download configuration file (BioInstaller package) and the annotation configuration file (anor).

+

anor supported databases will firstly be supported to download from original sites (exclude the authentication part) in BioInstaller. A portion of BioInstaller supported databases will be introduced in anor to as the candidate annotation databases (process method: remain unchanged, re-formate, re-analysis).

+
+
+

+Overview of supported database

+

The followed table shows all annotation names with its required download name.

+
+

The followed table shows all database names with its versions and description.

+
+

Besides, you can use the function download.database with parameter show.all.buildvers = TRUE get all available buildver.

+
x <- anor::download.database(download.name = "db_annovar_cosmic", show.all.buildvers = TRUE)
+as.data.frame(x)
+#>          db_annovar_cosmic
+#> cosmic70        hg38, hg19
+#> other                 hg19
+
+
+

+Gene and clincal annotation

+

Gene annotation databases contain the gene classification, gene function and phenotype correlation, such as HGNC, OMIM DoCM, CIVic, DisGeNET, ClinVar, and Gene Ontology (GO), .etc.

+
+
+

+Variant effect prediction

+

Variant effect prediction databases contain the various databases generated by the algorithms for prediction of variants effect on protein or RNA structural, such as SIFT, PolyPhen2, PROVEAN, MutationTaster, MutationAssessor, FATHMM, .etc.

+
+
+

+Population allele frequency

+

Population allele frequency databases contain the databases based on the population cohort genome sequencing data (mainly include whole genome sequencing and whole exome sequencing), such as 1000 Genome Project, NHLBI GO Exome Sequencing Project (ESP), gnomAD and ExAC, .etc.

+
+
+

+Cancer somatic mutation

+

Cancer somatic mutation databases generated by the cancer patients case-control paired genomic sequence data, such as COSMIC, Cancer Hotspots, intogen and Cancer Biomarkers database, .etc.

+
+
+

+RNA-seq variants

+

RNA-seq variants databases contributed by variants called from RNA-seq including expressed allele and RNA-editing. anor built an RNA-seq variants database, BRVar, based on 1285 cases B-cell lymphoblastic leukemia (B-ALL) patients RNA-seq data (Four different variants detection method be applied).

+
+
+

+Expression quantitative trait locus (eQTL)

+

eQTL databases contain the candidate locus of genome that have an candidate impact on gene expression level, such as Genotype-Tissue Expression (GTEx) QTL, seeQTL and PancanQTL, .etc.

+
+
+

+Non-coding RNA

+

Non-coding RNA databases contain the candidate biomarkers or non-coding RNA targeted transcriptional regulation region, such as Cancer-Specific CirRNA Database and (LNCediting)[http://bioinfo.life.hust.edu.cn/LNCediting/], .etc.

+
+
+ + + +
+ + + +
+

anor was developed by Jianfeng.

+
+ +
+

Developed by Jianfeng Li.

+

Site built by pkgdown.

