Clean-up, refactoring, commenting. Parameters file containts only options since Jalvi...

[jabaws.git] / webservices / compbio / ws / server / RNAalifoldWS.java

diff --git a/webservices/compbio/ws/server/RNAalifoldWS.java b/webservices/compbio/ws/server/RNAalifoldWS.java
index beca1dc..91081c4 100644 (file)
--- a/webservices/compbio/ws/server/RNAalifoldWS.java
+++ b/webservices/compbio/ws/server/RNAalifoldWS.java
@@ -9,13 +9,11 @@ import org.apache.log4j.Logger;
 import compbio.data.msa.JABAService;\r
 import compbio.data.msa.SequenceAnnotation;\r
 import compbio.data.sequence.FastaSequence;\r
-import compbio.data.sequence.RNAStructScoreManager;\r
 import compbio.engine.client.ConfiguredExecutable;\r
 import compbio.metadata.JobSubmissionException;\r
 import compbio.metadata.LimitExceededException;\r
 import compbio.metadata.Option;\r
 import compbio.metadata.Preset;\r
-import compbio.metadata.ResultNotAvailableException;\r
 import compbio.metadata.UnsupportedRuntimeException;\r
 import compbio.metadata.WrongParameterException;\r
 import compbio.runner.conservation.AACon;\r
@@ -31,15 +29,9 @@ public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
        public RNAalifoldWS() {\r
                super (new RNAalifold(), log);\r
        }\r
-\r
-       \r
-       // for testing\r
-       @Override\r
-       public RNAStructScoreManager getAnnotation(String jobId) \r
-                       throws ResultNotAvailableException {\r
-               return WSUtil.getAnnotation(jobId, log);\r
-       }\r
        \r
+       // Only purpose is to replace "analize" with "fold" method \r
+       // so that a clustal input file and not fasta will be generated\r
        @Override\r
        public String analize(List<FastaSequence> sequences)\r
                        throws UnsupportedRuntimeException, LimitExceededException,\r
@@ -50,6 +42,8 @@ public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
                                getLimit(""));\r
        }\r
 \r
+       // Only purpose is to replace "analize" with "fold" method \r
+       // so that a clustal input file and not fasta will be generated\r
        @Override\r
        public String customAnalize(List<FastaSequence> sequences,\r
                        List<Option<RNAalifold>> options) throws UnsupportedRuntimeException,\r