X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;h=5058e5fbfc0cf85aa4ac6fb407394c7d70cc1a89;hb=ed12859f49530c561c9d069c71333ddac9fc8a30;hp=3e0314ae75bb029642b1070d2d579621fd2e4f76;hpb=167476e350f385aa0fcb334b79722ddaa1b3a368;p=jalview.git

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 3e0314a..5058e5f 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program 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 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program 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 this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -148,7 +148,7 @@ public class FeaturesFile extends AlignFile
           }
           continue;
         }
-        String seqId="";
+        String seqId = "";
         while (st.hasMoreElements())
         {
 
@@ -201,11 +201,12 @@ public class FeaturesFile extends AlignFile
                 {
                   attributes.append("\t" + st.nextElement());
                 }
+                // TODO validate and split GFF2 attributes field ? parse out ([A-Za-z][A-Za-z0-9_]*) <value> ; and add as sf.setValue(attrib, val); 
                 sf.setValue("ATTRIBUTES", attributes.toString());
               }
 
               seq.addSequenceFeature(sf);
-              while ((seq=align.findName(seq, seqId, true))!=null)
+              while ((seq = align.findName(seq, seqId, true)) != null)
               {
                 seq.addSequenceFeature(new SequenceFeature(sf));
               }
@@ -234,12 +235,12 @@ public class FeaturesFile extends AlignFile
 
           if (!token.equals("ID_NOT_SPECIFIED"))
           {
-            seq = align.findName(seqId=token, true);
+            seq = align.findName(seqId = token, true);
             st.nextToken();
           }
           else
           {
-            seqId=null;
+            seqId = null;
             try
             {
               index = Integer.parseInt(st.nextToken());
@@ -285,7 +286,8 @@ public class FeaturesFile extends AlignFile
 
           seq.addSequenceFeature(sf);
 
-          while (seqId!=null && (seq=align.findName(seq, seqId, false))!=null)
+          while (seqId != null
+                  && (seq = align.findName(seq, seqId, false)) != null)
           {
             seq.addSequenceFeature(new SequenceFeature(sf));
           }
@@ -379,12 +381,15 @@ public class FeaturesFile extends AlignFile
 
   }
 
-/**
- * generate a features file for seqs
- * @param seqs source of sequence features
- * @param visible hash of feature types and colours 
- * @return features file contents
- */
+  /**
+   * generate a features file for seqs
+   * 
+   * @param seqs
+   *                source of sequence features
+   * @param visible
+   *                hash of feature types and colours
+   * @return features file contents
+   */
   public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)
   {
     return printJalviewFormat(seqs, visible, true);
@@ -392,9 +397,13 @@ public class FeaturesFile extends AlignFile
 
   /**
    * generate a features file for seqs with colours from visible (if any)
-   * @param seqs        source of features
-   * @param visible     hash of Colours for each feature type
-   * @param visOnly     when true only feature types in 'visible' will be output
+   * 
+   * @param seqs
+   *                source of features
+   * @param visible
+   *                hash of Colours for each feature type
+   * @param visOnly
+   *                when true only feature types in 'visible' will be output
    * @return features file contents
    */
   public String printJalviewFormat(SequenceI[] seqs, Hashtable visible,
@@ -409,7 +418,8 @@ public class FeaturesFile extends AlignFile
     }
     if (visible != null && visOnly)
     {
-      // write feature colours only if we're given them and we are generating viewed features
+      // write feature colours only if we're given them and we are generating
+      // viewed features
       Enumeration en = visible.keys();
       String type;
       int color;