+
+ +
+
+ + + + + + diff --git a/docs/articles/database_of_anor_files/crosstalk-1.1.0.1/css/crosstalk.css b/docs/articles/database_of_anor_files/crosstalk-1.1.0.1/css/crosstalk.css new file mode 100644 index 0000000..46befd2 --- /dev/null +++ b/docs/articles/database_of_anor_files/crosstalk-1.1.0.1/css/crosstalk.css @@ -0,0 +1,27 @@ +/* Adjust margins outwards, so column contents line up with the edges of the + parent of container-fluid. */ +.container-fluid.crosstalk-bscols { + margin-left: -30px; + margin-right: -30px; + white-space: normal; +} + +/* But don't adjust the margins outwards if we're directly under the body, + i.e. we were the top-level of something at the console. */ +body > .container-fluid.crosstalk-bscols { + margin-left: auto; + margin-right: auto; +} + +.crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column { + display: inline-block; + padding-right: 12px; + vertical-align: top; +} + +@media only screen and (max-width:480px) { + .crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column { + display: block; + padding-right: inherit; + } +} diff --git a/docs/articles/database_of_anor_files/crosstalk-1.1.0.1/js/crosstalk.js b/docs/articles/database_of_anor_files/crosstalk-1.1.0.1/js/crosstalk.js new file mode 100644 index 0000000..fd9eb53 --- /dev/null +++ b/docs/articles/database_of_anor_files/crosstalk-1.1.0.1/js/crosstalk.js @@ -0,0 +1,1474 @@ +(function(){function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error("Cannot find module '"+o+"'");throw f.code="MODULE_NOT_FOUND",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o b) { + return 1; + } +} + +/** + * @private + */ + +var FilterSet = function () { + function FilterSet() { + _classCallCheck(this, FilterSet); + + this.reset(); + } + + _createClass(FilterSet, [{ + key: "reset", + value: function reset() { + // Key: handle ID, Value: array of selected keys, or null + this._handles = {}; + // Key: key string, Value: count of handles that include it + this._keys = {}; + this._value = null; + this._activeHandles = 0; + } + }, { + key: "update", + value: function update(handleId, keys) { + if (keys !== null) { + keys = keys.slice(0); // clone before sorting + keys.sort(naturalComparator); + } + + var _diffSortedLists = (0, _util.diffSortedLists)(this._handles[handleId], keys), + added = _diffSortedLists.added, + removed = _diffSortedLists.removed; + + this._handles[handleId] = keys; + + for (var i = 0; i < added.length; i++) { + this._keys[added[i]] = (this._keys[added[i]] || 0) + 1; + } + for (var _i = 0; _i < removed.length; _i++) { + this._keys[removed[_i]]--; + } + + this._updateValue(keys); + } + + /** + * @param {string[]} keys Sorted array of strings that indicate + * a superset of possible keys. + * @private + */ + + }, { + key: "_updateValue", + value: function _updateValue() { + var keys = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : this._allKeys; + + var handleCount = Object.keys(this._handles).length; + if (handleCount === 0) { + this._value = null; + } else { + this._value = []; + for (var i = 0; i < keys.length; i++) { + var count = this._keys[keys[i]]; + if (count === handleCount) { + this._value.push(keys[i]); + } + } + } + } + }, { + key: "clear", + value: function clear(handleId) { + if (typeof this._handles[handleId] === "undefined") { + return; + } + + var keys = this._handles[handleId]; + if (!keys) { + keys = []; + } + + for (var i = 0; i < keys.length; i++) { + this._keys[keys[i]]--; + } + delete this._handles[handleId]; + + this._updateValue(); + } + }, { + key: "value", + get: function get() { + return this._value; + } + }, { + key: "_allKeys", + get: function get() { + var allKeys = Object.keys(this._keys); + allKeys.sort(naturalComparator); + return allKeys; + } + }]); + + return FilterSet; +}(); + +exports.default = FilterSet; + +},{"./util":11}],4:[function(require,module,exports){ +(function (global){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); + +var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }(); + +var _typeof = typeof Symbol === "function" && typeof Symbol.iterator === "symbol" ? function (obj) { return typeof obj; } : function (obj) { return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; }; + +exports.default = group; + +var _var2 = require("./var"); + +var _var3 = _interopRequireDefault(_var2); + +function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } + +function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } } + +// Use a global so that multiple copies of crosstalk.js can be loaded and still +// have groups behave as singletons across all copies. +global.__crosstalk_groups = global.__crosstalk_groups || {}; +var groups = global.__crosstalk_groups; + +function group(groupName) { + if (groupName && typeof groupName === "string") { + if (!groups.hasOwnProperty(groupName)) { + groups[groupName] = new Group(groupName); + } + return groups[groupName]; + } else if ((typeof groupName === "undefined" ? "undefined" : _typeof(groupName)) === "object" && groupName._vars && groupName.var) { + // Appears to already be a group object + return groupName; + } else if (Array.isArray(groupName) && groupName.length == 1 && typeof groupName[0] === "string") { + return group(groupName[0]); + } else { + throw new Error("Invalid groupName argument"); + } +} + +var Group = function () { + function Group(name) { + _classCallCheck(this, Group); + + this.name = name; + this._vars = {}; + } + + _createClass(Group, [{ + key: "var", + value: function _var(name) { + if (!name || typeof name !== "string") { + throw new Error("Invalid var name"); + } + + if (!this._vars.hasOwnProperty(name)) this._vars[name] = new _var3.default(this, name); + return this._vars[name]; + } + }, { + key: "has", + value: function has(name) { + if (!name || typeof name !== "string") { + throw new Error("Invalid var name"); + } + + return this._vars.hasOwnProperty(name); + } + }]); + + return Group; +}(); + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./var":12}],5:[function(require,module,exports){ +(function (global){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); + +var _group = require("./group"); + +var _group2 = _interopRequireDefault(_group); + +var _selection = require("./selection"); + +var _filter = require("./filter"); + +var _input = require("./input"); + +require("./input_selectize"); + +require("./input_checkboxgroup"); + +require("./input_slider"); + +function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } + +var defaultGroup = (0, _group2.default)("default"); + +function var_(name) { + return defaultGroup.var(name); +} + +function has(name) { + return defaultGroup.has(name); +} + +if (global.Shiny) { + global.Shiny.addCustomMessageHandler("update-client-value", function (message) { + if (typeof message.group === "string") { + (0, _group2.default)(message.group).var(message.name).set(message.value); + } else { + var_(message.name).set(message.value); + } + }); +} + +var crosstalk = { + group: _group2.default, + var: var_, + has: has, + SelectionHandle: _selection.SelectionHandle, + FilterHandle: _filter.FilterHandle, + bind: _input.bind +}; + +/** + * @namespace crosstalk + */ +exports.default = crosstalk; + +global.crosstalk = crosstalk; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./filter":2,"./group":4,"./input":6,"./input_checkboxgroup":7,"./input_selectize":8,"./input_slider":9,"./selection":10}],6:[function(require,module,exports){ +(function (global){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); +exports.register = register; +exports.bind = bind; +var $ = global.jQuery; + +var bindings = {}; + +function register(reg) { + bindings[reg.className] = reg; + if (global.document && global.document.readyState !== "complete") { + $(function () { + bind(); + }); + } else if (global.document) { + setTimeout(bind, 100); + } +} + +function bind() { + Object.keys(bindings).forEach(function (className) { + var binding = bindings[className]; + $("." + binding.className).not(".crosstalk-input-bound").each(function (i, el) { + bindInstance(binding, el); + }); + }); +} + +// Escape jQuery identifier +function $escape(val) { + return val.replace(/([!"#$%&'()*+,./:;<=>?@[\\\]^`{|}~])/g, "\\$1"); +} + +function bindEl(el) { + var $el = $(el); + Object.keys(bindings).forEach(function (className) { + if ($el.hasClass(className) && !$el.hasClass("crosstalk-input-bound")) { + var binding = bindings[className]; + bindInstance(binding, el); + } + }); +} + +function bindInstance(binding, el) { + var jsonEl = $(el).find("script[type='application/json'][data-for='" + $escape(el.id) + "']"); + var data = JSON.parse(jsonEl[0].innerText); + + var instance = binding.factory(el, data); + $(el).data("crosstalk-instance", instance); + $(el).addClass("crosstalk-input-bound"); +} + +if (global.Shiny) { + var inputBinding = new global.Shiny.InputBinding(); + var _$ = global.jQuery; + _$.extend(inputBinding, { + find: function find(scope) { + return _$(scope).find(".crosstalk-input"); + }, + initialize: function initialize(el) { + if (!_$(el).hasClass("crosstalk-input-bound")) { + bindEl(el); + } + }, + getId: function getId(el) { + return el.id; + }, + getValue: function getValue(el) {}, + setValue: function setValue(el, value) {}, + receiveMessage: function receiveMessage(el, data) {}, + subscribe: function subscribe(el, callback) { + _$(el).data("crosstalk-instance").resume(); + }, + unsubscribe: function unsubscribe(el) { + _$(el).data("crosstalk-instance").suspend(); + } + }); + global.Shiny.inputBindings.register(inputBinding, "crosstalk.inputBinding"); +} + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{}],7:[function(require,module,exports){ +(function (global){ +"use strict"; + +var _input = require("./input"); + +var input = _interopRequireWildcard(_input); + +var _filter = require("./filter"); + +function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } } + +var $ = global.jQuery; + +input.register({ + className: "crosstalk-input-checkboxgroup", + + factory: function factory(el, data) { + /* + * map: {"groupA": ["keyA", "keyB", ...], ...} + * group: "ct-groupname" + */ + var ctHandle = new _filter.FilterHandle(data.group); + + var lastKnownKeys = void 0; + var $el = $(el); + $el.on("change", "input[type='checkbox']", function () { + var checked = $el.find("input[type='checkbox']:checked"); + if (checked.length === 0) { + lastKnownKeys = null; + ctHandle.clear(); + } else { + var keys = {}; + checked.each(function () { + data.map[this.value].forEach(function (key) { + keys[key] = true; + }); + }); + var keyArray = Object.keys(keys); + keyArray.sort(); + lastKnownKeys = keyArray; + ctHandle.set(keyArray); + } + }); + + return { + suspend: function suspend() { + ctHandle.clear(); + }, + resume: function resume() { + if (lastKnownKeys) ctHandle.set(lastKnownKeys); + } + }; + } +}); + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./filter":2,"./input":6}],8:[function(require,module,exports){ +(function (global){ +"use strict"; + +var _input = require("./input"); + +var input = _interopRequireWildcard(_input); + +var _util = require("./util"); + +var util = _interopRequireWildcard(_util); + +var _filter = require("./filter"); + +function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } } + +var $ = global.jQuery; + +input.register({ + className: "crosstalk-input-select", + + factory: function factory(el, data) { + /* + * items: {value: [...], label: [...]} + * map: {"groupA": ["keyA", "keyB", ...], ...} + * group: "ct-groupname" + */ + + var first = [{ value: "", label: "(All)" }]; + var items = util.dataframeToD3(data.items); + var opts = { + options: first.concat(items), + valueField: "value", + labelField: "label", + searchField: "label" + }; + + var select = $(el).find("select")[0]; + + var selectize = $(select).selectize(opts)[0].selectize; + + var ctHandle = new _filter.FilterHandle(data.group); + + var lastKnownKeys = void 0; + selectize.on("change", function () { + if (selectize.items.length === 0) { + lastKnownKeys = null; + ctHandle.clear(); + } else { + var keys = {}; + selectize.items.forEach(function (group) { + data.map[group].forEach(function (key) { + keys[key] = true; + }); + }); + var keyArray = Object.keys(keys); + keyArray.sort(); + lastKnownKeys = keyArray; + ctHandle.set(keyArray); + } + }); + + return { + suspend: function suspend() { + ctHandle.clear(); + }, + resume: function resume() { + if (lastKnownKeys) ctHandle.set(lastKnownKeys); + } + }; + } +}); + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./filter":2,"./input":6,"./util":11}],9:[function(require,module,exports){ +(function (global){ +"use strict"; + +var _slicedToArray = function () { function sliceIterator(arr, i) { var _arr = []; var _n = true; var _d = false; var _e = undefined; try { for (var _i = arr[Symbol.iterator](), _s; !(_n = (_s = _i.next()).done); _n = true) { _arr.push(_s.value); if (i && _arr.length === i) break; } } catch (err) { _d = true; _e = err; } finally { try { if (!_n && _i["return"]) _i["return"](); } finally { if (_d) throw _e; } } return _arr; } return function (arr, i) { if (Array.isArray(arr)) { return arr; } else if (Symbol.iterator in Object(arr)) { return sliceIterator(arr, i); } else { throw new TypeError("Invalid attempt to destructure non-iterable instance"); } }; }(); + +var _input = require("./input"); + +var input = _interopRequireWildcard(_input); + +var _filter = require("./filter"); + +function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } } + +var $ = global.jQuery; +var strftime = global.strftime; + +input.register({ + className: "crosstalk-input-slider", + + factory: function factory(el, data) { + /* + * map: {"groupA": ["keyA", "keyB", ...], ...} + * group: "ct-groupname" + */ + var ctHandle = new _filter.FilterHandle(data.group); + + var opts = {}; + var $el = $(el).find("input"); + var dataType = $el.data("data-type"); + var timeFormat = $el.data("time-format"); + var round = $el.data("round"); + var timeFormatter = void 0; + + // Set up formatting functions + if (dataType === "date") { + timeFormatter = strftime.utc(); + opts.prettify = function (num) { + return timeFormatter(timeFormat, new Date(num)); + }; + } else if (dataType === "datetime") { + var timezone = $el.data("timezone"); + if (timezone) timeFormatter = strftime.timezone(timezone);else timeFormatter = strftime; + + opts.prettify = function (num) { + return timeFormatter(timeFormat, new Date(num)); + }; + } else if (dataType === "number") { + if (typeof round !== "undefined") opts.prettify = function (num) { + var factor = Math.pow(10, round); + return Math.round(num * factor) / factor; + }; + } + + $el.ionRangeSlider(opts); + + function getValue() { + var result = $el.data("ionRangeSlider").result; + + // Function for converting numeric value from slider to appropriate type. + var convert = void 0; + var dataType = $el.data("data-type"); + if (dataType === "date") { + convert = function convert(val) { + return formatDateUTC(new Date(+val)); + }; + } else if (dataType === "datetime") { + convert = function convert(val) { + // Convert ms to s + return +val / 1000; + }; + } else { + convert = function convert(val) { + return +val; + }; + } + + if ($el.data("ionRangeSlider").options.type === "double") { + return [convert(result.from), convert(result.to)]; + } else { + return convert(result.from); + } + } + + var lastKnownKeys = null; + + $el.on("change.crosstalkSliderInput", function (event) { + if (!$el.data("updating") && !$el.data("animating")) { + var _getValue = getValue(), + _getValue2 = _slicedToArray(_getValue, 2), + from = _getValue2[0], + to = _getValue2[1]; + + var keys = []; + for (var i = 0; i < data.values.length; i++) { + var val = data.values[i]; + if (val >= from && val <= to) { + keys.push(data.keys[i]); + } + } + keys.sort(); + ctHandle.set(keys); + lastKnownKeys = keys; + } + }); + + // let $el = $(el); + // $el.on("change", "input[type="checkbox"]", function() { + // let checked = $el.find("input[type="checkbox"]:checked"); + // if (checked.length === 0) { + // ctHandle.clear(); + // } else { + // let keys = {}; + // checked.each(function() { + // data.map[this.value].forEach(function(key) { + // keys[key] = true; + // }); + // }); + // let keyArray = Object.keys(keys); + // keyArray.sort(); + // ctHandle.set(keyArray); + // } + // }); + + return { + suspend: function suspend() { + ctHandle.clear(); + }, + resume: function resume() { + if (lastKnownKeys) ctHandle.set(lastKnownKeys); + } + }; + } +}); + +// Convert a number to a string with leading zeros +function padZeros(n, digits) { + var str = n.toString(); + while (str.length < digits) { + str = "0" + str; + }return str; +} + +// Given a Date object, return a string in yyyy-mm-dd format, using the +// UTC date. This may be a day off from the date in the local time zone. +function formatDateUTC(date) { + if (date instanceof Date) { + return date.getUTCFullYear() + "-" + padZeros(date.getUTCMonth() + 1, 2) + "-" + padZeros(date.getUTCDate(), 2); + } else { + return null; + } +} + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./filter":2,"./input":6}],10:[function(require,module,exports){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); +exports.SelectionHandle = undefined; + +var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }(); + +var _events = require("./events"); + +var _events2 = _interopRequireDefault(_events); + +var _group = require("./group"); + +var _group2 = _interopRequireDefault(_group); + +var _util = require("./util"); + +var util = _interopRequireWildcard(_util); + +function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } } + +function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } + +function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } } + +/** + * Use this class to read and write (and listen for changes to) the selection + * for a Crosstalk group. This is intended to be used for linked brushing. + * + * If two (or more) `SelectionHandle` instances in the same webpage share the + * same group name, they will share the same state. Setting the selection using + * one `SelectionHandle` instance will result in the `value` property instantly + * changing across the others, and `"change"` event listeners on all instances + * (including the one that initiated the sending) will fire. + * + * @param {string} [group] - The name of the Crosstalk group, or if none, + * null or undefined (or any other falsy value). This can be changed later + * via the [SelectionHandle#setGroup](#setGroup) method. + * @param {Object} [extraInfo] - An object whose properties will be copied to + * the event object whenever an event is emitted. + */ +var SelectionHandle = exports.SelectionHandle = function () { + function SelectionHandle() { + var group = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : null; + var extraInfo = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : null; + + _classCallCheck(this, SelectionHandle); + + this._eventRelay = new _events2.default(); + this._emitter = new util.SubscriptionTracker(this._eventRelay); + + // Name of the group we're currently tracking, if any. Can change over time. + this._group = null; + // The Var we're currently tracking, if any. Can change over time. + this._var = null; + // The event handler subscription we currently have on var.on("change"). + this._varOnChangeSub = null; + + this._extraInfo = util.extend({ sender: this }, extraInfo); + + this.setGroup(group); + } + + /** + * Changes the Crosstalk group membership of this SelectionHandle. The group + * being switched away from (if any) will not have its selection value + * modified as a result of calling `setGroup`, even if this handle was the + * most recent handle to set the selection of the group. + * + * The group being switched to (if any) will also not have its selection value + * modified as a result of calling `setGroup`. If you want to set the + * selection value of the new group, call `set` explicitly. + * + * @param {string} group - The name of the Crosstalk group, or null (or + * undefined) to clear the group. + */ + + + _createClass(SelectionHandle, [{ + key: "setGroup", + value: function setGroup(group) { + var _this = this; + + // If group is unchanged, do nothing + if (this._group === group) return; + // Treat null, undefined, and other falsy values the same + if (!this._group && !group) return; + + if (this._var) { + this._var.off("change", this._varOnChangeSub); + this._var = null; + this._varOnChangeSub = null; + } + + this._group = group; + + if (group) { + this._var = (0, _group2.default)(group).var("selection"); + var sub = this._var.on("change", function (e) { + _this._eventRelay.trigger("change", e, _this); + }); + this._varOnChangeSub = sub; + } + } + + /** + * Retrieves the current selection for the group represented by this + * `SelectionHandle`. + * + * - If no selection is active, then this value will be falsy. + * - If a selection is active, but no data points are selected, then this + * value will be an empty array. + * - If a selection is active, and data points are selected, then the keys + * of the selected data points will be present in the array. + */ + + }, { + key: "_mergeExtraInfo", + + + /** + * Combines the given `extraInfo` (if any) with the handle's default + * `_extraInfo` (if any). + * @private + */ + value: function _mergeExtraInfo(extraInfo) { + // Important incidental effect: shallow clone is returned + return util.extend({}, this._extraInfo ? this._extraInfo : null, extraInfo ? extraInfo : null); + } + + /** + * Overwrites the current selection for the group, and raises the `"change"` + * event among all of the group's '`SelectionHandle` instances (including + * this one). + * + * @fires SelectionHandle#change + * @param {string[]} selectedKeys - Falsy, empty array, or array of keys (see + * {@link SelectionHandle#value}). + * @param {Object} [extraInfo] - Extra properties to be included on the event + * object that's passed to listeners (in addition to any options that were + * passed into the `SelectionHandle` constructor). + */ + + }, { + key: "set", + value: function set(selectedKeys, extraInfo) { + if (this._var) this._var.set(selectedKeys, this._mergeExtraInfo(extraInfo)); + } + + /** + * Overwrites the current selection for the group, and raises the `"change"` + * event among all of the group's '`SelectionHandle` instances (including + * this one). + * + * @fires SelectionHandle#change + * @param {Object} [extraInfo] - Extra properties to be included on the event + * object that's passed to listeners (in addition to any that were passed + * into the `SelectionHandle` constructor). + */ + + }, { + key: "clear", + value: function clear(extraInfo) { + if (this._var) this.set(void 0, this._mergeExtraInfo(extraInfo)); + } + + /** + * Subscribes to events on this `SelectionHandle`. + * + * @param {string} eventType - Indicates the type of events to listen to. + * Currently, only `"change"` is supported. + * @param {SelectionHandle~listener} listener - The callback function that + * will be invoked when the event occurs. + * @return {string} - A token to pass to {@link SelectionHandle#off} to cancel + * this subscription. + */ + + }, { + key: "on", + value: function on(eventType, listener) { + return this._emitter.on(eventType, listener); + } + + /** + * Cancels event subscriptions created by {@link SelectionHandle#on}. + * + * @param {string} eventType - The type of event to unsubscribe. + * @param {string|SelectionHandle~listener} listener - Either the callback + * function previously passed into {@link SelectionHandle#on}, or the + * string that was returned from {@link SelectionHandle#on}. + */ + + }, { + key: "off", + value: function off(eventType, listener) { + return this._emitter.off(eventType, listener); + } + + /** + * Shuts down the `SelectionHandle` object. + * + * Removes all event listeners that were added through this handle. + */ + + }, { + key: "close", + value: function close() { + this._emitter.removeAllListeners(); + this.setGroup(null); + } + }, { + key: "value", + get: function get() { + return this._var ? this._var.get() : null; + } + }]); + + return SelectionHandle; +}(); + +/** + * @callback SelectionHandle~listener + * @param {Object} event - An object containing details of the event. For + * `"change"` events, this includes the properties `value` (the new + * value of the selection, or `undefined` if no selection is active), + * `oldValue` (the previous value of the selection), and `sender` (the + * `SelectionHandle` instance that made the change). + */ + +/** + * @event SelectionHandle#change + * @type {object} + * @property {object} value - The new value of the selection, or `undefined` + * if no selection is active. + * @property {object} oldValue - The previous value of the selection. + * @property {SelectionHandle} sender - The `SelectionHandle` instance that + * changed the value. + */ + +},{"./events":1,"./group":4,"./util":11}],11:[function(require,module,exports){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); + +var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }(); + +var _typeof = typeof Symbol === "function" && typeof Symbol.iterator === "symbol" ? function (obj) { return typeof obj; } : function (obj) { return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; }; + +exports.extend = extend; +exports.checkSorted = checkSorted; +exports.diffSortedLists = diffSortedLists; +exports.dataframeToD3 = dataframeToD3; + +function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } } + +function extend(target) { + for (var _len = arguments.length, sources = Array(_len > 1 ? _len - 1 : 0), _key = 1; _key < _len; _key++) { + sources[_key - 1] = arguments[_key]; + } + + for (var i = 0; i < sources.length; i++) { + var src = sources[i]; + if (typeof src === "undefined" || src === null) continue; + + for (var key in src) { + if (src.hasOwnProperty(key)) { + target[key] = src[key]; + } + } + } + return target; +} + +function checkSorted(list) { + for (var i = 1; i < list.length; i++) { + if (list[i] <= list[i - 1]) { + throw new Error("List is not sorted or contains duplicate"); + } + } +} + +function diffSortedLists(a, b) { + var i_a = 0; + var i_b = 0; + + if (!a) a = []; + if (!b) b = []; + + var a_only = []; + var b_only = []; + + checkSorted(a); + checkSorted(b); + + while (i_a < a.length && i_b < b.length) { + if (a[i_a] === b[i_b]) { + i_a++; + i_b++; + } else if (a[i_a] < b[i_b]) { + a_only.push(a[i_a++]); + } else { + b_only.push(b[i_b++]); + } + } + + if (i_a < a.length) a_only = a_only.concat(a.slice(i_a)); + if (i_b < b.length) b_only = b_only.concat(b.slice(i_b)); + return { + removed: a_only, + added: b_only + }; +} + +// Convert from wide: { colA: [1,2,3], colB: [4,5,6], ... } +// to long: [ {colA: 1, colB: 4}, {colA: 2, colB: 5}, ... ] +function dataframeToD3(df) { + var names = []; + var length = void 0; + for (var name in df) { + if (df.hasOwnProperty(name)) names.push(name); + if (_typeof(df[name]) !== "object" || typeof df[name].length === "undefined") { + throw new Error("All fields must be arrays"); + } else if (typeof length !== "undefined" && length !== df[name].length) { + throw new Error("All fields must be arrays of the same length"); + } + length = df[name].length; + } + var results = []; + var item = void 0; + for (var row = 0; row < length; row++) { + item = {}; + for (var col = 0; col < names.length; col++) { + item[names[col]] = df[names[col]][row]; + } + results.push(item); + } + return results; +} + +/** + * Keeps track of all event listener additions/removals and lets all active + * listeners be removed with a single operation. + * + * @private + */ + +var SubscriptionTracker = exports.SubscriptionTracker = function () { + function SubscriptionTracker(emitter) { + _classCallCheck(this, SubscriptionTracker); + + this._emitter = emitter; + this._subs = {}; + } + + _createClass(SubscriptionTracker, [{ + key: "on", + value: function on(eventType, listener) { + var sub = this._emitter.on(eventType, listener); + this._subs[sub] = eventType; + return sub; + } + }, { + key: "off", + value: function off(eventType, listener) { + var sub = this._emitter.off(eventType, listener); + if (sub) { + delete this._subs[sub]; + } + return sub; + } + }, { + key: "removeAllListeners", + value: function removeAllListeners() { + var _this = this; + + var current_subs = this._subs; + this._subs = {}; + Object.keys(current_subs).forEach(function (sub) { + _this._emitter.off(current_subs[sub], sub); + }); + } + }]); + + return SubscriptionTracker; +}(); + +},{}],12:[function(require,module,exports){ +(function (global){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); + +var _typeof = typeof Symbol === "function" && typeof Symbol.iterator === "symbol" ? function (obj) { return typeof obj; } : function (obj) { return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; }; + +var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }(); + +var _events = require("./events"); + +var _events2 = _interopRequireDefault(_events); + +function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } + +function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } } + +var Var = function () { + function Var(group, name, /*optional*/value) { + _classCallCheck(this, Var); + + this._group = group; + this._name = name; + this._value = value; + this._events = new _events2.default(); + } + + _createClass(Var, [{ + key: "get", + value: function get() { + return this._value; + } + }, { + key: "set", + value: function set(value, /*optional*/event) { + if (this._value === value) { + // Do nothing; the value hasn't changed + return; + } + var oldValue = this._value; + this._value = value; + // Alert JavaScript listeners that the value has changed + var evt = {}; + if (event && (typeof event === "undefined" ? "undefined" : _typeof(event)) === "object") { + for (var k in event) { + if (event.hasOwnProperty(k)) evt[k] = event[k]; + } + } + evt.oldValue = oldValue; + evt.value = value; + this._events.trigger("change", evt, this); + + // TODO: Make this extensible, to let arbitrary back-ends know that + // something has changed + if (global.Shiny && global.Shiny.onInputChange) { + global.Shiny.onInputChange(".clientValue-" + (this._group.name !== null ? this._group.name + "-" : "") + this._name, typeof value === "undefined" ? null : value); + } + } + }, { + key: "on", + value: function on(eventType, listener) { + return this._events.on(eventType, listener); + } + }, { + key: "off", + value: function off(eventType, listener) { + return this._events.off(eventType, listener); + } + }]); + + return Var; +}(); + +exports.default = Var; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./events":1}]},{},[5]) +//# sourceMappingURL=crosstalk.js.map diff --git a/docs/articles/database_of_anor_files/crosstalk-1.1.0.1/js/crosstalk.js.map b/docs/articles/database_of_anor_files/crosstalk-1.1.0.1/js/crosstalk.js.map new file mode 100644 index 0000000..cff94f0 --- /dev/null +++ b/docs/articles/database_of_anor_files/crosstalk-1.1.0.1/js/crosstalk.js.map @@ -0,0 +1,37 @@ +{ + "version": 3, + "sources": [ + "node_modules/browser-pack/_prelude.js", + "javascript/src/events.js", + "javascript/src/filter.js", + "javascript/src/filterset.js", + "javascript/src/group.js", + "javascript/src/index.js", + "javascript/src/input.js", + "javascript/src/input_checkboxgroup.js", + "javascript/src/input_selectize.js", + "javascript/src/input_slider.js", + "javascript/src/selection.js", + "javascript/src/util.js", + "javascript/src/var.js" + ], + "names": [], + "mappings": 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+ "file": "generated.js", + "sourceRoot": "", + "sourcesContent": [ + "(function(){function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require==\"function\"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error(\"Cannot find module '\"+o+\"'\");throw f.code=\"MODULE_NOT_FOUND\",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require==\"function\"&&require;for(var o=0;o {\n this._eventRelay.trigger(\"change\", e, this);\n });\n this._varOnChangeSub = sub;\n }\n }\n\n /**\n * Combine the given `extraInfo` (if any) with the handle's default\n * `_extraInfo` (if any).\n * @private\n */\n _mergeExtraInfo(extraInfo) {\n return util.extend({},\n this._extraInfo ? this._extraInfo : null,\n extraInfo ? extraInfo : null);\n }\n\n /**\n * Close the handle. This clears this handle's contribution to the filter set,\n * and unsubscribes all event listeners.\n */\n close() {\n this._emitter.removeAllListeners();\n this.clear();\n this.setGroup(null);\n }\n\n /**\n * Clear this handle's contribution to the filter set.\n *\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `FilterHandle` constructor).\n * \n * @fires FilterHandle#change\n */\n clear(extraInfo) {\n if (!this._filterSet)\n return;\n this._filterSet.clear(this._id);\n this._onChange(extraInfo);\n }\n\n /**\n * Set this handle's contribution to the filter set. This array should consist\n * of the keys of the rows that _should_ be displayed; any keys that are not\n * present in the array will be considered _filtered out_. Note that multiple\n * `FilterHandle` instances in the group may each contribute an array of keys,\n * and only those keys that appear in _all_ of the arrays make it through the\n * filter.\n *\n * @param {string[]} keys - Empty array, or array of keys. To clear the\n * filter, don't pass an empty array; instead, use the\n * {@link FilterHandle#clear} method.\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `FilterHandle` constructor).\n * \n * @fires FilterHandle#change\n */\n set(keys, extraInfo) {\n if (!this._filterSet)\n return;\n this._filterSet.update(this._id, keys);\n this._onChange(extraInfo);\n }\n\n /**\n * @return {string[]|null} - Either: 1) an array of keys that made it through\n * all of the `FilterHandle` instances, or, 2) `null`, which means no filter\n * is being applied (all data should be displayed).\n */\n get filteredKeys() {\n return this._filterSet ? this._filterSet.value : null;\n }\n\n /**\n * Subscribe to events on this `FilterHandle`.\n *\n * @param {string} eventType - Indicates the type of events to listen to.\n * Currently, only `\"change\"` is supported.\n * @param {FilterHandle~listener} listener - The callback function that\n * will be invoked when the event occurs.\n * @return {string} - A token to pass to {@link FilterHandle#off} to cancel\n * this subscription.\n */\n on(eventType, listener) {\n return this._emitter.on(eventType, listener);\n }\n\n /**\n * Cancel event subscriptions created by {@link FilterHandle#on}.\n *\n * @param {string} eventType - The type of event to unsubscribe.\n * @param {string|FilterHandle~listener} listener - Either the callback\n * function previously passed into {@link FilterHandle#on}, or the\n * string that was returned from {@link FilterHandle#on}.\n */\n off(eventType, listener) {\n return this._emitter.off(eventType, listener);\n }\n\n _onChange(extraInfo) {\n if (!this._filterSet)\n return;\n this._filterVar.set(this._filterSet.value, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * @callback FilterHandle~listener\n * @param {Object} event - An object containing details of the event. For\n * `\"change\"` events, this includes the properties `value` (the new\n * value of the filter set, or `null` if no filter set is active),\n * `oldValue` (the previous value of the filter set), and `sender` (the\n * `FilterHandle` instance that made the change).\n */\n\n}\n\n/**\n * @event FilterHandle#change\n * @type {object}\n * @property {object} value - The new value of the filter set, or `null`\n * if no filter set is active.\n * @property {object} oldValue - The previous value of the filter set.\n * @property {FilterHandle} sender - The `FilterHandle` instance that\n * changed the value.\n */\n", + "import { diffSortedLists } from \"./util\";\n\nfunction naturalComparator(a, b) {\n if (a === b) {\n return 0;\n } else if (a < b) {\n return -1;\n } else if (a > b) {\n return 1;\n }\n}\n\n/**\n * @private\n */\nexport default class FilterSet {\n constructor() {\n this.reset();\n }\n\n reset() {\n // Key: handle ID, Value: array of selected keys, or null\n this._handles = {};\n // Key: key string, Value: count of handles that include it\n this._keys = {};\n this._value = null;\n this._activeHandles = 0;\n }\n\n get value() {\n return this._value;\n }\n\n update(handleId, keys) {\n if (keys !== null) {\n keys = keys.slice(0); // clone before sorting\n keys.sort(naturalComparator);\n }\n\n let {added, removed} = diffSortedLists(this._handles[handleId], keys);\n this._handles[handleId] = keys;\n\n for (let i = 0; i < added.length; i++) {\n this._keys[added[i]] = (this._keys[added[i]] || 0) + 1;\n }\n for (let i = 0; i < removed.length; i++) {\n this._keys[removed[i]]--;\n }\n\n this._updateValue(keys);\n }\n\n /**\n * @param {string[]} keys Sorted array of strings that indicate\n * a superset of possible keys.\n * @private\n */\n _updateValue(keys = this._allKeys) {\n let handleCount = Object.keys(this._handles).length;\n if (handleCount === 0) {\n this._value = null;\n } else {\n this._value = [];\n for (let i = 0; i < keys.length; i++) {\n let count = this._keys[keys[i]];\n if (count === handleCount) {\n this._value.push(keys[i]);\n }\n }\n }\n }\n\n clear(handleId) {\n if (typeof(this._handles[handleId]) === \"undefined\") {\n return;\n }\n\n let keys = this._handles[handleId];\n if (!keys) {\n keys = [];\n }\n\n for (let i = 0; i < keys.length; i++) {\n this._keys[keys[i]]--;\n }\n delete this._handles[handleId];\n\n this._updateValue();\n }\n\n get _allKeys() {\n let allKeys = Object.keys(this._keys);\n allKeys.sort(naturalComparator);\n return allKeys;\n }\n}\n", + "import Var from \"./var\";\n\n// Use a global so that multiple copies of crosstalk.js can be loaded and still\n// have groups behave as singletons across all copies.\nglobal.__crosstalk_groups = global.__crosstalk_groups || {};\nlet groups = global.__crosstalk_groups;\n\nexport default function group(groupName) {\n if (groupName && typeof(groupName) === \"string\") {\n if (!groups.hasOwnProperty(groupName)) {\n groups[groupName] = new Group(groupName);\n }\n return groups[groupName];\n } else if (typeof(groupName) === \"object\" && groupName._vars && groupName.var) {\n // Appears to already be a group object\n return groupName;\n } else if (Array.isArray(groupName) &&\n groupName.length == 1 &&\n typeof(groupName[0]) === \"string\") {\n return group(groupName[0]);\n } else {\n throw new Error(\"Invalid groupName argument\");\n }\n}\n\nclass Group {\n constructor(name) {\n this.name = name;\n this._vars = {};\n }\n\n var(name) {\n if (!name || typeof(name) !== \"string\") {\n throw new Error(\"Invalid var name\");\n }\n\n if (!this._vars.hasOwnProperty(name))\n this._vars[name] = new Var(this, name);\n return this._vars[name];\n }\n\n has(name) {\n if (!name || typeof(name) !== \"string\") {\n throw new Error(\"Invalid var name\");\n }\n\n return this._vars.hasOwnProperty(name);\n }\n}\n", + "import group from \"./group\";\nimport { SelectionHandle } from \"./selection\";\nimport { FilterHandle } from \"./filter\";\nimport { bind } from \"./input\";\nimport \"./input_selectize\";\nimport \"./input_checkboxgroup\";\nimport \"./input_slider\";\n\nconst defaultGroup = group(\"default\");\n\nfunction var_(name) {\n return defaultGroup.var(name);\n}\n\nfunction has(name) {\n return defaultGroup.has(name);\n}\n\nif (global.Shiny) {\n global.Shiny.addCustomMessageHandler(\"update-client-value\", function(message) {\n if (typeof(message.group) === \"string\") {\n group(message.group).var(message.name).set(message.value);\n } else {\n var_(message.name).set(message.value);\n }\n });\n}\n\nconst crosstalk = {\n group: group,\n var: var_,\n has: has,\n SelectionHandle: SelectionHandle,\n FilterHandle: FilterHandle,\n bind: bind\n};\n\n/**\n * @namespace crosstalk\n */\nexport default crosstalk;\nglobal.crosstalk = crosstalk;\n", + "let $ = global.jQuery;\n\nlet bindings = {};\n\nexport function register(reg) {\n bindings[reg.className] = reg;\n if (global.document && global.document.readyState !== \"complete\") {\n $(() => {\n bind();\n });\n } else if (global.document) {\n setTimeout(bind, 100);\n }\n}\n\nexport function bind() {\n Object.keys(bindings).forEach(function(className) {\n let binding = bindings[className];\n $(\".\" + binding.className).not(\".crosstalk-input-bound\").each(function(i, el) {\n bindInstance(binding, el);\n });\n });\n}\n\n// Escape jQuery identifier\nfunction $escape(val) {\n return val.replace(/([!\"#$%&'()*+,./:;<=>?@[\\\\\\]^`{|}~])/g, \"\\\\$1\");\n}\n\nfunction bindEl(el) {\n let $el = $(el);\n Object.keys(bindings).forEach(function(className) {\n if ($el.hasClass(className) && !$el.hasClass(\"crosstalk-input-bound\")) {\n let binding = bindings[className];\n bindInstance(binding, el);\n }\n });\n}\n\nfunction bindInstance(binding, el) {\n let jsonEl = $(el).find(\"script[type='application/json'][data-for='\" + $escape(el.id) + \"']\");\n let data = JSON.parse(jsonEl[0].innerText);\n\n let instance = binding.factory(el, data);\n $(el).data(\"crosstalk-instance\", instance);\n $(el).addClass(\"crosstalk-input-bound\");\n}\n\nif (global.Shiny) {\n let inputBinding = new global.Shiny.InputBinding();\n let $ = global.jQuery;\n $.extend(inputBinding, {\n find: function(scope) {\n return $(scope).find(\".crosstalk-input\");\n },\n initialize: function(el) {\n if (!$(el).hasClass(\"crosstalk-input-bound\")) {\n bindEl(el);\n }\n },\n getId: function(el) {\n return el.id;\n },\n getValue: function(el) {\n\n },\n setValue: function(el, value) {\n\n },\n receiveMessage: function(el, data) {\n\n },\n subscribe: function(el, callback) {\n $(el).data(\"crosstalk-instance\").resume();\n },\n unsubscribe: function(el) {\n $(el).data(\"crosstalk-instance\").suspend();\n }\n });\n global.Shiny.inputBindings.register(inputBinding, \"crosstalk.inputBinding\");\n}\n", + "import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n className: \"crosstalk-input-checkboxgroup\",\n\n factory: function(el, data) {\n /*\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n let ctHandle = new FilterHandle(data.group);\n\n let lastKnownKeys;\n let $el = $(el);\n $el.on(\"change\", \"input[type='checkbox']\", function() {\n let checked = $el.find(\"input[type='checkbox']:checked\");\n if (checked.length === 0) {\n lastKnownKeys = null;\n ctHandle.clear();\n } else {\n let keys = {};\n checked.each(function() {\n data.map[this.value].forEach(function(key) {\n keys[key] = true;\n });\n });\n let keyArray = Object.keys(keys);\n keyArray.sort();\n lastKnownKeys = keyArray;\n ctHandle.set(keyArray);\n }\n });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n", + "import * as input from \"./input\";\nimport * as util from \"./util\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n className: \"crosstalk-input-select\",\n\n factory: function(el, data) {\n /*\n * items: {value: [...], label: [...]