Define path to UNIREF database in conf/Executable.properties

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

diff --git a/runner/compbio/runner/msa/Probcons.java b/runner/compbio/runner/msa/Probcons.java
index 58e4adb..872a5f8 100644 (file)
--- a/runner/compbio/runner/msa/Probcons.java
+++ b/runner/compbio/runner/msa/Probcons.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
@@ -30,7 +30,7 @@ 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
 public class Probcons extends SkeletalExecutable<Probcons>\r
                implements\r
@@ -40,11 +40,9 @@ public class Probcons extends SkeletalExecutable<Probcons>
 \r
        private final static String ANNOTATION = "annotation.txt";\r
 \r
-       public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
+       public static final String KEY_VALUE_SEPARATOR = " ";\r
 \r
        /**\r
-        * \r
-        * @param workDirectory\r
         */\r
        public Probcons() {\r
                addParameters(Arrays.asList("-v", "-clustalw", "-annot", ANNOTATION));\r
@@ -59,7 +57,7 @@ public class Probcons extends SkeletalExecutable<Probcons>
        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