X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=0b9a53764e5bb027ad53dd22ca98d3ac629b1720;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=837fee057af9a077f74739b64f351e33dff8c497;hpb=d7c00f48b00e3ede57c46ae4daf6a9203b9b6059;p=jalview.git
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 837fee0..0b9a537 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,19 +1,20 @@
/*
- * 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 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* 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
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
@@ -27,15 +28,6 @@ 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;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-
/**
* DOCUMENT ME!
*
@@ -74,7 +66,7 @@ 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();
}
@@ -85,22 +77,16 @@ 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
- * @throws InterruptedException
- * @throws ExceptionUnmatchedClosingParentheses
*/
- public AlignFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ 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