}\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n\n let first = [{value: \"\", label: \"(All)\"}];\n let items = util.dataframeToD3(data.items);\n let opts = {\n options: first.concat(items),\n valueField: \"value\",\n labelField: \"label\",\n searchField: \"label\"\n };\n\n let select = $(el).find(\"select\")[0];\n\n let selectize = $(select).selectize(opts)[0].selectize;\n\n let ctHandle = new FilterHandle(data.group);\n\n let lastKnownKeys;\n selectize.on(\"change\", function() {\n if (selectize.items.length === 0) {\n lastKnownKeys = null;\n ctHandle.clear();\n } else {\n let keys = {};\n selectize.items.forEach(function(group) {\n data.map[group].forEach(function(key) {\n keys[key] = true;\n });\n });\n let keyArray = Object.keys(keys);\n keyArray.sort();\n lastKnownKeys = keyArray;\n ctHandle.set(keyArray);\n }\n });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n", + "import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\nlet strftime = global.strftime;\n\ninput.register({\n className: \"crosstalk-input-slider\",\n\n factory: function(el, data) {\n /*\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n let ctHandle = new FilterHandle(data.group);\n\n let opts = {};\n let $el = $(el).find(\"input\");\n let dataType = $el.data(\"data-type\");\n let timeFormat = $el.data(\"time-format\");\n let round = $el.data(\"round\");\n let timeFormatter;\n\n // Set up formatting functions\n if (dataType === \"date\") {\n timeFormatter = strftime.utc();\n opts.prettify = function(num) {\n return timeFormatter(timeFormat, new Date(num));\n };\n\n } else if (dataType === \"datetime\") {\n let timezone = $el.data(\"timezone\");\n if (timezone)\n timeFormatter = strftime.timezone(timezone);\n else\n timeFormatter = strftime;\n\n opts.prettify = function(num) {\n return timeFormatter(timeFormat, new Date(num));\n };\n } else if (dataType === \"number\") {\n if (typeof round !== \"undefined\")\n opts.prettify = function(num) {\n let factor = Math.pow(10, round);\n return Math.round(num * factor) / factor;\n };\n }\n\n $el.ionRangeSlider(opts);\n\n function getValue() {\n let result = $el.data(\"ionRangeSlider\").result;\n\n // Function for converting numeric value from slider to appropriate type.\n let convert;\n let dataType = $el.data(\"data-type\");\n if (dataType === \"date\") {\n convert = function(val) {\n return formatDateUTC(new Date(+val));\n };\n } else if (dataType === \"datetime\") {\n convert = function(val) {\n // Convert ms to s\n return +val / 1000;\n };\n } else {\n convert = function(val) { return +val; };\n }\n\n if ($el.data(\"ionRangeSlider\").options.type === \"double\") {\n return [convert(result.from), convert(result.to)];\n } else {\n return convert(result.from);\n }\n }\n\n let lastKnownKeys = null;\n\n $el.on(\"change.crosstalkSliderInput\", function(event) {\n if (!$el.data(\"updating\") && !$el.data(\"animating\")) {\n let [from, to] = getValue();\n let keys = [];\n for (let i = 0; i < data.values.length; i++) {\n let val = data.values[i];\n if (val >= from && val <= to) {\n keys.push(data.keys[i]);\n }\n }\n keys.sort();\n ctHandle.set(keys);\n lastKnownKeys = keys;\n }\n });\n\n\n // let $el = $(el);\n // $el.on(\"change\", \"input[type=\"checkbox\"]\", function() {\n // let checked = $el.find(\"input[type=\"checkbox\"]:checked\");\n // if (checked.length === 0) {\n // ctHandle.clear();\n // } else {\n // let keys = {};\n // checked.each(function() {\n // data.map[this.value].forEach(function(key) {\n // keys[key] = true;\n // });\n // });\n // let keyArray = Object.keys(keys);\n // keyArray.sort();\n // ctHandle.set(keyArray);\n // }\n // });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n\n\n// Convert a number to a string with leading zeros\nfunction padZeros(n, digits) {\n let str = n.toString();\n while (str.length < digits)\n str = \"0\" + str;\n return str;\n}\n\n// Given a Date object, return a string in yyyy-mm-dd format, using the\n// UTC date. This may be a day off from the date in the local time zone.\nfunction formatDateUTC(date) {\n if (date instanceof Date) {\n return date.getUTCFullYear() + \"-\" +\n padZeros(date.getUTCMonth()+1, 2) + \"-\" +\n padZeros(date.getUTCDate(), 2);\n\n } else {\n return null;\n }\n}\n", + "import Events from \"./events\";\nimport grp from \"./group\";\nimport * as util from \"./util\";\n\n/**\n * Use this class to read and write (and listen for changes to) the selection\n * for a Crosstalk group. This is intended to be used for linked brushing.\n *\n * If two (or more) `SelectionHandle` instances in the same webpage share the\n * same group name, they will share the same state. Setting the selection using\n * one `SelectionHandle` instance will result in the `value` property instantly\n * changing across the others, and `\"change\"` event listeners on all instances\n * (including the one that initiated the sending) will fire.\n *\n * @param {string} [group] - The name of the Crosstalk group, or if none,\n * null or undefined (or any other falsy value). This can be changed later\n * via the [SelectionHandle#setGroup](#setGroup) method.\n * @param {Object} [extraInfo] - An object whose properties will be copied to\n * the event object whenever an event is emitted.\n */\nexport class SelectionHandle {\n\n constructor(group = null, extraInfo = null) {\n this._eventRelay = new Events();\n this._emitter = new util.SubscriptionTracker(this._eventRelay);\n\n // Name of the group we're currently tracking, if any. Can change over time.\n this._group = null;\n // The Var we're currently tracking, if any. Can change over time.\n this._var = null;\n // The event handler subscription we currently have on var.on(\"change\").\n this._varOnChangeSub = null;\n\n this._extraInfo = util.extend({ sender: this }, extraInfo);\n\n this.setGroup(group);\n }\n\n /**\n * Changes the Crosstalk group membership of this SelectionHandle. The group\n * being switched away from (if any) will not have its selection value\n * modified as a result of calling `setGroup`, even if this handle was the\n * most recent handle to set the selection of the group.\n *\n * The group being switched to (if any) will also not have its selection value\n * modified as a result of calling `setGroup`. If you want to set the\n * selection value of the new group, call `set` explicitly.\n *\n * @param {string} group - The name of the Crosstalk group, or null (or\n * undefined) to clear the group.\n */\n setGroup(group) {\n // If group is unchanged, do nothing\n if (this._group === group)\n return;\n // Treat null, undefined, and other falsy values the same\n if (!this._group && !group)\n return;\n\n if (this._var) {\n this._var.off(\"change\", this._varOnChangeSub);\n this._var = null;\n this._varOnChangeSub = null;\n }\n\n this._group = group;\n\n if (group) {\n this._var = grp(group).var(\"selection\");\n let sub = this._var.on(\"change\", (e) => {\n this._eventRelay.trigger(\"change\", e, this);\n });\n this._varOnChangeSub = sub;\n }\n }\n\n /**\n * Retrieves the current selection for the group represented by this\n * `SelectionHandle`.\n *\n * - If no selection is active, then this value will be falsy.\n * - If a selection is active, but no data points are selected, then this\n * value will be an empty array.\n * - If a selection is active, and data points are selected, then the keys\n * of the selected data points will be present in the array.\n */\n get value() {\n return this._var ? this._var.get() : null;\n }\n\n /**\n * Combines the given `extraInfo` (if any) with the handle's default\n * `_extraInfo` (if any).\n * @private\n */\n _mergeExtraInfo(extraInfo) {\n // Important incidental effect: shallow clone is returned\n return util.extend({},\n this._extraInfo ? this._extraInfo : null,\n extraInfo ? extraInfo : null);\n }\n\n /**\n * Overwrites the current selection for the group, and raises the `\"change\"`\n * event among all of the group's '`SelectionHandle` instances (including\n * this one).\n *\n * @fires SelectionHandle#change\n * @param {string[]} selectedKeys - Falsy, empty array, or array of keys (see\n * {@link SelectionHandle#value}).\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `SelectionHandle` constructor).\n */\n set(selectedKeys, extraInfo) {\n if (this._var)\n this._var.set(selectedKeys, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * Overwrites the current selection for the group, and raises the `\"change\"`\n * event among all of the group's '`SelectionHandle` instances (including\n * this one).\n *\n * @fires SelectionHandle#change\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any that were passed\n * into the `SelectionHandle` constructor).\n */\n clear(extraInfo) {\n if (this._var)\n this.set(void 0, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * Subscribes to events on this `SelectionHandle`.\n *\n * @param {string} eventType - Indicates the type of events to listen to.\n * Currently, only `\"change\"` is supported.\n * @param {SelectionHandle~listener} listener - The callback function that\n * will be invoked when the event occurs.\n * @return {string} - A token to pass to {@link SelectionHandle#off} to cancel\n * this subscription.\n */\n on(eventType, listener) {\n return this._emitter.on(eventType, listener);\n }\n\n /**\n * Cancels event subscriptions created by {@link SelectionHandle#on}.\n *\n * @param {string} eventType - The type of event to unsubscribe.\n * @param {string|SelectionHandle~listener} listener - Either the callback\n * function previously passed into {@link SelectionHandle#on}, or the\n * string that was returned from {@link SelectionHandle#on}.\n */\n off(eventType, listener) {\n return this._emitter.off(eventType, listener);\n }\n\n /**\n * Shuts down the `SelectionHandle` object.\n *\n * Removes all event listeners that were added through this handle.\n */\n close() {\n this._emitter.removeAllListeners();\n this.setGroup(null);\n }\n}\n\n/**\n * @callback SelectionHandle~listener\n * @param {Object} event - An object containing details of the event. For\n * `\"change\"` events, this includes the properties `value` (the new\n * value of the selection, or `undefined` if no selection is active),\n * `oldValue` (the previous value of the selection), and `sender` (the\n * `SelectionHandle` instance that made the change).\n */\n\n/**\n * @event SelectionHandle#change\n * @type {object}\n * @property {object} value - The new value of the selection, or `undefined`\n * if no selection is active.\n * @property {object} oldValue - The previous value of the selection.\n * @property {SelectionHandle} sender - The `SelectionHandle` instance that\n * changed the value.\n */\n", + "export function extend(target, ...sources) {\n for (let i = 0; i < sources.length; i++) {\n let src = sources[i];\n if (typeof(src) === \"undefined\" || src === null)\n continue;\n\n for (let key in src) {\n if (src.hasOwnProperty(key)) {\n target[key] = src[key];\n }\n }\n }\n return target;\n}\n\nexport function checkSorted(list) {\n for (let i = 1; i < list.length; i++) {\n if (list[i] <= list[i-1]) {\n throw new Error(\"List is not sorted or contains duplicate\");\n }\n }\n}\n\nexport function diffSortedLists(a, b) {\n let i_a = 0;\n let i_b = 0;\n\n if (!a) a = [];\n if (!b) b = [];\n\n let a_only = [];\n let b_only = [];\n\n checkSorted(a);\n checkSorted(b);\n\n while (i_a < a.length && i_b < b.length) {\n if (a[i_a] === b[i_b]) {\n i_a++;\n i_b++;\n } else if (a[i_a] < b[i_b]) {\n a_only.push(a[i_a++]);\n } else {\n b_only.push(b[i_b++]);\n }\n }\n\n if (i_a < a.length)\n a_only = a_only.concat(a.slice(i_a));\n if (i_b < b.length)\n b_only = b_only.concat(b.slice(i_b));\n return {\n removed: a_only,\n added: b_only\n };\n}\n\n// Convert from wide: { colA: [1,2,3], colB: [4,5,6], ... }\n// to long: [ {colA: 1, colB: 4}, {colA: 2, colB: 5}, ... ]\nexport function dataframeToD3(df) {\n let names = [];\n let length;\n for (let name in df) {\n if (df.hasOwnProperty(name))\n names.push(name);\n if (typeof(df[name]) !== \"object\" || typeof(df[name].length) === \"undefined\") {\n throw new Error(\"All fields must be arrays\");\n } else if (typeof(length) !== \"undefined\" && length !== df[name].length) {\n throw new Error(\"All fields must be arrays of the same length\");\n }\n length = df[name].length;\n }\n let results = [];\n let item;\n for (let row = 0; row < length; row++) {\n item = {};\n for (let col = 0; col < names.length; col++) {\n item[names[col]] = df[names[col]][row];\n }\n results.push(item);\n }\n return results;\n}\n\n/**\n * Keeps track of all event listener additions/removals and lets all active\n * listeners be removed with a single operation.\n *\n * @private\n */\nexport class SubscriptionTracker {\n constructor(emitter) {\n this._emitter = emitter;\n this._subs = {};\n }\n\n on(eventType, listener) {\n let sub = this._emitter.on(eventType, listener);\n this._subs[sub] = eventType;\n return sub;\n }\n\n off(eventType, listener) {\n let sub = this._emitter.off(eventType, listener);\n if (sub) {\n delete this._subs[sub];\n }\n return sub;\n }\n\n removeAllListeners() {\n let current_subs = this._subs;\n this._subs = {};\n Object.keys(current_subs).forEach((sub) => {\n this._emitter.off(current_subs[sub], sub);\n });\n }\n}\n", + "import Events from \"./events\";\n\nexport default class Var {\n constructor(group, name, /*optional*/ value) {\n this._group = group;\n this._name = name;\n this._value = value;\n this._events = new Events();\n }\n\n get() {\n return this._value;\n }\n\n set(value, /*optional*/ event) {\n if (this._value === value) {\n // Do nothing; the value hasn't changed\n return;\n }\n let oldValue = this._value;\n this._value = value;\n // Alert JavaScript listeners that the value has changed\n let evt = {};\n if (event && typeof(event) === \"object\") {\n for (let k in event) {\n if (event.hasOwnProperty(k))\n evt[k] = event[k];\n }\n }\n evt.oldValue = oldValue;\n evt.value = value;\n this._events.trigger(\"change\", evt, this);\n\n // TODO: Make this extensible, to let arbitrary back-ends know that\n // something has changed\n if (global.Shiny && global.Shiny.onInputChange) {\n global.Shiny.onInputChange(\n \".clientValue-\" +\n (this._group.name !== null ? this._group.name + \"-\" : \"\") +\n this._name,\n typeof(value) === \"undefined\" ? null : value\n );\n }\n }\n\n on(eventType, listener) {\n return this._events.on(eventType, listener);\n }\n\n off(eventType, listener) {\n return this._events.off(eventType, listener);\n }\n}\n" + ] +} \ No newline at end of file diff --git a/docs/articles/database_of_anor_files/crosstalk-1.1.0.1/js/crosstalk.min.js b/docs/articles/database_of_anor_files/crosstalk-1.1.0.1/js/crosstalk.min.js new file mode 100644 index 0000000..b7ec0ac --- /dev/null +++ b/docs/articles/database_of_anor_files/crosstalk-1.1.0.1/js/crosstalk.min.js @@ -0,0 +1,2 @@ +!function o(u,a,l){function s(n,e){if(!a[n]){if(!u[n]){var t="function"==typeof require&&require;if(!e&&t)return t(n,!0);if(f)return f(n,!0);var r=new Error("Cannot find module '"+n+"'");throw r.code="MODULE_NOT_FOUND",r}var i=a[n]={exports:{}};u[n][0].call(i.exports,function(e){var t=u[n][1][e];return s(t||e)},i,i.exports,o,u,a,l)}return a[n].exports}for(var f="function"==typeof require&&require,e=0;e?@[\\\]^`{|}~])/g,"\\$1")+"']"),r=JSON.parse(n[0].innerText),i=e.factory(t,r);o(t).data("crosstalk-instance",i),o(t).addClass("crosstalk-input-bound")}if(t.Shiny){var e=new t.Shiny.InputBinding,u=t.jQuery;u.extend(e,{find:function(e){return u(e).find(".crosstalk-input")},initialize:function(e){var t,n;u(e).hasClass("crosstalk-input-bound")||(n=o(t=e),Object.keys(r).forEach(function(e){n.hasClass(e)&&!n.hasClass("crosstalk-input-bound")&&i(r[e],t)}))},getId:function(e){return e.id},getValue:function(e){},setValue:function(e,t){},receiveMessage:function(e,t){},subscribe:function(e,t){u(e).data("crosstalk-instance").resume()},unsubscribe:function(e){u(e).data("crosstalk-instance").suspend()}}),t.Shiny.inputBindings.register(e,"crosstalk.inputBinding")}}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{}],7:[function(r,e,t){(function(e){"use strict";var t=function(e){{if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.prototype.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t}}(r("./input")),n=r("./filter");var a=e.jQuery;t.register({className:"crosstalk-input-checkboxgroup",factory:function(e,r){var i=new n.FilterHandle(r.group),o=void 0,u=a(e);return u.on("change","input[type='checkbox']",function(){var e=u.find("input[type='checkbox']:checked");if(0===e.length)o=null,i.clear();else{var t={};e.each(function(){r.map[this.value].forEach(function(e){t[e]=!0})});var n=Object.keys(t);n.sort(),o=n,i.set(n)}}),{suspend:function(){i.clear()},resume:function(){o&&i.set(o)}}}})}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{"./filter":2,"./input":6}],8:[function(r,e,t){(function(e){"use strict";var t=n(r("./input")),l=n(r("./util")),s=r("./filter");function n(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.prototype.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t}var f=e.jQuery;t.register({className:"crosstalk-input-select",factory:function(e,n){var t=l.dataframeToD3(n.items),r={options:[{value:"",label:"(All)"}].concat(t),valueField:"value",labelField:"label",searchField:"label"},i=f(e).find("select")[0],o=f(i).selectize(r)[0].selectize,u=new s.FilterHandle(n.group),a=void 0;return o.on("change",function(){if(0===o.items.length)a=null,u.clear();else{var t={};o.items.forEach(function(e){n.map[e].forEach(function(e){t[e]=!0})});var e=Object.keys(t);e.sort(),a=e,u.set(e)}}),{suspend:function(){u.clear()},resume:function(){a&&u.set(a)}}}})}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{"./filter":2,"./input":6,"./util":11}],9:[function(n,e,t){(function(e){"use strict";var d=function(e,t){if(Array.isArray(e))return e;if(Symbol.iterator in Object(e))return function(e,t){var n=[],r=!0,i=!1,o=void 0;try{for(var u,a=e[Symbol.iterator]();!(r=(u=a.next()).done)&&(n.push(u.value),!t||n.length!==t);r=!0);}catch(e){i=!0,o=e}finally{try{!r&&a.return&&a.return()}finally{if(i)throw o}}return n}(e,t);throw new TypeError("Invalid attempt to destructure non-iterable instance")},t=function(e){{if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.prototype.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t}}(n("./input")),a=n("./filter");var v=e.jQuery,p=e.strftime;function y(e,t){for(var n=e.toString();n.length {\n this._eventRelay.trigger(\"change\", e, this);\n });\n this._varOnChangeSub = sub;\n }\n }\n\n /**\n * Combine the given `extraInfo` (if any) with the handle's default\n * `_extraInfo` (if any).\n * @private\n */\n _mergeExtraInfo(extraInfo) {\n return util.extend({},\n this._extraInfo ? this._extraInfo : null,\n extraInfo ? extraInfo : null);\n }\n\n /**\n * Close the handle. This clears this handle's contribution to the filter set,\n * and unsubscribes all event listeners.\n */\n close() {\n this._emitter.removeAllListeners();\n this.clear();\n this.setGroup(null);\n }\n\n /**\n * Clear this handle's contribution to the filter set.\n *\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `FilterHandle` constructor).\n * \n * @fires FilterHandle#change\n */\n clear(extraInfo) {\n if (!this._filterSet)\n return;\n this._filterSet.clear(this._id);\n this._onChange(extraInfo);\n }\n\n /**\n * Set this handle's contribution to the filter set. This array should consist\n * of the keys of the rows that _should_ be displayed; any keys that are not\n * present in the array will be considered _filtered out_. Note that multiple\n * `FilterHandle` instances in the group may each contribute an array of keys,\n * and only those keys that appear in _all_ of the arrays make it through the\n * filter.\n *\n * @param {string[]} keys - Empty array, or array of keys. To clear the\n * filter, don't pass an empty array; instead, use the\n * {@link FilterHandle#clear} method.\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `FilterHandle` constructor).\n * \n * @fires FilterHandle#change\n */\n set(keys, extraInfo) {\n if (!this._filterSet)\n return;\n this._filterSet.update(this._id, keys);\n this._onChange(extraInfo);\n }\n\n /**\n * @return {string[]|null} - Either: 1) an array of keys that made it through\n * all of the `FilterHandle` instances, or, 2) `null`, which means no filter\n * is being applied (all data should be displayed).\n */\n get filteredKeys() {\n return this._filterSet ? this._filterSet.value : null;\n }\n\n /**\n * Subscribe to events on this `FilterHandle`.\n *\n * @param {string} eventType - Indicates the type of events to listen to.\n * Currently, only `\"change\"` is supported.\n * @param {FilterHandle~listener} listener - The callback function that\n * will be invoked when the event occurs.\n * @return {string} - A token to pass to {@link FilterHandle#off} to cancel\n * this subscription.\n */\n on(eventType, listener) {\n return this._emitter.on(eventType, listener);\n }\n\n /**\n * Cancel event subscriptions created by {@link FilterHandle#on}.\n *\n * @param {string} eventType - The type of event to unsubscribe.\n * @param {string|FilterHandle~listener} listener - Either the callback\n * function previously passed into {@link FilterHandle#on}, or the\n * string that was returned from {@link FilterHandle#on}.\n */\n off(eventType, listener) {\n return this._emitter.off(eventType, listener);\n }\n\n _onChange(extraInfo) {\n if (!this._filterSet)\n return;\n this._filterVar.set(this._filterSet.value, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * @callback FilterHandle~listener\n * @param {Object} event - An object containing details of the event. For\n * `\"change\"` events, this includes the properties `value` (the new\n * value of the filter set, or `null` if no filter set is active),\n * `oldValue` (the previous value of the filter set), and `sender` (the\n * `FilterHandle` instance that made the change).