From f8adfdfd7621e8612b5ac5702a241b2a31b38670 Mon Sep 17 00:00:00 2001 From: David Maddison Date: Fri, 29 Aug 2014 17:15:41 -0700 Subject: [PATCH 1/3] notices and install file for version 1.1.1 --- Web Site Files/install.xml | 8 ++++---- Web Site Files/notices.xml | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/Web Site Files/install.xml b/Web Site Files/install.xml index 469d5ee..a85087b 100644 --- a/Web Site Files/install.xml +++ b/Web Site Files/install.xml @@ -4,7 +4,7 @@ 1 - 612 + 620 8 alert Chromaseq @@ -12,13 +12,13 @@ Chromaseq version 1.11

- In order to install Chromaseq 1.11, you need to first update to Mesquite version 3.0. - You can get Mesquite 3.0 at https://mesquiteproject.wikispaces.com/Installation + In order to install Chromaseq 1.11, you need to first update to Mesquite version 3.0. + You can get Mesquite 3.0 at https://mesquiteproject.wikispaces.com/Installation ]]> - 619 + 644 13 update Chromaseq diff --git a/Web Site Files/notices.xml b/Web Site Files/notices.xml index 2bdd45a..1bc5a90 100644 --- a/Web Site Files/notices.xml +++ b/Web Site Files/notices.xml @@ -3,7 +3,7 @@ 1 - 612 + 620 8 alert Chromaseq @@ -11,8 +11,8 @@ Chromaseq version 1.11

