2 package org.forester.surfacing;
4 import java.text.DecimalFormat;
5 import java.text.NumberFormat;
6 import java.util.ArrayList;
7 import java.util.Collections;
8 import java.util.Comparator;
9 import java.util.HashMap;
10 import java.util.HashSet;
11 import java.util.List;
14 import java.util.SortedMap;
15 import java.util.SortedSet;
16 import java.util.TreeMap;
17 import java.util.TreeSet;
19 import org.forester.go.GoId;
20 import org.forester.surfacing.BinaryDomainCombination.DomainCombinationType;
21 import org.forester.util.BasicDescriptiveStatistics;
22 import org.forester.util.DescriptiveStatistics;
23 import org.forester.util.ForesterUtil;
25 public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDomains {
27 private final static NumberFormat FORMATTER = new DecimalFormat( "0.0E0" );
28 private static final Comparator<CombinableDomains> DESCENDING_KEY_DOMAIN_COUNT_ORDER = new Comparator<CombinableDomains>() {
31 public int compare( final CombinableDomains d1,
32 final CombinableDomains d2 ) {
33 if ( d1.getKeyDomainCount() < d2
34 .getKeyDomainCount() ) {
38 .getKeyDomainCount() > d2
39 .getKeyDomainCount() ) {
52 private static final Comparator<CombinableDomains> DESCENDING_KEY_DOMAIN_PROTEINS_COUNT_ORDER = new Comparator<CombinableDomains>() {
55 public int compare( final CombinableDomains d1,
56 final CombinableDomains d2 ) {
57 if ( d1.getKeyDomainProteinsCount() < d2
58 .getKeyDomainProteinsCount() ) {
62 .getKeyDomainProteinsCount() > d2
63 .getKeyDomainProteinsCount() ) {
76 private static final Comparator<CombinableDomains> DESCENDING_COMBINATIONS_COUNT_ORDER = new Comparator<CombinableDomains>() {
79 public int compare( final CombinableDomains d1,
80 final CombinableDomains d2 ) {
81 if ( d1.getNumberOfCombinableDomains() < d2
82 .getNumberOfCombinableDomains() ) {
86 .getNumberOfCombinableDomains() > d2
87 .getNumberOfCombinableDomains() ) {
100 final private SortedMap<DomainId, CombinableDomains> _combinable_domains_map;
101 final private Species _species;
102 final private DomainCombinationType _dc_type;
104 private BasicGenomeWideCombinableDomains( final Species species, final DomainCombinationType dc_type ) {
105 _combinable_domains_map = new TreeMap<DomainId, CombinableDomains>();
110 private void add( final DomainId key, final CombinableDomains cdc ) {
111 _combinable_domains_map.put( key, cdc );
115 public boolean contains( final DomainId key_id ) {
116 return _combinable_domains_map.containsKey( key_id );
120 public CombinableDomains get( final DomainId key_id ) {
121 return _combinable_domains_map.get( key_id );
125 public SortedMap<DomainId, CombinableDomains> getAllCombinableDomainsIds() {
126 return _combinable_domains_map;
130 public SortedSet<DomainId> getAllDomainIds() {
131 final SortedSet<DomainId> domains = new TreeSet<DomainId>();
132 for( final DomainId key : getAllCombinableDomainsIds().keySet() ) {
133 final CombinableDomains cb = getAllCombinableDomainsIds().get( key );
134 final List<DomainId> ds = cb.getAllDomains();
135 for( final DomainId d : ds ) {
143 public DomainCombinationType getDomainCombinationType() {
148 public SortedSet<DomainId> getMostPromiscuosDomain() {
149 final SortedSet<DomainId> doms = new TreeSet<DomainId>();
150 final int max = ( int ) getPerGenomeDomainPromiscuityStatistics().getMax();
151 for( final DomainId key : getAllCombinableDomainsIds().keySet() ) {
152 final CombinableDomains cb = getAllCombinableDomainsIds().get( key );
153 if ( cb.getNumberOfCombinableDomains() == max ) {
161 public DescriptiveStatistics getPerGenomeDomainPromiscuityStatistics() {
162 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
163 for( final DomainId key : getAllCombinableDomainsIds().keySet() ) {
