Merge pull request #26 from MesquiteProject/development

3.31 release

Source/mesquite/zephyr/aZephyrIntro/aZephyrIntro.java

@@ -1 +1 @@
-/* Mesquite.zephyr source code.  Copyright 2007 and onwards D. Maddison and W. Maddison. Mesquite.zephyr is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.Zephry's web site is http://zephyr.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.zephyr.aZephyrIntro;import mesquite.lib.MesquiteTrunk;import mesquite.lib.duties.*;/* ======================================================================== */public class aZephyrIntro extends PackageIntro {	/*.................................................................................................................*/	public boolean startJob(String arguments, Object condition, boolean hiredByName) { 		return true;  	 }  	 public Class getDutyClass(){  	 	return aZephyrIntro.class;  	 } 	/*.................................................................................................................*/	 public String getExplanation() {	return "Zephyr is a package of Mesquite modules providing tools for connecting to other phylogenetic inference programs.";	 }		/*.................................................................................................................*/		public String getManualPath(){			return getPackagePath() +"docs/introduction.html";  		}	/*.................................................................................................................*/    	 public String getName() {		return "Zephyr Package";   	 }	/*.................................................................................................................*/	/** Returns the name of the package of modules (e.g., "Basic Mesquite Package", "Rhetenor")*/ 	public String getPackageName(){ 		return "Zephyr Package"; 	}	/*.................................................................................................................*/	/** Returns citation for a package of modules*/ 	public String getPackageCitation(){ 		return "Maddison, D.R. & Maddison W.P. 2023. Zephyr: A Mesquite package for interacting with external phylogeny inference programs. Version "+getPackageVersion(); 	}	/*.................................................................................................................*/	/** Returns whether there is a splash banner*/	public boolean hasSplash(){ 		return true; 	}	/*.................................................................................................................*/	/** Returns version for a package of modules*/	public String getPackageVersion(){				return "3.30";	}	/*.................................................................................................................*/	/** Returns version for a package of modules as an integer*/	public int getPackageVersionInt(){		return 3300;	}	/*.................................................................................................................*/	public String getPackageDateReleased(){		return "9 April 2023";   	}	/*.................................................................................................................*/	/** Returns build number for a package of modules as an integer*/	public int getPackageBuildNumber(){		return 168;	}	/*  Release dates:	 *   1.0 (no build number stated):  29 August 2014	 *   1.0 (build 11):  20 September 2014	 *   1.1 (build 23):  6 January 2015	 *   2.0 (build 86):  12 September 2017	 *   2.01 (build 91):  19 September 2017	 *   2.1 (build 104):  4 May 2018	 *   2.11 (build 111):  28 June 2018	 *   3.0 (build 133):  27 December 2018	 *   3.1 (build 146):  26 December 2019	 *   3.11 (build 150):  3 January 2020	 *   3.20 (build 159):  21 August 2021	 *   3.30 (build 168):  9 April 2023	 * */	/*.................................................................................................................*/	public boolean isPrerelease(){		return false;  	}	/*.................................................................................................................*/	/** Returns the tag for the release tag*/	public String getReleaseTag(){		return "3.30";	}	/** Returns the URL for the release package*/	public String getReleaseURL(){		return "https://github.com/MesquiteProject/Mesquite-Zephyr/releases/download/v3.30/Zephyr.3.30.zip";	}	/*.................................................................................................................*/	/** Returns the kind of repository*/	public int getRepositoryKind(){		return GITHUBREPOSITORY;	}	/*.................................................................................................................*/	/** Returns the repository path on the repository server*/	public String getRepositoryPath(){		return "MesquiteProject/Mesquite-Zephyr";	}	/*.................................................................................................................*/	/** Returns the repository URL*/	public String getRepositoryFullURL(){		return "https://github.com/MesquiteProject/Mesquite-Zephyr";	}	/*.................................................................................................................*/	public String getPackageURL(){		return "http://zephyr.mesquiteproject.org";  	}/*.................................................................................................................*/	/** 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://zephyr.mesquiteproject.org/noticesAndUpdates/noticesDev.xml";		else if (isPrerelease()) 			return "http://zephyr.mesquiteproject.org/noticesAndUpdates/noticesPrerelease.xml";		else			return "http://zephyr.mesquiteproject.org/noticesAndUpdates/notices.xml";				/*	version 2.01 and before: 		if (MesquiteTrunk.debugMode)			return "http://mesquiteproject.org/package s/zephyr/noticesDev.xml";		else if (isPrerelease()) 			return "http://mesquiteproject.org/package s/zephyr/noticesPrerelease.xml";		else			return "http://mesquiteproject.org/package s/zephyr/notices.xml";			*/	}	/*.................................................................................................................*/	/** Returns the  integer version of the MesquiteCore version  that this package requires to function*/	public int getMinimumMesquiteVersionRequiredInt(){		return 380;  	}	/*.................................................................................................................*/	/** Returns the String version of the MesquiteCore version number that this package requires to function*/	public String getMinimumMesquiteVersionRequired(){		return "3.80";  	}	/*.................................................................................................................*/	public int getVersionOfFirstRelease(){		return 300;  	}}
