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Merge pull request #16 from MesquiteProject/development
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Chromaseq 1.31 Release
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@DMaddison
DMaddison authored May 4, 2018
2 parents 1096d0e + 34f8301 commit c3e0664
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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 getPackagePath() +"docs/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 true; } /*.................................................................................................................*/ /** Returns citation for a package of modules*/ public String getPackageCitation(){ if (isPrerelease()) return "Maddison, D.R., & W.P. Maddison. 2018. Chromaseq. A package for processing chromatograms and sequence data in Mesquite. Prerelease version " + getPackageVersion() + " (build " + getBuildVersion() + ")."; return "Maddison, D.R., & W.P. Maddison. 2018. Chromaseq. A package for processing chromatograms and sequence data in Mesquite. Version " + getPackageVersion() + "."; } /*.................................................................................................................*/ /** Returns version for a package of modules*/ public String getPackageVersion(){ return "1.3+"; } /*.................................................................................................................*/ /** Returns version for a package of modules as an integer*/ public int getPackageVersionInt(){ return 1300; } /*.................................................................................................................*/ public String getPackageDateReleased(){ return "1 May 2018 "; } /*.................................................................................................................*/ /** Returns build number for a package of modules as an integer*/ public int getPackageBuildNumber(){ return 51; }/* 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) 2 September 2014 1.2 (build 40) 27 June 2016 1.3 (build 48) 12 September 2017 */ /*.................................................................................................................*/ public String getPackageURL(){ return "http://mesquiteproject.github.io/chromaseq"; } /*.................................................................................................................*/ /** 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 getPackagePath() +"docs/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://chromaseq.mesquiteproject.org/noticesAndUpdates/noticesDev.xml"; else if (isPrerelease()) return "http://chromaseq.mesquiteproject.org/noticesAndUpdates/noticesPrerelease.xml"; else return "http://chromaseq.mesquiteproject.org/noticesAndUpdates/notices.xml"; /* version 1.3 and before: 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. 2018. Chromaseq. A package for processing chromatograms and sequence data in Mesquite. Prerelease version " + getPackageVersion() + " (build " + getBuildVersion() + ")."; return "Maddison, D.R., & W.P. Maddison. 2018. Chromaseq. A package for processing chromatograms and sequence data in Mesquite. Version " + getPackageVersion() + "."; } /*.................................................................................................................*/ /** Returns version for a package of modules*/ public String getPackageVersion(){ return "1.31"; } /*.................................................................................................................*/ /** Returns version for a package of modules as an integer*/ public int getPackageVersionInt(){ return 1310; } /*.................................................................................................................*/ public String getPackageDateReleased(){ return "4 May 2018 "; } /*.................................................................................................................*/ /** Returns build number for a package of modules as an integer*/ public int getPackageBuildNumber(){ return 53; }/* 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) 2 September 2014 1.2 (build 40) 27 June 2016 1.3 (build 48) 12 September 2017 1.31 (build 53) 4 May 2018 */ /*.................................................................................................................*/ public String getPackageURL(){ return "http://chromaseq.mesquiteproject.org"; } /*.................................................................................................................*/ /** Returns whether there is a splash banner*/ public boolean hasSplash(){ return true; } /*.................................................................................................................*/ public int getVersionOfFirstRelease(){ return 275; }}
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44 changes: 0 additions & 44 deletions Web Site Files/notices.xml
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10 changes: 5 additions & 5 deletions docs/CSS/mesquitePackage.css
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background-position: 0 0;
background-repeat: no-repeat;
font-family:Verdana, Lucida, Arial, sans-serif;
font-size:11px;
font-size:12px;
}


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}
.thrColFixHdr #sidebar1 {
float: left; /* since this element is floated, a width must be given */
width: 120px; /* the actual width of this div, in standards-compliant browsers, or standards mode in Internet Explorer will include the padding and border in addition to the width */
width: 140px; /* the actual width of this div, in standards-compliant browsers, or standards mode in Internet Explorer will include the padding and border in addition to the width */
background:#f4f0e2;
padding: 10px; /* padding keeps the content of the div away from the edges */
}
.thrColFixHdr #mainContent {
margin-left: 200px; /* remember that padding is the space inside the div box and margin is the space outside the div box */
margin-left: 230px; /* remember that padding is the space inside the div box and margin is the space outside the div box */
background:#FFFFFF;
color: #000000;
border: #000 thin;
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}


.thrColFixHdr #sidebar1 { width: 180px; }
.thrColFixHdr #sidebar1 { width: 210px; }
.thrColFixHdr #sidebar2 { width: 190px; }

.monospaced {
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}
.monospacedSmall {
font-family: "Courier New", Courier, monospace;
font-size: 10px;
font-size: 11px;
}


