X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=93803c80b460b85ec9dd3fe8fedcbbd3df84c49a;hb=62129a185d2d7f2bfc405851da4dada0900a2afc;hp=abc7a16fc614910f98a40404fa24bea9ab840bbd;hpb=57d863cc978bfd638da0e21a37b425be6251ce13;p=jalview.git
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index abc7a16..93803c8 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,26 +1,32 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * 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.
- *
+ *
* 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 .
+ * 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.datamodel.*;
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
/**
* DOCUMENT ME!
@@ -37,7 +43,7 @@ public abstract class AlignFile extends FileParse
/**
* Sequences to be added to form a new alignment.
*/
- protected Vector seqs;
+ protected Vector seqs;
/**
* annotation to be added to generated alignment object
@@ -73,10 +79,13 @@ 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 +100,17 @@ 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 getSeqs()
{
return seqs;
}