-/* 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.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
\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
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
\r
@SuppressWarnings("unchecked")\r
@Override\r
- public Class<Executable<Probcons>> getType() {\r
- return (Class<Executable<Probcons>>) this.getClass();\r
+ public Class<Probcons> getType() {\r
+ return (Class<Probcons>) this.getClass();\r
}\r
}\r