Fixed T-Coffee file scores parser to support extended format including residue numbers

diff --git a/.gitignore b/.gitignore
index f256683..3407192 100644 (file)
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,4 @@
+.project
 /dist
 /classes
+.externalToolBuilders/Jalview Release indices [Builder].launch

diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index 42a2caa..ad5f52a 100644 (file)
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -30,6 +30,8 @@ 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
@@ -138,7 +140,7 @@ 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()
@@ -393,6 +395,8 @@ 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.
    * 
@@ -452,6 +456,11 @@ 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);
@@ -540,7 +549,8 @@ 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;

diff --git a/test/jalview/io/TCoffeeScoreFileTest.java b/test/jalview/io/TCoffeeScoreFileTest.java
index 7308446..3147054 100644 (file)
--- a/test/jalview/io/TCoffeeScoreFileTest.java
+++ b/test/jalview/io/TCoffeeScoreFileTest.java
@@ -21,12 +21,9 @@ import static org.junit.Assert.*;
 import jalview.io.TCoffeeScoreFile.Block;
 import jalview.io.TCoffeeScoreFile.Header;
 
-import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileNotFoundException;
-import java.io.FileReader;
 import java.io.IOException;
-import java.io.StringReader;
 import java.util.List;
 
 import org.junit.Test;
@@ -34,14 +31,15 @@ import org.junit.Test;
 public class TCoffeeScoreFileTest {
 
        final static File SCORE_FILE = new File("test/jalview/io/tcoffee.score_ascii");
-        final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
+    final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
        
        @Test
        public void testReadHeader() throws IOException, FileNotFoundException {
 
-               TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
-               assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
-               Header header = scoreFile.header;
+           TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
+           assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
+               
+           Header header = scoreFile.header;
                assertNotNull(header);
                assertEquals( "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)", header.head );
                assertEquals( 90, header.score );
@@ -60,9 +58,10 @@ public class TCoffeeScoreFileTest {
        @Test
        public void testWrongFile() {
            try {
-               TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
-               assertFalse(result.isValid());
-           } catch (IOException x)
+                       TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
+                       assertFalse(result.isValid());
+           } 
+           catch (IOException x)
            {
              assertTrue("File not found exception thrown",x instanceof FileNotFoundException);
            }
@@ -173,6 +172,15 @@ public class TCoffeeScoreFileTest {
                
        } 
        
+       @Test
+       public void testHeightAndWidthWithResidueNumbers() throws IOException {
+               String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
+               TCoffeeScoreFile result = new TCoffeeScoreFile(file, FormatAdapter.FILE);
+               assertTrue(result.isValid());
+               assertEquals( 5, result.getHeight() );
+               assertEquals( 84, result.getWidth() );
+       }       
+       
        
        
 }

diff --git a/test/jalview/io/tcoffee.score_ascii_with_residue_numbers b/test/jalview/io/tcoffee.score_ascii_with_residue_numbers
new file mode 100644 (file)
index 0000000..ec518e3
--- /dev/null
+++ b/test/jalview/io/tcoffee.score_ascii_with_residue_numbers
@@ -0,0 +1,30 @@
+T-COFFEE, Version_9.01 (2011-10-13 19:18:54 - Revision 1115 - Build 6)
+Cedric Notredame 
+CPU TIME:0 sec.
+SCORE=45
+*
+ BAD AVG GOOD
+*
+1aboA   :  50
+1ycsB   :  50
+1pht    :  42
+1vie    :  41
+1ihvA   :  39
+cons    :  45
+
+1aboA       1 65-556---666667666555555665566-------66666-------54445665--5555-55556777665---   54 
+1ycsB       1 653556---665667776555666666667-------6666544-----44455565--5555-55557766655---   57 
+1pht        1 764567---765656566656666665555444445677776554455555544666556665-67667876655333   74 
+1vie        1 44-----------344--44455555555544555555555655------------5--5565444545666655---   48 
+1ihvA       1 75-4443444444444444-3445555556-------55555-------444--------------456665554---   45 
+cons        1 542344111454434444333444554444211112234333111111122222332112222122335655444111   78 
+
+
+1aboA      55 ---679   57 
+1ycsB      58 ---678   60 
+1pht       75 323578   80 
+1vie       49 ---678   51 
+1ihvA      46 --3579   49 
+cons       79 111568   84 
+
+