X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FRNAalifoldWS.java;h=ed94c23cdc071f3617cf1910dd5f87bdc8a0b3e5;hb=184bf3dce9500c599b5257140ec49edd80f8cea1;hp=34f0aaf4f6dcc2c323ab4db522180cb2a11df80b;hpb=42d82f347c559914cc57499c43daa49aed0573b8;p=jabaws.git

diff --git a/webservices/compbio/ws/server/RNAalifoldWS.java b/webservices/compbio/ws/server/RNAalifoldWS.java
index 34f0aaf..ed94c23 100644
--- a/webservices/compbio/ws/server/RNAalifoldWS.java
+++ b/webservices/compbio/ws/server/RNAalifoldWS.java
@@ -1,66 +1,70 @@
-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;
+
+import java.util.List;
+
+import javax.jws.WebService;
+
+import org.apache.log4j.Logger;
+
+import compbio.data.msa.JABAService;
+import compbio.data.msa.SequenceAnnotation;
+import compbio.data.sequence.FastaSequence;
+import compbio.engine.client.ConfiguredExecutable;
+import compbio.metadata.JobSubmissionException;
+import compbio.metadata.LimitExceededException;
+import compbio.metadata.Option;
+import compbio.metadata.Preset;
+import compbio.metadata.UnsupportedRuntimeException;
+import compbio.metadata.WrongParameterException;
+import compbio.runner.conservation.AACon;
+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(RNAalifoldWS.class);
+	
+	public RNAalifoldWS() {
+		super (new RNAalifold(), log);
+	}
+	
+	// Only purpose is to replace "analize" with "fold" method 
+	// so that a clustal input file and not fasta will be generated
+	@SuppressWarnings("unchecked")
+	@Override
+	public String analize(List<FastaSequence> sequences)
+			throws UnsupportedRuntimeException, LimitExceededException,
+			JobSubmissionException {
+		WSUtil.validateFastaInput(sequences);
+		ConfiguredExecutable<RNAalifoldWS> confRNAalifold = init(sequences);
+		return WSUtil.fold(sequences, confRNAalifold, log, "analize", getLimit(""));
+	}
+
+	// Only purpose is to replace "analize" with "fold" method 
+	// so that a clustal input file and not fasta will be generated
+	@SuppressWarnings("unchecked")
+	@Override
+	public String customAnalize(List<FastaSequence> sequences,
+			List<Option<RNAalifold>> options) throws UnsupportedRuntimeException,
+			LimitExceededException, JobSubmissionException,
+			WrongParameterException {
+		WSUtil.validateFastaInput(sequences);
+		ConfiguredExecutable<RNAalifold> confRNAalifold = init(sequences);
+		List<String> params = WSUtil.getCommands(options, RNAalifold.KEY_VALUE_SEPARATOR);
+		confRNAalifold.addParameters(params);
+		return WSUtil.fold(sequences, confRNAalifold, log, "customAnalize", getLimit(""));
+	}
+	
+	
+	/*
+	 * 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);
+	}
+}