Development

Source/mesquite/Mesquite.java

@@ -37,7 +37,7 @@ public class Mesquite extends MesquiteTrunk
 {
 	/*.................................................................................................................*/
 	public String getCitation() {
-		return "Maddison, W.P. & D.R. Maddison. 2018. Mesquite: A modular system for evolutionary analysis.  Version 3.5.  http://mesquiteproject.org";
+		return "Maddison, W.P. & D.R. Maddison. 2018. Mesquite: A modular system for evolutionary analysis.  Version 3.5.  http://www.mesquiteproject.org";
 	}
 	/*.................................................................................................................*/
 	public String getVersion() {
@@ -69,7 +69,7 @@ public String  getHomePhoneNumber(){
 			return "https://raw.githubusercontent.com/MesquiteProject/MesquiteCore/development/noticesAndUpdates/noticesPrerelease.xml";   
 
 
-	/* Version 3.2 through 3.40 
+	/* Version 3.2 through 3.4 
 		if (!isPrerelease() && !debugMode)
 			return "https://raw.githubusercontent.com/MesquiteProject/MesquiteCore/master/noticesAndUpdates/notices.xml";   
 		else
@@ -86,7 +86,7 @@ public String  getHomePhoneNumber(){
 	}
 	/*.................................................................................................................*/
 	public boolean isPrerelease(){
-		return true;
+		return false;
 	}
 	/*.................................................................................................................*/
 	public void getEmployeeNeeds(){  //This gets called on startup to harvest information; override this and inside, call registerEmployeeNeed
@@ -498,7 +498,7 @@ else if (prefsFile.exists() || prefsFileXML.exists()) {
 			//WelcomeDialog is being phased out
 			if (false && !MesquiteWindow.headless && !MesquiteThread.suppressInteractionAsLibrary){  //hackathon
 				String s = "Welcome to Mesquite.  If this is the first time you've run Mesquite, you might want to try the example files to learn about how to use it (example files in \"Mesquite_Folder/examples\").  You might also check the menu items in the Help menu for links to documentation.";
-				s += "\n\nAlso, please sign up to the Mesquite Discussion e-mail list to learn about bugs and updates (instructions for signing up at http://mesquiteproject.org).";
+				s += "\n\nAlso, please sign up to the Mesquite Discussion e-mail list to learn about bugs and updates (instructions for signing up at http://www.mesquiteproject.org).";
 				new WelcomeDialog(containerOfModule(), "Welcome to Mesquite", s);
 			}
 			if (makeNewPrefsDirectory) {
@@ -1260,7 +1260,7 @@ private void searchWeb(String queryTerm, MesquiteBoolean addMesquiteToSearch, Me
 		if (addMesquiteToSearch.getValue())
 			textToGoogle += "+" + "Mesquite";
 		if (restrictSearchToManual.getValue())
-			textToGoogle += "&as_sitesearch=http%3A%2F%2Fmesquitecore.mesquiteproject.org%2F";
+			textToGoogle += "&as_sitesearch=http%3A%2F%2Fwww.mesquiteproject.org%2F";
 		showWebPage("http://www.google.com/search?q=" + textToGoogle, false);
 	}
 	/*End new code added Feb.05.07 oliver*/

Source/mesquite/lib/MesquiteHTMLWindow.java

@@ -169,8 +169,6 @@ public synchronized void setExtraPanelText(String s) {
 	void goBack(){
 		if (pastTexts==null)
 			return;
-		//if (backEnabled && pastTexts.size() <= 1)  // WAYNECHECK: see how I changed this.  
-		// Encountered a case where backEnabled was true and pastTexts was empty so the lastElement called threw an exception
 		if (!backEnabled || pastTexts.size() <= 1)
 			return;
 		String t = (String)pastTexts.lastElement();

