X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=f73e250528d0f7771225137b261b6574ee8e810c;hb=bdba25716eaa9492681532cb443c18ed34237488;hp=a4fb83064032610e75fb73708b50ec56d98c9118;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index a4fb830..f73e250 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,26 +1,35 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
- * 
+ * 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/>.
+ * 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 java.io.*;
-import java.util.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
 
-import jalview.datamodel.*;
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
 
 /**
  * DOCUMENT ME!
@@ -37,7 +46,7 @@ public abstract class AlignFile extends FileParse
   /**
    * Sequences to be added to form a new alignment.
    */
-  protected Vector seqs;
+  protected Vector<SequenceI> seqs;
 
   /**
    * annotation to be added to generated alignment object
@@ -60,6 +69,10 @@ public abstract class AlignFile extends FileParse
    */
   public AlignFile()
   {
+    // Shouldn't we init data structures (JBPNote: not sure - initData is for
+    // initialising the structures used for reading from a datasource, and the
+    // bare constructor hasn't got any datasource)
+    initData();
   }
 
   /**
@@ -73,10 +86,13 @@ public abstract class AlignFile extends FileParse
   public AlignFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
-
     initData();
-
     parse();
+    // sets the index of each sequence in the alignment
+    for (int i = 0, c = seqs.size(); i < c; i++)
+    {
+      seqs.get(i).setIndex(i);
+    }
   }
 
   /**
@@ -91,12 +107,17 @@ public abstract class AlignFile extends FileParse
     super(source);
     initData();
     parse();
+    // sets the index of each sequence in the alignment
+    for (int i = 0, c = seqs.size(); i < c; i++)
+    {
+      seqs.get(i).setIndex(i);
+    }
   }
 
   /**
    * Return the seqs Vector
    */
-  public Vector getSeqs()
+  public Vector<SequenceI> getSeqs()
   {
     return seqs;
   }
@@ -176,8 +197,7 @@ public abstract class AlignFile extends FileParse
   {
     if (key == null)
     {
-      throw new Error(
-              "Implementation error: Cannot have null alignment property key.");
+      throw new Error(MessageManager.getString("error.implementation_error_cannot_have_null_alignment"));
     }
     if (value == null)
     {