Merge pull request #181 from TheJacksonLaboratory/develop

updates
TheJacksonLaboratory · Jul 5, 2024 · c4e7ee3 · c4e7ee3
2 parents d12954f + 2658acd
commit c4e7ee3
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Showing 18 changed files with 17 additions and 75 deletions.
diff --git a/isopret-cli/pom.xml b/isopret-cli/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.3.2</version>
+        <version>1.3.3</version>
     </parent>
 
     <artifactId>isopret-cli</artifactId>

diff --git a/isopret-cli/src/main/java/org/jax/isopret/cli/command/GoOverrepCommand.java b/isopret-cli/src/main/java/org/jax/isopret/cli/command/GoOverrepCommand.java
@@ -204,13 +204,10 @@ private void writeGoResultsToFile(GoAnalysisResults results,
                 try {
                     if (exportAll) {
                         bw.write("DGE\t" + cts.getRow(geneOntology) + "\n");
-                        outputDgeGoTerms++;
-
-                    } else {
-                        if (cts.passesThreshold(GO_PVAL_THRESHOLD))
-                            bw.write("DGE\t" + cts.getRow(geneOntology) + "\n");
-                        outputDgeGoTerms++;
+                    } else if (cts.passesThreshold(GO_PVAL_THRESHOLD)) {
+                        bw.write("DGE\t" + cts.getRow(geneOntology) + "\n");
                     }
+                    outputDgeGoTerms++;
                 } catch (Exception e) {
                     // some issue with getting terms, probably ontology is not in sync
                     LOGGER.error("Could not get data for {}: {}", cts, e.getLocalizedMessage());

diff --git a/isopret-core/pom.xml b/isopret-core/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.3.2</version>
+        <version>1.3.3</version>
     </parent>
 
     <artifactId>isopret-core</artifactId>

diff --git a/isopret-core/src/main/java/module-info.java b/isopret-core/src/main/java/module-info.java
@@ -4,7 +4,6 @@
     requires org.monarchinitiative.svart;
     requires org.monarchinitiative.phenol.analysis;
     requires jannovar.core;
-    requires org.apache.commons.net;
     requires org.monarchinitiative.phenol.io;
     requires guava;
     requires org.jax.isopret.data;

diff --git a/...-core/src/main/java/org/jax/isopret/core/impl/rnaseqdata/PosteriorErrorProbThreshold.java b/...-core/src/main/java/org/jax/isopret/core/impl/rnaseqdata/PosteriorErrorProbThreshold.java
@@ -6,7 +6,7 @@
 import java.util.stream.IntStream;
 
 /**
- * This class is used to calculate the threshold posterior error proibability (PEP) threshold that achieves a desired
+ * This class is used to calculate the threshold posterior error probability (PEP) threshold that achieves a desired
  * false-discovery rate (FDR) over the current dataset. Explanations can be found in
  * Käll L, Storey JD, MacCoss MJ, Noble WS. Posterior error probabilities and false discovery rates:
  * two sides of the same coin. J Proteome Res. 2008 Jan;7(1):40-4. PMID:18052118.

diff --git a/isopret-core/src/main/java/org/jax/isopret/visualization/EnsemblVisualizable.java b/isopret-core/src/main/java/org/jax/isopret/visualization/EnsemblVisualizable.java
@@ -176,8 +176,6 @@ public double getMostSignificantSplicingPval() {
 
     @Override
     public double getExpressionFoldChange() {
-       // double logFc = getExpressionLogFoldChange();
-       // return Math.exp(logFc);
         return this.hbaDealsResult.getExpressionFoldChange();
     }
 

diff --git a/...et-core/src/main/java/org/jax/isopret/visualization/HtmlGoAnnotationMatrixVisualizer.java b/...et-core/src/main/java/org/jax/isopret/visualization/HtmlGoAnnotationMatrixVisualizer.java
@@ -90,7 +90,6 @@ private String htmlTableHeader(GoAnnotationMatrix matrix) {
                margin: 20;
                font-size:14px;
             }
-
             body {
                font-family:"DIN Next", Helvetica, Arial, sans-serif;
                line-height:1.25;
@@ -99,18 +98,15 @@ private String htmlTableHeader(GoAnnotationMatrix matrix) {
                 margin-left:auto;
                 margin-right:auto;
              }
-             
              gotable, gotable.th, gotable.td {
                  border: 0.5px solid;
                  border-collapse: collapse;
              }
-
              gotable.th
              {
                vertical-align: bottom;
                text-align: center;
              }
-             
              gotable.th span
              {
                -ms-writing-mode: tb-rl;

