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: https://sites.google.com/site/cmzmasek/home/software/forester
28 package org.forester.surfacing;
31 import java.util.SortedMap;
32 import java.util.SortedSet;
33 import java.util.TreeMap;
34 import java.util.TreeSet;
36 import org.forester.util.ForesterUtil;
37 import org.forester.util.SequenceAccessionTools;
39 class PrintableSpeciesSpecificDcData implements SpeciesSpecificDcData {
41 final SortedMap<String, Integer> _combinable_domain_id_to_count_map;
42 final SortedSet<String> _key_domain_proteins;
43 final private int _combinable_domains_count;
44 final private int _key_domain_domains_count;
46 public PrintableSpeciesSpecificDcData( final int key_domain_domains_count, final int combinable_domains ) {
47 _key_domain_proteins = new TreeSet<String>();
48 _key_domain_domains_count = key_domain_domains_count;
49 _combinable_domains_count = combinable_domains;
50 _combinable_domain_id_to_count_map = new TreeMap<String, Integer>();
54 public void addKeyDomainProtein( final String protein ) {
55 if ( ForesterUtil.isEmpty( protein ) ) {
56 throw new IllegalArgumentException( "attempt to add null or empty protein" );
58 if ( getKeyDomainProteins().contains( protein ) ) {
59 throw new IllegalArgumentException( "protein \"" + protein + "\" is not unique" );
61 getKeyDomainProteins().add( protein );
65 public void addProteinsExhibitingCombinationCount( final String domain_id, final int count ) {
66 if ( getCombinableDomainIdToCountsMap().containsKey( domain_id ) ) {
67 throw new IllegalArgumentException( "Domain with id " + domain_id + " already exists" );
69 getCombinableDomainIdToCountsMap().put( domain_id, count );
73 public SortedMap<String, Integer> getCombinableDomainIdToCountsMap() {
74 return _combinable_domain_id_to_count_map;
78 public SortedSet<String> getKeyDomainProteins() {
79 return _key_domain_proteins;
83 public int getNumberOfProteinsExhibitingCombinationWith( final String domain_id ) {
84 if ( !getCombinableDomainIdToCountsMap().containsKey( domain_id ) ) {
85 throw new IllegalArgumentException( "Domain with id " + domain_id + " not found" );
87 return getCombinableDomainIdToCountsMap().get( domain_id );
91 public String toString() {
92 return toStringBuffer( DomainSimilarityCalculator.Detailedness.LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES, false )
97 public StringBuffer toStringBuffer( final DomainSimilarityCalculator.Detailedness detailedness, final boolean html ) {
98 final StringBuffer sb = new StringBuffer();
99 if ( detailedness == DomainSimilarityCalculator.Detailedness.PUNCTILIOUS ) {
104 sb.append( getKeyDomainDomainsCount() );
107 sb.append( "</td><td>" );
112 sb.append( getKeyDomainProteinsCount() );
114 // sb.append( ", " );
115 sb.append( "</td><td>" );
120 sb.append( getCombinableDomainsCount() );
121 if ( html /*&& !getCombinableDomainIdToCountsMap().isEmpty()*/) {
123 sb.append( "</td><td>" );
127 final Set<String> ids = getCombinableDomainIdToCountsMap().keySet();
128 for( final String domain_id : ids ) {
131 sb.append( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_id + "\">" + domain_id
135 sb.append( domain_id );
137 if ( detailedness == DomainSimilarityCalculator.Detailedness.PUNCTILIOUS ) {
139 sb.append( getCombinableDomainIdToCountsMap().get( domain_id ) );
143 boolean first = true;
144 for( final String p : getKeyDomainProteins() ) {
145 final String link = obtainSeqLink( p );
155 sb.append( "</td>" );
160 private int getCombinableDomainsCount() {
161 return _combinable_domains_count;
164 private int getKeyDomainDomainsCount() {
165 return _key_domain_domains_count;
168 private int getKeyDomainProteinsCount() {
169 return _key_domain_proteins.size();
172 private static String obtainSeqLink( final String p ) {
174 final String up_id = SequenceAccessionTools.parseUniProtAccessorFromString( p );
175 if ( !ForesterUtil.isEmpty( up_id ) ) {
176 link = "<a class=\"pl\" href=\"" + ForesterUtil.UNIPROT_KB + up_id + "\" target=\"_up_window\">" + up_id
180 final String gb_id = SequenceAccessionTools.parseGenbankProteinAccessorFromString( p );
181 if ( !ForesterUtil.isEmpty( gb_id ) ) {
182 link = "<a class=\"pl\" href=\"" + ForesterUtil.NCBI_PROTEIN + gb_id + "\" target=\"_up_window\">"
186 final String gi = SequenceAccessionTools.parseGInumberFromString( p );
187 if ( !ForesterUtil.isEmpty( gi ) ) {
188 link = "<a class=\"pl\" href=\"" + ForesterUtil.NCBI_GI + gi + "\" target=\"_up_window\">gi|" + gi
192 link = "<a class=\"ps\" href=\"" + "http://www.google.com/search?q=" + p
193 + "\" target=\"_g_window\">" + p + "</a>";