Merge remote-tracking branch 'origin/Tcoffee_JAL-1065' into develop

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

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index a4fb830..3ef7210 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -17,10 +17,15 @@
  */
 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.datamodel.*;
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
 
 /**
  * DOCUMENT ME!
@@ -37,7 +42,7 @@ 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
@@ -73,10 +78,12 @@ 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 +98,16 @@ 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;
   }