Replace Map<String, HashSet<Score>> with ScoreManager and ScoreHolder classes to...

[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 f43db89..fd76e55 100644 (file)
--- a/runner/compbio/runner/conservation/AACon.java
+++ b/runner/compbio/runner/conservation/AACon.java
@@ -20,13 +20,12 @@ import java.io.FileNotFoundException;
 import java.io.IOException;\r
 import java.io.InputStream;\r
 import java.util.Arrays;\r
-import java.util.HashSet;\r
 import java.util.List;\r
 \r
 import org.apache.log4j.Logger;\r
 \r
 import compbio.data.sequence.SMERFSConstraints;\r
-import compbio.data.sequence.Score;\r
+import compbio.data.sequence.ScoreManager;\r
 import compbio.data.sequence.SequenceUtil;\r
 import compbio.engine.client.CommandBuilder;\r
 import compbio.engine.client.Executable;\r
@@ -72,13 +71,14 @@ public class AACon extends SkeletalExecutable<AACon> {
        }\r
        // HashMap<Method, float[]>\r
        @Override\r
-       public HashSet<Score> getResults(String workDirectory)\r
+       public ScoreManager getResults(String workDirectory)\r
                        throws ResultNotAvailableException {\r
-               HashSet<Score> annotations = null;\r
+               ScoreManager annotations = null;\r
                try {\r
                        InputStream inStream = new FileInputStream(new File(workDirectory,\r
                                        getOutput()));\r
-                       annotations = SequenceUtil.readAAConResults(inStream);\r
+                       annotations = ScoreManager.newInstanceSingleSequence(SequenceUtil\r
+                                       .readAAConResults(inStream));\r
                        inStream.close();\r
                } catch (FileNotFoundException e) {\r
                        log.error(e.getMessage(), e.getCause());\r