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.protein.BinaryDomainCombination;
21 import org.forester.protein.BinaryDomainCombination.DomainCombinationType;
22 import org.forester.protein.Domain;
23 import org.forester.protein.DomainId;
24 import org.forester.protein.Protein;
25 import org.forester.species.Species;
26 import org.forester.util.BasicDescriptiveStatistics;
27 import org.forester.util.DescriptiveStatistics;
28 import org.forester.util.ForesterUtil;
30 public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDomains {
32 private final static NumberFormat FORMATTER = new DecimalFormat( "0.0E0" );
33 private static final Comparator<CombinableDomains> DESCENDING_KEY_DOMAIN_COUNT_ORDER = new Comparator<CombinableDomains>() {
36 public int compare( final CombinableDomains d1,
37 final CombinableDomains d2 ) {
38 if ( d1.getKeyDomainCount() < d2
39 .getKeyDomainCount() ) {
43 .getKeyDomainCount() > d2
44 .getKeyDomainCount() ) {
57 private static final Comparator<CombinableDomains> DESCENDING_KEY_DOMAIN_PROTEINS_COUNT_ORDER = new Comparator<CombinableDomains>() {
60 public int compare( final CombinableDomains d1,
61 final CombinableDomains d2 ) {
62 if ( d1.getKeyDomainProteinsCount() < d2
63 .getKeyDomainProteinsCount() ) {
67 .getKeyDomainProteinsCount() > d2
68 .getKeyDomainProteinsCount() ) {
81 private static final Comparator<CombinableDomains> DESCENDING_COMBINATIONS_COUNT_ORDER = new Comparator<CombinableDomains>() {
84 public int compare( final CombinableDomains d1,
85 final CombinableDomains d2 ) {
86 if ( d1.getNumberOfCombinableDomains() < d2
87 .getNumberOfCombinableDomains() ) {
91 .getNumberOfCombinableDomains() > d2
92 .getNumberOfCombinableDomains() ) {
105 final private SortedMap<DomainId, CombinableDomains> _combinable_domains_map;
106 final private Species _species;
107 final private DomainCombinationType _dc_type;
109 private BasicGenomeWideCombinableDomains( final Species species, final DomainCombinationType dc_type ) {
110 _combinable_domains_map = new TreeMap<DomainId, CombinableDomains>();
115 private void add( final DomainId key, final CombinableDomains cdc ) {
116 _combinable_domains_map.put( key, cdc );
120 public boolean contains( final DomainId key_id ) {
121 return _combinable_domains_map.containsKey( key_id );
125 public CombinableDomains get( final DomainId key_id ) {
126 return _combinable_domains_map.get( key_id );
130 public SortedMap<DomainId, CombinableDomains> getAllCombinableDomainsIds() {
131 return _combinable_domains_map;
135 public SortedSet<DomainId> getAllDomainIds() {
136 final SortedSet<DomainId> domains = new TreeSet<DomainId>();
137 for( final DomainId key : getAllCombinableDomainsIds().keySet() ) {
138 final CombinableDomains cb = getAllCombinableDomainsIds().get( key );
139 final List<DomainId> ds = cb.getAllDomains();
140 for( final DomainId d : ds ) {
148 public DomainCombinationType getDomainCombinationType() {
153 public SortedSet<DomainId> getMostPromiscuosDomain() {
154 final SortedSet<DomainId> doms = new TreeSet<DomainId>();
155 final int max = ( int ) getPerGenomeDomainPromiscuityStatistics().getMax();
156 for( final DomainId key : getAllCombinableDomainsIds().keySet() ) {
157 final CombinableDomains cb = getAllCombinableDomainsIds().get( key );
158 if ( cb.getNumberOfCombinableDomains() == max ) {
166 public DescriptiveStatistics getPerGenomeDomainPromiscuityStatistics() {
167 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
168 for( final DomainId key : getAllCombinableDomainsIds().keySet() ) {
169 final CombinableDomains cb = getAllCombinableDomainsIds().get( key );
170 stats.addValue( cb.getNumberOfCombinableDomains() );
176 public int getSize() {
177 return _combinable_domains_map.size();
181 public Species getSpecies() {
186 public SortedSet<BinaryDomainCombination> toBinaryDomainCombinations() {
187 final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
188 for( final DomainId key : getAllCombinableDomainsIds().keySet() ) {
189 final CombinableDomains cb = getAllCombinableDomainsIds().get( key );