\n */\n\n}\n\n/**\n * @event FilterHandle#change\n * @type {object}\n * @property {object} value - The new value of the filter set, or `null`\n * if no filter set is active.\n * @property {object} oldValue - The previous value of the filter set.\n * @property {FilterHandle} sender - The `FilterHandle` instance that\n * changed the value.\n */\n","import { diffSortedLists } from \"./util\";\n\nfunction naturalComparator(a, b) {\n if (a === b) {\n return 0;\n } else if (a < b) {\n return -1;\n } else if (a > b) {\n return 1;\n }\n}\n\n/**\n * @private\n */\nexport default class FilterSet {\n constructor() {\n this.reset();\n }\n\n reset() {\n // Key: handle ID, Value: array of selected keys, or null\n this._handles = {};\n // Key: key string, Value: count of handles that include it\n this._keys = {};\n this._value = null;\n this._activeHandles = 0;\n }\n\n get value() {\n return this._value;\n }\n\n update(handleId, keys) {\n if (keys !== null) {\n keys = keys.slice(0); // clone before sorting\n keys.sort(naturalComparator);\n }\n\n let {added, removed} = diffSortedLists(this._handles[handleId], keys);\n this._handles[handleId] = keys;\n\n for (let i = 0; i < added.length; i++) {\n this._keys[added[i]] = (this._keys[added[i]] || 0) + 1;\n }\n for (let i = 0; i < removed.length; i++) {\n this._keys[removed[i]]--;\n }\n\n this._updateValue(keys);\n }\n\n /**\n * @param {string[]} keys Sorted array of strings that indicate\n * a superset of possible keys.\n * @private\n */\n _updateValue(keys = this._allKeys) {\n let handleCount = Object.keys(this._handles).length;\n if (handleCount === 0) {\n this._value = null;\n } else {\n this._value = [];\n for (let i = 0; i < keys.length; i++) {\n let count = this._keys[keys[i]];\n if (count === handleCount) {\n this._value.push(keys[i]);\n }\n }\n }\n }\n\n clear(handleId) {\n if (typeof(this._handles[handleId]) === \"undefined\") {\n return;\n }\n\n let keys = this._handles[handleId];\n if (!keys) {\n keys = [];\n }\n\n for (let i = 0; i < keys.length; i++) {\n this._keys[keys[i]]--;\n }\n delete this._handles[handleId];\n\n this._updateValue();\n }\n\n get _allKeys() {\n let allKeys = Object.keys(this._keys);\n allKeys.sort(naturalComparator);\n return allKeys;\n }\n}\n","import Var from \"./var\";\n\n// Use a global so that multiple copies of crosstalk.js can be loaded and still\n// have groups behave as singletons across all copies.\nglobal.__crosstalk_groups = global.__crosstalk_groups || {};\nlet groups = global.__crosstalk_groups;\n\nexport default function group(groupName) {\n if (groupName && typeof(groupName) === \"string\") {\n if (!groups.hasOwnProperty(groupName)) {\n groups[groupName] = new Group(groupName);\n }\n return groups[groupName];\n } else if (typeof(groupName) === \"object\" && groupName._vars && groupName.var) {\n // Appears to already be a group object\n return groupName;\n } else if (Array.isArray(groupName) &&\n groupName.length == 1 &&\n typeof(groupName[0]) === \"string\") {\n return group(groupName[0]);\n } else {\n throw new Error(\"Invalid groupName argument\");\n }\n}\n\nclass Group {\n constructor(name) {\n this.name = name;\n this._vars = {};\n }\n\n var(name) {\n if (!name || typeof(name) !== \"string\") {\n throw new Error(\"Invalid var name\");\n }\n\n if (!this._vars.hasOwnProperty(name))\n this._vars[name] = new Var(this, name);\n return this._vars[name];\n }\n\n has(name) {\n if (!name || typeof(name) !== \"string\") {\n throw new Error(\"Invalid var name\");\n }\n\n return this._vars.hasOwnProperty(name);\n }\n}\n","import group from \"./group\";\nimport { SelectionHandle } from \"./selection\";\nimport { FilterHandle } from \"./filter\";\nimport { bind } from \"./input\";\nimport \"./input_selectize\";\nimport \"./input_checkboxgroup\";\nimport \"./input_slider\";\n\nconst defaultGroup = group(\"default\");\n\nfunction var_(name) {\n return defaultGroup.var(name);\n}\n\nfunction has(name) {\n return defaultGroup.has(name);\n}\n\nif (global.Shiny) {\n global.Shiny.addCustomMessageHandler(\"update-client-value\", function(message) {\n if (typeof(message.group) === \"string\") {\n group(message.group).var(message.name).set(message.value);\n } else {\n var_(message.name).set(message.value);\n }\n });\n}\n\nconst crosstalk = {\n group: group,\n var: var_,\n has: has,\n SelectionHandle: SelectionHandle,\n FilterHandle: FilterHandle,\n bind: bind\n};\n\n/**\n * @namespace crosstalk\n */\nexport default crosstalk;\nglobal.crosstalk = crosstalk;\n","let $ = global.jQuery;\n\nlet bindings = {};\n\nexport function register(reg) {\n bindings[reg.className] = reg;\n if (global.document && global.document.readyState !== \"complete\") {\n $(() => {\n bind();\n });\n } else if (global.document) {\n setTimeout(bind, 100);\n }\n}\n\nexport function bind() {\n Object.keys(bindings).forEach(function(className) {\n let binding = bindings[className];\n $(\".\" + binding.className).not(\".crosstalk-input-bound\").each(function(i, el) {\n bindInstance(binding, el);\n });\n });\n}\n\n// Escape jQuery identifier\nfunction $escape(val) {\n return val.replace(/([!\"#$%&'()*+,./:;<=>?@[\\\\\\]^`{|}~])/g, \"\\\\$1\");\n}\n\nfunction bindEl(el) {\n let $el = $(el);\n Object.keys(bindings).forEach(function(className) {\n if ($el.hasClass(className) && !$el.hasClass(\"crosstalk-input-bound\")) {\n let binding = bindings[className];\n bindInstance(binding, el);\n }\n });\n}\n\nfunction bindInstance(binding, el) {\n let jsonEl = $(el).find(\"script[type='application/json'][data-for='\" + $escape(el.id) + \"']\");\n let data = JSON.parse(jsonEl[0].innerText);\n\n let instance = binding.factory(el, data);\n $(el).data(\"crosstalk-instance\", instance);\n $(el).addClass(\"crosstalk-input-bound\");\n}\n\nif (global.Shiny) {\n let inputBinding = new global.Shiny.InputBinding();\n let $ = global.jQuery;\n $.extend(inputBinding, {\n find: function(scope) {\n return $(scope).find(\".crosstalk-input\");\n },\n initialize: function(el) {\n if (!$(el).hasClass(\"crosstalk-input-bound\")) {\n bindEl(el);\n }\n },\n getId: function(el) {\n return el.id;\n },\n getValue: function(el) {\n\n },\n setValue: function(el, value) {\n\n },\n receiveMessage: function(el, data) {\n\n },\n subscribe: function(el, callback) {\n $(el).data(\"crosstalk-instance\").resume();\n },\n unsubscribe: function(el) {\n $(el).data(\"crosstalk-instance\").suspend();\n }\n });\n global.Shiny.inputBindings.register(inputBinding, \"crosstalk.inputBinding\");\n}\n","import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n className: \"crosstalk-input-checkboxgroup\",\n\n factory: function(el, data) {\n /*\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n let ctHandle = new FilterHandle(data.group);\n\n let lastKnownKeys;\n let $el = $(el);\n $el.on(\"change\", \"input[type='checkbox']\", function() {\n let checked = $el.find(\"input[type='checkbox']:checked\");\n if (checked.length === 0) {\n lastKnownKeys = null;\n ctHandle.clear();\n } else {\n let keys = {};\n checked.each(function() {\n data.map[this.value].forEach(function(key) {\n keys[key] = true;\n });\n });\n let keyArray = Object.keys(keys);\n keyArray.sort();\n lastKnownKeys = keyArray;\n ctHandle.set(keyArray);\n }\n });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n","import * as input from \"./input\";\nimport * as util from \"./util\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n className: \"crosstalk-input-select\",\n\n factory: function(el, data) {\n /*\n * items: {value: [...], label: [...]}\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n\n let first = [{value: \"\", label: \"(All)\"}];\n let items = util.dataframeToD3(data.items);\n let opts = {\n options: first.concat(items),\n valueField: \"value\",\n labelField: \"label\",\n searchField: \"label\"\n };\n\n let select = $(el).find(\"select\")[0];\n\n let selectize = $(select).selectize(opts)[0].selectize;\n\n let ctHandle = new FilterHandle(data.group);\n\n let lastKnownKeys;\n selectize.on(\"change\", function() {\n if (selectize.items.length === 0) {\n lastKnownKeys = null;\n ctHandle.clear();\n } else {\n let keys = {};\n selectize.items.forEach(function(group) {\n data.map[group].forEach(function(key) {\n keys[key] = true;\n });\n });\n let keyArray = Object.keys(keys);\n keyArray.sort();\n lastKnownKeys = keyArray;\n ctHandle.set(keyArray);\n }\n });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n","import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\nlet strftime = global.strftime;\n\ninput.register({\n className: \"crosstalk-input-slider\",\n\n factory: function(el, data) {\n /*\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n let ctHandle = new FilterHandle(data.group);\n\n let opts = {};\n let $el = $(el).find(\"input\");\n let dataType = $el.data(\"data-type\");\n let timeFormat = $el.data(\"time-format\");\n let round = $el.data(\"round\");\n let timeFormatter;\n\n // Set up formatting functions\n if (dataType === \"date\") {\n timeFormatter = strftime.utc();\n opts.prettify = function(num) {\n return timeFormatter(timeFormat, new Date(num));\n };\n\n } else if (dataType === \"datetime\") {\n let timezone = $el.data(\"timezone\");\n if (timezone)\n timeFormatter = strftime.timezone(timezone);\n else\n timeFormatter = strftime;\n\n opts.prettify = function(num) {\n return timeFormatter(timeFormat, new Date(num));\n };\n } else if (dataType === \"number\") {\n if (typeof round !== \"undefined\")\n opts.prettify = function(num) {\n let factor = Math.pow(10, round);\n return Math.round(num * factor) / factor;\n };\n }\n\n $el.ionRangeSlider(opts);\n\n function getValue() {\n let result = $el.data(\"ionRangeSlider\").result;\n\n // Function for converting numeric value from slider to appropriate type.\n let convert;\n let dataType = $el.data(\"data-type\");\n if (dataType === \"date\") {\n convert = function(val) {\n return formatDateUTC(new Date(+val));\n };\n } else if (dataType === \"datetime\") {\n convert = function(val) {\n // Convert ms to s\n return +val / 1000;\n };\n } else {\n convert = function(val) { return +val; };\n }\n\n if ($el.data(\"ionRangeSlider\").options.type === \"double\") {\n return [convert(result.from), convert(result.to)];\n } else {\n return convert(result.from);\n }\n }\n\n let lastKnownKeys = null;\n\n $el.on(\"change.crosstalkSliderInput\", function(event) {\n if (!$el.data(\"updating\") && !$el.data(\"animating\")) {\n let [from, to] = getValue();\n let keys = [];\n for (let i = 0; i < data.values.length; i++) {\n let val = data.values[i];\n if (val >= from && val <= to) {\n keys.push(data.keys[i]);\n }\n }\n keys.sort();\n ctHandle.set(keys);\n lastKnownKeys = keys;\n }\n });\n\n\n // let $el = $(el);\n // $el.on(\"change\", \"input[type=\"checkbox\"]\", function() {\n // let checked = $el.find(\"input[type=\"checkbox\"]:checked\");\n // if (checked.length === 0) {\n // ctHandle.clear();\n // } else {\n // let keys = {};\n // checked.each(function() {\n // data.map[this.value].forEach(function(key) {\n // keys[key] = true;\n // });\n // });\n // let keyArray = Object.keys(keys);\n // keyArray.sort();\n // ctHandle.set(keyArray);\n // }\n // });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n\n\n// Convert a number to a string with leading zeros\nfunction padZeros(n, digits) {\n let str = n.toString();\n while (str.length < digits)\n str = \"0\" + str;\n return str;\n}\n\n// Given a Date object, return a string in yyyy-mm-dd format, using the\n// UTC date. This may be a day off from the date in the local time zone.\nfunction formatDateUTC(date) {\n if (date instanceof Date) {\n return date.getUTCFullYear() + \"-\" +\n padZeros(date.getUTCMonth()+1, 2) + \"-\" +\n padZeros(date.getUTCDate(), 2);\n\n } else {\n return null;\n }\n}\n","import Events from \"./events\";\nimport grp from \"./group\";\nimport * as util from \"./util\";\n\n/**\n * Use this class to read and write (and listen for changes to) the selection\n * for a Crosstalk group. This is intended to be used for linked brushing.\n *\n * If two (or more) `SelectionHandle` instances in the same webpage share the\n * same group name, they will share the same state. Setting the selection using\n * one `SelectionHandle` instance will result in the `value` property instantly\n * changing across the others, and `\"change\"` event listeners on all instances\n * (including the one that initiated the sending) will fire.\n *\n * @param {string} [group] - The name of the Crosstalk group, or if none,\n * null or undefined (or any other falsy value). This can be changed later\n * via the [SelectionHandle#setGroup](#setGroup) method.\n * @param {Object} [extraInfo] - An object whose properties will be copied to\n * the event object whenever an event is emitted.\n */\nexport class SelectionHandle {\n\n constructor(group = null, extraInfo = null) {\n this._eventRelay = new Events();\n this._emitter = new util.SubscriptionTracker(this._eventRelay);\n\n // Name of the group we're currently tracking, if any. Can change over time.\n this._group = null;\n // The Var we're currently tracking, if any. Can change over time.\n this._var = null;\n // The event handler subscription we currently have on var.on(\"change\").\n this._varOnChangeSub = null;\n\n this._extraInfo = util.extend({ sender: this }, extraInfo);\n\n this.setGroup(group);\n }\n\n /**\n * Changes the Crosstalk group membership of this SelectionHandle. The group\n * being switched away from (if any) will not have its selection value\n * modified as a result of calling `setGroup`, even if this handle was the\n * most recent handle to set the selection of the group.\n *\n * The group being switched to (if any) will also not have its selection value\n * modified as a result of calling `setGroup`. If you want to set the\n * selection value of the new group, call `set` explicitly.\n *\n * @param {string} group - The name of the Crosstalk group, or null (or\n * undefined) to clear the group.\n */\n setGroup(group) {\n // If group is unchanged, do nothing\n if (this._group === group)\n return;\n // Treat null, undefined, and other falsy values the same\n if (!this._group && !group)\n return;\n\n if (this._var) {\n this._var.off(\"change\", this._varOnChangeSub);\n this._var = null;\n this._varOnChangeSub = null;\n }\n\n this._group = group;\n\n if (group) {\n this._var = grp(group).var(\"selection\");\n let sub = this._var.on(\"change\", (e) => {\n this._eventRelay.trigger(\"change\", e, this);\n });\n this._varOnChangeSub = sub;\n }\n }\n\n /**\n * Retrieves the current selection for the group represented by this\n * `SelectionHandle`.\n *\n * - If no selection is active, then this value will be falsy.\n * - If a selection is active, but no data points are selected, then this\n * value will be an empty array.\n * - If a selection is active, and data points are selected, then the keys\n * of the selected data points will be present in the array.\n */\n get value() {\n return this._var ? this._var.get() : null;\n }\n\n /**\n * Combines the given `extraInfo` (if any) with the handle's default\n * `_extraInfo` (if any).\n * @private\n */\n _mergeExtraInfo(extraInfo) {\n // Important incidental effect: shallow clone is returned\n return util.extend({},\n this._extraInfo ? this._extraInfo : null,\n extraInfo ? extraInfo : null);\n }\n\n /**\n * Overwrites the current selection for the group, and raises the `\"change\"`\n * event among all of the group's '`SelectionHandle` instances (including\n * this one).\n *\n * @fires SelectionHandle#change\n * @param {string[]} selectedKeys - Falsy, empty array, or array of keys (see\n * {@link SelectionHandle#value}).\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `SelectionHandle` constructor).\n */\n set(selectedKeys, extraInfo) {\n if (this._var)\n this._var.set(selectedKeys, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * Overwrites the current selection for the group, and raises the `\"change\"`\n * event among all of the group's '`SelectionHandle` instances (including\n * this one).\n *\n * @fires SelectionHandle#change\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any that were passed\n * into the `SelectionHandle` constructor).\n */\n clear(extraInfo) {\n if (this._var)\n this.set(void 0, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * Subscribes to events on this `SelectionHandle`.\n *\n * @param {string} eventType - Indicates the type of events to listen to.\n * Currently, only `\"change\"` is supported.\n * @param {SelectionHandle~listener} listener - The callback function that\n * will be invoked when the event occurs.\n * @return {string} - A token to pass to {@link SelectionHandle#off} to cancel\n * this subscription.\n */\n on(eventType, listener) {\n return this._emitter.on(eventType, listener);\n }\n\n /**\n * Cancels event subscriptions created by {@link SelectionHandle#on}.\n *\n * @param {string} eventType - The type of event to unsubscribe.\n * @param {string|SelectionHandle~listener} listener - Either the callback\n * function previously passed into {@link SelectionHandle#on}, or the\n * string that was returned from {@link SelectionHandle#on}.\n */\n off(eventType, listener) {\n return this._emitter.off(eventType, listener);\n }\n\n /**\n * Shuts down the `SelectionHandle` object.\n *\n * Removes all event listeners that were added through this handle.\n */\n close() {\n this._emitter.removeAllListeners();\n this.setGroup(null);\n }\n}\n\n/**\n * @callback SelectionHandle~listener\n * @param {Object} event - An object containing details of the event. For\n * `\"change\"` events, this includes the properties `value` (the new\n * value of the selection, or `undefined` if no selection is active),\n * `oldValue` (the previous value of the selection), and `sender` (the\n * `SelectionHandle` instance that made the change).\n */\n\n/**\n * @event SelectionHandle#change\n * @type {object}\n * @property {object} value - The new value of the selection, or `undefined`\n * if no selection is active.\n * @property {object} oldValue - The previous value of the selection.\n * @property {SelectionHandle} sender - The `SelectionHandle` instance that\n * changed the value.\n */\n","export function extend(target, ...sources) {\n for (let i = 0; i < sources.length; i++) {\n let src = sources[i];\n if (typeof(src) === \"undefined\" || src === null)\n continue;\n\n for (let key in src) {\n if (src.hasOwnProperty(key)) {\n target[key] = src[key];\n }\n }\n }\n return target;\n}\n\nexport function checkSorted(list) {\n for (let i = 1; i < list.length; i++) {\n if (list[i] <= list[i-1]) {\n throw new Error(\"List is not sorted or contains duplicate\");\n }\n }\n}\n\nexport function diffSortedLists(a, b) {\n let i_a = 0;\n let i_b = 0;\n\n if (!a) a = [];\n if (!b) b = [];\n\n let a_only = [];\n let b_only = [];\n\n checkSorted(a);\n checkSorted(b);\n\n while (i_a < a.length && i_b < b.length) {\n if (a[i_a] === b[i_b]) {\n i_a++;\n i_b++;\n } else if (a[i_a] < b[i_b]) {\n a_only.push(a[i_a++]);\n } else {\n b_only.push(b[i_b++]);\n }\n }\n\n if (i_a < a.length)\n a_only = a_only.concat(a.slice(i_a));\n if (i_b < b.length)\n b_only = b_only.concat(b.slice(i_b));\n return {\n removed: a_only,\n added: b_only\n };\n}\n\n// Convert from wide: { colA: [1,2,3], colB: [4,5,6], ... }\n// to long: [ {colA: 1, colB: 4}, {colA: 2, colB: 5}, ... ]\nexport function dataframeToD3(df) {\n let names = [];\n let length;\n for (let name in df) {\n if (df.hasOwnProperty(name))\n names.push(name);\n if (typeof(df[name]) !== \"object\" || typeof(df[name].length) === \"undefined\") {\n throw new Error(\"All fields must be arrays\");\n } else if (typeof(length) !== \"undefined\" && length !== df[name].length) {\n throw new Error(\"All fields must be arrays of the same length\");\n }\n length = df[name].length;\n }\n let results = [];\n let item;\n for (let row = 0; row < length; row++) {\n item = {};\n for (let col = 0; col < names.length; col++) {\n item[names[col]] = df[names[col]][row];\n }\n results.push(item);\n }\n return results;\n}\n\n/**\n * Keeps track of all event listener additions/removals and lets all active\n * listeners be removed with a single operation.\n *\n * @private\n */\nexport class SubscriptionTracker {\n constructor(emitter) {\n this._emitter = emitter;\n this._subs = {};\n }\n\n on(eventType, listener) {\n let sub = this._emitter.on(eventType, listener);\n this._subs[sub] = eventType;\n return sub;\n }\n\n off(eventType, listener) {\n let sub = this._emitter.off(eventType, listener);\n if (sub) {\n delete this._subs[sub];\n }\n return sub;\n }\n\n removeAllListeners() {\n let current_subs = this._subs;\n this._subs = {};\n Object.keys(current_subs).forEach((sub) => {\n this._emitter.off(current_subs[sub], sub);\n });\n }\n}\n","import Events from \"./events\";\n\nexport default class Var {\n constructor(group, name, /*optional*/ value) {\n this._group = group;\n this._name = name;\n this._value = value;\n this._events = new Events();\n }\n\n get() {\n return this._value;\n }\n\n set(value, /*optional*/ event) {\n if (this._value === value) {\n // Do nothing; the value hasn't changed\n return;\n }\n let oldValue = this._value;\n this._value = value;\n // Alert JavaScript listeners that the value has changed\n let evt = {};\n if (event && typeof(event) === \"object\") {\n for (let k in event) {\n if (event.hasOwnProperty(k))\n evt[k] = event[k];\n }\n }\n evt.oldValue = oldValue;\n evt.value = value;\n this._events.trigger(\"change\", evt, this);\n\n // TODO: Make this extensible, to let arbitrary back-ends know that\n // something has changed\n if (global.Shiny && global.Shiny.onInputChange) {\n global.Shiny.onInputChange(\n \".clientValue-\" +\n (this._group.name !