X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FTCoffeeScoreFile.java;h=07d7be4c1cea172765e32a420837b6a2501def56;hb=9fc1c4d049a16cccb933e80b5be07ec36e6bda7f;hp=178caad7b56e64fc785fe97fa730a306394389be;hpb=28787d9646cca5dd77190930f59b7ff32cf995b4;p=jalview.git

diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index 178caad..07d7be4 100644
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -1,19 +1,22 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ * 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/>.
+ * 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;
 
@@ -30,15 +33,8 @@ import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
-
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 /**
  * A file parse for T-Coffee score ascii format. This file contains the
@@ -93,15 +89,15 @@ import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  * @author Paolo Di Tommaso
  * 
  */
-public class TCoffeeScoreFile extends AlignFile {
-	
-  public TCoffeeScoreFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+public class TCoffeeScoreFile extends AlignFile
+{
+  public TCoffeeScoreFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
 
   }
 
-  public TCoffeeScoreFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public TCoffeeScoreFile(FileParse source) throws IOException
   {
     super(source);
   }
@@ -146,7 +142,7 @@ 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()
@@ -401,6 +397,9 @@ 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.
    * 
@@ -460,6 +459,12 @@ 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);
@@ -520,8 +525,7 @@ public class TCoffeeScoreFile extends AlignFile {
   /**
    * TCOFFEE score colourscheme
    */
-  static final Color[] colors =
-  { new Color(102, 102, 255), // #6666FF
+  static final Color[] colors = { new Color(102, 102, 255), // #6666FF
       new Color(0, 255, 0), // #00FF00
       new Color(102, 255, 0), // #66FF00
       new Color(204, 255, 0), // #CCFF00
@@ -548,7 +552,11 @@ 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;