// 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;
public class ProteinDomain implements PhylogenyData {
- final public static double CONFIDENCE_DEFAULT = 0.0;
+ final public static double CONFIDENCE_DEFAULT = -1;
final public static String IDENTIFIER_DEFAULT = "";
final private String _name;
final private int _from;
_confidence = confidence;
}
+ @Override
public StringBuffer asSimpleText() {
return new StringBuffer( getName() );
}
+ @Override
public StringBuffer asText() {
final StringBuffer sb = new StringBuffer( getName() );
sb.append( " [" );
sb.append( " " );
sb.append( getId() );
}
- if ( getConfidence() != CONFIDENCE_DEFAULT ) {
+ if ( getConfidence() >= 0 ) {
sb.append( " " );
sb.append( getConfidence() );
}
return sb;
}
+ @Override
public PhylogenyData copy() {
if ( getId() == null ) {
return new ProteinDomain( getName(), getFrom(), getTo(), getConfidence() );
}
public int getLength() {
- return ( getTo() - getFrom() + 1 );
+ return ( ( getTo() - getFrom() ) + 1 );
}
public String getName() {
return _to;
}
+ @Override
public boolean isEqual( final PhylogenyData protein_domain ) {
if ( protein_domain == null ) {
return false;
return true;
}
+ @Override
public StringBuffer toNHX() {
throw new UnsupportedOperationException();
}
+ @Override
public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
writer.write( ForesterUtil.LINE_SEPARATOR );
writer.write( indentation );