AAConWS is working

[jabaws.git] / runner / compbio / runner / conservation / AACon.java

diff --git a/runner/compbio/runner/conservation/AACon.java b/runner/compbio/runner/conservation/AACon.java
index 5a1d752..ce4d293 100644 (file)
--- a/runner/compbio/runner/conservation/AACon.java
+++ b/runner/compbio/runner/conservation/AACon.java
@@ -20,12 +20,13 @@ import java.io.FileNotFoundException;
 import java.io.IOException;\r
 import java.io.InputStream;\r
 import java.util.Arrays;\r
-import java.util.HashMap;\r
+import java.util.HashSet;\r
 import java.util.List;\r
 \r
 import org.apache.log4j.Logger;\r
 \r
-import compbio.conservation.Method;\r
+import compbio.data.sequence.Score;\r
+import compbio.data.sequence.SequenceUtil;\r
 import compbio.engine.client.CommandBuilder;\r
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.SkeletalExecutable;\r
@@ -66,13 +67,13 @@ public class AACon extends SkeletalExecutable<AACon> {
        }\r
        // HashMap<Method, float[]>\r
        @Override\r
-       public HashMap<Method, float[]> getResults(String workDirectory)\r
+       public HashSet<Score> getResults(String workDirectory)\r
                        throws ResultNotAvailableException {\r
-               // MultiAnnotatedSequence<Method> annotations = null;\r
+               HashSet<Score> annotations = null;\r
                try {\r
                        InputStream inStream = new FileInputStream(new File(workDirectory,\r
                                        getOutput()));\r
-                       // annotations = SequenceUtil.readResults(inStream);\r
+                       annotations = SequenceUtil.readAAConResults(inStream);\r
                        inStream.close();\r
                } catch (FileNotFoundException e) {\r
                        log.error(e.getMessage(), e.getCause());\r
@@ -84,7 +85,7 @@ public class AACon extends SkeletalExecutable<AACon> {
                        log.error(e.getMessage(), e.getCause());\r
                        throw new ResultNotAvailableException(e);\r
                }\r
-               return null;\r
+               return annotations;\r
        }\r
 \r
        private static String getLibPath() {\r