Switch JpredWS from SequenceAnnotation to MsaWS

[jabaws.git] / runner / compbio / runner / predictors / Jpred.java

diff --git a/runner/compbio/runner/predictors/Jpred.java b/runner/compbio/runner/predictors/Jpred.java
index 7c27a37..12f9487 100644 (file)
--- a/runner/compbio/runner/predictors/Jpred.java
+++ b/runner/compbio/runner/predictors/Jpred.java
@@ -28,16 +28,14 @@ import java.util.List;
 \r
 import org.apache.log4j.Logger;\r
 \r
-import compbio.data.sequence.Alignment;\r
+import compbio.data.sequence.JpredAlignment;\r
 import compbio.data.sequence.AlignmentMetadata;\r
 import compbio.data.sequence.Program;\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
 import compbio.engine.client.SkeletalExecutable;\r
 import compbio.metadata.ResultNotAvailableException;\r
-import compbio.runner.Util;\r
 \r
 /**\r
  * Command line\r
@@ -62,16 +60,18 @@ public class Jpred extends SkeletalExecutable<Jpred> {
 \r
        public Jpred() {\r
                addParameters(Arrays.asList("-logfile " + STAT_FILE));\r
+               addParameters(Arrays.asList("-jabaws"));\r
        }\r
 \r
        // HashMap<Method, float[]>\r
+       @SuppressWarnings("unchecked")\r
        @Override\r
-       public Alignment getResults(String workDirectory)\r
+       public JpredAlignment getResults(String workDirectory)\r
                        throws ResultNotAvailableException {\r
-               Alignment annotations = null;\r
+               JpredAlignment annotations = null;\r
                try {\r
                        InputStream inStream = new FileInputStream(new File(workDirectory, getOutput()));\r
-                       annotations = new Alignment(SequenceUtil.readJpredFile(inStream), new AlignmentMetadata(Program.Jpred, '-'));\r
+                       annotations = new JpredAlignment(SequenceUtil.readJpredFile(inStream), new AlignmentMetadata(Program.Jpred, '-'));\r
                } catch (FileNotFoundException e) {\r
                        log.error(e.getMessage(), e.getCause());\r
                        throw new ResultNotAvailableException(e);\r