JAL-1503 update version in GPL header

[jalview.git] / src / jalview / io / TCoffeeScoreFile.java

diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index ac5f8d6..274f532 100644 (file)
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io;
 
 import jalview.analysis.SequenceIdMatcher;
@@ -7,17 +25,14 @@ 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
@@ -126,7 +141,7 @@ 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 +396,8 @@ 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 +457,11 @@ 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 +550,8 @@ 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;