Webservice works! but only supports some parameters. Replacing RNAstuct

[jabaws.git] / runner / compbio / runner / structure / RNAalifold.java

diff --git a/runner/compbio/runner/structure/RNAalifold.java b/runner/compbio/runner/structure/RNAalifold.java
index acb4a9e..3871ea9 100644 (file)
--- a/runner/compbio/runner/structure/RNAalifold.java
+++ b/runner/compbio/runner/structure/RNAalifold.java
@@ -31,17 +31,22 @@ public class RNAalifold extends SkeletalExecutable<RNAalifold>
        
        private static Logger log = Logger.getLogger(RNAalifold.class);
 
+       // May not be necessary as defult is "<space>" but still dont know
+       // How to deal with different key value separators for different params
+       public static final String KEY_VALUE_SEPARATOR = " ";
+       
+       public RNAalifold() {
+               super(KEY_VALUE_SEPARATOR);
+       }
        
        @Override
        public RNAalifold setOutput(String outFile) {
-               log.info("Set ouput file: " + outFile.toString());
                super.setOutput(outFile);
                return this;
        }
        
        @Override
        public RNAalifold setInput(String inFile) {
-               log.info("Set input file: " + inFile.toString());
                cbuilder.setLast(inFile);
                super.setInput(inFile);
                return this;
@@ -72,12 +77,11 @@ public class RNAalifold extends SkeletalExecutable<RNAalifold>
        }
 
 
-       // OLD :- the new methods for reading are found in 
+       // the new currently used methods for reading are found in 
        // - compbio.data.sequence.SequenceUtil and 
        // - compbio.runner.Util
        
        // Simple and generic methods for reading a whole file
-       // Should surfice until a more detailed datamodel and parser are developed
 //     private static String readRNAStruct(String workDirectory,
 //                     String structFile) throws IOException, FileNotFoundException {
 //             assert !compbio.util.Util.isEmpty(workDirectory);