X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FAAConWS.java;h=1625ded6d360d93d7eb1634a7d8ad88d7678691d;hb=99ab39d360a99ec101152070146b63773a1d6453;hp=cf382df632fe821d0fb7f3cbab7bef245bc848b8;hpb=fab6bab770b548a0c99ed6f5dfb46f5aa99f67c7;p=jabaws.git

diff --git a/webservices/compbio/ws/server/AAConWS.java b/webservices/compbio/ws/server/AAConWS.java
index cf382df..1625ded 100644
--- a/webservices/compbio/ws/server/AAConWS.java
+++ b/webservices/compbio/ws/server/AAConWS.java
@@ -1,6 +1,7 @@
 package compbio.ws.server;
 
 import java.io.File;
+import java.util.Arrays;
 import java.util.List;
 
 import javax.annotation.Resource;
@@ -9,14 +10,13 @@ import javax.xml.ws.WebServiceContext;
 
 import org.apache.log4j.Logger;
 
-import compbio.conservation.Method;
-import compbio.data.msa.Annotation;
+import compbio.data.msa.SequenceAnnotation;
 import compbio.data.sequence.FastaSequence;
-import compbio.data.sequence.JalviewAnnotation;
-import compbio.data.sequence.MultiAnnotatedSequence;
+import compbio.data.sequence.ScoreManager;
 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;
@@ -33,8 +33,8 @@ import compbio.metadata.WrongParameterException;
 import compbio.runner.Util;
 import compbio.runner.conservation.AACon;
 
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "MuscleWS")
-public class AAConWS implements Annotation<AACon> {
+@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "AAConWS")
+public class AAConWS implements SequenceAnnotation<AACon> {
 
 	// Ask for resource injection
 	@Resource
@@ -50,42 +50,50 @@ public class AAConWS implements Annotation<AACon> {
 	private static final PresetManager<AACon> aaconPresets = Util
 			.getPresets(AACon.class);
 
+	private static final LimitsManager<AACon> limitMan = compbio.engine.client.Util
+			.getLimits(new AACon().getType());
+
 	ConfiguredExecutable<AACon> init(List<FastaSequence> sequences)
 			throws JobSubmissionException {
 		AACon aacon = new AACon();
-		aacon.setInput("fasta.in").setOutput("fasta.out");
+		aacon.setInput(SkeletalExecutable.INPUT).setOutput(
+				SkeletalExecutable.OUTPUT);
 		return Configurator.configureExecutable(aacon, sequences);
 	}
 
-	@SuppressWarnings("unchecked")
-	public MultiAnnotatedSequence<Method> getResult(String jobId)
+	@Override
+	public ScoreManager getAnnotation(String jobId)
 			throws ResultNotAvailableException {
 		WSUtil.validateJobId(jobId);
 		AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
 		ConfiguredExecutable<AACon> aacon = (ConfiguredExecutable<AACon>) asyncEngine
 				.getResults(jobId);
-		MultiAnnotatedSequence<Method> mas = aacon.getResults();
-		// log(jobId, "getResults");
+		ScoreManager mas = aacon.getResults();
+		log.trace(jobId + " getConservation : " + mas);
 		return mas;
 	}
+	/*
+	 * @SuppressWarnings("unchecked") public JalviewAnnotation
+	 * getJalviewAnnotation(String jobId) throws ResultNotAvailableException {
+	 * MultiAnnotatedSequence<Method> result = getResult(jobId); // TODO //
+	 * log(jobId, "getResults"); return result.toJalviewAnnotation(); }
+	 */
 
-	@SuppressWarnings("unchecked")
-	public JalviewAnnotation getJalviewAnnotation(String jobId)
-			throws ResultNotAvailableException {
-		MultiAnnotatedSequence<Method> result = getResult(jobId);
-
-		// log(jobId, "getResults");
-		return result.toJalviewAnnotation();
-	}
-
+	@Override
 	public Limit<AACon> getLimit(String presetName) {
-		return new AACon().getLimit(presetName);
+		if (limitMan == null) {
+			// Limit is not defined
+			return null;
+		}
+		return limitMan.getLimitByName(presetName);
 	}
 