190 for( final BinaryDomainCombination b : cb.toBinaryDomainCombinations() ) {
191 binary_combinations.add( b );
194 return binary_combinations;
198 public String toString() {
199 return toStringBuilder( GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID ).toString();
202 // Produces something like:
203 // 2-oxoacid_dh 5 5 2 4.8E-67 Biotin_lipoyl [4], E3_binding [3]
205 public StringBuilder toStringBuilder( final GenomeWideCombinableDomainsSortOrder sort_order ) {
206 final StringBuilder sb = new StringBuilder();
207 final List<CombinableDomains> combinable_domains = new ArrayList<CombinableDomains>();
208 for( final DomainId key : getAllCombinableDomainsIds().keySet() ) {
209 final CombinableDomains cb = getAllCombinableDomainsIds().get( key );
210 combinable_domains.add( cb );
212 if ( sort_order == GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_COUNT ) {
213 Collections.sort( combinable_domains, BasicGenomeWideCombinableDomains.DESCENDING_KEY_DOMAIN_COUNT_ORDER );
215 else if ( sort_order == GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_PROTEINS_COUNT ) {
216 Collections.sort( combinable_domains,
217 BasicGenomeWideCombinableDomains.DESCENDING_KEY_DOMAIN_PROTEINS_COUNT_ORDER );
219 else if ( sort_order == GenomeWideCombinableDomainsSortOrder.COMBINATIONS_COUNT ) {
220 Collections.sort( combinable_domains, BasicGenomeWideCombinableDomains.DESCENDING_COMBINATIONS_COUNT_ORDER );
222 for( final CombinableDomains cb : combinable_domains ) {
223 sb.append( ForesterUtil.pad( new StringBuffer( cb.getKeyDomain().toString() ), 18, ' ', false ) );
224 sb.append( ForesterUtil.pad( new StringBuffer( "" + cb.getKeyDomainCount() ), 8, ' ', false ) );
225 sb.append( ForesterUtil.pad( new StringBuffer( "" + cb.getKeyDomainProteinsCount() ), 8, ' ', false ) );
226 sb.append( ForesterUtil.pad( new StringBuffer( "" + cb.getNumberOfCombinableDomains() ), 8, ' ', false ) );
227 sb.append( ForesterUtil.pad( new StringBuffer( ""
228 + FORMATTER.format( cb.getKeyDomainConfidenceDescriptiveStatistics()
233 sb.append( cb.getCombiningDomainIdsAsStringBuilder() );
234 sb.append( ForesterUtil.getLineSeparator() );
239 private static void countDomains( final Map<DomainId, Integer> domain_counts,
240 final Map<DomainId, Integer> domain_protein_counts,
241 final Map<DomainId, DescriptiveStatistics> stats,
242 final Set<DomainId> saw_c,
244 final double support ) {
245 if ( domain_counts.containsKey( id_i ) ) {
246 domain_counts.put( id_i, 1 + domain_counts.get( ( id_i ) ) );
247 if ( !saw_c.contains( id_i ) ) {
248 domain_protein_counts.put( id_i, 1 + domain_protein_counts.get( ( id_i ) ) );
252 stats.put( id_i, new BasicDescriptiveStatistics() );
253 domain_counts.put( id_i, 1 );
254 domain_protein_counts.put( id_i, 1 );
256 stats.get( id_i ).addValue( support );
260 public static BasicGenomeWideCombinableDomains createInstance( final List<Protein> protein_list,
261 final boolean ignore_combination_with_same_domain,
262 final Species species ) {
263 return createInstance( protein_list,
264 ignore_combination_with_same_domain,
267 DomainCombinationType.BASIC,
272 public static BasicGenomeWideCombinableDomains createInstance( final List<Protein> protein_list,
273 final boolean ignore_combination_with_same_domain,
274 final Species species,
275 final DomainCombinationType dc_type ) {
276 return createInstance( protein_list, ignore_combination_with_same_domain, species, null, dc_type, null, null );
279 public static BasicGenomeWideCombinableDomains createInstance( final List<Protein> protein_list,
280 final boolean ignore_combination_with_same_domain,
281 final Species species,
282 final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
283 final DomainCombinationType dc_type,
284 final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
285 final Map<String, DescriptiveStatistics> domain_number_stats_by_dc ) {
286 final BasicGenomeWideCombinableDomains instance = new BasicGenomeWideCombinableDomains( species, dc_type );
287 final Map<DomainId, Integer> domain_counts = new HashMap<DomainId, Integer>();
