X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=c0f85313ee804aa666ff9395e0e0ecbe0121205e;hb=6819474b5da8df0145cfe2c65ea9445609332c20;hp=a4fb83064032610e75fb73708b50ec56d98c9118;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index a4fb830..c0f8531 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,13 +1,13 @@
 /*
- * 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)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * 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 
@@ -17,10 +17,24 @@
  */
 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 java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import javax.xml.parsers.ParserConfigurationException;
 
-import jalview.datamodel.*;
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
 
 /**
  * DOCUMENT ME!
@@ -37,7 +51,7 @@ 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 +74,8 @@ 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();
   }
 
   /**
@@ -69,14 +85,18 @@ public abstract class AlignFile extends FileParse
    *          Filename to read from.
    * @param type
    *          What type of file to read from (File, URL)
+ * @throws Exception 
    */
-  public AlignFile(String inFile, String type) throws IOException
+  public AlignFile(String inFile, String type) throws Exception
   {
     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);
+    }
   }
 
   /**
@@ -84,19 +104,24 @@ public abstract class AlignFile extends FileParse
    * off.
    * 
    * @param source
-   * @throws IOException
+ * @throws Exception 
    */
-  public AlignFile(FileParse source) throws IOException
+  public AlignFile(FileParse source) throws Exception
   {
     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;
   }
@@ -226,8 +251,9 @@ public abstract class AlignFile extends FileParse
 
   /**
    * This method must be implemented to parse the contents of the file.
+
    */
-  public abstract void parse() throws IOException;
+  public abstract void parse() throws Exception;
 
   /**
    * Print out in alignment file format the Sequences in the seqs Vector.