Merge branch 'jims_annotate3d_update' into menard_finalsep2012

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

diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index 178caad..c020d99 100644 (file)
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -30,15 +30,8 @@ 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
@@ -94,14 +87,13 @@ import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  * 
  */
 public class TCoffeeScoreFile extends AlignFile {
-       
-  public TCoffeeScoreFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  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 +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()
@@ -401,6 +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.
    * 
@@ -460,6 +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);
@@ -548,7 +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;