fileFormat enum wip changes

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

diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index ac5f8d6..c3ec951 100644 (file)
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -1,3 +1,23 @@
+/*
+ * 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.
+ *  
+ * 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 +27,14 @@ 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
@@ -74,10 +91,10 @@ import java.util.Map;
  */
 public class TCoffeeScoreFile extends AlignFile
 {
-
-  public TCoffeeScoreFile(String inFile, String type) throws IOException
+  public TCoffeeScoreFile(String inFile, DataSourceType fileSourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, fileSourceType);
 
   }
 
@@ -126,7 +143,7 @@ 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()
@@ -197,6 +214,7 @@ public class TCoffeeScoreFile extends AlignFile
     return result;
   }
 
+  @Override
   public void parse() throws IOException
   {
     /*
@@ -381,6 +399,9 @@ 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.
    * 
@@ -440,6 +461,12 @@ 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);
@@ -500,8 +527,7 @@ 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
@@ -528,7 +554,11 @@ 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;
@@ -615,7 +645,7 @@ public class TCoffeeScoreFile extends AlignFile
   }
 
   @Override
-  public String print()
+  public String print(SequenceI[] sqs, boolean jvsuffix)
   {
     // TODO Auto-generated method stub
     return "Not valid.";