164 final CombinableDomains cb = getAllCombinableDomainsIds().get( key );
165 stats.addValue( cb.getNumberOfCombinableDomains() );
171 public int getSize() {
172 return _combinable_domains_map.size();
176 public Species getSpecies() {
181 public SortedSet<BinaryDomainCombination> toBinaryDomainCombinations() {
182 final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
183 for( final DomainId key : getAllCombinableDomainsIds().keySet() ) {
184 final CombinableDomains cb = getAllCombinableDomainsIds().get( key );
185 for( final BinaryDomainCombination b : cb.toBinaryDomainCombinations() ) {
186 binary_combinations.add( b );
189 return binary_combinations;
193 public String toString() {
194 return toStringBuilder( GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID ).toString();
197 // Produces something like:
198 // 2-oxoacid_dh 5 5 2 4.8E-67 Biotin_lipoyl [4], E3_binding [3]
200 public StringBuilder toStringBuilder( final GenomeWideCombinableDomainsSortOrder sort_order ) {
201 final StringBuilder sb = new StringBuilder();
202 final List<CombinableDomains> combinable_domains = new ArrayList<CombinableDomains>();
203 for( final DomainId key : getAllCombinableDomainsIds().keySet() ) {
204 final CombinableDomains cb = getAllCombinableDomainsIds().get( key );
205 combinable_domains.add( cb );
207 if ( sort_order == GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_COUNT ) {
208 Collections.sort( combinable_domains, BasicGenomeWideCombinableDomains.DESCENDING_KEY_DOMAIN_COUNT_ORDER );
210 else if ( sort_order == GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_PROTEINS_COUNT ) {
211 Collections.sort( combinable_domains,
212 BasicGenomeWideCombinableDomains.DESCENDING_KEY_DOMAIN_PROTEINS_COUNT_ORDER );
214 else if ( sort_order == GenomeWideCombinableDomainsSortOrder.COMBINATIONS_COUNT ) {
215 Collections.sort( combinable_domains, BasicGenomeWideCombinableDomains.DESCENDING_COMBINATIONS_COUNT_ORDER );
217 for( final CombinableDomains cb : combinable_domains ) {
218 sb.append( ForesterUtil.pad( new StringBuffer( cb.getKeyDomain().toString() ), 18, ' ', false ) );
219 sb.append( ForesterUtil.pad( new StringBuffer( "" + cb.getKeyDomainCount() ), 8, ' ', false ) );
220 sb.append( ForesterUtil.pad( new StringBuffer( "" + cb.getKeyDomainProteinsCount() ), 8, ' ', false ) );
221 sb.append( ForesterUtil.pad( new StringBuffer( "" + cb.getNumberOfCombinableDomains() ), 8, ' ', false ) );
222 sb.append( ForesterUtil.pad( new StringBuffer( ""
223 + FORMATTER.format( cb.getKeyDomainConfidenceDescriptiveStatistics()
228 sb.append( cb.getCombiningDomainIdsAsStringBuilder() );
229 sb.append( ForesterUtil.getLineSeparator() );
234 private static void countDomains( final Map<DomainId, Integer> domain_counts,
235 final Map<DomainId, Integer> domain_protein_counts,
236 final Map<DomainId, DescriptiveStatistics> stats,
237 final Set<DomainId> saw_c,
239 final double support ) {
240 if ( domain_counts.containsKey( id_i ) ) {
241 domain_counts.put( id_i, 1 + domain_counts.get( ( id_i ) ) );
242 if ( !saw_c.contains( id_i ) ) {
243 domain_protein_counts.put( id_i, 1 + domain_protein_counts.get( ( id_i ) ) );
247 stats.put( id_i, new BasicDescriptiveStatistics() );
248 domain_counts.put( id_i, 1 );
249 domain_protein_counts.put( id_i, 1 );
251 stats.get( id_i ).addValue( support );
255 public static BasicGenomeWideCombinableDomains createInstance( final List<Protein> protein_list,
256 final boolean ignore_combination_with_same_domain,
257 final Species species ) {
258 return createInstance( protein_list,
259 ignore_combination_with_same_domain,
262 DomainCombinationType.BASIC );
265 public static BasicGenomeWideCombinableDomains createInstance( final List<Protein> protein_list,
266 final boolean ignore_combination_with_same_domain,
