-/* 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
\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
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
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
\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