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 b360a82..6a43d35 100644 (file)
--- a/runner/compbio/runner/msa/Mafft.java
+++ b/runner/compbio/runner/msa/Mafft.java
@@ -31,7 +31,7 @@ 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
 /**\r
  * \r
@@ -51,7 +51,7 @@ public class Mafft extends SkeletalExecutable<Mafft> implements PipedExecutable<
 \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
@@ -64,7 +64,7 @@ public class Mafft extends SkeletalExecutable<Mafft> implements PipedExecutable<
        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