X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=runner%2Fcompbio%2Frunner%2Fdisorder%2FDisembl.java;h=716859f27d5dcf276195fc714d699970a5bb125f;hb=8033a51860de2200a54e64add0809d6780f5b092;hp=c6b278ff0b1322319e2e3a2fb3dc9b070efb7c0c;hpb=b413eee53fa3cc22a6bd4e03c9ac64bf26b7c834;p=jabaws.git

diff --git a/runner/compbio/runner/disorder/Disembl.java b/runner/compbio/runner/disorder/Disembl.java
index c6b278f..716859f 100644
--- a/runner/compbio/runner/disorder/Disembl.java
+++ b/runner/compbio/runner/disorder/Disembl.java
@@ -14,14 +14,12 @@
 
 package compbio.runner.disorder;
 
-import java.io.FileNotFoundException;
-import java.io.IOException;
 import java.util.Arrays;
+import java.util.Map;
 
 import org.apache.log4j.Logger;
 
-import compbio.data.sequence.Alignment;
-import compbio.data.sequence.UnknownFileFormatException;
+import compbio.data.sequence.Score;
 import compbio.engine.client.Executable;
 import compbio.engine.client.PipedExecutable;
 import compbio.engine.client.SkeletalExecutable;
@@ -46,8 +44,9 @@ import compbio.runner.Util;
  *      print 'Mode: "default"(nothing) or "scores" which will give scores per
  *      residue in TAB separated format'
  */
-public class Disembl extends SkeletalExecutable<Disembl> implements
-		PipedExecutable<Disembl> {
+public class Disembl extends SkeletalExecutable<Disembl>
+		implements
+			PipedExecutable<Disembl> {
 
 	private static Logger log = Logger.getLogger(Disembl.class);
 
@@ -65,23 +64,10 @@ public class Disembl extends SkeletalExecutable<Disembl> implements
 	}
 
 	@SuppressWarnings("unchecked")
-	public Alignment getResults(String workDirectory)
+	public Map<String, Score> getResults(String workDirectory)
 			throws ResultNotAvailableException {
-		try {
-			return Util.readClustalFile(workDirectory, getOutput());
-		} catch (FileNotFoundException e) {
-			log.error(e.getMessage(), e.getCause());
-			throw new ResultNotAvailableException(e);
-		} catch (IOException e) {
-			log.error(e.getMessage(), e.getCause());
-			throw new ResultNotAvailableException(e);
-		} catch (UnknownFileFormatException e) {
-			log.error(e.getMessage(), e.getCause());
-			throw new ResultNotAvailableException(e);
-		} catch (NullPointerException e) {
-			log.error(e.getMessage(), e.getCause());
-			throw new ResultNotAvailableException(e);
-		}
+
+		return null;
 	}
 
 	@Override