Switch JpredWS from SequenceAnnotation to MsaWS

[jabaws.git] / runner / compbio / runner / msa / Mafft.java

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