Source/mesquite/lib/MesquiteModule.java

@@ -67,12 +67,12 @@ public abstract class MesquiteModule extends EmployerEmployee implements Command
 	/*.................................................................................................................*/
 	/** returns build date of the Mesquite system (e.g., "22 September 2003") */
 	public final static String getBuildDate() {
-		return "3 May 2018";
+		return "4 May 2018";
 	}
 	/*.................................................................................................................*/
 	/** returns version of the Mesquite system */
 	public final static String getMesquiteVersion() {
-		return "3.40+";
+		return "3.5";
 	}
 	/*.................................................................................................................*/
 	/** returns letter in the build number of the Mesquite system (e.g., "e" of "e58") */
@@ -85,7 +85,7 @@ public final static String getBuildLetter() {
 	public final static int getBuildNumber() {
 		//as of 26 Dec 08, build naming changed from letter + number to just number.  Accordingly j105 became 473, based on
 		// highest build numbers of d51+e81+g97+h66+i69+j105 + 3 for a, b, c
-		return 886;  
+		return 888;  
 	}
 	//0.95.80    14 Mar 01 - first beta release 
 	//0.96  2 April 01 beta  - second beta release
@@ -134,6 +134,7 @@ public final static int getBuildNumber() {
 	//3.30  = 854 released 12 Sept 2O17
 	//3.31  = 858 released 20 Sept 2O17; 859 released 20 Sept
 	//3.40  = 877 released 27 Jan 2O18
+	//3.50  = 888 released 4 May 2O18
 	/*.................................................................................................................*/
 	/** returns a string if this is a special version of Mesquite */
 	public final static String getSpecialVersion() {

Source/mesquite/lib/MesquiteTree.java

@@ -2380,20 +2380,7 @@ else if (ancAnc==anc && candidate == firstDaughter[anc])
 		else
 			return candidate;
 	}
-	/*-----------------------------------------* WAYNECHECK
-
-	public  int lastDaughterOfNodeUR(int anc, int node) {
-		if (!nodeExists(node) && !nodeExists(anc))
-			return 0;
-		int first = firstDaughterOfNodeUR(anc, node);
-		int prev = first;
-		while (nodeExists(first)) {
-			prev = first;
-			first = nextSisterOfNodeUR(anc, node, first);
-		}
-		return prev;
-	}
-	*/
+	/*-----------------------------------------*/
 
 	/** Returns the first (left-most) daughter of node in an UNROOTED sense where the node
 	is treated as descendant from anc. This is one of the UR procedures, designed
@@ -3039,11 +3026,12 @@ else if ("<".equals(c)) {
 					fromWhichNamer = 4;
 				}
 				if (taxonNumber<0){
-					/* Debugg.  WAYNECHECK: DAVIDCHECK: there is a problem with this.  If you read in a Zephyr produced tree file by itself, not after
+					/* Note: There is a problem with this if permitTONames is on.  If you read in a Zephyr produced tree file by itself, not after
 					 * opening the file with the taxa in order, then you will likely get reticulations.  In particular, permitTONames not only
 					 * interprets "tx" as a taxon name, it presumes that the taxon number of this taxon number x.  The problem with this
 					 * is that in reading the treefile, it creates the taxa in the orders it encounters them.  If t88 is the first taxon in the first
 					 * treedescription, this will be taxon 0.  So if it reads t0, it will interpret it as taxon 0, even if it is the 99th taxon read in. 
+					 * Our solution to this has been to set permitTONames to false by default, and warn the user not to turn it on unless they need to.
 					 * */
 					if (MesquiteTree.permitT0Names && c != null && c.startsWith("t")){  //not found in taxon names, but as permits t0, t1 style names, look for it there 
 						String number = c.substring(1, c.length());

Source/mesquite/minimal/Installer/Installer.java

@@ -109,13 +109,13 @@ public String  getHomePhoneNumber(){
 	//See MesquiteModule for version reporter and error reporter URLs
 
 		if (!MesquiteTrunk.mesquiteTrunk.isPrerelease() && !MesquiteTrunk.debugMode) 
-			return "https://raw.githubusercontent.com/MesquiteProject/MesquiteCore/master/noticesAndUpdates/updates.xml";
+			return "http://www.mesquiteproject.org/noticesAndUpdates/updates.xml";
 		else
 			return "https://raw.githubusercontent.com/MesquiteProject/MesquiteCore/development/noticesAndUpdates/updatesPrerelease.xml";   
 
 
 
-		/* Version 3.2 through 3.40 
+		/* Version 3.2 through 3.4 
 		if (!MesquiteTrunk.mesquiteTrunk.isPrerelease() && !MesquiteTrunk.debugMode)
 			return "https://raw.githubusercontent.com/MesquiteProject/MesquiteCore/master/noticesAndUpdates/updates.xml";
 		else