+/* Mesquite.zephyr source code.  Copyright 2007 and onwards D. Maddison and W. Maddison. Mesquite.zephyr is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.Zephry's web site is http://zephyr.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.zephyr.aZephyrIntro;import mesquite.lib.MesquiteTrunk;import mesquite.lib.duties.*;/* ======================================================================== */public class aZephyrIntro extends PackageIntro {	/*.................................................................................................................*/	public boolean startJob(String arguments, Object condition, boolean hiredByName) { 		return true;  	 }  	 public Class getDutyClass(){  	 	return aZephyrIntro.class;  	 } 	/*.................................................................................................................*/	 public String getExplanation() {	return "Zephyr is a package of Mesquite modules providing tools for connecting to other phylogenetic inference programs.";	 }		/*.................................................................................................................*/		public String getManualPath(){			return getPackagePath() +"docs/introduction.html";  		}	/*.................................................................................................................*/    	 public String getName() {		return "Zephyr Package";   	 }	/*.................................................................................................................*/	/** Returns the name of the package of modules (e.g., "Basic Mesquite Package", "Rhetenor")*/ 	public String getPackageName(){ 		return "Zephyr Package"; 	}	/*.................................................................................................................*/	/** Returns citation for a package of modules*/ 	public String getPackageCitation(){ 		return "Maddison, D.R. & Maddison W.P. 2023. Zephyr: A Mesquite package for interacting with external phylogeny inference programs. Version "+getPackageVersion(); 	}	/*.................................................................................................................*/	/** Returns whether there is a splash banner*/	public boolean hasSplash(){ 		return true; 	}	/*.................................................................................................................*/	/** Returns version for a package of modules*/	public String getPackageVersion(){				return "3.31";	}	/*.................................................................................................................*/	/** Returns version for a package of modules as an integer*/	public int getPackageVersionInt(){		return 3310;	}	/*.................................................................................................................*/	public String getPackageDateReleased(){		return "20 April 2023";   	}	/*.................................................................................................................*/	/** Returns build number for a package of modules as an integer*/	public int getPackageBuildNumber(){		return 170;	}	/*  Release dates:	 *   1.0 (no build number stated):  29 August 2014	 *   1.0 (build 11):  20 September 2014	 *   1.1 (build 23):  6 January 2015	 *   2.0 (build 86):  12 September 2017	 *   2.01 (build 91):  19 September 2017	 *   2.1 (build 104):  4 May 2018	 *   2.11 (build 111):  28 June 2018	 *   3.0 (build 133):  27 December 2018	 *   3.1 (build 146):  26 December 2019	 *   3.11 (build 150):  3 January 2020	 *   3.20 (build 159):  21 August 2021	 *   3.30 (build 168):  9 April 2023	 *   3.31 (build 170):  20 April 2023	 * */	/*.................................................................................................................*/	public boolean isPrerelease(){		return false;  	}	/*.................................................................................................................*/	/** Returns the tag for the release tag*/	public String getReleaseTag(){		return "3.31";	}	/** Returns the URL for the release package*/	public String getReleaseURL(){		return "https://github.com/MesquiteProject/Mesquite-Zephyr/releases/download/v3.31/Zephyr.3.31.zip";	}	/*.................................................................................................................*/	/** Returns the kind of repository*/	public int getRepositoryKind(){		return GITHUBREPOSITORY;	}	/*.................................................................................................................*/	/** Returns the repository path on the repository server*/	public String getRepositoryPath(){		return "MesquiteProject/Mesquite-Zephyr";	}	/*.................................................................................................................*/	/** Returns the repository URL*/	public String getRepositoryFullURL(){		return "https://github.com/MesquiteProject/Mesquite-Zephyr";	}	/*.................................................................................................................*/	public String getPackageURL(){		return "http://zephyr.mesquiteproject.org";  	}/*.................................................................................................................*/	/** 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://zephyr.mesquiteproject.org/noticesAndUpdates/noticesDev.xml";		else if (isPrerelease()) 			return "http://zephyr.mesquiteproject.org/noticesAndUpdates/noticesPrerelease.xml";		else			return "http://zephyr.mesquiteproject.org/noticesAndUpdates/notices.xml";				/*	version 2.01 and before: 		if (MesquiteTrunk.debugMode)			return "http://mesquiteproject.org/package s/zephyr/noticesDev.xml";		else if (isPrerelease()) 			return "http://mesquiteproject.org/package s/zephyr/noticesPrerelease.xml";		else			return "http://mesquiteproject.org/package s/zephyr/notices.xml";			*/	}	/*.................................................................................................................*/	/** Returns the  integer version of the MesquiteCore version  that this package requires to function*/	public int getMinimumMesquiteVersionRequiredInt(){		return 380;  	}	/*.................................................................................................................*/	/** Returns the String version of the MesquiteCore version number that this package requires to function*/	public String getMinimumMesquiteVersionRequired(){		return "3.80";  	}	/*.................................................................................................................*/	public int getVersionOfFirstRelease(){		return 300;  	}}

