Remove Annotated and MuptiAnnotated Sequence use Score instead

[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 c6b278f..716859f 100644 (file)
--- a/runner/compbio/runner/disorder/Disembl.java
+++ b/runner/compbio/runner/disorder/Disembl.java
@@ -14,14 +14,12 @@
 \r
 package compbio.runner.disorder;\r
 \r
-import java.io.FileNotFoundException;\r
-import java.io.IOException;\r
 import java.util.Arrays;\r
+import java.util.Map;\r
 \r
 import org.apache.log4j.Logger;\r
 \r
-import compbio.data.sequence.Alignment;\r
-import compbio.data.sequence.UnknownFileFormatException;\r
+import compbio.data.sequence.Score;\r
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.PipedExecutable;\r
 import compbio.engine.client.SkeletalExecutable;\r
@@ -46,8 +44,9 @@ import compbio.runner.Util;
  *      print 'Mode: "default"(nothing) or "scores" which will give scores per\r
  *      residue in TAB separated format'\r
  */\r
-public class Disembl extends SkeletalExecutable<Disembl> implements\r
-               PipedExecutable<Disembl> {\r
+public class Disembl extends SkeletalExecutable<Disembl>\r
+               implements\r
+                       PipedExecutable<Disembl> {\r
 \r
        private static Logger log = Logger.getLogger(Disembl.class);\r
 \r
@@ -65,23 +64,10 @@ public class Disembl extends SkeletalExecutable<Disembl> implements
        }\r
 \r
        @SuppressWarnings("unchecked")\r
-       public Alignment getResults(String workDirectory)\r
+       public Map<String, Score> getResults(String workDirectory)\r
                        throws ResultNotAvailableException {\r
-               try {\r
-                       return Util.readClustalFile(workDirectory, getOutput());\r
-               } catch (FileNotFoundException e) {\r
-                       log.error(e.getMessage(), e.getCause());\r
-                       throw new ResultNotAvailableException(e);\r
-               } catch (IOException e) {\r
-                       log.error(e.getMessage(), e.getCause());\r
-                       throw new ResultNotAvailableException(e);\r
-               } catch (UnknownFileFormatException e) {\r
-                       log.error(e.getMessage(), e.getCause());\r
-                       throw new ResultNotAvailableException(e);\r
-               } catch (NullPointerException e) {\r
-                       log.error(e.getMessage(), e.getCause());\r
-                       throw new ResultNotAvailableException(e);\r
-               }\r
+\r
+               return null;\r
        }\r
 \r
        @Override\r