- In order to install Chromaseq 1.11, you need to first update to Mesquite version 3.0. - You can get Mesquite 3.0 at https://mesquiteproject.wikispaces.com/Installation + In order to install Chromaseq 1.11, you need to first update to Mesquite version 3.0. + You can get Mesquite 3.0 at https://mesquiteproject.wikispaces.com/Installation ]]> @@ -34,7 +34,7 @@ mesquite chromaseq - https://github.com/MesquiteProject/Chromaseq/releases/download/1.1.1/chromaseq.1.1.1.zip + https://github.com/MesquiteProject/Chromaseq/releases/download/1.1.1/Chromaseq.1.1.1.zip unzip 003 From bd8f09e04c32c459c2f9ac2983e9fa8a32e728ac Mon Sep 17 00:00:00 2001 From: wmaddisn Date: Tue, 2 Sep 2014 17:42:52 -0700 Subject: [PATCH 2/3] Fixed mustBeAfter method in ManageChromaseq --- .../chromaseq/ManageChromaseqBlock/ManageChromaseqBlock.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Source/mesquite/chromaseq/ManageChromaseqBlock/ManageChromaseqBlock.java b/Source/mesquite/chromaseq/ManageChromaseqBlock/ManageChromaseqBlock.java index 0b5d91b..f7727f0 100644 --- a/Source/mesquite/chromaseq/ManageChromaseqBlock/ManageChromaseqBlock.java +++ b/Source/mesquite/chromaseq/ManageChromaseqBlock/ManageChromaseqBlock.java @@ -773,7 +773,7 @@ public String getName(){ return "CHROMASEQ block"; } public boolean mustBeAfter(NexusBlock block){ - return false; + return (block.getBlockName().equalsIgnoreCase("TAXA") || block.getBlockName().equalsIgnoreCase("CHARACTERS") || block.getBlockName().equalsIgnoreCase("SETS") || block.getBlockName().equalsIgnoreCase("LABELS")); } public String getBlockName(){ return "CHROMASEQ"; From 7d121c058b80f1471a9c2e19c4934f4a8c57aacd Mon Sep 17 00:00:00 2001 From: David Maddison Date: Tue, 2 Sep 2014 19:57:09 -0700 Subject: [PATCH 3/3] Documentation tweaks to bring change version number to 1.12 --- .../aChromaseqIntro/aChromaseqIntro.java | 2 +- .../manual/Templates/ChromaseqTemplate.dwt | 4 ++-- .../manual/acknowledgements.html | 4 ++-- .../manual/appendingSequences.html | 4 ++-- .../aChromaseqIntro/manual/callingBases.html | 4 ++-- .../aChromaseqIntro/manual/chromaseqList.html | 4 ++-- .../aChromaseqIntro/manual/chromatograms.html | 4 ++-- .../aChromaseqIntro/manual/citation.html | 6 ++--- .../aChromaseqIntro/manual/conflicts.html | 4 ++-- .../aChromaseqIntro/manual/display.html | 4 ++-- .../aChromaseqIntro/manual/download.html | 4 ++-- .../manual/extraSequences.html | 4 ++-- .../chromaseq/aChromaseqIntro/manual/faq.html | 4 ++-- .../manual/fileNamingRules.html | 4 ++-- .../aChromaseqIntro/manual/future.html | 4 ++-- .../aChromaseqIntro/manual/genbank.html | 4 ++-- .../manual/helpfulMesquite.html | 4 ++-- .../aChromaseqIntro/manual/index.html | 4 ++-- .../manual/informationStrips.html | 4 ++-- .../aChromaseqIntro/manual/installation.html | 4 ++-- .../manual/interpretingResults.html | 4 ++-- .../aChromaseqIntro/manual/knownIssues.html | 4 ++-- .../aChromaseqIntro/manual/limitations.html | 4 ++-- .../aChromaseqIntro/manual/listWindow.html | 4 ++-- .../aChromaseqIntro/manual/matrixCells.html | 4 ++-- .../aChromaseqIntro/manual/navigation.html | 4 ++-- .../aChromaseqIntro/manual/otherPrograms.html | 4 ++-- .../aChromaseqIntro/manual/overview.html | 4 ++-- .../aChromaseqIntro/manual/phredphrap.html | 4 ++-- .../aChromaseqIntro/manual/postPhrap.html | 4 ++-- .../aChromaseqIntro/manual/preparation.html | 4 ++-- .../aChromaseqIntro/manual/primerSites.html | 4 ++-- .../aChromaseqIntro/manual/primers.html | 4 ++-- .../aChromaseqIntro/manual/purging.html | 4 ++-- .../aChromaseqIntro/manual/quality.html | 4 ++-- .../aChromaseqIntro/manual/quickstart.html | 4 ++-- .../aChromaseqIntro/manual/runningPP.html | 4 ++-- .../aChromaseqIntro/manual/sampleCode.html | 4 ++-- .../manual/segregatingChromatograms.html | 4 ++-- .../aChromaseqIntro/manual/sourceCode.html | 4 ++-- .../aChromaseqIntro/manual/technicalFAQ.html | 4 ++-- .../manual/troubleshooting.html | 4 ++-- .../aChromaseqIntro/manual/tutorial.html | 4 ++-- .../aChromaseqIntro/manual/versions.html | 4 ++-- .../aChromaseqIntro/manual/viewer.html | 4 ++-- .../aChromaseqIntro/manual/vouchers.html | 4 ++-- .../aChromaseqIntro/manual/workflow.html | 4 ++-- Web Site Files/install.xml | 18 +++++++------- Web Site Files/notices.xml | 24 +++++++++---------- 49 files changed, 115 insertions(+), 115 deletions(-) diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/aChromaseqIntro.java b/Source/mesquite/chromaseq/aChromaseqIntro/aChromaseqIntro.java index cc3fac5..2b2a871 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/aChromaseqIntro.java +++ b/Source/mesquite/chromaseq/aChromaseqIntro/aChromaseqIntro.java @@ -1 +1 @@ -/* Mesquite Chromaseq source code. Copyright 2005-2011 David Maddison and Wayne Maddison. Version 1.0 December 2011 Disclaimer: The Mesquite source code is lengthy and we are few. There are no doubt inefficiencies and goofs in this code. The commenting leaves much to be desired. Please approach this source code with the spirit of helping out. Perhaps with your help we can be more than a few, and make Mesquite better. Mesquite is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. Mesquite's web site is http://mesquiteproject.org This source code and its compiled class files are free and modifiable under the terms of GNU Lesser General Public License. (http://www.gnu.org/copyleft/lesser.html) */ package mesquite.chromaseq.aChromaseqIntro; import mesquite.lib.duties.