X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FAlignFile.java;h=0691d82d47e10dd93bb8721fb3866f8ce860a917;hb=b45345a4ee49f07b6f66e80535ca5f140a954e41;hp=d22dc12affec96ce09f97bd011adf368f81bb256;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index d22dc12..0691d82 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
@@ -39,6 +39,7 @@ public abstract class AlignFile extends FileParse
     Vector headers;
     long start;
     long end;
+    boolean jvSuffix = true;
 
     /**
      * Creates a new AlignFile object.
@@ -47,24 +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.
@@ -131,15 +114,17 @@ public abstract class AlignFile extends FileParse
     protected boolean isValidProteinSequence(String sequence)
     {
         for (int i = 0; i < sequence.length(); i++)
-            if (!jalview.schemes.ResidueProperties.aaHash.containsKey(
-                        String.valueOf(sequence.charAt(i))))
+            if (jalview.schemes.ResidueProperties.aaIndex[sequence.charAt(i)]==-1)
             {
+                invalidCharacter = sequence.charAt(i);
                 return false;
             }
 
         return true;
     }
 
+    char invalidCharacter;
+
     /**
      * This method must be implemented to parse the contents of the file.
      */
@@ -149,4 +134,45 @@ public abstract class AlignFile extends FileParse
      * Print out in alignment file format the Sequences in the seqs Vector.
      */
     public abstract String print();
+
+    public void addJVSuffix(boolean b)
+    {
+      jvSuffix = b;
+    }
+
+    /**
+     * A general parser for ids.
+     *
+     * @String id Id to be parsed
+     */
+    Sequence parseId(String id)
+    {
+      Sequence seq = null;
+      id = id.trim();
+      int space = id.indexOf(" ");
+      if(space>-1)
+      {
+        seq = new Sequence(id.substring(0, space),"");
+        seq.setDescription(id.substring(space+1));
+      }
+      else
+      {
+        seq = new Sequence(id, "");
+      }
+
+      return seq;
+    }
+
+    /**
+     * Creates the output id.
+     * Adds prefix Uniprot format source|id
+     * And suffix Jalview /start-end
+     *
+     * @String id Id to be parsed
+     */
+    String printId(SequenceI seq)
+    {
+     return seq.getDisplayId(jvSuffix);
+    }
+
 }