Merge branch 'JABAWS_Release_2_5' into develop

[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 43a0975..918918e 100644 (file)
--- a/runner/compbio/runner/structure/RNAalifold.java
+++ b/runner/compbio/runner/structure/RNAalifold.java
@@ -1,60 +1,64 @@
-package compbio.runner.structure;
-
-import java.util.Scanner; //temp
-import java.io.File; //temp
-
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import compbio.data.sequence.Alignment;
-import compbio.data.sequence.UnknownFileFormatException;
-import compbio.engine.client.SkeletalExecutable;
-import compbio.metadata.ResultNotAvailableException;
-import compbio.runner.Util;
-
-public class RNAalifold extends SkeletalExecutable<RNAalifold> {
-       
-       @SuppressWarnings("unchecked")
-       @Override
-       //temp
-       public String getResults(String resultFile)
-                       throws ResultNotAvailableException {
-               Scanner s;
-               try {
-                       System.out.println("testfrom RNAalifold.getResults");
-                       s = new Scanner(new File(resultFile));
-                       System.out.println(s.nextLine());
-                       return "null";
-               } catch (FileNotFoundException e) {
-                       System.out.println("file not found");
-                       throw new ResultNotAvailableException(e);
-               } 
-       }
-
-       
-       @Override
-       public RNAalifold setOutput(String outFile) {
-               System.out.println("Set ouput file: " + outFile.toString());
-               super.setOutput(outFile);
-               return this;
-       }
-       
-       @Override
-       public RNAalifold setInput(String inFile) {
-               System.out.println("Set input file: " + inFile.toString());
-               super.setInput(inFile);
-               return this;
-       }
-       
-       @SuppressWarnings("unchecked")
-       @Override
-       public Class<RNAalifold> getType() {
-               return (Class<RNAalifold>) this.getClass();
-       }
-       
-       
-}
+package compbio.runner.structure;\r
+\r
+\r
+import java.io.FileNotFoundException;\r
+import java.io.IOException;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import compbio.data.sequence.RNAStructScoreManager;\r
+import compbio.engine.client.PipedExecutable;\r
+import compbio.engine.client.SkeletalExecutable;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.runner.Util;\r
+\r
+public class RNAalifold extends SkeletalExecutable<RNAalifold> \r
+               implements PipedExecutable<RNAalifold> {\r
+       \r
+       \r
+       private static Logger log = Logger.getLogger(RNAalifold.class);\r
+\r
+       // May not be necessary as defult is "<space>" but still dont know\r
+       // How to deal with different key value separators for different params\r
+       public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
+       \r
+       public RNAalifold() {\r
+               super(KEY_VALUE_SEPARATOR);\r
+       }\r
+       \r
+       @Override\r
+       public RNAalifold setOutput(String outFile) {\r
+               super.setOutput(outFile);\r
+               return this;\r
+       }\r
+       \r
+       @Override\r
+       public RNAalifold setInput(String inFile) {\r
+               cbuilder.setLast(inFile);\r
+               super.setInput(inFile);\r
+               return this;\r
+       }\r
+       \r
+       @SuppressWarnings("unchecked")\r
+       @Override\r
+       public Class<RNAalifold> getType() {\r
+               return (Class<RNAalifold>) this.getClass();\r
+       }\r
+       \r
+       @SuppressWarnings("unchecked")\r
+       @Override\r
+       public RNAStructScoreManager getResults(String workDirectory)\r
+                       throws ResultNotAvailableException {\r
+               try {\r
+                       return Util.readRNAStruct(workDirectory, getOutput());\r
+                       \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
+               }\r
+       }\r
+\r
+}\r