*; import mesquite.lib.*; /* ======================================================================== */ public class aChromaseqIntro extends PackageIntro { /*.................................................................................................................*/ public boolean startJob(String arguments, Object condition, boolean hiredByName) { return true; } public Class getDutyClass(){ return aChromaseqIntro.class; } /*.................................................................................................................*/ public String getManualPath(){ return getPath() +"/manual/index.html"; } /** returns the URL of the notices file for this module so that it can phone home and check for messages */ /*.................................................................................................................*/ public String getHomePhoneNumber(){ if (MesquiteTrunk.debugMode) return "http://mesquiteproject.org/packages/chromaseq/noticesDev.xml"; else if (isPrerelease()) return "http://mesquiteproject.org/packages/chromaseq/noticesPrerelease.xml"; else return "http://mesquiteproject.org/packages/chromaseq/notices.xml"; } /*.................................................................................................................*/ public String getExplanation() { return "Chromaseq is a package of Mesquite modules providing tools for processing and displaying chromatograms and sequence data."; } /*.................................................................................................................*/ public String getName() { return "Chromaseq Package"; } /*.................................................................................................................*/ /** Returns the name of the package of modules (e.g., "Basic Mesquite Package", "Rhetenor")*/ public String getPackageName(){ return "Chromaseq Package"; } /*.................................................................................................................*/ public boolean isPrerelease(){ return false; } /*.................................................................................................................*/ /** Returns citation for a package of modules*/ public String getPackageCitation(){ if (isPrerelease()) return "Maddison, D.R., & W.P. Maddison. 2014. Chromaseq. A package for processing chromatograms and sequence data in Mesquite. Prerelease version " + getPackageVersion() + " (build " + getBuildVersion() + ")."; return "Maddison, D.R., & W.P. Maddison. 2014. Chromaseq. A package for processing chromatograms and sequence data in Mesquite. Version " + getPackageVersion() + "."; } /*.................................................................................................................*/ /** Returns version for a package of modules*/ public String getPackageVersion(){ return "1.11"; } /*.................................................................................................................*/ /** Returns version for a package of modules as an integer*/ public int getPackageVersionInt(){ return 1110; } /*.................................................................................................................*/ /** Returns build number for a package of modules as an integer*/ public int getPackageBuildNumber(){ return 35; } /* release history: 0.981, build 12 25 July 2010 - first beta release 0.982, build 15 14 August 2010 - second beta 0.983, build 18 21 September 2010 0.984, build 19 3 October 2010 0.986, build 21 1 June 2011 - third beta 0.990, build 25 4 October 2011 - first public release, fourth beta 1.0, build 28 23 December 2011 1.01 10 December 2013 1.1 19 August 2014 1.11 */ /*.................................................................................................................*/ public String getPackageURL(){ return "http://mesquiteproject.org/packages/chromaseq"; } public String getPackageDateReleased(){ return "21 August 2014 "; } /*.................................................................................................................*/ /** Returns whether there is a splash banner*/ public boolean hasSplash(){ return true; } /*.................................................................................................................*/ public int getVersionOfFirstRelease(){ return 275; } } \ No newline at end of file +/* Mesquite Chromaseq source code. Copyright 2005-2011 David Maddison and Wayne Maddison. Version 1.0 December 2011 Disclaimer: The Mesquite source code is lengthy and we are few. There are no doubt inefficiencies and goofs in this code. The commenting leaves much to be desired. Please approach this source code with the spirit of helping out. Perhaps with your help we can be more than a few, and make Mesquite better. Mesquite is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. Mesquite's web site is http://mesquiteproject.org This source code and its compiled class files are free and modifiable under the terms of GNU Lesser General Public License. (http://www.gnu.org/copyleft/lesser.html) */ package mesquite.chromaseq.aChromaseqIntro; import mesquite.lib.duties.