Add missing doc files

[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 34f0aaf..33208a0 100644 (file)
--- a/webservices/compbio/ws/server/RNAalifoldWS.java
+++ b/webservices/compbio/ws/server/RNAalifoldWS.java
@@ -1,66 +1,77 @@
-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> \r
+               implements\r
+                       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
+       @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
+       }\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
+                       LimitExceededException, JobSubmissionException,\r
+                       WrongParameterException {\r
+               WSUtil.validateFastaInput(sequences);\r
+               ConfiguredExecutable<RNAalifold> confRNAalifold = init(sequences);\r
+               \r
+               List<String> params = WSUtil.getCommands(options,\r
+                               RNAalifold.KEY_VALUE_SEPARATOR);\r
+               confRNAalifold.addParameters(params);\r
+               return WSUtil.fold(sequences, confRNAalifold, log, "customAnalize",\r
+                               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
+\r
+               return analize(sequences);\r
+       }\r
+}\r
+       \r
+       \r