-package compbio.ws.server;
-
-import java.io.File;
-import java.util.List;
-
-import javax.jws.WebParam;
-import javax.jws.WebService;
-
-import org.apache.log4j.Logger;
-
-import compbio.data.msa.FoldWS;
-import compbio.data.msa.JABAService;
-import compbio.data.msa.JManagement;
-import compbio.data.msa.Metadata;
-import compbio.data.msa.SequenceAnnotation;
-import compbio.data.sequence.Alignment;
-import compbio.data.sequence.RNAStruct;
-import compbio.data.sequence.FastaSequence;
-import compbio.engine.AsyncExecutor;
-import compbio.engine.Configurator;
-import compbio.engine.client.ConfiguredExecutable;
-import compbio.engine.client.SkeletalExecutable;
-import compbio.metadata.ChunkHolder;
-import compbio.metadata.JobStatus;
-import compbio.metadata.JobSubmissionException;
-import compbio.metadata.Limit;
-import compbio.metadata.LimitExceededException;
-import compbio.metadata.LimitsManager;
-import compbio.metadata.Option;
-import compbio.metadata.Preset;
-import compbio.metadata.PresetManager;
-import compbio.metadata.ResultNotAvailableException;
-import compbio.metadata.RunnerConfig;
-import compbio.metadata.UnsupportedRuntimeException;
-import compbio.metadata.WrongParameterException;
-import compbio.runner.Util;
-import compbio.runner.disorder.GlobPlot;
-import compbio.runner.structure.RNAalifold;
-
-@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "RNAalifoldWS")
-public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
- implements
- SequenceAnnotation<RNAalifold> {
-
- private static Logger log = Logger.getLogger(ClustalWS.class);
-
- public RNAalifoldWS() {
- super (new RNAalifold(), log);
- }
-
-
- /*
- * No presets are supported, thus the result of this call will be as simple
- * call to analize without parameters
- */
- @Override
- public String presetAnalize(List<FastaSequence> sequences,
- Preset<RNAalifold> preset) throws UnsupportedRuntimeException,
- LimitExceededException, JobSubmissionException,
- WrongParameterException {
-
- return analize(sequences);
- }
-}
-
-
+package compbio.ws.server;\r
+\r
+import java.util.List;\r
+\r
+import javax.jws.WebService;\r
+\r
+import org.apache.log4j.Logger;\r
+\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.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
+public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold> implements SequenceAnnotation<RNAalifold> {\r
+\r
+ private static Logger log = Logger.getLogger(RNAalifoldWS.class);\r
+ \r
+ public RNAalifoldWS() {\r
+ super (new RNAalifold(), 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
+ @SuppressWarnings("unchecked")\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", 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
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public String customAnalize(List<FastaSequence> sequences,\r
+ List<Option<RNAalifold>> options) throws UnsupportedRuntimeException,\r
+ LimitExceededException, JobSubmissionException,\r
+ WrongParameterException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ ConfiguredExecutable<RNAalifold> confRNAalifold = init(sequences);\r
+ List<String> params = WSUtil.getCommands(options, RNAalifold.KEY_VALUE_SEPARATOR);\r
+ confRNAalifold.addParameters(params);\r
+ return WSUtil.fold(sequences, confRNAalifold, log, "customAnalize", getLimit(""));\r
+ }\r
+ \r
+ \r
+ /*\r
+ * No presets are supported, thus the result of this call will be as simple\r
+ * call to analize without parameters\r
+ */\r
+ @Override\r
+ public String presetAnalize(List<FastaSequence> sequences,\r
+ Preset<RNAalifold> preset) throws UnsupportedRuntimeException,\r
+ LimitExceededException, JobSubmissionException,\r
+ WrongParameterException {\r
+ return analize(sequences);\r
+ }\r
+}\r