X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FTCoffeeScoreFile.java;h=c020d990d3ed0de148623cda879bbed1b6312438;hb=ac1d5169b86af13d4f06152a09cb125309ddf76f;hp=ac5f8d6096a6f1a59ebf42b98da468ab657d9ea9;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git

diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index ac5f8d6..c020d99 100644
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -1,3 +1,20 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
 package jalview.io;
 
 import jalview.analysis.SequenceIdMatcher;
@@ -7,17 +24,14 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
 import java.io.IOException;
-import java.io.Reader;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 /**
  * A file parse for T-Coffee score ascii format. This file contains the
@@ -72,9 +86,7 @@ import java.util.Map;
  * @author Paolo Di Tommaso
  * 
  */
-public class TCoffeeScoreFile extends AlignFile
-{
-
+public class TCoffeeScoreFile extends AlignFile {
   public TCoffeeScoreFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
@@ -126,7 +138,7 @@ public class TCoffeeScoreFile extends AlignFile
 
   /**
    * @return The 'width' of the score matrix i.e. the number of columns. Since
-   *         teh score value are supposd to be calculated for an 'aligned' MSA,
+   *         the score value are supposed to be calculated for an 'aligned' MSA,
    *         all the entries have to have the same width.
    */
   public int getWidth()
@@ -381,6 +393,8 @@ public class TCoffeeScoreFile extends AlignFile
     }
   }
 
+  static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern.compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
+  
   /**
    * Read a scores block ihe provided stream.
    * 
@@ -440,6 +454,11 @@ public class TCoffeeScoreFile extends AlignFile
       String id = line.substring(0, p).trim();
       String val = line.substring(p + 1).trim();
 
+      Matcher m = SCORES_WITH_RESIDUE_NUMS.matcher(val);
+      if( m.matches() ) {
+    	  val = m.group(1);
+      }
+      
       result.items.put(id, val);
 
     } while ((line = reader.nextLine()) != null);
@@ -528,7 +547,8 @@ public class TCoffeeScoreFile extends AlignFile
   {
     if (al.getHeight() != getHeight() || al.getWidth() != getWidth())
     {
-      warningMessage = "Alignment shape does not match T-Coffee score file shape.";
+      String info = String.format("align w: %s, h: %s; score: w: %s; h: %s ", al.getWidth(), al.getHeight(), getWidth(), getHeight() );
+      warningMessage = "Alignment shape does not match T-Coffee score file shape -- " + info;
       return false;
     }
     boolean added = false;