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Merge pull request #8 from DMaddison/master
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Fixed the NEXUS block ordering bug, updated to 1.1.2
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@DMaddison
DMaddison committed Sep 3, 2014
2 parents f4d1790 + 7d121c0 commit 592b5fa
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Showing 50 changed files with 121 additions and 121 deletions.
2 changes: 1 addition & 1 deletion Source/mesquite/chromaseq/ManageChromaseqBlock/ManageChromaseqBlock.java
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Expand Up @@ -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";
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2 changes: 1 addition & 1 deletion Source/mesquite/chromaseq/aChromaseqIntro/aChromaseqIntro.java
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/* Mesquite Chromaseq source code. Copyright 2005-2011 David Maddison and Wayne Maddison.Version 1.0 December 2011Disclaimer: 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.orgThis 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; }}
/* Mesquite Chromaseq source code. Copyright 2005-2011 David Maddison and Wayne Maddison.Version 1.0 December 2011Disclaimer: 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.orgThis 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; }}
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4 changes: 2 additions & 2 deletions Source/mesquite/chromaseq/aChromaseqIntro/manual/Templates/ChromaseqTemplate.dwt
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<td width="51%"><strong id="PackageTitle">Chromaseq</strong></td>
<td width="33%" align="right"><div id="subtitle"><!-- TemplateBeginEditable name="subtitle" -->subtitle<!-- TemplateEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
29 August 2014<br /></td>
<td width="14%">Version 1.12<br />
2 September 2014<br /></td>
</tr>
</table>

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4 changes: 2 additions & 2 deletions Source/mesquite/chromaseq/aChromaseqIntro/manual/acknowledgements.html
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<td width="51%"><strong id="PackageTitle">Chromaseq</strong></td>
<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Acknowledgements<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
29 August 2014<br /></td>
<td width="14%">Version 1.12<br />
2 September 2014<br /></td>
</tr>
</table>

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4 changes: 2 additions & 2 deletions Source/mesquite/chromaseq/aChromaseqIntro/manual/appendingSequences.html
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<td width="51%"><strong id="PackageTitle">Chromaseq</strong></td>
<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Processing Additional Chromatograms<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
29 August 2014<br /></td>
<td width="14%">Version 1.12<br />
2 September 2014<br /></td>
</tr>
</table>

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4 changes: 2 additions & 2 deletions Source/mesquite/chromaseq/aChromaseqIntro/manual/callingBases.html
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<td width="51%"><strong id="PackageTitle">Chromaseq</strong></td>
<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Calling Bases <!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
29 August 2014<br /></td>
<td width="14%">Version 1.12<br />
2 September 2014<br /></td>
</tr>
</table>

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4 changes: 2 additions & 2 deletions Source/mesquite/chromaseq/aChromaseqIntro/manual/chromaseqList.html
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<td width="51%"><strong id="PackageTitle">Chromaseq</strong></td>
<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Chromaseq E-mail List<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
29 August 2014<br /></td>
<td width="14%">Version 1.12<br />
2 September 2014<br /></td>
</tr>
</table>

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4 changes: 2 additions & 2 deletions Source/mesquite/chromaseq/aChromaseqIntro/manual/chromatograms.html
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<td width="51%"><strong id="PackageTitle">Chromaseq</strong></td>
<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Preparing Chromatograms<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
29 August 2014<br /></td>
<td width="14%">Version 1.12<br />
2 September 2014<br /></td>
</tr>
</table>

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6 changes: 3 additions & 3 deletions Source/mesquite/chromaseq/aChromaseqIntro/manual/citation.html
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<td width="51%"><strong id="PackageTitle">Chromaseq</strong></td>
<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Citation<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
29 August 2014<br /></td>
<td width="14%">Version 1.12<br />
2 September 2014<br /></td>
</tr>
</table>

