/*
- * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
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!
*
*/
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();
}
* 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<c; i++ ) {
- seqs.get(i).setIndex(i);
+ for (int i = 0, c = seqs.size(); i < c; i++)
+ {
+ seqs.get(i).setIndex(i);
}
}
*
* @param source
* @throws IOException
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionFileFormatOrSyntax
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
- * @throws ExceptionUnmatchedClosingParentheses
*/
- public AlignFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ 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);
}
}
/**
* This method must be implemented to parse the contents of the file.
- * @throws ExceptionFileFormatOrSyntax
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
- * @throws ExceptionUnmatchedClosingParentheses
*/
- public abstract void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses;
+ public abstract void parse() throws IOException;
/**
* Print out in alignment file format the Sequences in the seqs Vector.