Fixed: bug with phyml batch processing

ddarriba · Sep 1, 2011 · 7e3561b · 7e3561b
1 parent d4e67ff
commit 7e3561b
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Showing 4 changed files with 18 additions and 609 deletions.
diff --git a/src/main/java/es/uvigo/darwin/jmodeltest/exe/PhymlSingleModel.java b/src/main/java/es/uvigo/darwin/jmodeltest/exe/PhymlSingleModel.java
@@ -135,7 +135,7 @@ private void writePhyml3CommandLine(Model currentModel,
 		if (currentModel.ispF())
 			commandLine += " -f m"; // changed from -f e DP200509
 		else
-			commandLine += " -f 0.25 0.25 0.25 0.25";
+			commandLine += " -f 0.25,0.25,0.25,0.25";
 
 		// optimize pinvar if needed
 		if (currentModel.ispI())
@@ -168,6 +168,9 @@ private void writePhyml3CommandLine(Model currentModel,
 		if (numberOfThreads > 0) {
 			commandLine += " --num_threads " + numberOfThreads;
 		}
+
+		// avoid memory warning
+		commandLine += " --no_memory_check";
 
 		// do optimize topology?
 		/*
@@ -212,9 +215,17 @@ private void executeCommandLine() {
 		try {
 			File dir = new File(PHYML_PATH);
 
-			// to deal with spaces in path we need to fragment commandline (at
-			// least it works in MacOS X)
-			String[] executable = { PHYML_PATH + Utilities.getBinaryVersion() };
+			String[] executable = new String[1];
+
+			File phymlBinary = new File (PHYML_PATH + "phyml");
+			if (phymlBinary.exists() && phymlBinary.canExecute())
+			{
+				executable[0] = phymlBinary.getAbsolutePath();
+			}
+			else
+			{
+				executable[0] = PHYML_PATH + Utilities.getBinaryVersion();
+			}
 			String[] tokenizedCommandLine = commandLine.split(" ");
 			String[] cmd = Utilities.specialConcatStringArrays(executable,
 					tokenizedCommandLine);
@@ -408,6 +419,7 @@ else if (line.length() > 0
 		} catch (NullPointerException e) {
 			System.err.println("Error while parsing result data from "
 					+ currentModel.getName());
+			e.printStackTrace();
 		}
 		phymlStatFile.close();
 

diff --git a/src/main/java/es/uvigo/darwin/jmodeltest/exe/RunPhyml.java b/src/main/java/es/uvigo/darwin/jmodeltest/exe/RunPhyml.java
@@ -31,7 +31,7 @@
  * RunPhyml.java
  *
  * Description:		Makes phyml calculate likelihood scores for competing models
- * @author			Diego Darriba, University of Vigo / University of A Coru–a, Spain
+ * @author			Diego Darriba, University of Vigo / University of A Coruna, Spain
  * 					ddarriba@udc.es
  * @author			David Posada, University of Vigo, Spain  
  *					dposada@uvigo.es | darwin.uvigo.es

diff --git a/src/main/java/es/uvigo/darwin/jmodeltest/exe/RunPhymlMPJ.java b/src/main/java/es/uvigo/darwin/jmodeltest/exe/RunPhymlMPJ.java
@@ -37,7 +37,7 @@
  * RunPhymlMPJ.java
  *
  * Description:		Makes phyml calculate likelihood scores for competing models
- * @author			Diego Darriba, University of Vigo / University of A Coru–a, Spain
+ * @author			Diego Darriba, University of Vigo / University of A Coruna, Spain
  * 					ddarriba@udc.es
  * @author			David Posada, University of Vigo, Spain  
  *					dposada@uvigo.es | darwin.uvigo.es