*; import mesquite.lib.*; /* ======================================================================== */ public class aChromaseqIntro extends PackageIntro { /*.................................................................................................................*/ public boolean startJob(String arguments, Object condition, boolean hiredByName) { return true; } public Class getDutyClass(){ return aChromaseqIntro.class; } /*.................................................................................................................*/ public String getManualPath(){ return getPath() +"/manual/index.html"; } /** returns the URL of the notices file for this module so that it can phone home and check for messages */ /*.................................................................................................................*/ public String getHomePhoneNumber(){ if (MesquiteTrunk.debugMode) return "http://mesquiteproject.org/packages/chromaseq/noticesDev.xml"; else if (isPrerelease()) return "http://mesquiteproject.org/packages/chromaseq/noticesPrerelease.xml"; else return "http://mesquiteproject.org/packages/chromaseq/notices.xml"; } /*.................................................................................................................*/ public String getExplanation() { return "Chromaseq is a package of Mesquite modules providing tools for processing and displaying chromatograms and sequence data."; } /*.................................................................................................................*/ public String getName() { return "Chromaseq Package"; } /*.................................................................................................................*/ /** Returns the name of the package of modules (e.g., "Basic Mesquite Package", "Rhetenor")*/ public String getPackageName(){ return "Chromaseq Package"; } /*.................................................................................................................*/ public boolean isPrerelease(){ return false; } /*.................................................................................................................*/ /** Returns citation for a package of modules*/ public String getPackageCitation(){ if (isPrerelease()) return "Maddison, D.R., & W.P. Maddison. 2014. Chromaseq. A package for processing chromatograms and sequence data in Mesquite. Prerelease version " + getPackageVersion() + " (build " + getBuildVersion() + ")."; return "Maddison, D.R., & W.P. Maddison. 2014. Chromaseq. A package for processing chromatograms and sequence data in Mesquite. Version " + getPackageVersion() + "."; } /*.................................................................................................................*/ /** Returns version for a package of modules*/ public String getPackageVersion(){ return "1.12"; } /*.................................................................................................................*/ /** Returns version for a package of modules as an integer*/ public int getPackageVersionInt(){ return 1120; } /*.................................................................................................................*/ /** Returns build number for a package of modules as an integer*/ public int getPackageBuildNumber(){ return 36; } /* release history: 0.981, build 12 25 July 2010 - first beta release 0.982, build 15 14 August 2010 - second beta 0.983, build 18 21 September 2010 0.984, build 19 3 October 2010 0.986, build 21 1 June 2011 - third beta 0.990, build 25 4 October 2011 - first public release, fourth beta 1.0, build 28 23 December 2011 1.01 10 December 2013 1.1 19 August 2014 1.11 (build 35) 29 August 2014 1.12 (build 36) 29 August 2014 */ /*.................................................................................................................*/ public String getPackageURL(){ return "http://mesquiteproject.org/packages/chromaseq"; } public String getPackageDateReleased(){ return "29 August 2014 "; } /*.................................................................................................................*/ /** Returns whether there is a splash banner*/ public boolean hasSplash(){ return true; } /*.................................................................................................................*/ public int getVersionOfFirstRelease(){ return 275; } } \ No newline at end of file diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/Templates/ChromaseqTemplate.dwt b/Source/mesquite/chromaseq/aChromaseqIntro/manual/Templates/ChromaseqTemplate.dwt index b5c0d6b..237db96 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/Templates/ChromaseqTemplate.dwt +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/Templates/ChromaseqTemplate.dwt @@ -41,8 +41,8 @@ Chromaseq

