JWS-86 made few changes to text, plus couple of links were faulty so changed ClustalW...

[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 16b5734..2ce0d03 100644 (file)
--- a/runner/compbio/runner/msa/ClustalW.java
+++ b/runner/compbio/runner/msa/ClustalW.java
@@ -29,7 +29,7 @@ import compbio.data.sequence.Alignment;
 import compbio.data.sequence.UnknownFileFormatException;\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
@@ -67,7 +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
@@ -89,7 +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