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

[jabaws.git] / runner / compbio / runner / disorder / Disembl.java

diff --git a/runner/compbio/runner/disorder/Disembl.java b/runner/compbio/runner/disorder/Disembl.java
index 616b552..6b014ba 100644 (file)
--- a/runner/compbio/runner/disorder/Disembl.java
+++ b/runner/compbio/runner/disorder/Disembl.java
@@ -19,12 +19,10 @@ import java.io.FileInputStream;
 import java.io.FileNotFoundException;\r
 import java.io.IOException;\r
 import java.io.InputStream;\r
-import java.util.HashMap;\r
-import java.util.HashSet;\r
 \r
 import org.apache.log4j.Logger;\r
 \r
-import compbio.data.sequence.Score;\r
+import compbio.data.sequence.ScoreManager;\r
 import compbio.data.sequence.SequenceUtil;\r
 import compbio.data.sequence.UnknownFileFormatException;\r
 import compbio.engine.client.Executable;\r
@@ -85,15 +83,15 @@ public class Disembl extends SkeletalExecutable<Disembl>
 \r
        @SuppressWarnings("unchecked")\r
        @Override\r
-       public HashMap<String, HashSet<Score>> getResults(String workDirectory)\r
+       public ScoreManager getResults(String workDirectory)\r
                        throws ResultNotAvailableException {\r
 \r
                InputStream inStream = null;\r
-               HashMap<String, HashSet<Score>> results = null;\r
+               ScoreManager results = null;\r
 \r
                try {\r
                        inStream = new FileInputStream(new File(workDirectory, getOutput()));\r
-                       results = SequenceUtil.removeSequences(SequenceUtil\r
+                       results = ScoreManager.newInstance(SequenceUtil\r
                                        .readDisembl(inStream));\r
                        inStream.close();\r
                } catch (FileNotFoundException e) {\r
@@ -112,7 +110,6 @@ public class Disembl extends SkeletalExecutable<Disembl>
                log.trace("DRESULTS: " + results);\r
                return results;\r
        }\r
-\r
        @Override\r
        public Disembl setInput(String inFile) {\r
                super.setInput(inFile);\r