X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=runner%2Fcompbio%2Frunner%2Fstructure%2FRNAalifold.java;h=c0a50fe73fc1d6ae334cca147bd1f91a511a4bc5;hb=e6227b3fc0bb5abdf275bb24a87607b0555bce10;hp=52a784c0d5e7b7e8a85704d9a4485fe120669576;hpb=9072bd850138bedbd005509e5b14bb5e104574b4;p=jabaws.git

diff --git a/runner/compbio/runner/structure/RNAalifold.java b/runner/compbio/runner/structure/RNAalifold.java
index 52a784c..c0a50fe 100644
--- a/runner/compbio/runner/structure/RNAalifold.java
+++ b/runner/compbio/runner/structure/RNAalifold.java
@@ -1,117 +1,61 @@
-package compbio.runner.structure;
-
-
-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.RNAstruct;
-import compbio.data.sequence.UnknownFileFormatException;
-import compbio.engine.client.PipedExecutable;
-import compbio.engine.client.SkeletalExecutable;
-import compbio.metadata.ResultNotAvailableException;
-import compbio.runner.Util;
-
-
-import compbio.engine.client.CommandBuilder;
-
-public class RNAalifold extends SkeletalExecutable<RNAalifold> 
-		implements PipedExecutable<RNAalifold> {
-	
-	
-	private static Logger log = Logger.getLogger(RNAalifold.class);
-
-	// May not be necessary as defult is "<space>" but still dont know
-	// How to deal with different key value separators for different params
-	public static final String KEY_VALUE_SEPARATOR = " ";
-	
-	public RNAalifold() {
-		super(KEY_VALUE_SEPARATOR);
-	}
-	
-	@Override
-	public RNAalifold setOutput(String outFile) {
-		super.setOutput(outFile);
-		return this;
-	}
-	
-	@Override
-	public RNAalifold setInput(String inFile) {
-		cbuilder.setLast(inFile);
-		super.setInput(inFile);
-		return this;
-	}
-	
-	@SuppressWarnings("unchecked")
-	@Override
-	public Class<RNAalifold> getType() {
-		return (Class<RNAalifold>) this.getClass();
-	}
-	
-	@SuppressWarnings("unchecked")
-	@Override
-	// PlaceHolder method
-	public String getResults(String workDirectory)
-			throws ResultNotAvailableException {
-		try {
-			return Util.readRNAStruct(workDirectory, getOutput());
-			
-		} catch (FileNotFoundException e) {
-			log.error(e.getMessage(), e.getCause());
-			throw new ResultNotAvailableException(e);
-		} catch (IOException e) {
-			log.error(e.getMessage(), e.getCause());
-			throw new ResultNotAvailableException(e);
-		}
-	}
-
-
-	// the new currently used methods for reading are found in 
-	// - compbio.data.sequence.SequenceUtil and 
-	// - compbio.runner.Util
-	
-	// Simple and generic methods for reading a whole file
-//	private static String readRNAStruct(String workDirectory,
-//			String structFile) throws IOException, FileNotFoundException {
-//		assert !compbio.util.Util.isEmpty(workDirectory);
-//		assert !compbio.util.Util.isEmpty(structFile);
-//		File sfile = new File(compbio.engine.client.Util.getFullPath(
-//				workDirectory, structFile));
-//		log.trace("RNAALIFOLD OUTPUT FILE PATH: " + sfile.getAbsolutePath());
-//		if(!(sfile.exists() && sfile.length() > 0)) {
-//			throw new FileNotFoundException("Result for the jobId "
-//					+ workDirectory + "with file name " + structFile
-//					+ " is not found!");
-//		}
-//		return readFile(sfile);
-//	}
-//	
-//	private static BufferedReader input;
-//	public static String readFile(File inputFile) throws 
-//			FileNotFoundException, IOException {
-//		
-//		input	= new BufferedReader(new FileReader(inputFile));
-//		
-//		String file = new String();
-//		String line = new String();
-//		
-//		while (true) {
-//			line = input.readLine();
-//			
-//			if (line != null) {
-//				file = file + line + "\r\n";
-//			} else break;
-//		}
-//		// Close file
-//		input.close();
-//		return file;
-//	}
-	
-}
+package compbio.runner.structure;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+
+import org.apache.log4j.Logger;
+
+import compbio.data.sequence.RNAStructScoreManager;
+import compbio.engine.client.PipedExecutable;
+import compbio.engine.client.SkeletalExecutable;
+import compbio.metadata.ResultNotAvailableException;
+import compbio.runner.RunnerUtil;
+
+public class RNAalifold extends SkeletalExecutable<RNAalifold> 
+		implements PipedExecutable<RNAalifold> {
+
+	private static Logger log = Logger.getLogger(RNAalifold.class);
+
+	// May not be necessary as defult is "<space>" but still dont know
+	// How to deal with different key value separators for different params
+	public static final String KEY_VALUE_SEPARATOR = " ";
+	
+	public RNAalifold() {
+		super(KEY_VALUE_SEPARATOR);
+	}
+	
+	@Override
+	public RNAalifold setOutput(String outFile) {
+		super.setOutput(outFile);
+		return this;
+	}
+	
+	@Override
+	public RNAalifold setInput(String inFile) {
+		cbuilder.setLast(inFile);
+		super.setInput(inFile);
+		return this;
+	}
+	
+	@SuppressWarnings("unchecked")
+	@Override
+	public Class<RNAalifold> getType() {
+		return (Class<RNAalifold>) this.getClass();
+	}
+	
+	@SuppressWarnings("unchecked")
+	@Override
+	public RNAStructScoreManager getResults(String workDirectory)
+			throws ResultNotAvailableException {
+		try {
+			return RunnerUtil.readRNAStruct(workDirectory, getOutput());
+		} catch (FileNotFoundException e) {
+			log.error(e.getMessage(), e.getCause());
+			throw new ResultNotAvailableException(e);
+		} catch (IOException e) {
+			log.error(e.getMessage(), e.getCause());
+			throw new ResultNotAvailableException(e);
+		}
+	}
+
+}