// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
// 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
// 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.
// 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
// 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
- final private DomainId _key_domain;
- private int _key_domain_count;
- private int _key_domain_proteins_count;
- final private Species _species;
- final private TreeMap<DomainId, Integer> _combining_domains;
- private DescriptiveStatistics _key_domain_confidence_statistics;
+ final private TreeMap<String, Integer> _combining_domains;
+ final private String _key_domain;
+ private int _key_domain_count;
+ final private Set<String> _proteins_with_key_domain;
+ final private Species _species;
if ( getCombiningDomains().containsKey( protein_domain ) ) {
getCombiningDomains().put( protein_domain, getCombiningDomains().get( protein_domain ) + 1 );
}
if ( getCombiningDomains().containsKey( protein_domain ) ) {
getCombiningDomains().put( protein_domain, getCombiningDomains().get( protein_domain ) + 1 );
}
- public List<DomainId> getAllDomains() {
- final List<DomainId> domains = getCombinableDomains();
+ @Override
+ public void addKeyDomainProtein( final String protein ) {
+ if ( ForesterUtil.isEmpty( protein ) ) {
+ throw new IllegalArgumentException( "attempt to add null or empty protein" );
+ }
+ getKeyDomainProteins().add( protein );
+ }
+
+ @Override
+ public List<String> getAllDomains() {
+ final List<String> domains = getCombinableDomains();
- public List<DomainId> getCombinableDomains() {
- final List<DomainId> domains = new ArrayList<DomainId>( getNumberOfCombinableDomains() );
- for( final DomainId domain : getCombiningDomains().keySet() ) {
+ @Override
+ public List<String> getCombinableDomains() {
+ final List<String> domains = new ArrayList<String>( getNumberOfCombinableDomains() );
+ for( final String domain : getCombiningDomains().keySet() ) {
- public SortedMap<DomainId, Integer> getCombinableDomainsIds() {
- final SortedMap<DomainId, Integer> ids = new TreeMap<DomainId, Integer>();
- for( final DomainId domain : getCombiningDomains().keySet() ) {
- final DomainId pd = domain;
+ @Override
+ public SortedMap<String, Integer> getCombinableDomainsIds() {
+ final SortedMap<String, Integer> ids = new TreeMap<String, Integer>();
+ for( final String domain : getCombiningDomains().keySet() ) {
+ final String pd = domain;
public StringBuilder getCombiningDomainIdsAsStringBuilder() {
final StringBuilder sb = new StringBuilder();
public StringBuilder getCombiningDomainIdsAsStringBuilder() {
final StringBuilder sb = new StringBuilder();
- for( final Iterator<DomainId> iter = getCombiningDomains().keySet().iterator(); iter.hasNext(); ) {
- final DomainId key = iter.next();
+ for( final Iterator<String> iter = getCombiningDomains().keySet().iterator(); iter.hasNext(); ) {
+ final String key = iter.next();
- protected TreeMap<DomainId, Integer> getCombiningDomains() {
- return _combining_domains;
- }
-
- public DomainId getKeyDomain() {
+ @Override
+ public String getKeyDomain() {
if ( getCombiningDomains().containsKey( protein_domain ) ) {
return getCombiningDomains().get( protein_domain );
}
if ( getCombiningDomains().containsKey( protein_domain ) ) {
return getCombiningDomains().get( protein_domain );
}
- private void init() {
- _key_domain_count = 0;
- _key_domain_proteins_count = 0;
- _key_domain_confidence_statistics = null;
- }
-
- public boolean isCombinable( final DomainId protein_domain ) {
+ @Override
+ public boolean isCombinable( final String protein_domain ) {
@Override
public List<BinaryDomainCombination> toBinaryDomainCombinations() {
final List<BinaryDomainCombination> binary_combinations = new ArrayList<BinaryDomainCombination>( getNumberOfCombinableDomains() );
@Override
public List<BinaryDomainCombination> toBinaryDomainCombinations() {
final List<BinaryDomainCombination> binary_combinations = new ArrayList<BinaryDomainCombination>( getNumberOfCombinableDomains() );
- for( final DomainId domain : getCombiningDomains().keySet() ) {
- binary_combinations.add( new BasicBinaryDomainCombination( getKeyDomain(), domain ) );
+ for( final String domain : getCombiningDomains().keySet() ) {
+ // binary_combinations.add( new BasicBinaryDomainCombination( getKeyDomain(), domain ) );
+ binary_combinations.add( BasicBinaryDomainCombination.obtainInstance( getKeyDomain(), domain ) );