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/*
* This file is part of Artemis
*
* Copyright (C) 2013 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.
*
*/
package uk.ac.sanger.artemis.io;
import java.io.IOException;
import java.net.URL;
import junit.framework.Assert;
import uk.ac.sanger.artemis.Options;
import uk.ac.sanger.artemis.io.DocumentEntryFactory;
import uk.ac.sanger.artemis.io.Entry;
import uk.ac.sanger.artemis.io.EntryInformationException;
import uk.ac.sanger.artemis.sequence.AminoAcidSequence;
import uk.ac.sanger.artemis.sequence.Bases;
import uk.ac.sanger.artemis.util.Document;
import uk.ac.sanger.artemis.util.DocumentFactory;
import uk.ac.sanger.artemis.util.StringVector;
public class Utils
{
protected static Entry getEntry(final String fileName)
{
try
{
URL entryFile = ValidateFeatureTest.class.getResource(fileName);
final Document doc = DocumentFactory.makeDocument(entryFile.getFile());
return DocumentEntryFactory.makeDocumentEntry(
Options.getArtemisEntryInformation(),doc,null);
}
catch(EntryInformationException e)
{
Assert.fail(e.getMessage());
}
catch(IOException e)
{
Assert.fail(e.getMessage());
}
return null;
}
/**
* Method to change the translation table being used
* @param n - genetic code table number
*/
protected static void changeTranslationTable(String n)
{
StringVector options_file_table =
Options.getOptions().getOptionValues("translation_table_"+n);
StringVector table = Options.getOptions().getOptionValues("translation_table_1");
for(String cod_plus_aa: options_file_table)
{
final int codon_index = Bases.getIndexOfBase(cod_plus_aa.charAt(0)) * 16 +
Bases.getIndexOfBase(cod_plus_aa.charAt(1)) * 4 +
Bases.getIndexOfBase(cod_plus_aa.charAt(2));
table.setElementAt(cod_plus_aa.substring(3), codon_index);
}
StringBuffer sbuff = new StringBuffer();
for(int i = 0; i < 64; ++i)
sbuff.append(table.elementAt(i)+" ");
Options.getOptions().setGeneticCode(sbuff.toString());
options_file_table =
Options.getOptions().getOptionValues("start_codons_"+n);
sbuff = new StringBuffer();
for(String start: options_file_table)
sbuff.append(start+" ");
Options.getOptions().setProperty("start_codons",sbuff.toString());
AminoAcidSequence.setGeneCode();
}
}