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 b07882a..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
@@ -45,7 +43,7 @@ public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
        }\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
+       // 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