Expand Down Expand Up @@ -192,7 +192,7 @@ <h3>&nbsp;</h3>
<p><font >This version of Chromaseq should be cited as:</font></p>
<p><strong><font ><br />
Maddison, D.R., &amp; W.P. Maddison. 2014. Chromaseq: a Mesquite
package for analyzing sequence chromatograms. Version 1.1. http://mesquiteproject.org/packages/chromaseq</font></strong></p>
package for analyzing sequence chromatograms. Version 1.12. http://mesquiteproject.org/packages/chromaseq</font></strong></p>
<p><font >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). </font></p>
<p>&nbsp;</p>
<!-- InstanceEndEditable -->
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4 changes: 2 additions & 2 deletions Source/mesquite/chromaseq/aChromaseqIntro/manual/conflicts.html
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<td width="51%"><strong id="PackageTitle">Chromaseq</strong></td>
<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Detecting Conflicts<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
29 August 2014<br /></td>
<td width="14%">Version 1.12<br />
2 September 2014<br /></td>
</tr>
</table>

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4 changes: 2 additions & 2 deletions Source/mesquite/chromaseq/aChromaseqIntro/manual/display.html
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<td width="51%"><strong id="PackageTitle">Chromaseq</strong></td>
<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Other Display Options <!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
29 August 2014<br /></td>
<td width="14%">Version 1.12<br />
2 September 2014<br /></td>
</tr>
</table>

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4 changes: 2 additions & 2 deletions Source/mesquite/chromaseq/aChromaseqIntro/manual/download.html
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<td width="51%"><strong id="PackageTitle">Chromaseq</strong></td>
<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Download<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
29 August 2014<br /></td>
<td width="14%">Version 1.12<br />
2 September 2014<br /></td>
</tr>
</table>

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4 changes: 2 additions & 2 deletions Source/mesquite/chromaseq/aChromaseqIntro/manual/extraSequences.html
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<td width="51%"><strong id="PackageTitle">Chromaseq</strong></td>
<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Multiple Reads/Contigs at Once<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
29 August 2014<br /></td>
<td width="14%">Version 1.12<br />
2 September 2014<br /></td>
</tr>
</table>

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4 changes: 2 additions & 2 deletions Source/mesquite/chromaseq/aChromaseqIntro/manual/faq.html
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<td width="51%"><strong id="PackageTitle">Chromaseq</strong></td>
<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Frequently Asked Questions <!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
29 August 2014<br /></td>
<td width="14%">Version 1.12<br />
2 September 2014<br /></td>
</tr>
</table>

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4 changes: 2 additions & 2 deletions Source/mesquite/chromaseq/aChromaseqIntro/manual/fileNamingRules.html
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<td width="51%"><strong id="PackageTitle">Chromaseq</strong></td>
<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->File Naming Rules<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
29 August 2014<br /></td>
<td width="14%">Version 1.12<br />
2 September 2014<br /></td>
</tr>
</table>

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4 changes: 2 additions & 2 deletions Source/mesquite/chromaseq/aChromaseqIntro/manual/future.html
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<td width="51%"><strong id="PackageTitle">Chromaseq</strong></td>
<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Future Directions <!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
29 August 2014<br /></td>
<td width="14%">Version 1.12<br />
2 September 2014<br /></td>
</tr>
</table>

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4 changes: 2 additions & 2 deletions Source/mesquite/chromaseq/aChromaseqIntro/manual/genbank.html
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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Submitting
Sequences to GenBank<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
29 August 2014<br /></td>
<td width="14%">Version 1.12<br />
2 September 2014<br /></td>
</tr>
</table>

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4 changes: 2 additions & 2 deletions Source/mesquite/chromaseq/aChromaseqIntro/manual/helpfulMesquite.html
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<td width="51%"><strong id="PackageTitle">Chromaseq</strong></td>
<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Helpful Mesquite features<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
29 August 2014<br /></td>
<td width="14%">Version 1.12<br />
2 September 2014<br /></td>
</tr>
</table>

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4 changes: 2 additions & 2 deletions Source/mesquite/chromaseq/aChromaseqIntro/manual/index.html
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<td width="51%"><strong id="PackageTitle">Chromaseq</strong></td>
<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" --><!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
29 August 2014<br /></td>
<td width="14%">Version 1.12<br />
2 September 2014<br /></td>
</tr>
</table>

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4 changes: 2 additions & 2 deletions Source/mesquite/chromaseq/aChromaseqIntro/manual/informationStrips.html
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<td width="51%"><strong id="PackageTitle">Chromaseq</strong></td>
<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Matrix information strips<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
29 August 2014<br /></td>
<td width="14%">Version 1.12<br />
2 September 2014<br /></td>
</tr>
</table>

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