+	@Override
 	public LimitsManager<AACon> getLimits() {
-		return new AACon().getLimits();
+		return limitMan;
 	}
 
+	@Override
 	public ChunkHolder pullExecStatistics(String jobId, long position) {
 		WSUtil.validateJobId(jobId);
 		String file = Configurator.getWorkDirectory(jobId) + File.separator
@@ -93,30 +101,54 @@ public class AAConWS implements Annotation<AACon> {
 		return WSUtil.pullFile(file, position);
 	}
 
+	@Override
 	public boolean cancelJob(String jobId) {
 		WSUtil.validateJobId(jobId);
 		return WSUtil.cancelJob(jobId);
 	}
 
+	@Override
 	public JobStatus getJobStatus(String jobId) {
 		WSUtil.validateJobId(jobId);
 		return WSUtil.getJobStatus(jobId);
 	}
 
+	@Override
 	public PresetManager<AACon> getPresets() {
 		return aaconPresets;
 	}
 
+	@Override
 	public RunnerConfig<AACon> getRunnerOptions() {
 		return aaconOptions;
 	}
 
+	private String analize(List<FastaSequence> sequences,
+			ConfiguredExecutable<AACon> confExec, Logger log, String method,
+			Limit<AACon> limit) throws JobSubmissionException {
+		if (limit != null && limit.isExceeded(sequences)) {
+			throw LimitExceededException.newLimitExceeded(limit, sequences);
+		}
+
+		compbio.runner.Util.writeInput(sequences, confExec);
+		AsyncExecutor engine = Configurator.getAsyncEngine(confExec);
+		String jobId = engine.submitJob(confExec);
+		return jobId;
+	}
+
 	@Override
 	public String analize(List<FastaSequence> sequences)
 			throws UnsupportedRuntimeException, LimitExceededException,
 			JobSubmissionException {
-		// TODO Auto-generated method stub
-		return null;
+
+		WSUtil.validateAAConInput(sequences);
+		ConfiguredExecutable<AACon> confAAcon = init(sequences);
+
+		// set default conservation method to fastest - SHENKIN
+		// TODO: This violates encapsulation, should be moved to the runners
+		// level.
+		confAAcon.addParameters(Arrays.asList("-m=SHENKIN"));
+		return analize(sequences, confAAcon, null, "analize", getLimit(""));
 	}
 
 	@Override
@@ -124,8 +156,16 @@ public class AAConWS implements Annotation<AACon> {
 			List<Option<AACon>> options) throws UnsupportedRuntimeException,
 			LimitExceededException, JobSubmissionException,
 			WrongParameterException {
-		// TODO Auto-generated method stub
-		return null;
+		WSUtil.validateAAConInput(sequences);
+		ConfiguredExecutable<AACon> confAACon = init(sequences);
+		// Could not do that! Space separated values
+		// will all be treated as keys! thus duplicates removed
+		// String params = cbuilder.getCommand();
+		List<String> params = WSUtil.getCommands(options,
+				AACon.KEY_VALUE_SEPARATOR);
+		confAACon.addParameters(params);
+		return analize(sequences, confAACon, null, "customAnalize",
+				getLimit(""));
 	}
 
 	@Override
@@ -133,8 +173,14 @@ public class AAConWS implements Annotation<AACon> {
 			Preset<AACon> preset) throws UnsupportedRuntimeException,
 			LimitExceededException, JobSubmissionException,
 			WrongParameterException {
-		// TODO Auto-generated method stub
-		return null;
+		WSUtil.validateAAConInput(sequences);
+		if (preset == null) {
+			throw new WrongParameterException("Preset must be provided!");
+		}
+		ConfiguredExecutable<AACon> confAAcon = init(sequences);
+		confAAcon.addParameters(preset.getOptions());
+		Limit<AACon> limit = getLimit(preset.getName());
+		return WSUtil.align(sequences, confAAcon, null, "presetAnalize", limit);
 	}
 
 }