X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FAlignFile.java;h=a800f0652d6b73e5273369cd5d2164817ebe38b3;hb=141ad7e898f94594bacb1c77eabbcd837505409c;hp=ceec54bcf0f384508583fff26806511762c7ab69;hpb=8d3d3b4edf47e543b8b352c1b2c247cfc59122a4;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index ceec54b..a800f06 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 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
@@ -36,7 +36,7 @@ public abstract class AlignFile extends FileParse
     int noSeqs = 0;
     int maxLength = 0;
     Vector seqs;
-    Vector headers;
+    Vector annotations;
     long start;
     long end;
     boolean jvSuffix = true;
@@ -48,24 +48,6 @@ public abstract class AlignFile extends FileParse
     {
     }
 
-    /**
-     * Creates a new AlignFile object.
-     *
-     * @param inStr DOCUMENT ME!
-     */
-    public AlignFile(String inStr)
-    {
-        initData();
-        System.out.println("is this ever called??");
-
-        try
-        {
-            parse();
-        }
-        catch (Exception ex)
-        {
-        }
-    }
 
     /**
      * Constructor which parses the data from a file of some specified type.
@@ -104,13 +86,24 @@ public abstract class AlignFile extends FileParse
         return s;
     }
 
+    public void addAnnotations(Alignment al)
+    {
+      for(int i=0; i<annotations.size(); i++)
+      {
+        al.addAnnotation(
+            (AlignmentAnnotation)annotations.elementAt(i)
+            );
+      }
+
+    }
+
     /**
      * Initialise objects to store sequence data in.
      */
     protected void initData()
     {
         seqs = new Vector();
-        headers = new Vector();
+        annotations = new Vector();
     }
 
     /**
@@ -129,13 +122,12 @@ public abstract class AlignFile extends FileParse
     }
 
     // Checks whether sequence is valid aa characters
-    protected boolean isValidProteinSequence(String sequence)
+    protected boolean isValidProteinSequence(char [] sequence)
     {
-        for (int i = 0; i < sequence.length(); i++)
-            if (!jalview.schemes.ResidueProperties.aaHash.containsKey(
-                        String.valueOf(sequence.charAt(i))))
+        for (int i = 0; i < sequence.length; i++)
+            if (jalview.schemes.ResidueProperties.aaIndex[sequence[i]]==-1)
             {
-                invalidCharacter = sequence.charAt(i);
+                invalidCharacter = sequence[i];
                 return false;
             }