== null ? this._group.name + \"-\" : \"\") +\n this._name,\n typeof(value) === \"undefined\" ? null : value\n );\n }\n }\n\n on(eventType, listener) {\n return this._events.on(eventType, listener);\n }\n\n off(eventType, listener) {\n return this._events.off(eventType, listener);\n }\n}\n"]} \ No newline at end of file diff --git a/docs/articles/database_of_anor_files/datatables-binding-0.13/datatables.js b/docs/articles/database_of_anor_files/datatables-binding-0.13/datatables.js new file mode 100644 index 0000000..1053375 --- /dev/null +++ b/docs/articles/database_of_anor_files/datatables-binding-0.13/datatables.js @@ -0,0 +1,1320 @@ +(function() { + +// some helper functions: using a global object DTWidget so that it can be used +// in JS() code, e.g. datatable(options = list(foo = JS('code'))); unlike R's +// dynamic scoping, when 'code' is eval()'ed, JavaScript does not know objects +// from the "parent frame", e.g. JS('DTWidget') will not work unless it was made +// a global object +var DTWidget = {}; + +// 123456666.7890 -> 123,456,666.7890 +var markInterval = function(d, digits, interval, mark, decMark, precision) { + x = precision ? d.toPrecision(digits) : d.toFixed(digits); + if (!/^-?[\d.]+$/.test(x)) return x; + var xv = x.split('.'); + if (xv.length > 2) return x; // should have at most one decimal point + xv[0] = xv[0].replace(new RegExp('\\B(?=(\\d{' + interval + '})+(?!\\d))', 'g'), mark); + return xv.join(decMark); +}; + +DTWidget.formatCurrency = function(data, currency, digits, interval, mark, decMark, before) { + var d = parseFloat(data); + if (isNaN(d)) return ''; + var res = markInterval(d, digits, interval, mark, decMark); + res = before ? (/^-/.test(res) ? '-' + currency + res.replace(/^-/, '') : currency + res) : + res + currency; + return res; +}; + +DTWidget.formatString = function(data, prefix, suffix) { + var d = data; + if (d === null) return ''; + return prefix + d + suffix; +}; + +DTWidget.formatPercentage = function(data, digits, interval, mark, decMark) { + var d = parseFloat(data); + if (isNaN(d)) return ''; + return markInterval(d * 100, digits, interval, mark, decMark) + '%'; +}; + +DTWidget.formatRound = function(data, digits, interval, mark, decMark) { + var d = parseFloat(data); + if (isNaN(d)) return ''; + return markInterval(d, digits, interval, mark, decMark); +}; + +DTWidget.formatSignif = function(data, digits, interval, mark, decMark) { + var d = parseFloat(data); + if (isNaN(d)) return ''; + return markInterval(d, digits, interval, mark, decMark, true); +}; + +DTWidget.formatDate = function(data, method, params) { + var d = data; + if (d === null) return ''; + // (new Date('2015-10-28')).toDateString() may return 2015-10-27 because the + // actual time created could be like 'Tue Oct 27 2015 19:00:00 GMT-0500 (CDT)', + // i.e. the date-only string is treated as UTC time instead of local time + if ((method === 'toDateString' || method === 'toLocaleDateString') && /^\d{4,}\D\d{2}\D\d{2}$/.test(d)) { + d = d.split(/\D/); + d = new Date(d[0], d[1] - 1, d[2]); + } else { + d = new Date(d); + } + return d[method].apply(d, params); +}; + +window.DTWidget = DTWidget; + +var transposeArray2D = function(a) { + return a.length === 0 ? a : HTMLWidgets.transposeArray2D(a); +}; + +var crosstalkPluginsInstalled = false; + +function maybeInstallCrosstalkPlugins() { + if (crosstalkPluginsInstalled) + return; + crosstalkPluginsInstalled = true; + + $.fn.dataTable.ext.afnFiltering.push( + function(oSettings, aData, iDataIndex) { + var ctfilter = oSettings.nTable.ctfilter; + if (ctfilter && !ctfilter[iDataIndex]) + return false; + + var ctselect = oSettings.nTable.ctselect; + if (ctselect && !ctselect[iDataIndex]) + return false; + + return true; + } + ); +} + +HTMLWidgets.widget({ + name: "datatables", + type: "output", + renderOnNullValue: true, + initialize: function(el, width, height) { + $(el).html(' '); + return { + data: null, + ctfilterHandle: new crosstalk.FilterHandle(), + ctfilterSubscription: null, + ctselectHandle: new crosstalk.SelectionHandle(), + ctselectSubscription: null + }; + }, + renderValue: function(el, data, instance) { + if (el.offsetWidth === 0 || el.offsetHeight === 0) { + instance.data = data; + return; + } + instance.data = null; + var $el = $(el); + $el.empty(); + + if (data === null) { + $el.append(' '); + // clear previous Shiny inputs (if any) + for (var i in instance.clearInputs) instance.clearInputs[i](); + instance.clearInputs = {}; + return; + } + + var crosstalkOptions = data.crosstalkOptions; + if (!crosstalkOptions) crosstalkOptions = { + 'key': null, 'group': null + }; + if (crosstalkOptions.group) { + maybeInstallCrosstalkPlugins(); + instance.ctfilterHandle.setGroup(crosstalkOptions.group); + instance.ctselectHandle.setGroup(crosstalkOptions.group); + } + + // If we are in a flexdashboard scroll layout then we: + // (a) Always want to use pagination (otherwise we'll have + // a "double scroll bar" effect on the phone); and + // (b) Never want to fill the container (we want the pagination + // level to determine the size of the container) + if (window.FlexDashboard && !window.FlexDashboard.isFillPage()) { + data.options.bPaginate = true; + data.fillContainer = false; + } + + // if we are in the viewer then we always want to fillContainer and + // and autoHideNavigation (unless the user has explicitly set these) + if (window.HTMLWidgets.viewerMode) { + if (!data.hasOwnProperty("fillContainer")) + data.fillContainer = true; + if (!data.hasOwnProperty("autoHideNavigation")) + data.autoHideNavigation = true; + } + + // propagate fillContainer to instance (so we have it in resize) + instance.fillContainer = data.fillContainer; + + var cells = data.data; + + if (cells instanceof Array) cells = transposeArray2D(cells); + + $el.append(data.container); + var $table = $el.find('table'); + if (data.class) $table.addClass(data.class); + if (data.caption) $table.prepend(data.caption); + + if (!data.selection) data.selection = { + mode: 'none', selected: null, target: 'row' + }; + if (HTMLWidgets.shinyMode && data.selection.mode !== 'none' && + data.selection.target === 'row+column') { + if ($table.children('tfoot').length === 0) { + $table.append($('')); + $table.find('thead tr').clone().appendTo($table.find('tfoot')); + } + } + + // column filters + var filterRow; + switch (data.filter) { + case 'top': + $table.children('thead').append(data.filterHTML); + filterRow = $table.find('thead tr:last td'); + break; + case 'bottom': + if ($table.children('tfoot').length === 0) { + $table.append($('')); + } + $table.children('tfoot').prepend(data.filterHTML); + filterRow = $table.find('tfoot tr:first td'); + break; + } + + var options = { searchDelay: 1000 }; + if (cells !== null) $.extend(options, { + data: cells + }); + + // options for fillContainer + var bootstrapActive = typeof($.fn.popover) != 'undefined'; + if (instance.fillContainer) { + + // force scrollX/scrollY and turn off autoWidth + options.scrollX = true; + options.scrollY = "100px"; // can be any value, we'll adjust below + + // if we aren't paginating then move around the info/filter controls + // to save space at the bottom and rephrase the info callback + if (data.options.bPaginate === false) { + + // we know how to do this cleanly for bootstrap, not so much + // for other themes/layouts + if (bootstrapActive) { + options.dom = "<'row'<'col-sm-4'i><'col-sm-8'f>>" + + "<'row'<'col-sm-12'tr>>"; + } + + options.fnInfoCallback = function(oSettings, iStart, iEnd, + iMax, iTotal, sPre) { + return Number(iTotal).toLocaleString() + " records"; + }; + } + } + + // auto hide navigation if requested + if (data.autoHideNavigation === true) { + if (bootstrapActive && data.options.bPaginate !== false) { + // strip all nav if length >= cells + if ((cells instanceof Array) && data.options.iDisplayLength >= cells.length) + options.dom = "<'row'<'col-sm-12'tr>>"; + // alternatively lean things out for flexdashboard mobile portrait + else if (window.FlexDashboard && window.FlexDashboard.isMobilePhone()) + options.dom = "<'row'<'col-sm-12'f>>" + + "<'row'<'col-sm-12'tr>>" + + "<'row'<'col-sm-12'p>>"; + } + } + + $.extend(true, options, data.options || {}); + + var searchCols = options.searchCols; + if (searchCols) { + searchCols = searchCols.map(function(x) { + return x === null ? '' : x.search; + }); + // FIXME: this means I don't respect the escapeRegex setting + delete options.searchCols; + } + + // server-side processing? + var server = options.serverSide === true; + + // use the dataSrc function to pre-process JSON data returned from R + var DT_rows_all = [], DT_rows_current = []; + if (server && HTMLWidgets.shinyMode && typeof options.ajax === 'object' && + /^session\/[\da-z]+\/dataobj/.test(options.ajax.url) && !options.ajax.dataSrc) { + options.ajax.dataSrc = function(json) { + DT_rows_all = $.makeArray(json.DT_rows_all); + DT_rows_current = $.makeArray(json.DT_rows_current); + var data = json.data; + if (!colReorderEnabled()) return data; + var table = $table.DataTable(), order = table.colReorder.order(), flag = true, i, j, row; + for (i = 0; i < order.length; ++i) if (order[i] !== i) flag = false; + if (flag) return data; + for (i = 0; i < data.length; ++i) { + row = data[i].slice(); + for (j = 0; j < order.length; ++j) data[i][j] = row[order[j]]; + } + return data; + }; + } + + var thiz = this; + if (instance.fillContainer) $table.on('init.dt', function(e) { + thiz.fillAvailableHeight(el, $(el).innerHeight()); + }); + // If the page contains serveral datatables and one of which enables colReorder, + // the table.colReorder.order() function will exist but throws error when called. + // So it seems like the only way to know if colReorder is enabled or not is to + // check the options. + var colReorderEnabled = function() { return "colReorder" in options; }; + var table = $table.DataTable(options); + $el.data('datatable', table); + + // Unregister previous Crosstalk event subscriptions, if they exist + if (instance.ctfilterSubscription) { + instance.ctfilterHandle.off("change", instance.ctfilterSubscription); + instance.ctfilterSubscription = null; + } + if (instance.ctselectSubscription) { + instance.ctselectHandle.off("change", instance.ctselectSubscription); + instance.ctselectSubscription = null; + } + + if (!crosstalkOptions.group) { + $table[0].ctfilter = null; + $table[0].ctselect = null; + } else { + var key = crosstalkOptions.key; + function keysToMatches(keys) { + if (!keys) { + return null; + } else { + var selectedKeys = {}; + for (var i = 0; i < keys.length; i++) { + selectedKeys[keys[i]] = true; + } + var matches = {}; + for (var j = 0; j < key.length; j++) { + if (selectedKeys[key[j]]) + matches[j] = true; + } + return matches; + } + } + + function applyCrosstalkFilter(e) { + $table[0].ctfilter = keysToMatches(e.value); + table.draw(); + } + instance.ctfilterSubscription = instance.ctfilterHandle.on("change", applyCrosstalkFilter); + applyCrosstalkFilter({value: instance.ctfilterHandle.filteredKeys}); + + function applyCrosstalkSelection(e) { + if (e.sender !== instance.ctselectHandle) { + table + .rows('.' + selClass, {search: 'applied'}) + .nodes() + .to$() + .removeClass(selClass); + if (selectedRows) + changeInput('rows_selected', selectedRows(), void 0, true); + } + + if (e.sender !== instance.ctselectHandle && e.value && e.value.length) { + var matches = keysToMatches(e.value); + + // persistent selection with plotly (& leaflet) + var ctOpts = crosstalk.var("plotlyCrosstalkOpts").get() || {}; + if (ctOpts.persistent === true) { + var matches = $.extend(matches, $table[0].ctselect); + } + + $table[0].ctselect = matches; + table.draw(); + } else { + if ($table[0].ctselect) { + $table[0].ctselect = null; + table.draw(); + } + } + } + instance.ctselectSubscription = instance.ctselectHandle.on("change", applyCrosstalkSelection); + // TODO: This next line doesn't seem to work when renderDataTable is used + applyCrosstalkSelection({value: instance.ctselectHandle.value}); + } + + var inArray = function(val, array) { + return $.inArray(val, $.makeArray(array)) > -1; + }; + + // encode + to %2B when searching in the table on server side, because + // shiny::parseQueryString() treats + as spaces, and DataTables does not + // encode + to %2B (or % to %25) when sending the request + var encode_plus = function(x) { + return server ? x.replace(/%/g, '%25').replace(/\+/g, '%2B') : x; + }; + + // search the i-th column + var searchColumn = function(i, value) { + var regex = false, ci = true; + if (options.search) { + regex = options.search.regex, + ci = options.search.caseInsensitive !== false; + } + return table.column(i).search(encode_plus(value), regex, !regex, ci); + }; + + if (data.filter !== 'none') { + + filterRow.each(function(i, td) { + + var $td = $(td), type = $td.data('type'), filter; + var $input = $td.children('div').first().children('input'); + $input.prop('disabled', !table.settings()[0].aoColumns[i].bSearchable || type === 'disabled'); + $input.on('input blur', function() { + $input.next('span').toggle(Boolean($input.val())); + }); + // Bootstrap sets pointer-events to none and we won't be able to click + // the clear button + $input.next('span').css('pointer-events', 'auto').hide().click(function() { + $(this).hide().prev('input').val('').trigger('input').focus(); + }); + var searchCol; // search string for this column + if (searchCols && searchCols[i]) { + searchCol = searchCols[i]; + $input.val(searchCol).trigger('input'); + } + var $x = $td.children('div').last(); + + // remove the overflow: hidden attribute of the scrollHead + // (otherwise the scrolling table body obscures the filters) + // The workaround and the discussion from + // https://github.com/rstudio/DT/issues/554#issuecomment-518007347 + // Otherwise the filter selection will not be anchored to the values + // when the columns number is many and scrollX is enabled. + var scrollHead = $(el).find('.dataTables_scrollHead,.dataTables_scrollFoot'); + var cssOverflowHead = scrollHead.css('overflow'); + var scrollBody = $(el).find('.dataTables_scrollBody'); + var cssOverflowBody = scrollBody.css('overflow'); + var scrollTable = $(el).find('.dataTables_scroll'); + var cssOverflowTable = scrollTable.css('overflow'); + if (cssOverflowHead === 'hidden') { + $x.on('show hide', function(e) { + if (e.type === 'show') { + scrollHead.css('overflow', 'visible'); + scrollBody.css('overflow', 'visible'); + scrollTable.css('overflow-x', 'scroll'); + } else { + scrollHead.css('overflow', cssOverflowHead); + scrollBody.css('overflow', cssOverflowBody); + scrollTable.css('overflow-x', cssOverflowTable); + } + }); + $x.css('z-index', 25); + } + + if (inArray(type, ['factor', 'logical'])) { + $input.on({ + click: function() { + $input.parent().hide(); $x.show().trigger('show'); filter[0].selectize.focus(); + }, + input: function() { + if ($input.val() === '') filter[0].selectize.setValue([]); + } + }); + var $input2 = $x.children('select'); + filter = $input2.selectize({ + options: $input2.data('options').map(function(v, i) { + return ({text: v, value: v}); + }), + plugins: ['remove_button'], + hideSelected: true, + onChange: function(value) { + if (value === null) value = []; // compatibility with jQuery 3.0 + $input.val(value.length ? JSON.stringify(value) : ''); + if (value.length) $input.trigger('input'); + $input.attr('title', $input.val()); + if (server) { + table.column(i).search(value.length ? encode_plus(JSON.stringify(value)) : '').draw(); + return; + } + // turn off filter if nothing selected + $td.data('filter', value.length > 0); + table.draw(); // redraw table, and filters will be applied + } + }); + if (searchCol) filter[0].selectize.setValue(JSON.parse(searchCol)); + filter[0].selectize.on('blur', function() { + $x.hide().trigger('hide'); $input.parent().show(); $input.trigger('blur'); + }); + filter.next('div').css('margin-bottom', 'auto'); + } else if (type === 'character') { + var fun = function() { + searchColumn(i, $input.val()).draw(); + }; + if (server) { + fun = $.fn.dataTable.util.throttle(fun, options.searchDelay); + } + $input.on('input', fun); + } else if (inArray(type, ['number', 'integer', 'date', 'time'])) { + var $x0 = $x; + $x = $x0.children('div').first(); + $x0.css({ + 'background-color': '#fff', + 'border': '1px #ddd solid', + 'border-radius': '4px', + 'padding': '20px 20px 10px 20px' + }); + var $spans = $x0.children('span').css({ + 'margin-top': '10px', + 'white-space': 'nowrap' + }); + var $span1 = $spans.first(), $span2 = $spans.last(); + var r1 = +$x.data('min'), r2 = +$x.data('max'); + // when the numbers are too small or have many decimal places, the + // slider may have numeric precision problems (#150) + var scale = Math.pow(10, Math.max(0, +$x.data('scale') || 0)); + r1 = Math.round(r1 * scale); r2 = Math.round(r2 * scale); + var scaleBack = function(x, scale) { + if (scale === 1) return x; + var d = Math.round(Math.log(scale) / Math.log(10)); + // to avoid problems like 3.423/100 -> 0.034230000000000003 + return (x / scale).toFixed(d); + }; + $input.on({ + focus: function() { + $x0.show().trigger('show'); + // first, make sure the slider div leaves at least 20px between + // the two (slider value) span's + $x0.width(Math.max(160, $span1.outerWidth() + $span2.outerWidth() + 20)); + // then, if the input is really wide, make the slider the same + // width as the input + if ($x0.outerWidth() < $input.outerWidth()) { + $x0.outerWidth($input.outerWidth()); + } + // make sure the slider div does not reach beyond the right margin + if ($(window).width() < $x0.offset().left + $x0.width()) { + $x0.offset({ + 'left': $input.offset().left + $input.outerWidth() - $x0.outerWidth() + }); + } + }, + blur: function() { + $x0.hide().trigger('hide'); + }, + input: function() { + if ($input.val() === '') filter.val([r1, r2]); + }, + change: function() { + var v = $input.val().replace(/\s/g, ''); + if (v === '') return; + v = v.split('...'); + if (v.length !== 2) { + $input.parent().addClass('has-error'); + return; + } + if (v[0] === '') v[0] = r1; + if (v[1] === '') v[1] = r2; + $input.parent().removeClass('has-error'); + // treat date as UTC time at midnight + var strTime = function(x) { + var s = type === 'date' ? 'T00:00:00Z' : ''; + var t = new Date(x + s).getTime(); + // add 10 minutes to date since it does not hurt the date, and + // it helps avoid the tricky floating point arithmetic problems, + // e.g. sometimes the date may be a few milliseconds earlier + // than the midnight due to precision problems in noUiSlider + return type === 'date' ? t + 3600000 : t; + }; + if (inArray(type, ['date', 'time'])) { + v[0] = strTime(v[0]); + v[1] = strTime(v[1]); + } + if (v[0] != r1) v[0] *= scale; + if (v[1] != r2) v[1] *= scale; + filter.val(v); + } + }); + var formatDate = function(d, isoFmt) { + d = scaleBack(d, scale); + if (type === 'number') return d; + if (type === 'integer') return parseInt(d); + var x = new Date(+d); + var fmt = ('filterDateFmt' in data) ? data.filterDateFmt[i] : undefined; + if (fmt !== undefined && isoFmt === false) return x[fmt.method].apply(x, fmt.params); + if (type === 'date') { + var pad0 = function(x) { + return ('0' + x).substr(-2, 2); + }; + return x.getUTCFullYear() + '-' + pad0(1 + x.getUTCMonth()) + + '-' + pad0(x.getUTCDate()); + } else { + return x.toISOString(); + } + }; + var opts = type === 'date' ? { step: 60 * 60 * 1000 } : + type === 'integer' ? { step: 1 } : {}; + filter = $x.noUiSlider($.extend({ + start: [r1, r2], + range: {min: r1, max: r2}, + connect: true + }, opts)); + if (scale > 1) (function() { + var t1 = r1, t2 = r2; + var val = filter.val(); + while (val[0] > r1 || val[1] < r2) { + if (val[0] > r1) { + t1 -= val[0] - r1; + } + if (val[1] < r2) { + t2 += r2 - val[1]; + } + filter = $x.noUiSlider($.extend({ + start: [t1, t2], + range: {min: t1, max: t2}, + connect: true + }, opts), true); + val = filter.val(); + } + r1 = t1; r2 = t2; + })(); + var updateSliderText = function(v1, v2) { + $span1.text(formatDate(v1, false)); $span2.text(formatDate(v2, false)); + }; + updateSliderText(r1, r2); + var updateSlider = function(e) { + var val = filter.val(); + // turn off filter if in full range + $td.data('filter', val[0] > r1 || val[1] < r2); + var v1 = formatDate(val[0]), v2 = formatDate(val[1]), ival; + if ($td.data('filter')) { + ival = v1 + ' ... ' + v2; + $input.attr('title', ival).val(ival).trigger('input'); + } else { + $input.attr('title', '').val(''); + } + updateSliderText(val[0], val[1]); + if (e.type === 'slide') return; // no searching when sliding only + if (server) { + table.column(i).search($td.data('filter') ? ival : '').draw(); + return; + } + table.draw(); + }; + filter.on({ + set: updateSlider, + slide: updateSlider + }); + } + + // server-side processing will be handled by R (or whatever server + // language you use); the following code is only needed for client-side + // processing + if (server) { + // if a search string has been pre-set, search now + if (searchCol) searchColumn(i, searchCol).draw(); + return; + } + + var customFilter = function(settings, data, dataIndex) { + // there is no way to attach a search function to a specific table, + // and we need to make sure a global search function is not applied to + // all tables (i.e. a range filter in a previous table should not be + // applied to the current table); we use the settings object to + // determine if we want to perform searching on the current table, + // since settings.sTableId will be different to different tables + if (table.settings()[0] !== settings) return true; + // no filter on this column or no need to filter this column + if (typeof filter === 'undefined' || !