subtitle
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/acknowledgements.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/acknowledgements.html index 25bc2bd..75f9005 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/acknowledgements.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/acknowledgements.html @@ -40,8 +40,8 @@ Chromaseq
Acknowledgements
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/appendingSequences.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/appendingSequences.html index 43c655f..19f5150 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/appendingSequences.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/appendingSequences.html @@ -41,8 +41,8 @@ Chromaseq
Processing Additional Chromatograms
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/callingBases.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/callingBases.html index 61ed18e..42078a5 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/callingBases.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/callingBases.html @@ -43,8 +43,8 @@ Chromaseq
Calling Bases
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/chromaseqList.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/chromaseqList.html index 8c06585..4fdab56 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/chromaseqList.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/chromaseqList.html @@ -41,8 +41,8 @@ Chromaseq
Chromaseq E-mail List
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/chromatograms.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/chromatograms.html index d178bcc..e3b56ab 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/chromatograms.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/chromatograms.html @@ -41,8 +41,8 @@ Chromaseq
Preparing Chromatograms
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/citation.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/citation.html index 2886f3a..32f6da5 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/citation.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/citation.html @@ -49,8 +49,8 @@ Chromaseq
Citation
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
@@ -192,7 +192,7 @@

 

This version of Chromaseq should be cited as:


Maddison, D.R., & W.P. Maddison. 2014. Chromaseq: a Mesquite - package for analyzing sequence chromatograms. Version 1.1. http://mesquiteproject.org/packages/chromaseq

+ package for analyzing sequence chromatograms. Version 1.12. http://mesquiteproject.org/packages/chromaseq

If your analysis involved Phred and Phrap (which virtually all uses of Chromaseq would), then you must also cite Phred and Phrap (see the Phred and Phrap documentation for details).

 

diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/conflicts.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/conflicts.html index 131a655..9c70771 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/conflicts.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/conflicts.html @@ -41,8 +41,8 @@ Chromaseq
Detecting Conflicts
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/display.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/display.html index f3fd27c..41cd5bb 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/display.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/display.html @@ -43,8 +43,8 @@ Chromaseq
Other Display Options
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/download.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/download.html index 2733499..292fbbb 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/download.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/download.html @@ -40,8 +40,8 @@ Chromaseq
Download
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/extraSequences.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/extraSequences.html index b246605..9b07c3e 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/extraSequences.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/extraSequences.html @@ -41,8 +41,8 @@ Chromaseq
Multiple Reads/Contigs at Once
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/faq.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/faq.html index abf5ec2..87b6c6a 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/faq.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/faq.html @@ -40,8 +40,8 @@ Chromaseq
Frequently Asked Questions
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/fileNamingRules.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/fileNamingRules.html index 3267c3d..e766f3e 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/fileNamingRules.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/fileNamingRules.html @@ -41,8 +41,8 @@ Chromaseq
File Naming Rules
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/future.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/future.html index a94c685..5f97048 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/future.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/future.html @@ -40,8 +40,8 @@ Chromaseq
Future Directions
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/genbank.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/genbank.html index 2c0efaf..37f6189 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/genbank.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/genbank.html @@ -41,8 +41,8 @@
Submitting Sequences to GenBank
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/helpfulMesquite.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/helpfulMesquite.html index 68a6531..6d33975 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/helpfulMesquite.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/helpfulMesquite.html @@ -41,8 +41,8 @@ Chromaseq
Helpful Mesquite features
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/index.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/index.html index 391d77f..1352d53 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/index.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/index.html @@ -49,8 +49,8 @@ Chromaseq
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/informationStrips.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/informationStrips.html index 81bdac6..3b1c71a 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/informationStrips.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/informationStrips.html @@ -41,8 +41,8 @@ Chromaseq
Matrix information strips
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/installation.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/installation.html index c5f2049..bafbb9d 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/installation.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/installation.html @@ -67,8 +67,8 @@ Chromaseq
Installation
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/interpretingResults.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/interpretingResults.html index 2e7816d..eed9c72 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/interpretingResults.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/interpretingResults.html @@ -41,8 +41,8 @@ Chromaseq
Interpreting Results
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/knownIssues.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/knownIssues.html index 23dea42..31c7b0e 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/knownIssues.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/knownIssues.html @@ -41,8 +41,8 @@ Chromaseq
Known Issues
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/limitations.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/limitations.html index 3d2e918..da2e813 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/limitations.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/limitations.html @@ -41,8 +41,8 @@ Chromaseq
Limitations
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/listWindow.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/listWindow.html index c51502a..c1ba645 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/listWindow.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/listWindow.html @@ -41,8 +41,8 @@ Chromaseq
List window features
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/matrixCells.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/matrixCells.html index eafbd10..22f5054 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/matrixCells.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/matrixCells.html @@ -41,8 +41,8 @@ Chromaseq
Matrix Colors
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/navigation.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/navigation.html index 28b5c0b..4adfe86 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/navigation.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/navigation.html @@ -40,8 +40,8 @@ Chromaseq
Chromatogram Navigation
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/otherPrograms.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/otherPrograms.html index 1010d09..1687f05 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/otherPrograms.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/otherPrograms.html @@ -40,8 +40,8 @@ Chromaseq
Chromaseq and other programs
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/overview.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/overview.html index 292ede6..d320eda 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/overview.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/overview.html @@ -40,8 +40,8 @@ Chromaseq
Overview
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/phredphrap.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/phredphrap.html index 0e5f9cf..0afb4a2 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/phredphrap.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/phredphrap.html @@ -40,8 +40,8 @@ Chromaseq
Phred & Phrap Options
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/postPhrap.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/postPhrap.html index e002ea0..97d9c3c 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/postPhrap.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/postPhrap.html @@ -40,8 +40,8 @@ Chromaseq
Post-Phrap Options
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/preparation.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/preparation.html index acf0d84..bd55d0d 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/preparation.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/preparation.html @@ -43,8 +43,8 @@ Chromaseq
Preparation & Processing
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/primerSites.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/primerSites.html index 5dd6385..8545793 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/primerSites.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/primerSites.html @@ -41,8 +41,8 @@ Chromaseq
Displaying Primer Sites
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/primers.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/primers.html index c1cea47..89c2d3d 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/primers.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/primers.html @@ -46,8 +46,8 @@ Chromaseq
Primer & Gene Information
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/purging.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/purging.html index 0319de6..055a8fd 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/purging.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/purging.html @@ -41,8 +41,8 @@ Chromaseq
Purging Chromaseq Data
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/quality.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/quality.html index b1e1b93..366ba4a 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/quality.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/quality.html @@ -40,8 +40,8 @@ Chromaseq
Quality Scores and Colors
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/quickstart.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/quickstart.html index 9597b2a..d9a3429 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/quickstart.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/quickstart.html @@ -48,8 +48,8 @@ Chromaseq
Quickstart
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/runningPP.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/runningPP.html index 79a4379..495e464 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/runningPP.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/runningPP.html @@ -40,8 +40,8 @@ Chromaseq
Running Phred and Phrap
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/sampleCode.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/sampleCode.html index a6a862b..5fda836 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/sampleCode.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/sampleCode.html @@ -51,8 +51,8 @@

Samples & Sequence Names

  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/segregatingChromatograms.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/segregatingChromatograms.html index 3bf5548..3cbcdc8 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/segregatingChromatograms.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/segregatingChromatograms.html @@ -41,8 +41,8 @@ Chromaseq
Segregating Chromatograms
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/sourceCode.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/sourceCode.html index 2e8a463..657e0ca 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/sourceCode.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/sourceCode.html @@ -45,8 +45,8 @@ Chromaseq
Source Code
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/technicalFAQ.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/technicalFAQ.html index 8f4d6b4..63c1281 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/technicalFAQ.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/technicalFAQ.html @@ -41,8 +41,8 @@ Chromaseq
Technical FAQ
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/troubleshooting.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/troubleshooting.html index 6ed8193..4ef5321 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/troubleshooting.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/troubleshooting.html @@ -41,8 +41,8 @@ Chromaseq
Troubleshooting
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/tutorial.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/tutorial.html index 69579b4..eb8e865 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/tutorial.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/tutorial.html @@ -47,8 +47,8 @@