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2 changes: 1 addition & 1 deletion docs/SpryAssets/SpryCollapsiblePanel.css
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* CollapsiblePanel panel tab container.
*/
.CollapsiblePanelTab {
font-size: 10px;
font-size: 12px;
font-weight:bold;
margin: 0px;
padding: 2px;
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22 changes: 11 additions & 11 deletions docs/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 1.3<br />
12 September 2017<br /></td>
<td width="14%">Version 1.31<br />
4 May 2018<br /></td>
</tr>
</table>

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</div>

<div id="GettingStartedPanel" class="CollapsiblePanel">
<div class="CollapsiblePanelTab" tabindex="0">Getting Started</div>
<div class="CollapsiblePanelTab" tabindex="0">Getting Started ˇ</div>
<div class="CollapsiblePanelContent" style="display: block">
<table width="100%" border="0" cellpadding="1">
<tr><td><a href="javascript:pageLink('download.html');">Download</a></td></tr>
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</div>
</div>
<div id="PreparingDataPanel" class="CollapsiblePanel">
<div class="CollapsiblePanelTab" tabindex="0">Preparing Data</div>
<div class="CollapsiblePanelTab" tabindex="0">Preparing Data ˇ</div>
<div class="CollapsiblePanelContent" style="display: block">
<table width="100%" border="0" cellpadding="1">
<tr><td><a href="javascript:pageLink('chromatograms.html');">Chromatograms</a></td></tr>
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</div>

<div id="ProcessingChromatoPanel" class="CollapsiblePanel">
<div class="CollapsiblePanelTab" tabindex="0">Processing Chromatograms</div>
<div class="CollapsiblePanelTab" tabindex="0">Processing Chromatograms ˇ</div>
<div class="CollapsiblePanelContent" style="display: block">
<table width="100%" border="0" cellpadding="1">
<tr> <td><a href="javascript:pageLink('preparation.html');">Preparation & Processing</a></td></tr>
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<div id="ChromatogramViewerPanel" class="CollapsiblePanel">
<div class="CollapsiblePanelTab" tabindex="0">Chromatogram Viewer</div>
<div class="CollapsiblePanelTab" tabindex="0">Chromatogram Viewer ˇ</div>
<div class="CollapsiblePanelContent" style="display: block">
<table width="100%" border="0" cellpadding="1">
<tr><td><a href="javascript:pageLink('viewer.html');">Viewing Chromatograms</a></td></tr>
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</div>

<div id="OtherFeaturesPanel" class="CollapsiblePanel">
<div class="CollapsiblePanelTab" tabindex="0">Other Features</div>
<div class="CollapsiblePanelTab" tabindex="0">Other Features ˇ</div>
<div class="CollapsiblePanelContent" style="display: block">
<table width="100%" border="0" cellpadding="1">
<tr><td><a href="javascript:pageLink('genbank.html');">GenBank Submissions</a></td></tr>
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</div>

<div id="HelpPanel" class="CollapsiblePanel">
<div class="CollapsiblePanelTab" tabindex="0">Help & Info</div>
<div class="CollapsiblePanelTab" tabindex="0">Help & Info ˇ</div>
<div class="CollapsiblePanelContent" style="display: block">
<table width="100%" border="0" cellpadding="1">
<tr><td><a href="javascript:pageLink('tutorial.html');">Tutorial</a></td></tr>
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</div>

<div id="TechnicalPanel" class="CollapsiblePanel">
<div class="CollapsiblePanelTab" tabindex="0">Technical Details</div>
<div class="CollapsiblePanelTab" tabindex="0">Technical Details ˇ</div>
<div class="CollapsiblePanelContent" style="display: block">
<table width="100%" border="0" cellpadding="1">
<tr><td><a href="javascript:pageLink('sourceCode.html');">Source Code</a></td></tr>
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</div>

<div id="CreditPanel" class="CollapsiblePanel">
<div class="CollapsiblePanelTab" tabindex="0">Citation & Credit</div>
<div class="CollapsiblePanelTab" tabindex="0">Citation & Credit ˇ</div>
<div class="CollapsiblePanelContent" style="display: block">
<table width="100%" border="0" cellpadding="1">
<tr><td><a href="javascript:pageLink('citation.html');">How to Cite</a></td></tr>
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</div>
<!-- This clearing element should immediately follow the #mainContent div in order to force the #container div to contain all child floats --><br class="clearfloat" />
<div id="footer">
<p> ©2017 David R. Maddison &amp; Wayne P. Maddison</p>
<p> ©2018 David R. Maddison &amp; Wayne P. Maddison</p>
<!-- end #footer --></div>
<!-- end #container --></div>

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