forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java

   1 // $Id:
   2 // 22:09:42 cmzmasek Exp $
   3 //
   4 // FORESTER -- software libraries and applications
   5 // for evolutionary biology research and applications.
   6 //
   7 // Copyright (C) 2008-2009 Christian M. Zmasek
   8 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   9 // All rights reserved
  10 //
  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.
  15 //
  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.
  20 //
  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
  24 //
  25 // Contact: phylosoft @ gmail . com
  26 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  27
  28 package org.forester.surfacing;
  29
  30 import java.util.Set;
  31 import java.util.SortedMap;
  32 import java.util.SortedSet;
  33 import java.util.TreeMap;
  34 import java.util.TreeSet;
  35
  36 import org.forester.util.ForesterUtil;
  37 import org.forester.util.SequenceAccessionTools;
  38
  39 class PrintableSpeciesSpecificDcData implements SpeciesSpecificDcData {
  40
  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;
  45
  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>();
  51     }
  52
  53     @Override
  54     public void addKeyDomainProtein( final String protein ) {
  55         if ( ForesterUtil.isEmpty( protein ) ) {
  56             throw new IllegalArgumentException( "attempt to add null or empty protein" );
  57         }
  58         if ( getKeyDomainProteins().contains( protein ) ) {
  59             throw new IllegalArgumentException( "protein \"" + protein + "\" is not unique" );
  60         }
  61         getKeyDomainProteins().add( protein );
  62     }
  63
  64     @Override
  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" );
  68         }
  69         getCombinableDomainIdToCountsMap().put( domain_id, count );
  70     }
  71
  72     @Override
  73     public SortedMap<String, Integer> getCombinableDomainIdToCountsMap() {
  74         return _combinable_domain_id_to_count_map;
  75     }
  76
  77     @Override
  78     public SortedSet<String> getKeyDomainProteins() {
  79         return _key_domain_proteins;
  80     }
  81
  82     @Override
  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" );
  86         }
  87         return getCombinableDomainIdToCountsMap().get( domain_id );
  88     }
  89
  90     @Override
  91     public String toString() {
  92         return toStringBuffer( DomainSimilarityCalculator.Detailedness.LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES, false )
  93                 .toString();
  94     }
  95
  96     @Override
  97     public StringBuffer toStringBuffer( final DomainSimilarityCalculator.Detailedness detailedness, final boolean html ) {
  98         final StringBuffer sb = new StringBuffer();
  99         if ( detailedness == DomainSimilarityCalculator.Detailedness.PUNCTILIOUS ) {
 100             if ( html ) {
 101                 sb.append( " " );
 102             }
 103             sb.append( getKeyDomainDomainsCount() );
 104             if ( html ) {
 105                 sb.append( ", " );
 106             }
 107             else {
 108                 sb.append( "\t" );
 109             }
 110             sb.append( getKeyDomainProteinsCount() );
 111             if ( html ) {
 112                 sb.append( ", " );
 113             }
 114             else {
 115                 sb.append( "\t" );
 116             }
 117             sb.append( getCombinableDomainsCount() );
 118             if ( html && !getCombinableDomainIdToCountsMap().isEmpty() ) {
 119                 sb.append( ":" );
 120             }
 121         }
 122         if ( html ) {
 123             final Set<String> ids = getCombinableDomainIdToCountsMap().keySet();
 124             for( final String domain_id : ids ) {
 125                 sb.append( " " );
 126                 if ( html ) {
 127                     sb.append( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_id + "\">" + domain_id
 128                             + "</a>" );
 129                 }
 130                 else {
 131                     sb.append( domain_id );
 132                 }
 133                 if ( detailedness == DomainSimilarityCalculator.Detailedness.PUNCTILIOUS ) {
 134                     sb.append( ":" );
 135                     sb.append( getCombinableDomainIdToCountsMap().get( domain_id ) );
 136                 }
 137             }
 138             sb.append( " [" );
 139             boolean first = true;
 140             for( final String p : getKeyDomainProteins() ) {
 141                 final String link = obtainSeqLink( p );
 142                 if ( first ) {
 143                     first = false;
 144                 }
 145                 else {
 146                     sb.append( ", " );
 147                 }
 148                 sb.append( link );
 149             }
 150             sb.append( "]" );
 151         }
 152         return sb;
 153     }
 154
 155     private int getCombinableDomainsCount() {
 156         return _combinable_domains_count;
 157     }
 158
 159     private int getKeyDomainDomainsCount() {
 160         return _key_domain_domains_count;
 161     }
 162
 163     private int getKeyDomainProteinsCount() {
 164         return _key_domain_proteins.size();
 165     }
 166
 167     private static String obtainSeqLink( final String p ) {
 168         String link;
 169         final String up_id = SequenceAccessionTools.parseUniProtAccessorFromString( p );
 170         if ( !ForesterUtil.isEmpty( up_id ) ) {
 171             link = "<a class=\"pl\" href=\"" + ForesterUtil.UNIPROT_KB + up_id + "\" target=\"_up_window\">" + up_id
 172                     + "</a>";
 173         }
 174         else {
 175             final String gb_id = SequenceAccessionTools.parseGenbankProteinAccessorFromString( p );
 176             if ( !ForesterUtil.isEmpty( gb_id ) ) {
 177                 link = "<a class=\"pl\" href=\"" + ForesterUtil.NCBI_PROTEIN + gb_id + "\" target=\"_up_window\">"
 178                         + gb_id + "</a>";
 179             }
 180             else {
 181                 final String gi = SequenceAccessionTools.parseGInumberFromString( p );
 182                 if ( !ForesterUtil.isEmpty( gi ) ) {
 183                     link = "<a class=\"pl\" href=\"" + ForesterUtil.NCBI_GI + gi + "\" target=\"_up_window\">gi|" + gi
 184                             + "</a>";
 185                 }
 186                 else {
 187                     link = "<a class=\"ps\" href=\"" + "http://www.google.com/search?q=" + p
 188                             + "\" target=\"_g_window\">" + p + "</a>";
 189                 }
 190             }
 191         }
 192         return link;
 193     }
 194 }