Alifold results are now parsed and stored in a ScoreManager object

[jabaws.git] / runner / compbio / runner / structure / RNAalifold.java

diff --git a/runner/compbio/runner/structure/RNAalifold.java b/runner/compbio/runner/structure/RNAalifold.java
index 3871ea9..0e9e20f 100644 (file)
--- a/runner/compbio/runner/structure/RNAalifold.java
+++ b/runner/compbio/runner/structure/RNAalifold.java
@@ -6,16 +6,14 @@ import java.io.IOException;
 import java.util.Arrays;
 import java.util.List;
 
-//imports for filereader method
-import java.io.FileReader;
-import java.io.BufferedReader;
-import java.io.File;
+
 
 
 
 import org.apache.log4j.Logger;
 
-import compbio.data.sequence.RNAstruct;
+import compbio.data.sequence.ScoreManager;
+import compbio.data.sequence.RNAStruct;
 import compbio.data.sequence.UnknownFileFormatException;
 import compbio.engine.client.PipedExecutable;
 import compbio.engine.client.SkeletalExecutable;
@@ -61,11 +59,10 @@ public class RNAalifold extends SkeletalExecutable<RNAalifold>
        @SuppressWarnings("unchecked")
        @Override
        // PlaceHolder method
-       public RNAstruct getResults(String workDirectory)
+       public ScoreManager getResults(String workDirectory)
                        throws ResultNotAvailableException {
                try {
-                       // System.out.println("Specialread " + Util.readRNAStructFile(workDirectory, getOutput()).toString());
-                       return Util.readRNAStructFile(workDirectory, getOutput());
+                       return Util.readRNAStruct(workDirectory, getOutput());
                        
                } catch (FileNotFoundException e) {
                        log.error(e.getMessage(), e.getCause());