import compbio.data.msa.JABAService;\r
import compbio.data.msa.SequenceAnnotation;\r
import compbio.data.sequence.FastaSequence;\r
import compbio.data.msa.JABAService;\r
import compbio.data.msa.SequenceAnnotation;\r
import compbio.data.sequence.FastaSequence;\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.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.UnsupportedRuntimeException;\r
import compbio.metadata.WrongParameterException;\r
import compbio.runner.conservation.AACon;\r
import compbio.runner.structure.RNAalifold;\r
\r
@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "RNAalifoldWS")\r
import compbio.metadata.UnsupportedRuntimeException;\r
import compbio.metadata.WrongParameterException;\r
import compbio.runner.conservation.AACon;\r
import compbio.runner.structure.RNAalifold;\r
\r
@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "RNAalifoldWS")\r
\r
private static Logger log = Logger.getLogger(RNAalifoldWS.class);\r
\r
public RNAalifoldWS() {\r
super (new RNAalifold(), log);\r
}\r
\r
private static Logger log = Logger.getLogger(RNAalifoldWS.class);\r
\r
public RNAalifoldWS() {\r
super (new RNAalifold(), log);\r
}\r
@Override\r
public String analize(List<FastaSequence> sequences)\r
throws UnsupportedRuntimeException, LimitExceededException,\r
JobSubmissionException {\r
WSUtil.validateFastaInput(sequences);\r
ConfiguredExecutable<RNAalifoldWS> confRNAalifold = init(sequences);\r
@Override\r
public String analize(List<FastaSequence> sequences)\r
throws UnsupportedRuntimeException, LimitExceededException,\r
JobSubmissionException {\r
WSUtil.validateFastaInput(sequences);\r
ConfiguredExecutable<RNAalifoldWS> confRNAalifold = init(sequences);\r
- return WSUtil.fold(sequences, confRNAalifold, log, "analize",\r
- getLimit(""));\r
+ return WSUtil.fold(sequences, confRNAalifold, log, "analize", getLimit(""));\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
+ @SuppressWarnings("unchecked")\r
@Override\r
public String customAnalize(List<FastaSequence> sequences,\r
List<Option<RNAalifold>> options) throws UnsupportedRuntimeException,\r
@Override\r
public String customAnalize(List<FastaSequence> sequences,\r
List<Option<RNAalifold>> options) throws UnsupportedRuntimeException,\r
WrongParameterException {\r
WSUtil.validateFastaInput(sequences);\r
ConfiguredExecutable<RNAalifold> confRNAalifold = init(sequences);\r
WrongParameterException {\r
WSUtil.validateFastaInput(sequences);\r
ConfiguredExecutable<RNAalifold> confRNAalifold = init(sequences);\r
- return WSUtil.fold(sequences, confRNAalifold, log, "customAnalize",\r
- getLimit(""));\r
+ return WSUtil.fold(sequences, confRNAalifold, log, "customAnalize", getLimit(""));\r
Preset<RNAalifold> preset) throws UnsupportedRuntimeException,\r
LimitExceededException, JobSubmissionException,\r
WrongParameterException {\r
Preset<RNAalifold> preset) throws UnsupportedRuntimeException,\r
LimitExceededException, JobSubmissionException,\r
WrongParameterException {\r