2 // 22:09:42 cmzmasek Exp $
4 // FORESTER -- software libraries and applications
5 // for evolutionary biology research and applications.
7 // Copyright (C) 2008-2009 Christian M. Zmasek
8 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
11 // This library is free software; you can redistribute it and/or
12 // modify it under the terms of the GNU Lesser General Public
13 // License as published by the Free Software Foundation; either
14 // version 2.1 of the License, or (at your option) any later version.
16 // This library is distributed in the hope that it will be useful,
17 // but WITHOUT ANY WARRANTY; without even the implied warranty of
18 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 // Lesser General Public License for more details.
21 // You should have received a copy of the GNU Lesser General Public
22 // License along with this library; if not, write to the Free Software
23 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
25 // Contact: phylosoft @ gmail . com
26 // WWW: www.phylosoft.org/forester
28 package org.forester.surfacing;
30 import java.text.DecimalFormat;
31 import java.text.NumberFormat;
33 import java.util.SortedMap;
34 import java.util.TreeMap;
36 import org.forester.protein.DomainId;
37 import org.forester.util.DescriptiveStatistics;
39 class PrintableSpeciesSpecificDomainSimilariyData implements SpeciesSpecificDomainSimilariyData {
41 private final static NumberFormat FORMATTER = new DecimalFormat( "0.0E0" );
42 final SortedMap<DomainId, Integer> _combinable_domain_id_to_count_map;
43 final private int _key_domain_proteins_count;
44 final private int _key_domain_domains_count;
45 final private int _combinable_domains_count;
46 final private DescriptiveStatistics _key_domain_confidence_descriptive_statistics;
48 public PrintableSpeciesSpecificDomainSimilariyData( final int key_domain_proteins_count,
49 final int key_domain_domains_count,
50 final int combinable_domains,
51 final DescriptiveStatistics key_domain_confidence_descriptive_statistics ) {
52 _key_domain_proteins_count = key_domain_proteins_count;
53 _key_domain_domains_count = key_domain_domains_count;
54 _combinable_domains_count = combinable_domains;
55 _key_domain_confidence_descriptive_statistics = key_domain_confidence_descriptive_statistics;
56 _combinable_domain_id_to_count_map = new TreeMap<DomainId, Integer>();
60 public void addProteinsExhibitingCombinationCount( final DomainId domain_id, final int count ) {
61 if ( getCombinableDomainIdToCountsMap().containsKey( domain_id ) ) {
62 throw new IllegalArgumentException( "Domain with id " + domain_id + " already exists" );
64 getCombinableDomainIdToCountsMap().put( domain_id, count );
68 public SortedMap<DomainId, Integer> getCombinableDomainIdToCountsMap() {
69 return _combinable_domain_id_to_count_map;
72 private int getCombinableDomainsCount() {
73 return _combinable_domains_count;
76 private DescriptiveStatistics getKeyDomainConfidenceDescriptiveStatistics() {
77 return _key_domain_confidence_descriptive_statistics;
80 private int getKeyDomainDomainsCount() {
81 return _key_domain_domains_count;
84 private int getKeyDomainProteinsCount() {
85 return _key_domain_proteins_count;
89 public int getNumberOfProteinsExhibitingCombinationWith( final DomainId domain_id ) {
90 if ( !getCombinableDomainIdToCountsMap().containsKey( domain_id ) ) {
91 throw new IllegalArgumentException( "Domain with id " + domain_id + " not found" );
93 return getCombinableDomainIdToCountsMap().get( domain_id );
97 public String toString() {
98 return toStringBuffer( DomainSimilarityCalculator.Detailedness.LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES, false )
103 public StringBuffer toStringBuffer( final DomainSimilarityCalculator.Detailedness detailedness, final boolean html ) {
104 final StringBuffer sb = new StringBuffer();
105 if ( detailedness == DomainSimilarityCalculator.Detailedness.PUNCTILIOUS ) {
107 sb.append( getKeyDomainDomainsCount() );
109 sb.append( getKeyDomainProteinsCount() );
111 sb.append( getCombinableDomainsCount() );
116 sb.append( FORMATTER.format( getKeyDomainConfidenceDescriptiveStatistics().arithmeticMean() ) );
120 if ( !getCombinableDomainIdToCountsMap().isEmpty() ) {
124 final Set<DomainId> ids = getCombinableDomainIdToCountsMap().keySet();
126 for( final DomainId domain_id : ids ) {
130 sb.append( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_id.getId() + "\">"
131 + domain_id.getId() + "</a>" );
134 sb.append( domain_id.getId() );
136 if ( detailedness == DomainSimilarityCalculator.Detailedness.PUNCTILIOUS ) {
138 sb.append( getCombinableDomainIdToCountsMap().get( domain_id ) );
140 if ( i < ( ids.size() - 1 ) ) {