288 final Map<DomainId, Integer> domain_protein_counts = new HashMap<DomainId, Integer>();
289 final Map<DomainId, DescriptiveStatistics> stats = new HashMap<DomainId, DescriptiveStatistics>();
290 for( final Protein protein : protein_list ) {
291 if ( !protein.getSpecies().equals( species ) ) {
292 throw new IllegalArgumentException( "species (" + protein.getSpecies()
293 + ") does not match species of combinable domains collection (" + species + ")" );
295 final Set<DomainId> saw_i = new HashSet<DomainId>();
296 final Set<DomainId> saw_c = new HashSet<DomainId>();
297 for( int i = 0; i < protein.getProteinDomains().size(); ++i ) {
298 final Domain pd_i = protein.getProteinDomain( i );
299 final DomainId id_i = pd_i.getDomainId();
300 final int current_start = pd_i.getFrom();
301 BasicGenomeWideCombinableDomains.countDomains( domain_counts,
302 domain_protein_counts,
306 pd_i.getPerSequenceEvalue() );
307 if ( !saw_i.contains( id_i ) ) {
308 if ( dc_type == DomainCombinationType.BASIC ) {
311 CombinableDomains domain_combination = null;
312 if ( instance.contains( id_i ) ) {
313 domain_combination = instance.get( id_i );
316 if ( dc_type == DomainCombinationType.DIRECTED_ADJACTANT ) {
317 domain_combination = new AdjactantDirectedCombinableDomains( pd_i.getDomainId(), species );
319 else if ( dc_type == DomainCombinationType.DIRECTED ) {
320 domain_combination = new DirectedCombinableDomains( pd_i.getDomainId(), species );
323 domain_combination = new BasicCombinableDomains( pd_i.getDomainId(), species );
325 if ( ( domain_id_to_go_ids_map != null )
326 && domain_id_to_go_ids_map.containsKey( pd_i.getDomainId() ) ) {
327 final List<GoId> go_ids = domain_id_to_go_ids_map.get( pd_i.getDomainId() );
328 for( final GoId go_id : go_ids ) {
329 domain_combination.getKeyDomain().addGoId( go_id );
332 instance.add( id_i, domain_combination );
334 final Set<DomainId> saw_j = new HashSet<DomainId>();
335 if ( ignore_combination_with_same_domain ) {
338 Domain closest = null;
339 for( int j = 0; j < protein.getNumberOfProteinDomains(); ++j ) {
340 if ( ( dc_type != DomainCombinationType.BASIC )
341 && ( current_start >= protein.getProteinDomain( j ).getFrom() ) ) {
345 final DomainId id = protein.getProteinDomain( j ).getDomainId();
346 if ( !saw_j.contains( id ) ) {
348 if ( dc_type != DomainCombinationType.DIRECTED_ADJACTANT ) {
350 .addCombinableDomain( protein.getProteinDomain( j ).getDomainId() );
353 if ( closest == null ) {
354 closest = protein.getProteinDomain( j );
357 if ( protein.getProteinDomain( j ).getFrom() < closest.getFrom() ) {
358 closest = protein.getProteinDomain( j );
365 if ( ( dc_type == DomainCombinationType.DIRECTED_ADJACTANT ) && ( closest != null ) ) {
366 domain_combination.addCombinableDomain( closest.getDomainId() );
368 if ( protein_length_stats_by_dc != null ) {
369 final List<BinaryDomainCombination> dcs = domain_combination.toBinaryDomainCombinations();
370 for( final BinaryDomainCombination dc : dcs ) {
371 final String dc_str = dc.toString();
372 if ( !protein_length_stats_by_dc.containsKey( dc_str ) ) {
373 protein_length_stats_by_dc.put( dc_str, new BasicDescriptiveStatistics() );
375 protein_length_stats_by_dc.get( dc_str ).addValue( protein.getLength() );
378 if ( domain_number_stats_by_dc != null ) {
379 final List<BinaryDomainCombination> dcs = domain_combination.toBinaryDomainCombinations();
380 for( final BinaryDomainCombination dc : dcs ) {
381 final String dc_str = dc.toString();
382 if ( !domain_number_stats_by_dc.containsKey( dc_str ) ) {
383 domain_number_stats_by_dc.put( dc_str, new BasicDescriptiveStatistics() );
385 domain_number_stats_by_dc.get( dc_str ).addValue( protein.getNumberOfProteinDomains() );
392 for( final DomainId key_id : domain_counts.keySet() ) {
393 instance.get( key_id ).setKeyDomainCount( domain_counts.get( key_id ) );
394 instance.get( key_id ).setKeyDomainProteinsCount( domain_protein_counts.get( key_id ) );
395 instance.get( key_id ).setKeyDomainConfidenceDescriptiveStatistics( stats.get( key_id ) );