X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=81d0ae48a503265a04942f4c41b7490de6b9cc53;hb=6fb502e4a8749d1d98f5442c3b8156ab47996b77;hp=c5d44edab913e4720eb8602080d1df54e0db16bb;hpb=a7f8fa9c06d82efbbdbc6a0bf1054bb21610b353;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index c5d44ed..81d0ae4 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 
@@ -27,14 +27,6 @@ import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.Vector;
 
-import javax.xml.parsers.ParserConfigurationException;
-
-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;
-
 /**
  * DOCUMENT ME!
  * 
@@ -73,7 +65,7 @@ public abstract class AlignFile extends FileParse
    */
   public AlignFile()
   {
-	  // Shouldn't we init data structures
+	  // 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();
   }
 
@@ -84,20 +76,16 @@ public abstract class AlignFile extends FileParse
    *          Filename to read from.
    * @param type
    *          What type of file to read from (File, URL)
- * @throws SAXException 
- * @throws ParserConfigurationException 
- * @throws ExceptionFileFormatOrSyntax 
- * @throws ExceptionLoadingFailed 
- * @throws ExceptionPermissionDenied 
    */
-  public AlignFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
+  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);  
+    for (int i = 0, c = seqs.size(); i < c; i++)
+    {
+      seqs.get(i).setIndex(i);
     }
   }
 
@@ -107,20 +95,16 @@ public abstract class AlignFile extends FileParse
    * 
    * @param source
    * @throws IOException
- * @throws SAXException 
- * @throws ParserConfigurationException 
- * @throws ExceptionFileFormatOrSyntax 
- * @throws ExceptionLoadingFailed 
- * @throws ExceptionPermissionDenied 
    */
-  public AlignFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
+  public AlignFile(FileParse source) throws IOException
   {
     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);  
+    for (int i = 0, c = seqs.size(); i < c; i++)
+    {
+      seqs.get(i).setIndex(i);
     }
   }
 
@@ -257,13 +241,8 @@ public abstract class AlignFile extends FileParse
 
   /**
    * This method must be implemented to parse the contents of the file.
- * @throws ExceptionFileFormatOrSyntax 
- * @throws SAXException 
- * @throws ParserConfigurationException 
- * @throws ExceptionLoadingFailed 
- * @throws ExceptionPermissionDenied 
    */
-  public abstract void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed;
+  public abstract void parse() throws IOException;
 
   /**
    * Print out in alignment file format the Sequences in the seqs Vector.