diff --git a/isopret-core/src/main/java/org/jax/isopret/visualization/HtmlUtil.java b/isopret-core/src/main/java/org/jax/isopret/visualization/HtmlUtil.java
@@ -6,7 +6,6 @@ public class HtmlUtil {
     public static final String header = """
             <!doctype html>
             <html class="no-js" lang="">
-                        
             <head>
               <meta charset="utf-8">
               <meta http-equiv="x-ua-compatible" content="ie=edge">
@@ -25,73 +24,58 @@ public class HtmlUtil {
                 -webkit-box-sizing: border-box;
                 box-sizing: border-box
             }
-                        
             html, body, h1, li, a, article, aside, footer, header, main, nav, section {
             	padding: 0;
             	margin: 0;
             }
-                        
             html, body {
             	font-size:14px;
             }
-                        
             body {
             	font-family:"DIN Next", Helvetica, Arial, sans-serif;
             	line-height:1.25;
             	background-color: white;
             }
-                        
-                        
             body > header, nav, main, body > section, footer {
             max-width:1200px;
             margin-left:auto;
             margin-right:auto;
             }
-                        
             @media(min-width:1440px) {
             body > header, nav, main, body > section, footer {
                 width:90%;
                 max-width:unset;
                 }
             }
-                        
             main, body > section {
             	margin-top:1.5rem;
             	margin-bottom:1.5rem;
             }
-                        
             body > header, body > section {
             	padding:2.1rem 2rem 1.6rem;
             }
-                        
             .fr {
               float: right;
             }
-                        
             a[href] {
             	color:#05396b;
             }
-                        
             a[href]:hover {
             	color:#009ed0;
             }
-                        
             p {
             	padding:0;
             	margin:0.75rem 0;
             }
-                        
             h1 {
             	font-family:"DIN Next", Helvetica, Arial, sans-serif;
             	font-weight:700;
             	font-size:1.8rem;
             	line-height:1;
             }
-                        
             .center {
               text-align: center;
             }
-                        
             main > section > a[name="othergenes"] > h3,
             h2 {
             	font-family:"DIN Next", Helvetica, Arial, sans-serif;
@@ -101,7 +85,6 @@ public class HtmlUtil {
             	margin:0 0 0.5rem;
             	padding:0;
             }
-                        
             h3 {
             	font-family:"DIN Next", Helvetica, Arial, sans-serif;
             	font-weight:700;
@@ -110,32 +93,25 @@ public class HtmlUtil {
             	margin:0 0 0.5rem;
             	padding:0;
             }
-                        
-                        
-                        
             main ul, main ol {
             	margin:0.5rem 0 0.5rem 1.4rem;
             	padding:0;
             }
-                        
             main li {
             	margin:0.25rem 0;
             	padding:0;
             }
-                        
             .banner {
             	background-color: #05396b;
             	color: white;
             }
-                        
             nav {
             	background-color: #4DA8DA;
             	margin-top:1px;
             	overflow:auto;
             	zoom:1;
             	padding:0;
             }
-                        
             nav a[href] {
             	color:white;
             	text-decoration:none;
@@ -145,58 +121,48 @@ public class HtmlUtil {
             	padding:1rem;
             	font-weight:400;
             }
-                        
             nav li:last-child a[href] {
             	padding-right:2.25rem;
             }
-                        
             nav a[href]:hover {
             	color:#05396b;
             	background-color:#04c3ff;
             }
-                        
             #navi ul {
             	display:table;
             	float:right;
             	margin:0;
             }
-                        
             #navi li {
             	display:block;
             	float:left;
             }
-                        
             main > section:first-child {
             	margin-top:1.5rem;
             	margin-bottom:1.5rem;
             	background-color:white;
             	padding:2.1rem 2rem 1.6rem;
             }
-                        
             main > section {
             	margin-top:1.5rem;
             	margin-bottom:0;
             	background-color:white;
             	padding: .5rem;
             }
-                        
             main > section > article {
             	padding: 1.5rem;
             	margin-top:1px;
             	background-color:white;
             }
-                        
             table {
             	border-collapse: collapse;
             	width:100%;
             	margin:0.5rem 0;
             }
-                        
             th, td {
             	text-align:left;
             	padding:0.4rem 0.5rem 0.25rem;
             }
-                        
             th {
             	background-color: #e0e3ea;
             	border-bottom:1px solid white;
@@ -215,15 +181,13 @@ public class HtmlUtil {
                padding: 5px 10px;
                 margin: 0 auto;
              }
-                             
             .svgrow{
                 width: 90%;
                 min-height: 100px;
                 margin: 0 auto;
                 display: -webkit-flex; /* Safari */
                 display: flex; /* Standard syntax */
             }
-                
             div.go {
                border: 0.5rem outset black;
                 border-radius: 4px;
@@ -232,29 +196,23 @@ public class HtmlUtil {
                 padding: 1rem;
                 outline-offset: 0.5rem;
             }
-                        
-                                
             footer {
             	background-color: #05396b;
             	color: white;
             	padding: 1rem 2rem;
             }
-                        
             /* The following links are in the SVG for the differentials */
             a.svg:link, a.svg:visited {
               cursor: pointer;
             }
-                        
             a.svg text,
             text a.svg {
               fill: blue; /* Even for text, SVG uses fill over color */
               text-decoration: underline;
             }
-                        
             a.svg:hover, a.svg:active {
               outline: dotted 1px blue;
             }
-
             .table-btn {
                 display: block;
                 font-weight: bold;
@@ -264,7 +222,6 @@ public class HtmlUtil {
                 color: white;
                 cursor: pointer;
             }
-  
             </style>
             """;
 