$td.data('filter')) return true; + + var r = filter.val(), v, r0, r1; + var i_data = function(i) { + if (!colReorderEnabled()) return i; + var order = table.colReorder.order(), k; + for (k = 0; k < order.length; ++k) if (order[k] === i) return k; + return i; // in theory it will never be here... + } + v = data[i_data(i)]; + if (type === 'number' || type === 'integer') { + v = parseFloat(v); + // how to handle NaN? currently exclude these rows + if (isNaN(v)) return(false); + r0 = parseFloat(scaleBack(r[0], scale)) + r1 = parseFloat(scaleBack(r[1], scale)); + if (v >= r0 && v <= r1) return true; + } else if (type === 'date' || type === 'time') { + v = new Date(v); + r0 = new Date(r[0] / scale); r1 = new Date(r[1] / scale); + if (v >= r0 && v <= r1) return true; + } else if (type === 'factor') { + if (r.length === 0 || inArray(v, r)) return true; + } else if (type === 'logical') { + if (r.length === 0) return true; + if (inArray(v === '' ? 'na' : v, r)) return true; + } + return false; + }; + + $.fn.dataTable.ext.search.push(customFilter); + + // search for the preset search strings if it is non-empty + if (searchCol) { + if (inArray(type, ['factor', 'logical'])) { + filter[0].selectize.setValue(JSON.parse(searchCol)); + } else if (type === 'character') { + $input.trigger('input'); + } else if (inArray(type, ['number', 'integer', 'date', 'time'])) { + $input.trigger('change'); + } + } + + }); + + } + + // highlight search keywords + var highlight = function() { + var body = $(table.table().body()); + // removing the old highlighting first + body.unhighlight(); + + // don't highlight the "not found" row, so we get the rows using the api + if (table.rows({ filter: 'applied' }).data().length === 0) return; + // highlight global search keywords + body.highlight($.trim(table.search()).split(/\s+/)); + // then highlight keywords from individual column filters + if (filterRow) filterRow.each(function(i, td) { + var $td = $(td), type = $td.data('type'); + if (type !== 'character') return; + var $input = $td.children('div').first().children('input'); + var column = table.column(i).nodes().to$(), + val = $.trim($input.val()); + if (type !== 'character' || val === '') return; + column.highlight(val.split(/\s+/)); + }); + }; + + if (options.searchHighlight) { + table + .on('draw.dt.dth column-visibility.dt.dth column-reorder.dt.dth', highlight) + .on('destroy', function() { + // remove event handler + table.off('draw.dt.dth column-visibility.dt.dth column-reorder.dt.dth'); + }); + + // Set the option for escaping regex characters in our search string. This will be used + // for all future matching. + jQuery.fn.highlight.options.escapeRegex = (!options.search || !options.search.regex); + + // initial highlight for state saved conditions and initial states + highlight(); + } + + // run the callback function on the table instance + if (typeof data.callback === 'function') data.callback(table); + + // double click to edit the cell, row, column, or all cells + if (data.editable) table.on('dblclick.dt', 'tbody td', function(e) { + // only bring up the editor when the cell itself is dbclicked, and ignore + // other dbclick events bubbled up (e.g. from the ) + if (e.target !== this) return; + var target = [], immediate = false; + switch (data.editable.target) { + case 'cell': + target = [this]; + immediate = true; // edit will take effect immediately + break; + case 'row': + target = table.cells(table.cell(this).index().row, '*').nodes(); + break; + case 'column': + target = table.cells('*', table.cell(this).index().column).nodes(); + break; + case 'all': + target = table.cells().nodes(); + break; + default: + throw 'The editable parameter must be "cell", "row", "column", or "all"'; + } + var disableCols = data.editable.disable ? data.editable.disable.columns : null; + for (var i = 0; i < target.length; i++) { + (function(cell, current) { + var $cell = $(cell), html = $cell.html(); + var _cell = table.cell(cell), value = _cell.data(); + var $input = $(''), changed = false; + if (!immediate) { + $cell.data('input', $input).data('html', html); + $input.attr('title', 'Hit Ctrl+Enter to finish editing, or Esc to cancel'); + } + $input.val(value); + if (inArray(_cell.index().column, disableCols)) { + $input.attr('readonly', '').css('filter', 'invert(25%)'); + } + $cell.empty().append($input); + if (cell === current) $input.focus(); + $input.css('width', '100%'); + + if (immediate) $input.on('change', function() { + changed = true; + var valueNew = $input.val(); + if (valueNew != value) { + _cell.data(valueNew); + if (HTMLWidgets.shinyMode) { + changeInput('cell_edit', [cellInfo(cell)], 'DT.cellInfo', null, {priority: "event"}); + } + // for server-side processing, users have to call replaceData() to update the table + if (!server) table.draw(false); + } else { + $cell.html(html); + } + $input.remove(); + }).on('blur', function() { + if (!changed) $input.trigger('change'); + }).on('keyup', function(e) { + // hit Escape to cancel editing + if (e.keyCode === 27) $input.trigger('blur'); + }); + + // bulk edit (row, column, or all) + if (!immediate) $input.on('keyup', function(e) { + var removeInput = function($cell, restore) { + $cell.data('input').remove(); + if (restore) $cell.html($cell.data('html')); + } + if (e.keyCode === 27) { + for (var i = 0; i < target.length; i++) { + removeInput($(target[i]), true); + } + } else if (e.keyCode === 13 && e.ctrlKey) { + // Ctrl + Enter + var cell, $cell, _cell, cellData = []; + for (var i = 0; i < target.length; i++) { + cell = target[i]; $cell = $(cell); _cell = table.cell(cell); + _cell.data($cell.data('input').val()); + HTMLWidgets.shinyMode && cellData.push(cellInfo(cell)); + removeInput($cell, false); + } + if (HTMLWidgets.shinyMode) { + changeInput('cell_edit', cellData, 'DT.cellInfo', null, {priority: "event"}); + } + if (!server) table.draw(false); + } + }); + })(target[i], this); + } + }); + + // interaction with shiny + if (!HTMLWidgets.shinyMode && !crosstalkOptions.group) return; + + var methods = {}; + var shinyData = {}; + + methods.updateCaption = function(caption) { + if (!caption) return; + $table.children('caption').replaceWith(caption); + } + + // register clear functions to remove input values when the table is removed + instance.clearInputs = {}; + + var changeInput = function(id, value, type, noCrosstalk, opts) { + var event = id; + id = el.id + '_' + id; + if (type) id = id + ':' + type; + // do not update if the new value is the same as old value + if (event !== 'cell_edit' && shinyData.hasOwnProperty(id) && shinyData[id] === JSON.stringify(value)) + return; + shinyData[id] = JSON.stringify(value); + if (HTMLWidgets.shinyMode && Shiny.setInputValue) { + Shiny.setInputValue(id, value, opts); + if (!instance.clearInputs[id]) instance.clearInputs[id] = function() { + Shiny.setInputValue(id, null); + } + } + + // HACK + if (event === "rows_selected" && !noCrosstalk) { + if (crosstalkOptions.group) { + var keys = crosstalkOptions.key; + var selectedKeys = null; + if (value) { + selectedKeys = []; + for (var i = 0; i < value.length; i++) { + // The value array's contents use 1-based row numbers, so we must + // convert to 0-based before indexing into the keys array. + selectedKeys.push(keys[value[i] - 1]); + } + } + instance.ctselectHandle.set(selectedKeys); + } + } + }; + + var addOne = function(x) { + return x.map(function(i) { return 1 + i; }); + }; + + var unique = function(x) { + var ux = []; + $.each(x, function(i, el){ + if ($.inArray(el, ux) === -1) ux.push(el); + }); + return ux; + } + + // change the row index of a cell + var tweakCellIndex = function(cell) { + var info = cell.index(); + // some cell may not be valid. e.g, #759 + // when using the RowGroup extension, datatables will + // generate the row label and the cells are not part of + // the data thus contain no row/col info + if (info === undefined) + return {row: null, col: null}; + if (server) { + info.row = DT_rows_current[info.row]; + } else { + info.row += 1; + } + return {row: info.row, col: info.column}; + } + + // a flag to indicates if select extension is initialized or not + var flagSelectExt = table.settings()[0]._select !== undefined; + // the Select extension should only be used in the client mode and + // when the selection.mode is set to none + if (data.selection.mode === 'none' && !server && flagSelectExt) { + var updateRowsSelected = function() { + var rows = table.rows({selected: true}); + var selected = []; + $.each(rows.indexes().toArray(), function(i, v) { + selected.push(v + 1); + }); + changeInput('rows_selected', selected); + } + var updateColsSelected = function() { + var columns = table.columns({selected: true}); + changeInput('columns_selected', columns.indexes().toArray()); + } + var updateCellsSelected = function() { + var cells = table.cells({selected: true}); + var selected = []; + cells.every(function() { + var row = this.index().row; + var col = this.index().column; + selected = selected.concat([[row + 1, col]]); + }); + changeInput('cells_selected', transposeArray2D(selected), 'shiny.matrix'); + } + table.on('select deselect', function(e, dt, type, indexes) { + updateRowsSelected(); + updateColsSelected(); + updateCellsSelected(); + }) + } + + var selMode = data.selection.mode, selTarget = data.selection.target; + if (inArray(selMode, ['single', 'multiple'])) { + var selClass = inArray(data.style, ['bootstrap', 'bootstrap4']) ? 'active' : 'selected'; + var selected = data.selection.selected, selected1, selected2; + // selected1: row indices; selected2: column indices + if (selected === null) { + selected1 = selected2 = []; + } else if (selTarget === 'row') { + selected1 = $.makeArray(selected); + } else if (selTarget === 'column') { + selected2 = $.makeArray(selected); + } else if (selTarget === 'row+column') { + selected1 = $.makeArray(selected.rows); + selected2 = $.makeArray(selected.cols); + } + + // After users reorder the rows or filter the table, we cannot use the table index + // directly. Instead, we need this function to find out the rows between the two clicks. + // If user filter the table again between the start click and the end click, the behavior + // would be undefined, but it should not be a problem. + var shiftSelRowsIndex = function(start, end) { + var indexes = server ? DT_rows_all : table.rows({ search: 'applied' }).indexes().toArray(); + start = indexes.indexOf(start); end = indexes.indexOf(end); + // if start is larger than end, we need to swap + if (start > end) { + var tmp = end; end = start; start = tmp; + } + return indexes.slice(start, end + 1); + } + + var serverRowIndex = function(clientRowIndex) { + return server ? DT_rows_current[clientRowIndex] : clientRowIndex + 1; + } + + // row, column, or cell selection + var lastClickedRow; + if (inArray(selTarget, ['row', 'row+column'])) { + var selectedRows = function() { + var rows = table.rows('.' + selClass); + var idx = rows.indexes().toArray(); + if (!server) return addOne(idx); + idx = idx.map(function(i) { + return DT_rows_current[i]; + }); + selected1 = selMode === 'multiple' ? unique(selected1.concat(idx)) : idx; + return selected1; + } + table.on('mousedown.dt', 'tbody tr', function(e) { + var $this = $(this), thisRow = table.row(this); + if (selMode === 'multiple') { + if (e.shiftKey && lastClickedRow !== undefined) { + // select or de-select depends on the last clicked row's status + var flagSel = !$this.hasClass(selClass); + var crtClickedRow = serverRowIndex(thisRow.index()); + if (server) { + var rowsIndex = shiftSelRowsIndex(lastClickedRow, crtClickedRow); + // update current page's selClass + rowsIndex.map(function(i) { + var rowIndex = DT_rows_current.indexOf(i); + if (rowIndex >= 0) { + var row = table.row(rowIndex).nodes().to$(); + var flagRowSel = !row.hasClass(selClass); + if (flagSel === flagRowSel) row.toggleClass(selClass); + } + }); + // update selected1 + if (flagSel) { + selected1 = unique(selected1.concat(rowsIndex)); + } else { + selected1 = selected1.filter(function(index) { + return !inArray(index, rowsIndex); + }); + } + } else { + // js starts from 0 + shiftSelRowsIndex(lastClickedRow - 1, crtClickedRow - 1).map(function(value) { + var row = table.row(value).nodes().to$(); + var flagRowSel = !row.hasClass(selClass); + if (flagSel === flagRowSel) row.toggleClass(selClass); + }); + } + e.preventDefault(); + } else { + $this.toggleClass(selClass); + } + } else { + if ($this.hasClass(selClass)) { + $this.removeClass(selClass); + } else { + table.$('tr.' + selClass).removeClass(selClass); + $this.addClass(selClass); + } + } + if (server && !$this.hasClass(selClass)) { + var id = DT_rows_current[thisRow.index()]; + // remove id from selected1 since its class .selected has been removed + if (inArray(id, selected1)) selected1.splice($.inArray(id, selected1), 1); + } + changeInput('rows_selected', selectedRows()); + changeInput('row_last_clicked', serverRowIndex(thisRow.index())); + lastClickedRow = serverRowIndex(thisRow.index()); + }); + changeInput('rows_selected', selected1); + var selectRows = function() { + table.$('tr.' + selClass).removeClass(selClass); + if (selected1.length === 0) return; + if (server) { + table.rows({page: 'current'}).every(function() { + if (inArray(DT_rows_current[this.index()], selected1)) { + $(this.node()).addClass(selClass); + } + }); + } else { + var selected0 = selected1.map(function(i) { return i - 1; }); + $(table.rows(selected0).nodes()).addClass(selClass); + } + } + selectRows(); // in case users have specified pre-selected rows + // restore selected rows after the table is redrawn (e.g. sort/search/page); + // client-side tables will preserve the selections automatically; for + // server-side tables, we have to *real* row indices are in `selected1` + if (server) table.on('draw.dt', selectRows); + methods.selectRows = function(selected) { + selected1 = $.makeArray(selected); + selectRows(); + changeInput('rows_selected', selected1); + } + } + + if (inArray(selTarget, ['column', 'row+column'])) { + if (selTarget === 'row+column') { + $(table.columns().footer()).css('cursor', 'pointer'); + } + var callback = function() { + var colIdx = selTarget === 'column' ? table.cell(this).index().column : + $.inArray(this, table.columns().footer()), + thisCol = $(table.column(colIdx).nodes()); + if (colIdx === -1) return; + if (thisCol.hasClass(selClass)) { + thisCol.removeClass(selClass); + selected2.splice($.inArray(colIdx, selected2), 1); + } else { + if (selMode === 'single') $(table.cells().nodes()).removeClass(selClass); + thisCol.addClass(selClass); + selected2 = selMode === 'single' ? [colIdx] : unique(selected2.concat([colIdx])); + } + changeInput('columns_selected', selected2); + } + if (selTarget === 'column') { + $(table.table().body()).on('click.dt', 'td', callback); + } else { + $(table.table().footer()).on('click.dt', 'tr th', callback); + } + changeInput('columns_selected', selected2); + var selectCols = function() { + table.columns().nodes().flatten().to$().removeClass(selClass); + if (selected2.length > 0) + table.columns(selected2).nodes().flatten().to$().addClass(selClass); + } + selectCols(); // in case users have specified pre-selected columns + if (server) table.on('draw.dt', selectCols); + methods.selectColumns = function(selected) { + selected2 = $.makeArray(selected); + selectCols(); + changeInput('columns_selected', selected2); + } + } + + if (selTarget === 'cell') { + var selected3; + if (selected === null) { + selected3 = []; + } else { + selected3 = selected; + } + var findIndex = function(ij) { + for (var i = 0; i < selected3.length; i++) { + if (ij[0] === selected3[i][0] && ij[1] === selected3[i][1]) return i; + } + return -1; + } + table.on('click.dt', 'tbody td', function() { + var $this = $(this), info = tweakCellIndex(table.cell(this)); + if ($this.hasClass(selClass)) { + $this.removeClass(selClass); + selected3.splice(findIndex([info.row, info.col]), 1); + } else { + if (selMode === 'single') $(table.cells().nodes()).removeClass(selClass); + $this.addClass(selClass); + selected3 = selMode === 'single' ? [[info.row, info.col]] : + unique(selected3.concat([[info.row, info.col]])); + } + changeInput('cells_selected', transposeArray2D(selected3), 'shiny.matrix'); + }); + changeInput('cells_selected', transposeArray2D(selected3), 'shiny.matrix'); + var selectCells = function() { + table.$('td.' + selClass).removeClass(selClass); + if (selected3.length === 0) return; + if (server) { + table.cells({page: 'current'}).every(function() { + var info = tweakCellIndex(this); + if (findIndex([info.row, info.col], selected3) > -1) + $(this.node()).addClass(selClass); + }); + } else { + selected3.map(function(ij) { + $(table.cell(ij[0] - 1, ij[1]).node()).addClass(selClass); + }); + } + }; + selectCells(); // in case users have specified pre-selected columns + if (server) table.on('draw.dt', selectCells); + methods.selectCells = function(selected) { + selected3 = selected ? selected : []; + selectCells(); + changeInput('cells_selected', transposeArray2D(selected3), 'shiny.matrix'); + } + } + } + + // expose some table info to Shiny + var updateTableInfo = function(e, settings) { + // TODO: is anyone interested in the page info? + // changeInput('page_info', table.page.info()); + var updateRowInfo = function(id, modifier) { + var idx; + if (server) { + idx = modifier.page === 'current' ? DT_rows_current : DT_rows_all; + } else { + var rows = table.rows($.extend({ + search: 'applied', + page: 'all' + }, modifier)); + idx = addOne(rows.indexes().toArray()); + } + changeInput('rows' + '_' + id, idx); + }; + updateRowInfo('current', {page: 'current'}); + updateRowInfo('all', {}); + } + table.on('draw.dt', updateTableInfo); + updateTableInfo(); + + // state info + table.on('draw.dt column-visibility.dt', function() { + changeInput('state', table.state()); + }); + changeInput('state', table.state()); + + // search info + var updateSearchInfo = function() { + changeInput('search', table.search()); + if (filterRow) changeInput('search_columns', filterRow.toArray().map(function(td) { + return $(td).find('input').first().val(); + })); + } + table.on('draw.dt', updateSearchInfo); + updateSearchInfo(); + + var cellInfo = function(thiz) { + var info = tweakCellIndex(table.cell(thiz)); + info.value = table.cell(thiz).data(); + return info; + } + // the current cell clicked on + table.on('click.dt', 'tbody td', function() { + changeInput('cell_clicked', cellInfo(this)); + }) + changeInput('cell_clicked', {}); + + // do not trigger table selection when clicking on links unless they have classes + table.on('click.dt', 'tbody td a', function(e) { + if (this.className === '') e.stopPropagation(); + }); + + methods.addRow = function(data, rowname) { + var data0 = table.row(0).data(), n = data0.length, d = n - data.length; + if (d === 1) { + data = rowname.concat(data) + } else if (d !== 0) { + console.log(data); + console.log(data0); + throw 'New data must be of the same length as current data (' + n + ')'; + }; + table.row.add(data).draw(); + } + + methods.updateSearch = function(keywords) { + if (keywords.global !