Source/mesquite/zephyr/lib/RAxMLRunnerBasic.java

@@ -44,7 +44,6 @@ public abstract class RAxMLRunnerBasic extends RAxMLRunner  implements KeyListen
 	protected boolean showIntermediateTrees = true;
 
 
-	protected SingleLineTextField MPISetupField;
 	protected IntegerField numProcessorsField;
 	protected RadioButtons threadingRadioButtons;
 
@@ -159,7 +158,7 @@ public String maxNumProcessorsMessage() {
 	/*.................................................................................................................*/
 	public void checkFields() {
 		int max = getMaxCores();
-		if (MesquiteInteger.isCombinable(max) && numProcessorsField.isValidInteger() && numProcessorsField.getValue()>max) {
+		if (numProcessorsField!=null && MesquiteInteger.isCombinable(max) && numProcessorsField.isValidInteger() && numProcessorsField.getValue()>max) {
 			MesquiteMessage.notifyUser("Number of processors used cannot exceed "+max +maxNumProcessorsMessage());			
 			numProcessorsField.setValue(max);
 		}

Source/mesquite/zephyr/lib/RAxMLRunnerBasicOld.java

@@ -46,8 +46,6 @@ public abstract class RAxMLRunnerBasicOld extends RAxMLRunnerBasic  implements K
 
 	protected boolean showIntermediateTrees = true;
 
-	protected SingleLineTextField MPISetupField;
-	protected IntegerField numProcessorsField;
 	protected RadioButtons threadingRadioButtons;
 	protected Checkbox RAxML814orLaterCheckbox;
 

Source/mesquite/zephyr/lib/TNTRunner.java

@@ -713,7 +713,8 @@ public void setTaxonTranslation(Taxa taxa) {
 
 	}
 	int[] taxonNumberTranslation = null;
-
+	FileInterpreterI exporter;
+
 	/*.................................................................................................................*/
 	public Tree getTrees(TreeVector trees, Taxa taxa, MCharactersDistribution matrix, long seed, MesquiteDouble finalScore) {
 		if (!initializeGetTrees(CategoricalData.class, taxa, matrix))
@@ -730,7 +731,7 @@ public Tree getTrees(TreeVector trees, Taxa taxa, MCharactersDistribution matrix
 		String dataFileName = "data.ss";   //replace this with actual file name?
 		String dataFilePath = tempDir +  dataFileName;
 
-		FileInterpreterI exporter = ZephyrUtil.getFileInterpreter(this,"#InterpretTNT");
+		exporter = ZephyrUtil.getFileInterpreter(this,"#InterpretTNT");
 		if (exporter==null)
 			return null;
 		boolean fileSaved = false;
@@ -764,6 +765,7 @@ public Tree getTrees(TreeVector trees, Taxa taxa, MCharactersDistribution matrix
 
 		if (StringUtil.blank(programCommand)) {
 			MesquiteMessage.discreetNotifyUser("Path to TNT not specified!");
+			((InterpretHennig86Base)exporter).setTaxonNamer(null);
 			return null;
 		}
 
@@ -804,6 +806,7 @@ public Tree getTrees(TreeVector trees, Taxa taxa, MCharactersDistribution matrix
 			data.decrementEditInhibition();
 		externalProcRunner.setLeaveAnalysisDirectoryIntact(true);  // we don't want to delete the directory here
 		externalProcRunner.finalCleanup();
+		((InterpretHennig86Base)exporter).setTaxonNamer(null);
 		return null;
 	}	
 
@@ -871,6 +874,8 @@ public Tree retrieveTreeBlock(TreeVector treeList, MesquiteDouble finalScore) {
 			data.decrementEditInhibition();
 		//	manager.deleteElement(tv);  // get rid of temporary tree block
 		externalProcRunner.finalCleanup();
+		if (exporter!=null)
+			((InterpretHennig86Base)exporter).setTaxonNamer(null);
 		if (success) 
 			return t;
 		return null;

docs/GARLIOverview.html

@@ -41,7 +41,7 @@
     <td width="51%"><img src="images/zephyrBannerNarrow.jpg" width="628" height="110" /></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->GARLI<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.30<br />      
+    <td width="14%">Version 3.31<br />      
     April 2023<br /></td>
   </tr>
 </table>

docs/IQTREEOverview.html

@@ -41,7 +41,7 @@
     <td width="51%"><img src="images/zephyrBannerNarrow.jpg" width="628" height="110" /></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->IQ-TREE<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.30<br />      
+    <td width="14%">Version 3.31<br />      
     April 2023<br /></td>
   </tr>
 </table>

docs/PAUPOverview.html

@@ -41,7 +41,7 @@
     <td width="51%"><img src="images/zephyrBannerNarrow.jpg" width="628" height="110" /></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->PAUP*<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.30<br />      
+    <td width="14%">Version 3.31<br />      
     April 2023<br /></td>
   </tr>
 </table>

docs/RAxMLOverview.html

@@ -41,7 +41,7 @@
     <td width="51%"><img src="images/zephyrBannerNarrow.jpg" width="628" height="110" /></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->RAxML-NG and RAxML<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.30<br />      
+    <td width="14%">Version 3.31<br />      
     April 2023<br /></td>
   </tr>
 </table>

docs/SOWHintroduction.html

@@ -41,7 +41,7 @@
     <td width="51%"><img src="images/zephyrBannerNarrow.jpg" width="628" height="110" /></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->SOWH Introduction<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.30<br />      
+    <td width="14%">Version 3.31<br />      
     April 2023<br /></td>
   </tr>
 </table>

docs/SOWHpreparing.html

@@ -41,7 +41,7 @@
     <td width="51%"><img src="images/zephyrBannerNarrow.jpg" width="628" height="110" /></td>
     <td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Preparing for SOWH<!-- InstanceEndEditable --></div></td>
     <td width="2%">&nbsp;</td>
-    <td width="14%">Version 3.30<br />      
+    <td width="14%">Version 3.31<br />      
     April 2023<br /></td>
   </tr>
 </table>