Merge pull request #24 from MesquiteProject/development

Development -> master for Zephyr 3.20 release
MesquiteProject · Aug 21, 2021 · 2e3b9be · 2e3b9be
2 parents e537e7c + c00865d
commit 2e3b9be
Show file tree

Hide file tree

Showing 65 changed files with 537 additions and 181 deletions.
diff --git a/Source/mesquite/zephyr/GarliRunnerLocal/GarliRunnerLocal.java b/Source/mesquite/zephyr/GarliRunnerLocal/GarliRunnerLocal.java
@@ -48,6 +48,11 @@ public Class getExternalProcessRunnerClass(){
 			return LocalScriptRunner.class;
 	 }
 
+		/*.................................................................................................................*/
+		public boolean mayHaveProblemsWithDeletingRunningOnReconnect() {
+			return true;
+		}
+
 	 /*.................................................................................................................*/
 	 public Object getProgramArguments(String dataFileName, String configFileName, boolean isPreflight) {
 
@@ -64,7 +69,6 @@ public Object getProgramArguments(String dataFileName, String configFileName, bo
 		public String getLogText() {
 			return externalProcRunner.getStdOut();
 		}
-
 	/*.................................................................................................................*/
 	public void appendToConfigFileGeneral(StringBuffer config) {
 		if (config!=null) {

diff --git a/Source/mesquite/zephyr/IQTreeRunnerLocal/IQTreeRunnerLocal.java b/Source/mesquite/zephyr/IQTreeRunnerLocal/IQTreeRunnerLocal.java
@@ -46,6 +46,11 @@ public Class getDutyClass() {
 		return IQTreeRunnerLocal.class;
 	}
 
+	/*.................................................................................................................*/
+	public boolean mayHaveProblemsWithDeletingRunningOnReconnect() {
+		return true;
+	}
+
 	/*.................................................................................................................*/
 	/** returns the version number at which this module was first released.  If 0, then no version number is claimed.  If a POSITIVE integer
 	 * then the number refers to the Mesquite version.  This should be used only by modules part of the core release of Mesquite.

diff --git a/Source/mesquite/zephyr/LocalScriptRunner/LocalScriptRunner.java b/Source/mesquite/zephyr/LocalScriptRunner/LocalScriptRunner.java
@@ -313,8 +313,13 @@ else if (scriptBasedCheckBox!=null)
 			scriptBased = scriptBasedCheckBox.getState();
 		return true;
 	}
+	/*.................................................................................................................*/
+	public static boolean isMacOSXCatalinaOrLater(){
+		return System.getProperty("os.name").startsWith("Mac OS X") && (MesquiteTrunk.getOSXVersion()>=15);
+	} 	
+
 	public boolean visibleTerminalOptionAllowed(){
-		return ShellScriptRunner.localScriptRunsCanDisplayTerminalWindow() && !processRequester.localScriptRunsRequireTerminalWindow();
+		return ShellScriptRunner.localScriptRunsCanDisplayTerminalWindow() && !processRequester.localScriptRunsRequireTerminalWindow() && !isMacOSXCatalinaOrLater();
 	}
 	public boolean getDirectProcessConnectionAllowed(){
 		return processRequester.getDirectProcessConnectionAllowed() && MesquiteTrunk.isJavaGreaterThanOrEqualTo(1.7);
@@ -328,7 +333,13 @@ public String getDirectoryPath(){
 		return localRootDir;
 	}
 
-
+	/*.................................................................................................................*/
+	public void deleteRunningFile(){  
+		if (scriptRunner!=null)
+			scriptRunner.deleteRunningFile();
+	}
+
+
 	/*.................................................................................................................*
 	public String getShellScript(String programCommand, String args) {
 		runningFilePath = rootDir + "running";//+ MesquiteFile.massageStringToFilePathSafe(unique);

diff --git a/Source/mesquite/zephyr/PAUPDistanceRunnerLocal/PAUPDistanceRunnerLocal.java b/Source/mesquite/zephyr/PAUPDistanceRunnerLocal/PAUPDistanceRunnerLocal.java
@@ -41,6 +41,10 @@ public Class getExternalProcessRunnerClass(){
 	public String getName() {
 		return "PAUP Trees (Distance) [Local] Runner";
 	}
+	/*.................................................................................................................*/
+	public boolean mayHaveProblemsWithDeletingRunningOnReconnect() {
+		return true;
+	}
 
 
 

diff --git a/Source/mesquite/zephyr/PAUPLikelihoodRunnerLocal/PAUPLikelihoodRunnerLocal.java b/Source/mesquite/zephyr/PAUPLikelihoodRunnerLocal/PAUPLikelihoodRunnerLocal.java
@@ -40,6 +40,10 @@ public Class getExternalProcessRunnerClass(){
 	public String getName() {
 		return getProgramName() + " Trees (Likelihood) [Local] Runner";
 	}
+	/*.................................................................................................................*/
+	public boolean mayHaveProblemsWithDeletingRunningOnReconnect() {
+		return true;
+	}
 