Source/mesquite/trunk/AboutPanel.java

@@ -52,7 +52,7 @@ public void paint(Graphics g) {
 			//StringUtil.highlightString(g, "Touch on red alert symbol in windows for information.", 25,45);
 			g.drawImage(InfoBar.prereleaseImage,3,3,(ImageObserver)this);
 		}
-		g.drawString("http://mesquiteproject.org", 5,210);
+		g.drawString("http://www.mesquiteproject.org", 5,210);
 		g.drawString("Copyright (c) 1997-2018 W. & D. Maddison.", 5,225);
 
 		MesquiteWindow.uncheckDoomed(this);

docs/Acknowledgements.html

@@ -41,7 +41,7 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</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 3.41<br />
+    <td width="14%">Version 3.5<br />
       4 May 2018<br /></td>
   </tr>
 </table>
@@ -58,7 +58,7 @@
     <a href="javascript:pageLink('http://www.mesquiteproject.org')">Mesquite Website Home</a>
   </div>
   <div id="NonCollapsiblePanel">
-    <a href="javascript:pageLink('home.html')">Introduction to Mesquite</a>
+    <a href="javascript:pageLink('home.html')">Introduction</a>
   </div>
   <div id="NonCollapsiblePanel">
     <a href="javascript:pageLink('Installation.html')">Download & Installation</a>

docs/Additional Mesquite Packages.html

@@ -41,7 +41,7 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Additional Packages<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.41<br />
+    <td width="14%">Version 3.5<br />
       4 May 2018<br /></td>
   </tr>
 </table>
@@ -58,7 +58,7 @@
     <a href="javascript:pageLink('http://www.mesquiteproject.org')">Mesquite Website Home</a>
   </div>
   <div id="NonCollapsiblePanel">
-    <a href="javascript:pageLink('home.html')">Introduction to Mesquite</a>
+    <a href="javascript:pageLink('home.html')">Introduction</a>
   </div>
   <div id="NonCollapsiblePanel">
     <a href="javascript:pageLink('Installation.html')">Download & Installation</a>
@@ -221,7 +221,7 @@ <h2 id="toc3"><a name="Additional Mesquite Packages-TreeSetViz"></a>TreeSetViz</
 <hr />
 <h2 id="toc4"><a name="Additional Mesquite Packages-Chromaseq"></a>Chromaseq</h2>
  <h2 id="toc5"><img src="files/Chromaseqsplash.gif" alt="Chromaseqsplash.gif" title="Chromaseqsplash.gif" /></h2>
- <span style="line-height: 1.5;">For deriving and editing DNA sequences from chromatograms, <a  href="http://mesquiteproject.org/packages/chromaseq/" rel="nofollow">Chromaseq</a> provides integration of chromatogram viewing and base calling with Mesquite's matrix editor, alignment and other functions.</span><br />
+ <span style="line-height: 1.5;">For deriving and editing DNA sequences from chromatograms, <a  href="http://chromaseq.mesquiteproject.org" rel="nofollow">Chromaseq</a> provides integration of chromatogram viewing and base calling with Mesquite's matrix editor, alignment and other functions.</span><br />
 <br />
 <hr />
 <h2 id="toc6"><a name="Additional Mesquite Packages-Opal and Opalescent"></a><strong><span style="line-height: 1.5;">Opal and Opalescent</span></strong></h2>

docs/Align.html

@@ -41,7 +41,7 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Sequence Alignment<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.41<br />
+    <td width="14%">Version 3.5<br />
       4 May 2018<br /></td>
   </tr>
 </table>
@@ -58,7 +58,7 @@
     <a href="javascript:pageLink('http://www.mesquiteproject.org')">Mesquite Website Home</a>
   </div>
   <div id="NonCollapsiblePanel">
-    <a href="javascript:pageLink('home.html')">Introduction to Mesquite</a>
+    <a href="javascript:pageLink('home.html')">Introduction</a>
   </div>
   <div id="NonCollapsiblePanel">
     <a href="javascript:pageLink('Installation.html')">Download & Installation</a>
@@ -312,7 +312,7 @@ <h3 id="toc1"><a name="Visualization Features-Coloring Cells for Alignment"></a>
 	  <h2 id="toc0"><a name="Citation"></a>Citation</h2>
 	  The Align package should be cited as:<br />
 <br />
-<strong>Maddison, D.R., T.J. Wheeler, and W.P. Maddison. 2016. Align: a Mesquite package for aligning sequence data. Version 1.8. <a href="http://mesquiteproject.org/Align.html">http://mesquiteproject.org/Align.html</a></strong>
+<strong>Maddison, D.R., T.J. Wheeler, and W.P. Maddison. 2016. Align: a Mesquite package for aligning sequence data. Version 1.8. <a href="http://www.mesquiteproject.org/Align.html">http://www.mesquiteproject.org/Align.html</a></strong>
 
