// 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.surfacing;
import org.forester.go.GoNameSpace;
import org.forester.go.GoTerm;
import org.forester.go.GoXRef;
+import org.forester.protein.DomainId;
+import org.forester.species.Species;
import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
import org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput;
import org.forester.util.ForesterUtil;
}
}
+ @Override
public int compareTo( final DomainSimilarity domain_similarity ) {
if ( this == domain_similarity ) {
return PrintableDomainSimilarity.EQUAL;
throw new AssertionError( "Unknown sort method: " + getSortField() );
}
+ @Override
public SortedSet<DomainId> getCombinableDomainIds( final Species species_of_combinable_domain ) {
final SortedSet<DomainId> sorted_ids = new TreeSet<DomainId>();
if ( getSpeciesData().containsKey( species_of_combinable_domain ) ) {
return _detailedness;
}
+ @Override
public DomainId getDomainId() {
return getCombinableDomains().getKeyDomain();
}
return _go_namespace_limit;
}
+ @Override
public int getMaximalDifference() {
return _max_difference;
}
return _max_difference_in_counts;
}
+ @Override
public double getMaximalSimilarityScore() {
return _max;
}
+ @Override
public double getMeanSimilarityScore() {
return _mean;
}
+ @Override
public double getMinimalSimilarityScore() {
return _min;
}
+ @Override
public int getN() {
return _n;
}
return _sort_field;
}
+ @Override
public SortedSet<Species> getSpecies() {
final SortedSet<Species> species = new TreeSet<Species>();
for( final Species s : getSpeciesData().keySet() ) {
return _species_order;
}
+ @Override
public SortedMap<Species, SpeciesSpecificDomainSimilariyData> getSpeciesData() {
return _species_data;
}
return sb;
}
+ @Override
public double getStandardDeviationOfSimilarityScore() {
return _sd;
}
return toStringBuffer( null ).toString();
}
+ @Override
public StringBuffer toStringBuffer( final PrintableDomainSimilarity.PRINT_OPTION print_option ) {
switch ( print_option ) {
case SIMPLE_TAB_DELIMITED: