X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=runner%2Fcompbio%2Frunner%2FUtil.java;h=6f0ec09bc576e9475b53ef88e849460be04e68ff;hb=4b647613e686c4edffd44702d86662c6facb2d5a;hp=c6cb33fc6b71f69dc0ee00d94e00071022725648;hpb=9072bd850138bedbd005509e5b14bb5e104574b4;p=jabaws.git

diff --git a/runner/compbio/runner/Util.java b/runner/compbio/runner/Util.java
index c6cb33f..6f0ec09 100644
--- a/runner/compbio/runner/Util.java
+++ b/runner/compbio/runner/Util.java
@@ -25,16 +25,30 @@ import java.io.BufferedReader;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
+import java.util.Arrays;
 import java.util.List;
+import java.util.ArrayList;
 import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
+import java.util.TreeMap;
+import java.util.regex.Pattern;
+import java.util.regex.Matcher;
+import java.util.Scanner;
+
+
+
 
 import org.apache.log4j.Logger;
 
 import compbio.data.sequence.Alignment;
 import compbio.data.sequence.ClustalAlignmentUtil;
 import compbio.data.sequence.FastaSequence;
-import compbio.data.sequence.RNAstruct;
+import compbio.data.sequence.RNAStructScoreManager;
 import compbio.data.sequence.Score;
+import compbio.data.sequence.ScoreManager;
+import compbio.data.sequence.Range;
+import compbio.data.sequence.RNAStructReader;
 import compbio.data.sequence.SequenceUtil;
 import compbio.data.sequence.UnknownFileFormatException;
 import compbio.engine.client.ConfExecutable;
@@ -152,38 +166,39 @@ public final class Util {
 						+ e.getLocalizedMessage(), e);
 		}
 	}
+
 	
-	// OUT OF USE
-	
-//	public static final RNAstruct readRNAStructFile(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));
-//		if(!(sfile.exists() && sfile.length() > 0)) {
-//			throw new FileNotFoundException("Result for the jobId "
-//					+ workDirectory + "with file name " + structFile
-//					+ " is not found!");
-//		}
-//		return compbio.data.sequence.SequenceUtil.readRNAalifoldResults(
-//				new FileInputStream(sfile));
-//	}
-	
-	public static String readRNAStruct(String workDirectory,
+	public static RNAStructScoreManager 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(
+		// The stdout from RNAalifold
+		File sFile = new File(compbio.engine.client.Util.getFullPath(
 				workDirectory, structFile));
-		if(!(sfile.exists() && sfile.length() > 0)) {
+		// Base pair probability matrix (-p option)
+		File aliFile = new File(compbio.engine.client.Util.getFullPath(
+				workDirectory, "alifold.out"));
+		// Check that stdout file exists
+		if(!(sFile.exists() && sFile.length() > 0)) {
 			throw new FileNotFoundException("Result for the jobId "
 					+ workDirectory + "with file name " + structFile
 					+ " is not found!");
 		}
-		return readFile(sfile);
+		// Check that base pair probability file exists
+		if(!aliFile.exists()) {
+			log.warn("The file alifold.out is not found for the jobId "
+					+ workDirectory + "Is the -p or --MEA option not specified?");
+			return RNAStructReader.readRNAStructStream(new FileInputStream(sFile));
+			
+		} else {
+			return RNAStructReader.readRNAStructStream(new FileInputStream(sFile), 
+					new FileInputStream(aliFile));
+		}
 	}
 	
+
+	
 	public static String readFile(File inputFile) throws 
 			FileNotFoundException, IOException {
 
@@ -203,7 +218,6 @@ public final class Util {
 		input.close();
 		return file;
 	}
-	
-	
-
 }
+
+