X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=runner%2Fcompbio%2Frunner%2Fmsa%2FMafft.java;h=b360a8225a8758ca0a76435327d72abe14d29f0e;hb=c9680e9b3771037dcb4c92e821a628c8dc6b1684;hp=508d5f787edce5ad0dcfd46a4b8ca0dacf4b3539;hpb=b6814b6b8761dba56f9e5fe34164f783af1aca4f;p=jabaws.git

diff --git a/runner/compbio/runner/msa/Mafft.java b/runner/compbio/runner/msa/Mafft.java
index 508d5f7..b360a82 100644
--- a/runner/compbio/runner/msa/Mafft.java
+++ b/runner/compbio/runner/msa/Mafft.java
@@ -1,6 +1,6 @@
-/* Copyright (c) 2009 Peter Troshin
+/* Copyright (c) 2011 Peter Troshin
  *  
- *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     
  * 
  *  This library is free software; you can redistribute it and/or modify it under the terms of the
  *  Apache License version 2 as published by the Apache Software Foundation
@@ -27,14 +27,23 @@ import org.apache.log4j.Logger;
 
 import compbio.data.sequence.Alignment;
 import compbio.data.sequence.UnknownFileFormatException;
+
 import compbio.engine.client.PipedExecutable;
 import compbio.engine.client.SkeletalExecutable;
 import compbio.metadata.ResultNotAvailableException;
 import compbio.runner.Util;
 
-public class Mafft extends SkeletalExecutable<Mafft>
-		implements
-			PipedExecutable<Mafft> {
+/**
+ * 
+ * @author pvtroshin
+ *
+ */
+public class Mafft extends SkeletalExecutable<Mafft> implements PipedExecutable<Mafft> {
+/*
+ * TODO get rid of piping: Mafft now supports --out option for output file. 
+ * Multi-threading supported with e.g. "thread 4" only for Linux, so JABAWS 
+ * will not support it for now, it also need editing of mafft makefile  
+ */
 
 	private static Logger log = Logger.getLogger(Mafft.class);
 
@@ -88,31 +97,11 @@ public class Mafft extends SkeletalExecutable<Mafft>
 		return this;
 	}
 
+
+	
 	@SuppressWarnings("unchecked")
 	@Override
 	public Class<Mafft> getType() {
 		return (Class<Mafft>) this.getClass();
 	}
-
-	/*
-	 * @Override public List<String> getParameters(
-	 * compbio.runner.Executable.ExecProvider provider) { for (int i = 0; i <
-	 * param.size(); i++) { String par = param.get(i); if
-	 * (isMatrixParameter(par)) { String matrixName = getValue(i); if (new
-	 * File(matrixName).isAbsolute()) { // Matrix can be found so no actions
-	 * necessary // This method has been called already and the matrix name //
-	 * is modified to contain full path // no further actions is necessary
-	 * break; } String matrixPath = Util.getExecProperty("matrix.path", this);
-	 * String absMatrixPath = Util.convertToAbsolute(matrixPath); param.remove(i
-	 * + 1); param.remove(i); super.addParameter(MATRIX_PAR_NAME);
-	 * super.addParameter(absMatrixPath + File.separator + matrixName); break; }
-	 * } return super.getParameters(provider); }
-	 * 
-	 * boolean isMatrixParameter(String parameter) { assert
-	 * !compbio.util.Util.isEmpty(parameter); if
-	 * (parameter.toUpperCase().startsWith(MATRIX_PAR_NAME)) { return true; }
-	 * return false; }
-	 * 
-	 * String getValue(int i) { return param.get(i + 1); }
-	 */
 }