Define path to UNIREF database in conf/Executable.properties

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

diff --git a/runner/compbio/runner/msa/ClustalW.java b/runner/compbio/runner/msa/ClustalW.java
index 88f6358..2ce0d03 100644 (file)
--- a/runner/compbio/runner/msa/ClustalW.java
+++ b/runner/compbio/runner/msa/ClustalW.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
@@ -27,10 +27,9 @@ import org.apache.log4j.Logger;
 \r
 import compbio.data.sequence.Alignment;\r
 import compbio.data.sequence.UnknownFileFormatException;\r
-import compbio.engine.client.Executable;\r
 import compbio.engine.client.SkeletalExecutable;\r
 import compbio.metadata.ResultNotAvailableException;\r
-import compbio.runner.Util;\r
+import compbio.runner.RunnerUtil;\r
 \r
 public class ClustalW extends SkeletalExecutable<ClustalW> {\r
 \r
@@ -68,7 +67,7 @@ public class ClustalW extends SkeletalExecutable<ClustalW> {
        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
@@ -90,7 +89,7 @@ public class ClustalW extends SkeletalExecutable<ClustalW> {
                                convertInputNameToTreeName());\r
        }\r
 \r
-       /*\r
+       /**\r
         * Clustal output tree with same name as input file but .dnd extension e.g.\r
         * this methods do similar conversion TO122.fasta -> TO122.dnd or\r
         * TO122.fasta.in -> TO122.fasta.dnd It does not seems that there is any\r
@@ -114,8 +113,8 @@ public class ClustalW extends SkeletalExecutable<ClustalW> {
 \r
        @SuppressWarnings("unchecked")\r
        @Override\r
-       public Class<Executable<ClustalW>> getType() {\r
-               return (Class<Executable<ClustalW>>) this.getClass();\r
+       public Class<ClustalW> getType() {\r
+               return (Class<ClustalW>) this.getClass();\r
        }\r
 \r
 }\r