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
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
- \r
- // Only purpose of Overrides is to replace "analize" with "fold" method \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
getLimit(""));\r
}\r
\r
- // Only purpose of Overrides is to replace "analize" with "fold" method \r
- // so that a clustal input file and not fasta will be generated\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
ConfiguredExecutable<RNAalifold> confRNAalifold = init(sequences);\r
\r
List<String> params = WSUtil.getCommands(options,\r
- AACon.KEY_VALUE_SEPARATOR);\r
+ RNAalifold.KEY_VALUE_SEPARATOR);\r
confRNAalifold.addParameters(params);\r
return WSUtil.fold(sequences, confRNAalifold, log, "customAnalize",\r
getLimit(""));\r