Tutorial

  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/versions.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/versions.html index f535ddd..1392afa 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/versions.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/versions.html @@ -41,8 +41,8 @@ Chromaseq
Versions
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/viewer.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/viewer.html index 66aea3a..95090df 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/viewer.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/viewer.html @@ -40,8 +40,8 @@ Chromaseq
Chromatogram Viewer
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/vouchers.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/vouchers.html index c0b7a35..fb11737 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/vouchers.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/vouchers.html @@ -41,8 +41,8 @@ Chromaseq
Voucher Information
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Source/mesquite/chromaseq/aChromaseqIntro/manual/workflow.html b/Source/mesquite/chromaseq/aChromaseqIntro/manual/workflow.html index ddb4ff1..3c878cc 100644 --- a/Source/mesquite/chromaseq/aChromaseqIntro/manual/workflow.html +++ b/Source/mesquite/chromaseq/aChromaseqIntro/manual/workflow.html @@ -41,8 +41,8 @@ Chromaseq
Workflow Suggestions
  - Version 1.11
- 29 August 2014
+ Version 1.12
+ 2 September 2014
diff --git a/Web Site Files/install.xml b/Web Site Files/install.xml index a85087b..7bbf557 100644 --- a/Web Site Files/install.xml +++ b/Web Site Files/install.xml @@ -5,25 +5,25 @@ 620 - 8 + 9 alert Chromaseq - 008 - Chromaseq version 1.11 + 009 + Chromaseq version 1.12

- In order to install Chromaseq 1.11, you need to first update to Mesquite version 3.0. + In order to install Chromaseq 1.12, you need to first update to Mesquite version 3.0. You can get Mesquite 3.0 at https://mesquiteproject.wikispaces.com/Installation ]]> 644 - 13 + 14 update Chromaseq - 013 - Chromaseq version 1.11 + 014 + Chromaseq version 1.12 This may take a while to download; please wait until a message appears saying it's finished.

@@ -36,9 +36,9 @@ mesquite chromaseq - https://github.com/MesquiteProject/Chromaseq/releases/download/1.1.1/chromaseq.1.1.1.zip + https://github.com/MesquiteProject/Chromaseq/releases/download/1.1.2/chromaseq.1.1.2.zip unzip - 013 + 014 diff --git a/Web Site Files/notices.xml b/Web Site Files/notices.xml index 1bc5a90..fdaa6a8 100644 --- a/Web Site Files/notices.xml +++ b/Web Site Files/notices.xml @@ -4,39 +4,39 @@ 1 620 - 8 + 9 alert Chromaseq - 008 - Chromaseq version 1.11 + 009 + Chromaseq version 1.12

- In order to install Chromaseq 1.11, you need to first update to Mesquite version 3.0. + In order to install Chromaseq 1.12, you need to first update to Mesquite version 3.0. You can get Mesquite 3.0 at https://mesquiteproject.wikispaces.com/Installation ]]> - 1.11 - 1110 + 1.12 + 1120 http://mesquiteproject.org/packages/chromaseq/manual/download.html - 1010 + 1110 update chromaseq - Chromaseq 1.1 + Chromaseq 1.12 - 013 - 013 + 014 + 014 mesquite chromaseq - https://github.com/MesquiteProject/Chromaseq/releases/download/1.1.1/Chromaseq.1.1.1.zip + https://github.com/MesquiteProject/Chromaseq/releases/download/1.1.2/Chromaseq.1.1.2.zip unzip - 003 + 014