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

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