From 89f3a6dd9c54aa2c178d45db4d36c781ab5ae2a1 Mon Sep 17 00:00:00 2001
From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Wed, 24 Nov 2010 13:07:42 +0000
Subject: [PATCH] More work on AAConWS not finished yet!

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3383 e3abac25-378b-4346-85de-24260fe3988d
---
 runner/compbio/runner/conservation/AACon.java |   12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/runner/compbio/runner/conservation/AACon.java b/runner/compbio/runner/conservation/AACon.java
index 5d20d5d..f514e24 100644
--- a/runner/compbio/runner/conservation/AACon.java
+++ b/runner/compbio/runner/conservation/AACon.java
@@ -21,12 +21,10 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.util.Arrays;
 import java.util.List;
+import java.util.Map;
 
 import org.apache.log4j.Logger;
 
-import compbio.conservation.Method;
-import compbio.conservation.ResultReader;
-import compbio.data.sequence.MultiAnnotatedSequence;
 import compbio.engine.client.CommandBuilder;
 import compbio.engine.client.Executable;
 import compbio.engine.client.SkeletalExecutable;
@@ -68,13 +66,13 @@ public class AACon extends SkeletalExecutable<AACon> {
 
 	@SuppressWarnings("unchecked")
 	@Override
-	public MultiAnnotatedSequence<Method> getResults(String workDirectory)
+	public Map getResults(String workDirectory)
 			throws ResultNotAvailableException {
-		MultiAnnotatedSequence<Method> annotations = null;
+		// MultiAnnotatedSequence<Method> annotations = null;
 		try {
 			InputStream inStream = new FileInputStream(new File(workDirectory,
 					getOutput()));
-			annotations = ResultReader.readResults(inStream);
+			// annotations = SequenceUtil.readResults(inStream);
 			inStream.close();
 		} catch (FileNotFoundException e) {
 			log.error(e.getMessage(), e.getCause());
@@ -86,7 +84,7 @@ public class AACon extends SkeletalExecutable<AACon> {
 			log.error(e.getMessage(), e.getCause());
 			throw new ResultNotAvailableException(e);
 		}
-		return annotations;
+		return null;
 	}
 
 	private static String getLibPath() {
-- 
1.7.10.2