Merge branch 'develop' into menard

[jalview.git] / src / jalview / io / AlignFile.java

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index c5d44ed..1d6b76b 100755 (executable)
--- 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 
@@ -34,6 +34,7 @@ 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!
@@ -89,15 +90,18 @@ public abstract class AlignFile extends FileParse
  * @throws ExceptionFileFormatOrSyntax 
  * @throws ExceptionLoadingFailed 
  * @throws ExceptionPermissionDenied 
+ * @throws InterruptedException 
+ * @throws ExceptionUnmatchedClosingParentheses 
    */
-  public AlignFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
+  public AlignFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     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);
     }
   }
 
@@ -112,15 +116,18 @@ public abstract class AlignFile extends FileParse
  * @throws ExceptionFileFormatOrSyntax 
  * @throws ExceptionLoadingFailed 
  * @throws ExceptionPermissionDenied 
+ * @throws InterruptedException 
+ * @throws ExceptionUnmatchedClosingParentheses 
    */
-  public AlignFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
+  public AlignFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     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);
     }
   }
 
@@ -262,8 +269,10 @@ public abstract class AlignFile extends FileParse
  * @throws ParserConfigurationException 
  * @throws ExceptionLoadingFailed 
  * @throws ExceptionPermissionDenied 
+ * @throws InterruptedException 
+ * @throws ExceptionUnmatchedClosingParentheses 
    */
-  public abstract void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed;
+  public abstract void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses;
 
   /**
    * Print out in alignment file format the Sequences in the seqs Vector.