// Copyright (C) 2008-2010 Christian M. Zmasek
// Copyright (C) 2008-2010 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.surfacing;
import java.util.SortedMap;
import java.util.TreeMap;
+import org.forester.protein.Domain;
+import org.forester.protein.Protein;
+import org.forester.species.Species;
import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
public class DomainLengthsTable {
- private final static DecimalFormat DF = new DecimalFormat( "#.0" );
- final SortedMap<DomainId, DomainLengths> _domain_lengths;
- final List<Species> _species;
+ private final static DecimalFormat DF = new DecimalFormat( "#.0" );
+ final SortedMap<String, DomainLengths> _domain_lengths;
+ final List<Species> _species;
public DomainLengthsTable() {
- _domain_lengths = new TreeMap<DomainId, DomainLengths>();
+ _domain_lengths = new TreeMap<String, DomainLengths>();
_species = new ArrayList<Species>();
}
getDomainLengths().put( domain_lengths.getDomainId(), domain_lengths );
}
- private void addLength( final DomainId domain_id, final Species species, final int domain_length ) {
+ private void addLength( final String domain_id, final Species species, final int domain_length ) {
if ( !getDomainLengths().containsKey( domain_id ) ) {
addDomainLengths( new DomainLengths( domain_id ) );
}
return stats;
}
- public DescriptiveStatistics calculateMeanBasedStatisticsForDomain( final DomainId domain_id ) {
+ public DescriptiveStatistics calculateMeanBasedStatisticsForDomain( final String domain_id ) {
return getDomainLengths( domain_id ).calculateMeanBasedStatistics();
}
return sb;
}
- private SortedMap<DomainId, DomainLengths> getDomainLengths() {
+ private SortedMap<String, DomainLengths> getDomainLengths() {
return _domain_lengths;
}
- public DomainLengths getDomainLengths( final DomainId domain_id ) {
+ public DomainLengths getDomainLengths( final String domain_id ) {
return getDomainLengths().get( domain_id );
}
return list;
}
- public DescriptiveStatistics getLengthStatistic( final DomainId domain_id, final Species species ) {
+ public DescriptiveStatistics getLengthStatistic( final String domain_id, final Species species ) {
return getDomainLengths( domain_id ).getLengthStatistic( species );
}