Define path to UNIREF database in conf/Executable.properties

[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 55d6e2b..6a43d35 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
@@ -31,29 +31,27 @@ import compbio.data.sequence.UnknownFileFormatException;
 import compbio.engine.client.PipedExecutable;\r
 import compbio.engine.client.SkeletalExecutable;\r
 import compbio.metadata.ResultNotAvailableException;\r
-import compbio.runner.Util;\r
+import compbio.runner.RunnerUtil;\r
 \r
 /**\r
  * \r
  * @author pvtroshin\r
  *\r
  */\r
-public class Mafft extends SkeletalExecutable<Mafft>\r
-               implements\r
-                       PipedExecutable<Mafft> {\r
-       /*\r
-        * TODO get rid of piping: Mafft now supports --out option for output file. \r
-     * Multithreading support does not seem to work reliably!  \r
-        */\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
        private static String autoOption = "--auto";\r
 \r
        private final String MATRIX_PAR_NAME = "--aamatrix";\r
 \r
-       public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
+       public static final String KEY_VALUE_SEPARATOR = " ";\r
 \r
        public Mafft() {\r
                // remove default input to prevent it to appear in the parameters list\r
@@ -66,7 +64,7 @@ public class Mafft extends SkeletalExecutable<Mafft>
        public Alignment getResults(String workDirectory)\r
                        throws ResultNotAvailableException {\r
                try {\r
-                       return Util.readClustalFile(workDirectory, getOutput());\r
+                       return RunnerUtil.readClustalFile(workDirectory, getOutput());\r
                } catch (FileNotFoundException e) {\r
                        log.error(e.getMessage(), e.getCause());\r
                        throw new ResultNotAvailableException(e);\r
@@ -106,26 +104,4 @@ public class Mafft extends SkeletalExecutable<Mafft>
        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