X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=runner%2Fcompbio%2Frunner%2Fconservation%2FAACon.java;h=0f96077ee97280ae8c0e5c4a6fb4f87ab6f804fa;hb=c9680e9b3771037dcb4c92e821a628c8dc6b1684;hp=5d20d5d10cb8c55ece0ee457b42d8f16b67a7ea6;hpb=fab6bab770b548a0c99ed6f5dfb46f5aa99f67c7;p=jabaws.git

diff --git a/runner/compbio/runner/conservation/AACon.java b/runner/compbio/runner/conservation/AACon.java
index 5d20d5d..0f96077 100644
--- a/runner/compbio/runner/conservation/AACon.java
+++ b/runner/compbio/runner/conservation/AACon.java
@@ -1,15 +1,19 @@
-/*
- * Copyright (c) 2009 Peter Troshin JAva Bioinformatics Analysis Web Services
- * (JABAWS) @version: 1.0 This library is free software; you can redistribute it
- * and/or modify it under the terms of the Apache License version 2 as published
- * by the Apache Software Foundation This library is distributed in the hope
- * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
- * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * Apache License for more details. A copy of the license is in
- * apache_license.txt. It is also available here:
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt Any republication or
- * derived work distributed in source code form must include this copyright and
- * license notice.
+/* Copyright (c) 2011 Peter Troshin
+ *  
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     
+ * 
+ *  This library is free software; you can redistribute it and/or modify it under the terms of the
+ *  Apache License version 2 as published by the Apache Software Foundation
+ * 
+ *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
+ *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache 
+ *  License for more details.
+ * 
+ *  A copy of the license is in apache_license.txt. It is also available here:
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
+ * 
+ * Any republication or derived work distributed in source code form
+ * must include this copyright and license notice.
  */
 
 package compbio.runner.conservation;
@@ -24,16 +28,13 @@ import java.util.List;
 
 import org.apache.log4j.Logger;
 
-import compbio.conservation.Method;
-import compbio.conservation.ResultReader;
-import compbio.data.sequence.MultiAnnotatedSequence;
+import compbio.data.sequence.SMERFSConstraints;
+import compbio.data.sequence.ScoreManager;
+import compbio.data.sequence.SequenceUtil;
 import compbio.engine.client.CommandBuilder;
 import compbio.engine.client.Executable;
 import compbio.engine.client.SkeletalExecutable;
-import compbio.metadata.Limit;
-import compbio.metadata.LimitsManager;
 import compbio.metadata.ResultNotAvailableException;
-import compbio.runner.Util;
 
 /**
  * Command line
@@ -53,28 +54,29 @@ public class AACon extends SkeletalExecutable<AACon> {
 	 */
 	private int ncoreNumber = 0;
 
-	private final String ncorePrm = "-n=";
-
-	// Cache for Limits information
-	private static LimitsManager<AACon> limits;
+	private final String ncorePrm = "-t=";
 
-	public static final String KEY_VALUE_SEPARATOR = Util.SPACE;
+	public static final String KEY_VALUE_SEPARATOR = "=";
 	public static final String STAT_FILE = "stat.txt";
 
+	private final int windowWidth = SMERFSConstraints.DEFAULT_WINDOW_SIZE;
+	private final SMERFSConstraints colScoreMethod = SMERFSConstraints.MID_SCORE;
+	private final double gapTreshold = SMERFSConstraints.DEFAULT_GAP_THRESHOLD;
+
 	public AACon() {
 		addParameters(Arrays.asList("-jar", getLibPath(), "-d=" + STAT_FILE,
 				"-f=RESULT_NO_ALIGNMENT"));
 	}
-
-	@SuppressWarnings("unchecked")
+	// HashMap<Method, float[]>
 	@Override
-	public MultiAnnotatedSequence<Method> getResults(String workDirectory)
+	public ScoreManager getResults(String workDirectory)
 			throws ResultNotAvailableException {
-		MultiAnnotatedSequence<Method> annotations = null;
+		ScoreManager annotations = null;
 		try {
 			InputStream inStream = new FileInputStream(new File(workDirectory,
 					getOutput()));
-			annotations = ResultReader.readResults(inStream);
+			annotations = ScoreManager.newInstanceSingleSequence(SequenceUtil
+					.readAAConResults(inStream));
 			inStream.close();
 		} catch (FileNotFoundException e) {
 			log.error(e.getMessage(), e.getCause());
@@ -98,7 +100,7 @@ public class AACon extends SkeletalExecutable<AACon> {
 							+ "and initialize it with the location of jronn jar file");
 		}
 		if (new File(settings).isAbsolute()) {
-			// Jronn jar can be found so no actions necessary
+			// the jar can be found so no actions necessary
 			// no further actions is necessary
 			return settings;
 		}
@@ -124,40 +126,10 @@ public class AACon extends SkeletalExecutable<AACon> {
 		return this;
 	}
 
+	@SuppressWarnings("unchecked")
 	@Override
-	public Limit<AACon> getLimit(String presetName) {
-		if (limits == null) {
-			limits = getLimits();
-		}
-		Limit<AACon> limit = null;
-		if (limits != null) {
-			// this returns default limit if preset is undefined!
-			limit = limits.getLimitByName(presetName);
-		}
-		// If limit is not defined for a particular preset, then return default
-		// limit
-		if (limit == null) {
-			log.debug("Limit for the preset " + presetName
-					+ " is not found. Using default");
-			limit = limits.getDefaultLimit();
-		}
-		return limit;
-	}
-
-	@Override
-	public LimitsManager<AACon> getLimits() {
-		// synchronise on static field
-		synchronized (log) {
-			if (limits == null) {
-				limits = Util.getLimits(this.getClass());
-			}
-		}
-		return limits;
-	}
-
-	@Override
-	public Class<? extends Executable<?>> getType() {
-		return this.getClass();
+	public Class<AACon> getType() {
+		return (Class<AACon>) this.getClass();
 	}
 
 	public static String getStatFile() {