 <p>&nbsp;</p>
 <p>&nbsp;</p>

docs/Analyzing Continuous Characters.html

@@ -41,7 +41,7 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Continuous characters<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.41<br />
+    <td width="14%">Version 3.5<br />
       4 May 2018<br /></td>
   </tr>
 </table>
@@ -58,7 +58,7 @@
     <a href="javascript:pageLink('http://www.mesquiteproject.org')">Mesquite Website Home</a>
   </div>
   <div id="NonCollapsiblePanel">
-    <a href="javascript:pageLink('home.html')">Introduction to Mesquite</a>
+    <a href="javascript:pageLink('home.html')">Introduction</a>
   </div>
   <div id="NonCollapsiblePanel">
     <a href="javascript:pageLink('Installation.html')">Download & Installation</a>

docs/Analyzing Molecular Data.html

@@ -41,7 +41,7 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Molecular Data<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.41<br />
+    <td width="14%">Version 3.5<br />
       4 May 2018<br /></td>
   </tr>
 </table>
@@ -58,7 +58,7 @@
     <a href="javascript:pageLink('http://www.mesquiteproject.org')">Mesquite Website Home</a>
   </div>
   <div id="NonCollapsiblePanel">
-    <a href="javascript:pageLink('home.html')">Introduction to Mesquite</a>
+    <a href="javascript:pageLink('home.html')">Introduction</a>
   </div>
   <div id="NonCollapsiblePanel">
     <a href="javascript:pageLink('Installation.html')">Download & Installation</a>

docs/Ancestral States.html

@@ -41,7 +41,7 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Ancestral States<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.41<br />
+    <td width="14%">Version 3.5<br />
       4 May 2018<br /></td>
   </tr>
 </table>
@@ -58,7 +58,7 @@
     <a href="javascript:pageLink('http://www.mesquiteproject.org')">Mesquite Website Home</a>
   </div>
   <div id="NonCollapsiblePanel">
-    <a href="javascript:pageLink('home.html')">Introduction to Mesquite</a>
+    <a href="javascript:pageLink('home.html')">Introduction</a>
   </div>
   <div id="NonCollapsiblePanel">
     <a href="javascript:pageLink('Installation.html')">Download & Installation</a>

docs/Are strepsipterans related to flies?.html

@@ -41,7 +41,7 @@
     <td width="51%"><strong id="PackageTitle">Mesquite</strong></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Hypothesis testing<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.41<br />
+    <td width="14%">Version 3.5<br />
       4 May 2018<br /></td>
   </tr>
 </table>
@@ -58,7 +58,7 @@
     <a href="javascript:pageLink('http://www.mesquiteproject.org')">Mesquite Website Home</a>
   </div>
   <div id="NonCollapsiblePanel">
-    <a href="javascript:pageLink('home.html')">Introduction to Mesquite</a>
+    <a href="javascript:pageLink('home.html')">Introduction</a>
   </div>
   <div id="NonCollapsiblePanel">
     <a href="javascript:pageLink('Installation.html')">Download & Installation</a>
@@ -276,7 +276,7 @@ <h3 id="toc5"><a name="Are strepsipterans related to flies? Exploring long branc
 Swofford, D. L. 2003. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4 beta 10. Sinauer Associates, Sunderland, Massachusetts.<br />
 <hr />
 <h4 id="toc7"><a name="Are strepsipterans related to flies? Exploring long branch attraction--References-Citation for this page"></a>Citation for this page</h4>
- Maddison, D.R. 2004. Are strepsipterans related to flies? Exploring long branch attraction. Study 2 in Mesquite: a modular system for evolutionary analysis, version 2.54, <a  href="http://mesquiteproject.org" rel="nofollow">http://mesquiteproject.org</a>.
+ Maddison, D.R. 2004. Are strepsipterans related to flies? Exploring long branch attraction. Study 2 in Mesquite: a modular system for evolutionary analysis, version 2.54, <a  href="http://www.mesquiteproject.org" rel="nofollow">http://www.mesquiteproject.org</a>.
 <!-- InstanceEndEditable -->