 
 }
diff --git a/Source/mesquite/zephyr/PAUPParsimonyRunnerLocal/PAUPParsimonyRunnerLocal.java b/Source/mesquite/zephyr/PAUPParsimonyRunnerLocal/PAUPParsimonyRunnerLocal.java
@@ -40,5 +40,9 @@ public String getName() {
 		return getProgramName() + " Trees (Parsimony) [Local] Runner";
 	}
 
+	/*.................................................................................................................*/
+	public boolean mayHaveProblemsWithDeletingRunningOnReconnect() {
+		return true;
+	}
 
 }
diff --git a/Source/mesquite/zephyr/PAUPSVDRunnerLocal/PAUPSVDRunnerLocal.java b/Source/mesquite/zephyr/PAUPSVDRunnerLocal/PAUPSVDRunnerLocal.java
@@ -43,6 +43,10 @@ public Class getExternalProcessRunnerClass(){
 	public String getName() {
 		return "PAUP Trees (SVD) [Local] Runner";
 	}
+	/*.................................................................................................................*/
+	public boolean mayHaveProblemsWithDeletingRunningOnReconnect() {
+		return true;
+	}
 
 
 

diff --git a/Source/mesquite/zephyr/RAxMLRunnerLocal/RAxMLRunnerLocal.java b/Source/mesquite/zephyr/RAxMLRunnerLocal/RAxMLRunnerLocal.java
@@ -44,9 +44,11 @@ public Class getDutyClass() {
 		return RAxMLRunnerLocal.class;
 	}
 	/*.................................................................................................................*/
-	public String getTestedProgramVersions(){
-		return "8.0.0–8.2.11";
+	public boolean mayHaveProblemsWithDeletingRunningOnReconnect() {
+		return true;
 	}
+
+
 	/*.................................................................................................................*/
 	/** returns the version number at which this module was first released.  If 0, then no version number is claimed.  If a POSITIVE integer
 	 * then the number refers to the Mesquite version.  This should be used only by modules part of the core release of Mesquite.

diff --git a/Source/mesquite/zephyr/TreeInferenceCoordinator/TreeInferenceCoordinator.java b/Source/mesquite/zephyr/TreeInferenceCoordinator/TreeInferenceCoordinator.java
@@ -90,7 +90,10 @@ TreeInferenceHandler findHandlerByID(int id){
 	}
 	/*.................................................................................................................*/
 	String getExtraLinks(TreeInferenceHandler e) {
-		return e.getExtraLinks();
+		if (StringUtil.blank(e.getCommandOfTextCommandLink()) || StringUtil.blank(e.getTitleOfTextCommandLink()))
+			return "";
+		String extraLinks = "(<a href = \"extra-" + e.getCommandOfTextCommandLink() + "-"+e.getID() + "\">" +e.getTitleOfTextCommandLink() + "</a>) ";
+		return extraLinks;
 	}
 	/*.................................................................................................................*/
 	String getNameForStopLink(TreeInferenceHandler e) {
@@ -287,7 +290,7 @@ else if (checker.compare(this.getClass(), "link touched", null, commandName, "li
 				int id = MesquiteInteger.fromString(idString);
 				TreeInferenceHandler handler = findHandlerByID(id);
 				if (handler != null) {
-					handler.dealWithExtraLink(command);
+					handler.processUserClickingOnTextCommandLink(command);
 					return null;
 				}
 			}

diff --git a/Source/mesquite/zephyr/TreeInferenceLiaison/TreeInferenceLiaison.java b/Source/mesquite/zephyr/TreeInferenceLiaison/TreeInferenceLiaison.java
@@ -54,13 +54,21 @@ public String getMessageIfCloseFileRequested (){
 		return null;
 	}
 	/*.................................................................................................................*/
-	public String getExtraLinks() {
-		//return "(<a href = \"extra-harvest-" + this.getID() + "\">Harvest Results</a>) ";
-		return "";
+	public String getTitleOfTextCommandLink() {
+		if (inferenceTask==null)
+			return "";
+		return inferenceTask.getTitleOfTextCommandLink();
 	}
 	/*.................................................................................................................*/
-	public void dealWithExtraLink(String command) {
-		//logln("User request to harvest trees");
+	public String getCommandOfTextCommandLink() {
+		if (inferenceTask==null)
+			return "";
+		return inferenceTask.getCommandOfTextCommandLink();
+	}
+	/*.................................................................................................................*/
+	public void processUserClickingOnTextCommandLink(String command) {
+		if (inferenceTask!=null)
+			inferenceTask.processUserClickingOnTextCommandLink(command);
 	}
 
 	/*.................................................................................................................*/