267 final Species species,
268 final DomainCombinationType dc_type ) {
269 return createInstance( protein_list, ignore_combination_with_same_domain, species, null, dc_type );
272 public static BasicGenomeWideCombinableDomains createInstance( final List<Protein> protein_list,
273 final boolean ignore_combination_with_same_domain,
274 final Species species,
275 final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
276 final DomainCombinationType dc_type ) {
277 final BasicGenomeWideCombinableDomains instance = new BasicGenomeWideCombinableDomains( species, dc_type );
278 final Map<DomainId, Integer> domain_counts = new HashMap<DomainId, Integer>();
279 final Map<DomainId, Integer> domain_protein_counts = new HashMap<DomainId, Integer>();
280 final Map<DomainId, DescriptiveStatistics> stats = new HashMap<DomainId, DescriptiveStatistics>();
281 for( final Protein protein : protein_list ) {
282 if ( !protein.getSpecies().equals( species ) ) {
283 throw new IllegalArgumentException( "species (" + protein.getSpecies()
284 + ") does not match species of combinable domains collection (" + species + ")" );
286 final Set<DomainId> saw_i = new HashSet<DomainId>();
287 final Set<DomainId> saw_c = new HashSet<DomainId>();
288 for( int i = 0; i < protein.getProteinDomains().size(); ++i ) {
289 final Domain pd_i = protein.getProteinDomain( i );
290 final DomainId id_i = pd_i.getDomainId();
291 final int current_start = pd_i.getFrom();
292 BasicGenomeWideCombinableDomains.countDomains( domain_counts,
293 domain_protein_counts,
297 pd_i.getPerSequenceEvalue() );
298 if ( !saw_i.contains( id_i ) ) {
299 if ( dc_type == DomainCombinationType.BASIC ) {
302 CombinableDomains domain_combination = null;
303 if ( instance.contains( id_i ) ) {
304 domain_combination = instance.get( id_i );
307 if ( dc_type == DomainCombinationType.DIRECTED_ADJACTANT ) {
308 domain_combination = new AdjactantDirectedCombinableDomains( pd_i.getDomainId(), species );
310 else if ( dc_type == DomainCombinationType.DIRECTED ) {
311 domain_combination = new DirectedCombinableDomains( pd_i.getDomainId(), species );
314 domain_combination = new BasicCombinableDomains( pd_i.getDomainId(), species );
316 if ( ( domain_id_to_go_ids_map != null )
317 && domain_id_to_go_ids_map.containsKey( pd_i.getDomainId() ) ) {
318 final List<GoId> go_ids = domain_id_to_go_ids_map.get( pd_i.getDomainId() );
319 for( final GoId go_id : go_ids ) {
320 domain_combination.getKeyDomain().addGoId( go_id );
323 instance.add( id_i, domain_combination );
325 final Set<DomainId> saw_j = new HashSet<DomainId>();
326 if ( ignore_combination_with_same_domain ) {
329 Domain closest = null;
330 for( int j = 0; j < protein.getNumberOfProteinDomains(); ++j ) {
331 if ( ( dc_type != DomainCombinationType.BASIC )
332 && ( current_start >= protein.getProteinDomain( j ).getFrom() ) ) {
336 final DomainId id = protein.getProteinDomain( j ).getDomainId();
337 if ( !saw_j.contains( id ) ) {
339 if ( dc_type != DomainCombinationType.DIRECTED_ADJACTANT ) {
341 .addCombinableDomain( protein.getProteinDomain( j ).getDomainId() );
344 if ( closest == null ) {
345 closest = protein.getProteinDomain( j );
348 if ( protein.getProteinDomain( j ).getFrom() < closest.getFrom() ) {
349 closest = protein.getProteinDomain( j );
356 if ( ( dc_type == DomainCombinationType.DIRECTED_ADJACTANT ) && ( closest != null ) ) {
357 domain_combination.addCombinableDomain( closest.getDomainId() );
362 for( final DomainId key_id : domain_counts.keySet() ) {
363 instance.get( key_id ).setKeyDomainCount( domain_counts.get( key_id ) );
364 instance.get( key_id ).setKeyDomainProteinsCount( domain_protein_counts.get( key_id ) );
365 instance.get( key_id ).setKeyDomainConfidenceDescriptiveStatistics( stats.get( key_id ) );