@@ -315,15 +272,14 @@ function showTooltip(evt, text) {
                 tooltip.style.left = evt.pageX + 10 + 'px';
                 tooltip.style.top = evt.pageY + 10 + 'px';
               }
-                        
               function hideTooltip() {
                 var tooltip = document.getElementById("tooltip");
                 tooltip.style.display = "none";
               }
             </script>
             </body>
             </html>
-            """;
+           """;
 
 
     public static String wrap(String html) {
@@ -337,7 +293,7 @@ public static String cssWrap(String html) {
             <html class="no-js" lang="">
             <head>
               <meta charset="utf-8">
-                """ +
+            """ +
                 css +
                 "</head>\n" +
                html

diff --git a/isopret-core/src/main/java/org/jax/isopret/visualization/HtmlVisualizer.java b/isopret-core/src/main/java/org/jax/isopret/visualization/HtmlVisualizer.java
@@ -23,7 +23,7 @@ public class HtmlVisualizer implements Visualizer {
     public final String HBADEALS_A = """
         <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02072-6"
          target=__blank>HBA-DEALS</a>
-         """;
+        """;
 
     public HtmlVisualizer(String experiment) {
         this.experiment = experiment;

diff --git a/isopret-core/src/main/java/org/jax/isopret/visualization/TranscriptSvgGenerator.java b/isopret-core/src/main/java/org/jax/isopret/visualization/TranscriptSvgGenerator.java
@@ -369,8 +369,6 @@ private int getRegionOfSvgCanvas(double xpos) {
     private void writeTranscriptName(Transcript tmod, double minX, double maxX, int ypos, Writer writer) throws IOException {
         String symbol = tmod.hgvsSymbol();
         AccessionNumber accession = tmod.accessionId();
-       // String positionString = String.format("%s:%d-%d (%s strand)", chrom, start, end, strand);
-       // String geneName = String.format("%s (%s)", symbol, accession.getAccessionString());
         double y = Y_SKIP_BENEATH_TRANSCRIPTS + ypos;
         int region = getRegionOfSvgCanvas(minX);
         String textAnchor = "start";

diff --git a/isopret-data/pom.xml b/isopret-data/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.3.2</version>
+        <version>1.3.3</version>
     </parent>
 
     <artifactId>isopret-data</artifactId>

diff --git a/isopret-exception/pom.xml b/isopret-exception/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.3.2</version>
+        <version>1.3.3</version>
     </parent>
 
     <artifactId>isopret-exception</artifactId>

diff --git a/isopret-gui/pom.xml b/isopret-gui/pom.xml
@@ -9,7 +9,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.3.2</version>
+        <version>1.3.3</version>
     </parent>
 
     <artifactId>isopret-gui</artifactId>