X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;h=462ee22dd65d8260f500437db9f2b22d4abc7bfe;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=03a7a8393a7c44223599fcbb9f084d5d2151cfc7;hpb=6750fadacf73cce0289645dbc387be9331016b1e;p=jalview.git

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 03a7a83..462ee22 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 = "";
         while (st.hasMoreElements())
         {
 
@@ -156,8 +156,8 @@ public class FeaturesFile extends AlignFile
           {
             // Still possible this is an old Jalview file,
             // which does not have type colours at the beginning
-            token = st.nextToken();
-            seq = align.findName(token, true);
+            seqId = token = st.nextToken();
+            seq = align.findName(seqId, true);
             if (seq != null)
             {
               desc = st.nextToken();
@@ -205,7 +205,10 @@ public class FeaturesFile extends AlignFile
               }
 
               seq.addSequenceFeature(sf);
-
+              while ((seq = align.findName(seq, seqId, true)) != null)
+              {
+                seq.addSequenceFeature(new SequenceFeature(sf));
+              }
               break;
             }
           }
@@ -231,11 +234,12 @@ public class FeaturesFile extends AlignFile
 
           if (!token.equals("ID_NOT_SPECIFIED"))
           {
-            seq = align.findName(token, true);
+            seq = align.findName(seqId = token, true);
             st.nextToken();
           }
           else
           {
+            seqId = null;
             try
             {
               index = Integer.parseInt(st.nextToken());
@@ -266,8 +270,6 @@ public class FeaturesFile extends AlignFile
 
           sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
 
-          seq.addSequenceFeature(sf);
-
           if (groupLink != null && removeHTML)
           {
             sf.addLink(groupLink);
@@ -281,6 +283,13 @@ public class FeaturesFile extends AlignFile
 
           parseDescriptionHTML(sf, removeHTML);
 
+          seq.addSequenceFeature(sf);
+
+          while (seqId != null
+                  && (seq = align.findName(seq, seqId, false)) != null)
+          {
+            seq.addSequenceFeature(new SequenceFeature(sf));
+          }
           // If we got here, its not a GFFFile
           GFFFile = false;
         }
@@ -371,12 +380,15 @@ 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);
@@ -384,9 +396,13 @@ 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,
@@ -401,7 +417,8 @@ 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;