== null) + $(table.table().container()).find('input[type=search]').first() + .val(keywords.global).trigger('input'); + var columns = keywords.columns; + if (!filterRow || columns === null) return; + filterRow.toArray().map(function(td, i) { + var v = typeof columns === 'string' ? columns : columns[i]; + if (typeof v === 'undefined') { + console.log('The search keyword for column ' + i + ' is undefined') + return; + } + $(td).find('input').first().val(v); + searchColumn(i, v); + }); + table.draw(); + } + + methods.hideCols = function(hide, reset) { + if (reset) table.columns().visible(true, false); + table.columns(hide).visible(false); + } + + methods.showCols = function(show, reset) { + if (reset) table.columns().visible(false, false); + table.columns(show).visible(true); + } + + methods.colReorder = function(order, origOrder) { + table.colReorder.order(order, origOrder); + } + + methods.selectPage = function(page) { + if (table.page.info().pages < page || page < 1) { + throw 'Selected page is out of range'; + }; + table.page(page - 1).draw(false); + } + + methods.reloadData = function(resetPaging, clearSelection) { + // empty selections first if necessary + if (methods.selectRows && inArray('row', clearSelection)) methods.selectRows([]); + if (methods.selectColumns && inArray('column', clearSelection)) methods.selectColumns([]); + if (methods.selectCells && inArray('cell', clearSelection)) methods.selectCells([]); + table.ajax.reload(null, resetPaging); + } + + table.shinyMethods = methods; + }, + resize: function(el, width, height, instance) { + if (instance.data) this.renderValue(el, instance.data, instance); + + // dynamically adjust height if fillContainer = TRUE + if (instance.fillContainer) + this.fillAvailableHeight(el, height); + + this.adjustWidth(el); + }, + + // dynamically set the scroll body to fill available height + // (used with fillContainer = TRUE) + fillAvailableHeight: function(el, availableHeight) { + + // see how much of the table is occupied by header/footer elements + // and use that to compute a target scroll body height + var dtWrapper = $(el).find('div.dataTables_wrapper'); + var dtScrollBody = $(el).find($('div.dataTables_scrollBody')); + var framingHeight = dtWrapper.innerHeight() - dtScrollBody.innerHeight(); + var scrollBodyHeight = availableHeight - framingHeight; + + // set the height + dtScrollBody.height(scrollBodyHeight + 'px'); + }, + + // adjust the width of columns; remove the hard-coded widths on table and the + // scroll header when scrollX/Y are enabled + adjustWidth: function(el) { + var $el = $(el), table = $el.data('datatable'); + if (table) table.columns.adjust(); + $el.find('.dataTables_scrollHeadInner').css('width', '') + .children('table').css('margin-left', ''); + } +}); + + if (!HTMLWidgets.shinyMode) return; + + Shiny.addCustomMessageHandler('datatable-calls', function(data) { + var id = data.id; + var el = document.getElementById(id); + var table = el ? $(el).data('datatable') : null; + if (!table) { + console.log("Couldn't find table with id " + id); + return; + } + + var methods = table.shinyMethods, call = data.call; + if (methods[call.method]) { + methods[call.method].apply(table, call.args); + } else { + console.log("Unknown method " + call.method); + } + }); + +})(); diff --git a/docs/articles/database_of_anor_files/datatables-css-0.0.0/datatables-crosstalk.css b/docs/articles/database_of_anor_files/datatables-css-0.0.0/datatables-crosstalk.css new file mode 100644 index 0000000..fb5bae8 --- /dev/null +++ b/docs/articles/database_of_anor_files/datatables-css-0.0.0/datatables-crosstalk.css @@ -0,0 +1,23 @@ +.dt-crosstalk-fade { + opacity: 0.2; +} + +html body div.DTS div.dataTables_scrollBody { + background: none; +} + + +/* +Fix https://github.com/rstudio/DT/issues/563 +If the `table.display` is set to "block" (e.g., pkgdown), the browser will display +datatable objects strangely. The search panel and the page buttons will still be +in full-width but the table body will be "compact" and shorter. +In therory, having this attributes will affect `dom="t"` +with `display: block` users. But in reality, there should be no one. +We may remove the below lines in the future if the upstream agree to have this there. +See https://github.com/DataTables/DataTablesSrc/issues/160 +*/ + +table.dataTable { + display: table; +} diff --git a/docs/articles/database_of_anor_files/dt-core-1.10.20/css/jquery.dataTables.extra.css b/docs/articles/database_of_anor_files/dt-core-1.10.20/css/jquery.dataTables.extra.css new file mode 100644 index 0000000..b2dd141 --- /dev/null +++ b/docs/articles/database_of_anor_files/dt-core-1.10.20/css/jquery.dataTables.extra.css @@ -0,0 +1,28 @@ +/* Selected rows/cells */ +table.dataTable tr.selected td, table.dataTable td.selected { + background-color: #b0bed9 !important; +} +/* In case of scrollX/Y or FixedHeader */ +.dataTables_scrollBody .dataTables_sizing { + visibility: hidden; +} + +/* The datatables' theme CSS file doesn't define +the color but with white background. It leads to an issue that +when the HTML's body color is set to 'white', the user can't +see the text since the background is white. One case happens in the +RStudio's IDE when inline viewing the DT table inside an Rmd file, +if the IDE theme is set to "Cobalt". + +See https://github.com/rstudio/DT/issues/447 for more info + +This fixes should have little side-effects because all the other elements +of the default theme use the #333 font color. + +TODO: The upstream may use relative colors for both the table background +and the color. It means the table can display well without this patch +then. At that time, we need to remove the below CSS attributes. +*/ +div.datatables { + color: #333; +} diff --git a/docs/articles/database_of_anor_files/dt-core-1.10.20/css/jquery.dataTables.min.css b/docs/articles/database_of_anor_files/dt-core-1.10.20/css/jquery.dataTables.min.css new file mode 100644 index 0000000..71ae98a --- /dev/null +++ b/docs/articles/database_of_anor_files/dt-core-1.10.20/css/jquery.dataTables.min.css @@ -0,0 +1 @@ +table.dataTable{width:100%;margin:0 auto;clear:both;border-collapse:separate;border-spacing:0}table.dataTable thead th,table.dataTable tfoot th{font-weight:bold}table.dataTable thead th,table.dataTable thead td{padding:10px 18px;border-bottom:1px solid #111}table.dataTable thead th:active,table.dataTable thead td:active{outline:none}table.dataTable tfoot th,table.dataTable tfoot td{padding:10px 18px 6px 18px;border-top:1px solid #111}table.dataTable thead .sorting,table.dataTable thead .sorting_asc,table.dataTable thead .sorting_desc,table.dataTable 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entries",sLoadingRecords:"Loading...",sProcessing:"Processing...",sSearch:"Search:",sSearchPlaceholder:"",sUrl:"",sZeroRecords:"No matching records found"},oSearch:f.extend({},q.models.oSearch),sAjaxDataProp:"data", +sAjaxSource:null,sDom:"lfrtip",searchDelay:null,sPaginationType:"simple_numbers",sScrollX:"",sScrollXInner:"",sScrollY:"",sServerMethod:"GET",renderer:null,rowId:"DT_RowId"};H(q.defaults);q.defaults.column={aDataSort:null,iDataSort:-1,asSorting:["asc","desc"],bSearchable:!0,bSortable:!0,bVisible:!0,fnCreatedCell:null,mData:null,mRender:null,sCellType:"td",sClass:"",sContentPadding:"",sDefaultContent:null,sName:"",sSortDataType:"std",sTitle:null,sType:null,sWidth:null};H(q.defaults.column);q.models.oSettings= +{oFeatures:{bAutoWidth:null,bDeferRender:null,bFilter:null,bInfo:null,bLengthChange:null,bPaginate:null,bProcessing:null,bServerSide:null,bSort:null,bSortMulti:null,bSortClasses:null,bStateSave:null},oScroll:{bCollapse:null,iBarWidth:0,sX:null,sXInner:null,sY:null},oLanguage:{fnInfoCallback:null},oBrowser:{bScrollOversize:!1,bScrollbarLeft:!1,bBounding:!1,barWidth:0},ajax:null,aanFeatures:[],aoData:[],aiDisplay:[],aiDisplayMaster:[],aIds:{},aoColumns:[],aoHeader:[],aoFooter:[],oPreviousSearch:{}, +aoPreSearchCols:[],aaSorting:null,aaSortingFixed:[],asStripeClasses:null,asDestroyStripes:[],sDestroyWidth:0,aoRowCallback:[],aoHeaderCallback:[],aoFooterCallback:[],aoDrawCallback:[],aoRowCreatedCallback:[],aoPreDrawCallback:[],aoInitComplete:[],aoStateSaveParams:[],aoStateLoadParams:[],aoStateLoaded:[],sTableId:"",nTable:null,nTHead:null,nTFoot:null,nTBody:null,nTableWrapper:null,bDeferLoading:!1,bInitialised:!1,aoOpenRows:[],sDom:null,searchDelay:null,sPaginationType:"two_button",iStateDuration:0, +aoStateSave:[],aoStateLoad:[],oSavedState:null,oLoadedState:null,sAjaxSource:null,sAjaxDataProp:null,bAjaxDataGet:!0,jqXHR:null,json:p,oAjaxData:p,fnServerData:null,aoServerParams:[],sServerMethod:null,fnFormatNumber:null,aLengthMenu:null,iDraw:0,bDrawing:!1,iDrawError:-1,_iDisplayLength:10,_iDisplayStart:0,_iRecordsTotal:0,_iRecordsDisplay:0,oClasses:{},bFiltered:!1,bSorted:!1,bSortCellsTop:null,oInit:null,aoDestroyCallback:[],fnRecordsTotal:function(){return"ssp"==D(this)?1*this._iRecordsTotal: +this.aiDisplayMaster.length},fnRecordsDisplay:function(){return"ssp"==D(this)?1*this._iRecordsDisplay:this.aiDisplay.length},fnDisplayEnd:function(){var a=this._iDisplayLength,b=this._iDisplayStart,c=b+a,d=this.aiDisplay.length,e=this.oFeatures,f=e.bPaginate;return e.bServerSide?!1===f||-1===a?b+d:Math.min(b+a,this._iRecordsDisplay):!f||c>d||-1===a?d:c},oInstance:null,sInstance:null,iTabIndex:0,nScrollHead:null,nScrollFoot:null,aLastSort:[],oPlugins:{},rowIdFn:null,rowId:null};q.ext=C={buttons:{}, +classes:{},builder:"-source-",errMode:"alert",feature:[],search:[],selector:{cell:[],column:[],row:[]},internal:{},legacy:{ajax:null},pager:{},renderer:{pageButton:{},header:{}},order:{},type:{detect:[],search:{},order:{}},_unique:0,fnVersionCheck:q.fnVersionCheck,iApiIndex:0,oJUIClasses:{},sVersion:q.version};f.extend(C,{afnFiltering:C.search,aTypes:C.type.detect,ofnSearch:C.type.search,oSort:C.type.order,afnSortData:C.order,aoFeatures:C.feature,oApi:C.internal,oStdClasses:C.classes,oPagination:C.pager}); +f.extend(q.ext.classes,{sTable:"dataTable",sNoFooter:"no-footer",sPageButton:"paginate_button",sPageButtonActive:"current",sPageButtonDisabled:"disabled",sStripeOdd:"odd",sStripeEven:"even",sRowEmpty:"dataTables_empty",sWrapper:"dataTables_wrapper",sFilter:"dataTables_filter",sInfo:"dataTables_info",sPaging:"dataTables_paginate paging_",sLength:"dataTables_length",sProcessing:"dataTables_processing",sSortAsc:"sorting_asc",sSortDesc:"sorting_desc",sSortable:"sorting",sSortableAsc:"sorting_asc_disabled", +sSortableDesc:"sorting_desc_disabled",sSortableNone:"sorting_disabled",sSortColumn:"sorting_",sFilterInput:"",sLengthSelect:"",sScrollWrapper:"dataTables_scroll",sScrollHead:"dataTables_scrollHead",sScrollHeadInner:"dataTables_scrollHeadInner",sScrollBody:"dataTables_scrollBody",sScrollFoot:"dataTables_scrollFoot",sScrollFootInner:"dataTables_scrollFootInner",sHeaderTH:"",sFooterTH:"",sSortJUIAsc:"",sSortJUIDesc:"",sSortJUI:"",sSortJUIAscAllowed:"",sSortJUIDescAllowed:"",sSortJUIWrapper:"",sSortIcon:"", +sJUIHeader:"",sJUIFooter:""});var Pb=q.ext.pager;f.extend(Pb,{simple:function(a,b){return["previous","next"]},full:function(a,b){return["first","previous","next","last"]},numbers:function(a,b){return[ka(a,b)]},simple_numbers:function(a,b){return["previous",ka(a,b),"next"]},full_numbers:function(a,b){return["first","previous",ka(a,b),"next","last"]},first_last_numbers:function(a,b){return["first",ka(a,b),"last"]},_numbers:ka,numbers_length:7});f.extend(!0,q.ext.renderer,{pageButton:{_:function(a,b, +c,d,e,h){var g=a.oClasses,k=a.oLanguage.oPaginate,l=a.oLanguage.oAria.paginate||{},n,m,q=0,t=function(b,d){var p,r=g.sPageButtonDisabled,u=function(b){Xa(a,b.data.action,!0)};var w=0;for(p=d.length;w").appendTo(b);t(x,v)}else{n=null;m=v;x=a.iTabIndex;switch(v){case "ellipsis":b.append('…');break;case "first":n=k.sFirst;0===e&&(x=-1,m+=" "+r);break;case "previous":n=k.sPrevious;0===e&&(x=-1,m+= +" "+r);break;case "next":n=k.sNext;e===h-1&&(x=-1,m+=" "+r);break;case "last":n=k.sLast;e===h-1&&(x=-1,m+=" "+r);break;default:n=v+1,m=e===v?g.sPageButtonActive:""}null!==n&&(x=f("",{"class":g.sPageButton+" "+m,"aria-controls":a.sTableId,"aria-label":l[v],"data-dt-idx":q,tabindex:x,id:0===c&&"string"===typeof v?a.sTableId+"_"+v:null}).html(n).appendTo(b),$a(x,{action:v},u),q++)}}};try{var v=f(b).find(y.activeElement).data("dt-idx")}catch(mc){}t(f(b).empty(),d);v!==p&&f(b).find("[data-dt-idx="+ +v+"]").focus()}}});f.extend(q.ext.type.detect,[function(a,b){b=b.oLanguage.sDecimal;return db(a,b)?"num"+b:null},function(a,b){if(a&&!(a instanceof Date)&&!cc.test(a))return null;b=Date.parse(a);return null!==b&&!isNaN(b)||P(a)?"date":null},function(a,b){b=b.oLanguage.sDecimal;return db(a,b,!0)?"num-fmt"+b:null},function(a,b){b=b.oLanguage.sDecimal;return Ub(a,b)?"html-num"+b:null},function(a,b){b=b.oLanguage.sDecimal;return Ub(a,b,!0)?"html-num-fmt"+b:null},function(a,b){return P(a)||"string"=== +typeof a&&-1!==a.indexOf("<")?"html":null}]);f.extend(q.ext.type.search,{html:function(a){return P(a)?a:"string"===typeof a?a.replace(Rb," ").replace(Ea,""):""},string:function(a){return P(a)?a:"string"===typeof a?a.replace(Rb," "):a}});var Da=function(a,b,c,d){if(0!==a&&(!a||"-"===a))return-Infinity;b&&(a=Tb(a,b));a.replace&&(c&&(a=a.replace(c,"")),d&&(a=a.replace(d,"")));return 1*a};f.extend(C.type.order,{"date-pre":function(a){a=Date.parse(a);return isNaN(a)?-Infinity:a},"html-pre":function(a){return P(a)? +"":a.replace?a.replace(/<.*?>/g,"").toLowerCase():a+""},"string-pre":function(a){return P(a)?"":"string"===typeof a?a.toLowerCase():a.toString?a.toString():""},"string-asc":function(a,b){return ab?1:0},"string-desc":function(a,b){return ab?-1:0}});Ha("");f.extend(!0,q.ext.renderer,{header:{_:function(a,b,c,d){f(a.nTable).on("order.dt.DT",function(e,f,g,k){a===f&&(e=c.idx,b.removeClass(c.sSortingClass+" "+d.sSortAsc+" "+d.sSortDesc).addClass("asc"==k[e]?d.sSortAsc:"desc"==k[e]?d.sSortDesc: +c.sSortingClass))})},jqueryui:function(a,b,c,d){f("
").addClass(d.sSortJUIWrapper).append(b.contents()).append(f("").addClass(d.sSortIcon+" "+c.sSortingClassJUI)).appendTo(b);f(a.nTable).on("order.dt.DT",function(e,f,g,k){a===f&&(e=c.idx,b.removeClass(d.sSortAsc+" "+d.sSortDesc).addClass("asc"==k[e]?d.sSortAsc:"desc"==k[e]?d.sSortDesc:c.sSortingClass),b.find("span."+d.sSortIcon).removeClass(d.sSortJUIAsc+" "+d.sSortJUIDesc+" "+d.sSortJUI+" "+d.sSortJUIAscAllowed+" "+d.sSortJUIDescAllowed).addClass("asc"== +k[e]?d.sSortJUIAsc:"desc"==k[e]?d.sSortJUIDesc:c.sSortingClassJUI))})}}});var ib=function(a){return"string"===typeof a?a.replace(//g,">").replace(/"/g,"""):a};q.render={number:function(a,b,c,d,e){return{display:function(f){if("number"!==typeof f&&"string"!==typeof f)return f;var g=0>f?"-":"",h=parseFloat(f);if(isNaN(h))return ib(f);h=h.toFixed(c);f=Math.abs(h);h=parseInt(f,10);f=c?b+(f-h).toFixed(c).substring(2):"";return g+(d||"")+h.toString().replace(/\B(?=(\d{3})+(?!\d))/g, +a)+f+(e||"")}}},text:function(){return{display:ib,filter:ib}}};f.extend(q.ext.internal,{_fnExternApiFunc:Qb,_fnBuildAjax:va,_fnAjaxUpdate:qb,_fnAjaxParameters:zb,_fnAjaxUpdateDraw:Ab,_fnAjaxDataSrc:wa,_fnAddColumn:Ia,_fnColumnOptions:ma,_fnAdjustColumnSizing:aa,_fnVisibleToColumnIndex:ba,_fnColumnIndexToVisible:ca,_fnVisbleColumns:W,_fnGetColumns:oa,_fnColumnTypes:Ka,_fnApplyColumnDefs:nb,_fnHungarianMap:H,_fnCamelToHungarian:L,_fnLanguageCompat:Ga,_fnBrowserDetect:lb,_fnAddData:R,_fnAddTr:pa,_fnNodeToDataIndex:function(a, +b){return b._DT_RowIndex!==p?b._DT_RowIndex:null},_fnNodeToColumnIndex:function(a,b,c){return f.inArray(c,a.aoData[b].anCells)},_fnGetCellData:I,_fnSetCellData:ob,_fnSplitObjNotation:Na,_fnGetObjectDataFn:U,_fnSetObjectDataFn:Q,_fnGetDataMaster:Oa,_fnClearTable:qa,_fnDeleteIndex:ra,_fnInvalidate:ea,_fnGetRowElements:Ma,_fnCreateTr:La,_fnBuildHead:pb,_fnDrawHead:ha,_fnDraw:S,_fnReDraw:V,_fnAddOptionsHtml:sb,_fnDetectHeader:fa,_fnGetUniqueThs:ua,_fnFeatureHtmlFilter:ub,_fnFilterComplete:ia,_fnFilterCustom:Db, +_fnFilterColumn:Cb,_fnFilter:Bb,_fnFilterCreateSearch:Ta,_fnEscapeRegex:Ua,_fnFilterData:Eb,_fnFeatureHtmlInfo:xb,_fnUpdateInfo:Hb,_fnInfoMacros:Ib,_fnInitialise:ja,_fnInitComplete:xa,_fnLengthChange:Va,_fnFeatureHtmlLength:tb,_fnFeatureHtmlPaginate:yb,_fnPageChange:Xa,_fnFeatureHtmlProcessing:vb,_fnProcessingDisplay:K,_fnFeatureHtmlTable:wb,_fnScrollDraw:na,_fnApplyToChildren:N,_fnCalculateColumnWidths:Ja,_fnThrottle:Sa,_fnConvertToWidth:Jb,_fnGetWidestNode:Kb,_fnGetMaxLenString:Lb,_fnStringToCss:B, +_fnSortFlatten:Y,_fnSort:rb,_fnSortAria:Nb,_fnSortListener:Za,_fnSortAttachListener:Qa,_fnSortingClasses:Aa,_fnSortData:Mb,_fnSaveState:Ba,_fnLoadState:Ob,_fnSettingsFromNode:Ca,_fnLog:O,_fnMap:M,_fnBindAction:$a,_fnCallbackReg:E,_fnCallbackFire:A,_fnLengthOverflow:Wa,_fnRenderer:Ra,_fnDataSource:D,_fnRowAttributes:Pa,_fnExtend:ab,_fnCalculateEnd:function(){}});f.fn.dataTable=q;q.$=f;f.fn.dataTableSettings=q.settings;f.fn.dataTableExt=q.ext;f.fn.DataTable=function(a){return f(this).dataTable(a).api()}; +f.each(q,function(a,b){f.fn.DataTable[a]=b});return f.fn.dataTable}); diff --git a/docs/articles/database_of_anor_files/dt-ext-buttons-1.10.20/css/buttons.dataTables.min.css b/docs/articles/database_of_anor_files/dt-ext-buttons-1.10.20/css/buttons.dataTables.min.css new file mode 100644 index 0000000..19a1f1d --- /dev/null +++ b/docs/articles/database_of_anor_files/dt-ext-buttons-1.10.20/css/buttons.dataTables.min.css @@ -0,0 +1 @@ +@keyframes dtb-spinner{100%{transform:rotate(360deg)}}@-o-keyframes dtb-spinner{100%{-o-transform:rotate(360deg);transform:rotate(360deg)}}@-ms-keyframes dtb-spinner{100%{-ms-transform:rotate(360deg);transform:rotate(360deg)}}@-webkit-keyframes dtb-spinner{100%{-webkit-transform:rotate(360deg);transform:rotate(360deg)}}@-moz-keyframes dtb-spinner{100%{-moz-transform:rotate(360deg);transform:rotate(360deg)}}div.dt-button-info{position:fixed;top:50%;left:50%;width:400px;margin-top:-100px;margin-left:-200px;background-color:white;border:2px solid #111;box-shadow:3px 3px 8px rgba(0,0,0,0.3);border-radius:3px;text-align:center;z-index:21}div.dt-button-info h2{padding:0.5em;margin:0;font-weight:normal;border-bottom:1px solid #ddd;background-color:#f3f3f3}div.dt-button-info>div{padding:1em}div.dt-button-collection-title{text-align:center;padding:0.3em 0 0.5em;font-size:0.9em}div.dt-button-collection-title:empty{display:none}button.dt-button,div.dt-button,a.dt-button{position:relative;display:inline-block;box-sizing:border-box;margin-right:0.333em;margin-bottom:0.333em;padding:0.5em 1em;border:1px solid #999;border-radius:2px;cursor:pointer;font-size:0.88em;line-height:1.6em;color:black;white-space:nowrap;overflow:hidden;background-color:#e9e9e9;background-image:-webkit-linear-gradient(top, #fff 0%, #e9e9e9 100%);background-image:-moz-linear-gradient(top, #fff 0%, #e9e9e9 100%);background-image:-ms-linear-gradient(top, #fff 0%, #e9e9e9 100%);background-image:-o-linear-gradient(top, #fff 0%, #e9e9e9 100%);background-image:linear-gradient(to bottom, #fff 0%, #e9e9e9 100%);filter:progid:DXImageTransform.Microsoft.gradient(GradientType=0,StartColorStr='white', EndColorStr='#e9e9e9');-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;user-select:none;text-decoration:none;outline:none;text-overflow:ellipsis}button.dt-button.disabled,div.dt-button.disabled,a.dt-button.disabled{color:#999;border:1px solid #d0d0d0;cursor:default;background-color:#f9f9f9;background-image:-webkit-linear-gradient(top, #fff 0%, #f9f9f9 100%);background-image:-moz-linear-gradient(top, #fff 0%, #f9f9f9 100%);background-image:-ms-linear-gradient(top, #fff 0%, #f9f9f9 100%);background-image:-o-linear-gradient(top, #fff 0%, #f9f9f9 100%);background-image:linear-gradient(to bottom, #fff 0%, #f9f9f9 100%);filter:progid:DXImageTransform.Microsoft.gradient(GradientType=0,StartColorStr='#ffffff', EndColorStr='#f9f9f9')}button.dt-button:active:not(.disabled),button.dt-button.active:not(.disabled),div.dt-button:active:not(.disabled),div.dt-button.active:not(.disabled),a.dt-button:active:not(.disabled),a.dt-button.active:not(.disabled){background-color:#e2e2e2;background-image:-webkit-linear-gradient(top, #f3f3f3 0%, #e2e2e2 100%);background-image:-moz-linear-gradient(top, #f3f3f3 0%, #e2e2e2 100%);background-image:-ms-linear-gradient(top, #f3f3f3 0%, #e2e2e2 100%);background-image:-o-linear-gradient(top, #f3f3f3 0%, #e2e2e2 100%);background-image:linear-gradient(to bottom, #f3f3f3 0%, #e2e2e2 100%);filter:progid:DXImageTransform.Microsoft.gradient(GradientType=0,StartColorStr='#f3f3f3', EndColorStr='#e2e2e2');box-shadow:inset 1px 1px 3px #999999}button.dt-button:active:not(.disabled):hover:not(.disabled),button.dt-button.active:not(.disabled):hover:not(.disabled),div.dt-button:active:not(.disabled):hover:not(.disabled),div.dt-button.active:not(.disabled):hover:not(.disabled),a.dt-button:active:not(.disabled):hover:not(.disabled),a.dt-button.active:not(.disabled):hover:not(.disabled){box-shadow:inset 1px 1px 3px #999999;background-color:#cccccc;background-image:-webkit-linear-gradient(top, #eaeaea 0%, #ccc 100%);background-image:-moz-linear-gradient(top, #eaeaea 0%, #ccc 100%);background-image:-ms-linear-gradient(top, #eaeaea 0%, #ccc 100%);background-image:-o-linear-gradient(top, #eaeaea 0%, #ccc 100%);background-image:linear-gradient(to bottom, #eaeaea 0%, #ccc 100%);filter:progid:DXImageTransform.Microsoft.gradient(GradientType=0,StartColorStr='#eaeaea', EndColorStr='#cccccc')}button.dt-button:hover,div.dt-button:hover,a.dt-button:hover{text-decoration:none}button.dt-button:hover:not(.disabled),div.dt-button:hover:not(.disabled),a.dt-button:hover:not(.disabled){border:1px solid #666;background-color:#e0e0e0;background-image:-webkit-linear-gradient(top, #f9f9f9 0%, #e0e0e0 100%);background-image:-moz-linear-gradient(top, #f9f9f9 0%, #e0e0e0 100%);background-image:-ms-linear-gradient(top, #f9f9f9 0%, #e0e0e0 100%);background-image:-o-linear-gradient(top, #f9f9f9 0%, #e0e0e0 100%);background-image:linear-gradient(to bottom, #f9f9f9 0%, #e0e0e0 100%);filter:progid:DXImageTransform.Microsoft.gradient(GradientType=0,StartColorStr='#f9f9f9', EndColorStr='#e0e0e0')}button.dt-button:focus:not(.disabled),div.dt-button:focus:not(.disabled),a.dt-button:focus:not(.disabled){border:1px solid #426c9e;text-shadow:0 1px 0 #c4def1;outline:none;background-color:#79ace9;background-image:-webkit-linear-gradient(top, #bddef4 0%, #79ace9 100%);background-image:-moz-linear-gradient(top, #bddef4 0%, #79ace9 100%);background-image:-ms-linear-gradient(top, #bddef4 0%, #79ace9 100%);background-image:-o-linear-gradient(top, #bddef4 0%, #79ace9 100%);background-image:linear-gradient(to bottom, #bddef4 0%, #79ace9 100%);filter:progid:DXImageTransform.Microsoft.gradient(GradientType=0,StartColorStr='#bddef4', EndColorStr='#79ace9')}.dt-button embed{outline:none}div.dt-buttons{position:relative;float:left}div.dt-buttons.buttons-right{float:right}div.dt-button-collection{position:absolute;top:0;left:0;width:150px;margin-top:3px;padding:8px 8px 4px 8px;border:1px solid #ccc;border:1px solid rgba(0,0,0,0.4);background-color:white;overflow:hidden;z-index:2002;border-radius:5px;box-shadow:3px 3px 5px rgba(0,0,0,0.3);box-sizing:border-box}div.dt-button-collection button.dt-button,div.dt-button-collection div.dt-button,div.dt-button-collection a.dt-button{position:relative;left:0;right:0;width:100%;display:block;float:none;margin-bottom:4px;margin-right:0}div.dt-button-collection button.dt-button:active:not(.disabled),div.dt-button-collection button.dt-button.active:not(.disabled),div.dt-button-collection div.dt-button:active:not(.disabled),div.dt-button-collection div.dt-button.active:not(.disabled),div.dt-button-collection a.dt-button:active:not(.disabled),div.dt-button-collection a.dt-button.active:not(.disabled){background-color:#dadada;background-image:-webkit-linear-gradient(top, #f0f0f0 0%, #dadada 100%);background-image:-moz-linear-gradient(top, #f0f0f0 0%, #dadada 100%);background-image:-ms-linear-gradient(top, #f0f0f0 0%, #dadada 100%);background-image:-o-linear-gradient(top, #f0f0f0 0%, #dadada 100%);background-image:linear-gradient(to bottom, #f0f0f0 0%, #dadada 100%);filter:progid:DXImageTransform.Microsoft.gradient(GradientType=0,StartColorStr='#f0f0f0', EndColorStr='#dadada');box-shadow:inset 1px 1px 3px 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