Define path to UNIREF database in conf/Executable.properties

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

diff --git a/runner/compbio/runner/msa/Muscle.java b/runner/compbio/runner/msa/Muscle.java
index c37b73a..8576a04 100644 (file)
--- a/runner/compbio/runner/msa/Muscle.java
+++ b/runner/compbio/runner/msa/Muscle.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
@@ -29,10 +29,9 @@ 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 Muscle extends SkeletalExecutable<Muscle> {\r
 \r
@@ -44,14 +43,13 @@ public class Muscle extends SkeletalExecutable<Muscle> {
 \r
        private static final String EXEC_STAT_FILE = "stat.log";\r
 \r
-       public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
+       public static final String KEY_VALUE_SEPARATOR = " ";\r
 \r
        /**\r
         * Default options are\r
         * \r
         * -clwstrict - write output in clustal format\r
         * \r
-        * @param workDirectory\r
         */\r
        public Muscle() {\r
                /*\r
@@ -61,7 +59,8 @@ public class Muscle extends SkeletalExecutable<Muscle> {
                 * completes. So –quiet and –verbose are not contradictory."-quiet",\r
                 * "-verbose"\r
                 */\r
-               addParameters(Arrays.asList("-clwstrict", "-quiet", "-verbose"));\r
+               addParameters(Arrays.asList("-clwstrict", "-quiet", "-verbose",\r
+                               "-nocore"));\r
                cbuilder.setParam("-log", EXEC_STAT_FILE);\r
        }\r
 \r
@@ -84,7 +83,7 @@ public class Muscle extends SkeletalExecutable<Muscle> {
        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
@@ -111,8 +110,8 @@ public class Muscle extends SkeletalExecutable<Muscle> {
 \r
        @SuppressWarnings("unchecked")\r
        @Override\r
-       public Class<Executable<Muscle>> getType() {\r
-               return (Class<Executable<Muscle>>) this.getClass();\r
+       public Class<Muscle> getType() {\r
+               return (Class<Muscle>) this.getClass();\r
        }\r
 \r
 }\r