X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=runner%2Fcompbio%2Frunner%2Fdisorder%2FGlobPlot.java;h=6530f5fb280ba04afe10dc6ba839c8a472806276;hb=fa61eaad52ffe5ee0db449c3dd9ec5fa67aec43f;hp=22846714fae2b65f370f86800feef6c92374c618;hpb=ecb4bc6237a7407063f45e3044353e73a3bd1829;p=jabaws.git

diff --git a/runner/compbio/runner/disorder/GlobPlot.java b/runner/compbio/runner/disorder/GlobPlot.java
index 2284671..6530f5f 100644
--- a/runner/compbio/runner/disorder/GlobPlot.java
+++ b/runner/compbio/runner/disorder/GlobPlot.java
@@ -19,19 +19,14 @@ import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
-import java.util.Map;
-import java.util.Set;
 
 import org.apache.log4j.Logger;
 
-import compbio.data.sequence.Score;
+import compbio.data.sequence.ScoreManager;
 import compbio.data.sequence.SequenceUtil;
 import compbio.data.sequence.UnknownFileFormatException;
-import compbio.engine.client.Executable;
 import compbio.engine.client.PipedExecutable;
 import compbio.engine.client.SkeletalExecutable;
-import compbio.metadata.Limit;
-import compbio.metadata.LimitsManager;
 import compbio.metadata.ResultNotAvailableException;
 import compbio.runner.Util;
 
@@ -57,9 +52,6 @@ public class GlobPlot extends SkeletalExecutable<GlobPlot>
 
 	private static Logger log = Logger.getLogger(GlobPlot.class);
 
-	// Cache for Limits information
-	private static LimitsManager<GlobPlot> limits;
-
 	public static final String KEY_VALUE_SEPARATOR = Util.SPACE;
 
 	/* The parameter list there must not contain same values! */
@@ -69,16 +61,17 @@ public class GlobPlot extends SkeletalExecutable<GlobPlot>
 		// super.setInput("");
 	}
 
+	@Override
 	@SuppressWarnings("unchecked")
-	public Map<String, Set<Score>> getResults(String workDirectory)
+	public ScoreManager getResults(String workDirectory)
 			throws ResultNotAvailableException {
 
 		InputStream inStream = null;
-		Map<String, Set<Score>> results = null;
+		ScoreManager results = null;
 		// How about getting ranges?
 		try {
 			inStream = new FileInputStream(new File(workDirectory, getOutput()));
-			results = SequenceUtil.removeSequences(SequenceUtil
+			results = ScoreManager.newInstance(SequenceUtil
 					.readGlobPlot(inStream));
 			inStream.close();
 		} catch (FileNotFoundException e) {
@@ -105,41 +98,10 @@ public class GlobPlot extends SkeletalExecutable<GlobPlot>
 		return this;
 	}
 
+	@SuppressWarnings("unchecked")
 	@Override
-	public Limit<GlobPlot> getLimit(String presetName) {
-		if (limits == null) {
-			limits = getLimits();
-		}
-
-		Limit<GlobPlot> 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<GlobPlot> 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<GlobPlot> getType() {
+		return (Class<GlobPlot>) this.getClass();
 	}
 
 }