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.util.DescriptiveStatistics;
38 class PrintableSpeciesSpecificDomainSimilariyData implements SpeciesSpecificDomainSimilariyData {
40 private final static NumberFormat FORMATTER = new DecimalFormat( "0.0E0" );
41 final SortedMap<DomainId, Integer> _combinable_domain_id_to_count_map;
42 final private int _key_domain_proteins_count;
43 final private int _key_domain_domains_count;
44 final private int _combinable_domains_count;
45 final private DescriptiveStatistics _key_domain_confidence_descriptive_statistics;
47 public PrintableSpeciesSpecificDomainSimilariyData( final int key_domain_proteins_count,
48 final int key_domain_domains_count,
49 final int combinable_domains,
50 final DescriptiveStatistics key_domain_confidence_descriptive_statistics ) {
51 _key_domain_proteins_count = key_domain_proteins_count;
52 _key_domain_domains_count = key_domain_domains_count;
53 _combinable_domains_count = combinable_domains;
54 _key_domain_confidence_descriptive_statistics = key_domain_confidence_descriptive_statistics;
55 _combinable_domain_id_to_count_map = new TreeMap<DomainId, Integer>();
59 public void addProteinsExhibitingCombinationCount( final DomainId domain_id, final int count ) {
60 if ( getCombinableDomainIdToCountsMap().containsKey( domain_id ) ) {
61 throw new IllegalArgumentException( "Domain with id " + domain_id + " already exists" );
63 getCombinableDomainIdToCountsMap().put( domain_id, count );
67 public SortedMap<DomainId, Integer> getCombinableDomainIdToCountsMap() {
68 return _combinable_domain_id_to_count_map;
71 private int getCombinableDomainsCount() {
72 return _combinable_domains_count;
75 private DescriptiveStatistics getKeyDomainConfidenceDescriptiveStatistics() {
76 return _key_domain_confidence_descriptive_statistics;
79 private int getKeyDomainDomainsCount() {
80 return _key_domain_domains_count;
83 private int getKeyDomainProteinsCount() {
84 return _key_domain_proteins_count;
88 public int getNumberOfProteinsExhibitingCombinationWith( final DomainId domain_id ) {
89 if ( !getCombinableDomainIdToCountsMap().containsKey( domain_id ) ) {
90 throw new IllegalArgumentException( "Domain with id " + domain_id + " not found" );
92 return getCombinableDomainIdToCountsMap().get( domain_id );
96 public String toString() {
97 return toStringBuffer( DomainSimilarityCalculator.Detailedness.LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES, false )
102 public StringBuffer toStringBuffer( final DomainSimilarityCalculator.Detailedness detailedness, final boolean html ) {
103 final StringBuffer sb = new StringBuffer();
104 if ( detailedness == DomainSimilarityCalculator.Detailedness.PUNCTILIOUS ) {
106 sb.append( getKeyDomainDomainsCount() );
108 sb.append( getKeyDomainProteinsCount() );
110 sb.append( getCombinableDomainsCount() );
115 sb.append( FORMATTER.format( getKeyDomainConfidenceDescriptiveStatistics().arithmeticMean() ) );
119 if ( !getCombinableDomainIdToCountsMap().isEmpty() ) {
123 final Set<DomainId> ids = getCombinableDomainIdToCountsMap().keySet();
125 for( final DomainId domain_id : ids ) {
129 sb.append( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_id.getId() + "\">"
130 + domain_id.getId() + "</a>" );
133 sb.append( domain_id.getId() );
135 if ( detailedness == DomainSimilarityCalculator.Detailedness.PUNCTILIOUS ) {
137 sb.append( getCombinableDomainIdToCountsMap().get( domain_id ) );
139 if ( i < ids.size() - 1 ) {