// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.phylogeny.data;
import java.io.IOException;
import java.io.Writer;
+import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.List;
import java.util.SortedMap;
public class DomainArchitecture implements PhylogenyData {
- public final static String NHX_SEPARATOR = ">";
- private static final double INCREASE_KEY = 0.0001;
- private SortedMap<Double, ProteinDomain> _domains;
- private int _total_length;
+ public final static String NHX_SEPARATOR = ">";
+ private static final BigDecimal INCREASE_KEY = new BigDecimal( "0.00001" );
+ private SortedMap<BigDecimal, ProteinDomain> _domains;
+ private int _total_length;
public DomainArchitecture() {
init();
}
}
catch ( final Exception e ) {
- throw new IllegalArgumentException( "Malformed format for domain structure \"" + da_str + "\": "
+ throw new IllegalArgumentException( "malformed format for domain structure \"" + da_str + "\": "
+ e.getMessage() );
}
if ( to > total_length ) {
}
public void addDomain( final ProteinDomain pd ) {
- Double key = new Double( pd.getFrom() );
+ BigDecimal key = new BigDecimal( "" + pd.getFrom() );
while ( _domains.containsKey( key ) ) {
- key = new Double( key.doubleValue() + DomainArchitecture.INCREASE_KEY );
+ key = new BigDecimal( "" + ( key.doubleValue() + DomainArchitecture.INCREASE_KEY.doubleValue() ) );
}
_domains.put( key, pd );
}
+ @Override
public StringBuffer asSimpleText() {
final StringBuffer sb = new StringBuffer();
for( int i = 0; i < getDomains().size(); ++i ) {
return sb;
}
+ @Override
public StringBuffer asText() {
final StringBuffer sb = new StringBuffer();
for( int i = 0; i < getDomains().size(); ++i ) {
return sb;
}
+ @Override
public PhylogenyData copy() {
final List<PhylogenyData> domains = new ArrayList<PhylogenyData>( getDomains().size() );
for( int i = 0; i < getDomains().size(); ++i ) {
return ( ProteinDomain ) _domains.values().toArray()[ i ];
}
- public SortedMap<Double, ProteinDomain> getDomains() {
+ public SortedMap<BigDecimal, ProteinDomain> getDomains() {
return _domains;
}
}
private void init() {
- _domains = new TreeMap<Double, ProteinDomain>();
+ _domains = new TreeMap<BigDecimal, ProteinDomain>();
_total_length = 0;
}
*
*
*/
+ @Override
public boolean isEqual( final PhylogenyData domain_architecture ) {
if ( domain_architecture == null ) {
return false;
_total_length = total_length;
}
+ @Override
public StringBuffer toNHX() {
final StringBuffer sb = new StringBuffer();
sb.append( ":" );
return sb;
}
+ @Override
public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
writer.write( ForesterUtil.LINE_SEPARATOR );
writer.write( indentation );