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/* ComparisonDataFactory.java
*
* created: Thu Jul 15 1999
*
* This file is part of Artemis
*
* Copyright (C) 1999-2002 Genome Research Limited
*
* This program 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 2
* of the License, or (at your option) any later version.
*
* This program 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 this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
* $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/ComparisonDataFactory.java,v 1.1 2004-06-09 09:44:16 tjc Exp $
*/
package uk.ac.sanger.artemis;
import uk.ac.sanger.artemis.util.*;
import uk.ac.sanger.artemis.util.LinePushBackReader;
import java.io.*;
/**
* This class contains the method readComparisonData (), which returns an
* appropriate ComparisonData object for a given Document.
*
* @author Kim Rutherford
* @version $Id: ComparisonDataFactory.java,v 1.1 2004-06-09 09:44:16 tjc Exp $
**/
public class ComparisonDataFactory {
/**
* This method creates an appropriate ComparisonData object from a Document.
**/
static public ComparisonData readComparisonData (Document data_document)
throws IOException {
final Reader in_file = data_document.getReader ();
final LinePushBackReader pushback_reader =
new LinePushBackReader (in_file);
final String line = pushback_reader.readLine ();
if (line == null) {
throw new IOException ("End of file while reading from: " +
data_document);
}
pushback_reader.pushBack (line);
if (MSPcrunchComparisonData.formatCorrect (line)) {
return new MSPcrunchComparisonData (pushback_reader);
} else {
if (SSAHAComparisonData.formatCorrect (line)) {
return new SSAHAComparisonData (pushback_reader);
} else {
if (BlastM8ComparisonData.formatCorrect (line)) {
return new BlastM8ComparisonData (pushback_reader);
} else {
if (MegaBlastComparisonData.formatCorrect (line)) {
return new MegaBlastComparisonData (pushback_reader);
} else {
// if (tokenizer.countTokens () < 8) {
// return new MUMmerComparisonData (pushback_reader);
// } else {
throw new IOException ("cannot understand the comparison file format");
// }
}
}
}
}
}
}