forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDomainSimilariyData.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: www.phylosoft.org/forester
  27
  28 package org.forester.surfacing;
  29
  30 import java.text.DecimalFormat;
  31 import java.text.NumberFormat;
  32 import java.util.Set;
  33 import java.util.SortedMap;
  34 import java.util.TreeMap;
  35
  36 import org.forester.util.DescriptiveStatistics;
  37
  38 class PrintableSpeciesSpecificDomainSimilariyData implements SpeciesSpecificDomainSimilariyData {
  39
  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;
  46
  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>();
  56     }
  57
  58     @Override
  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" );
  62         }
  63         getCombinableDomainIdToCountsMap().put( domain_id, count );
  64     }
  65
  66     @Override
  67     public SortedMap<DomainId, Integer> getCombinableDomainIdToCountsMap() {
  68         return _combinable_domain_id_to_count_map;
  69     }
  70
  71     private int getCombinableDomainsCount() {
  72         return _combinable_domains_count;
  73     }
  74
  75     private DescriptiveStatistics getKeyDomainConfidenceDescriptiveStatistics() {
  76         return _key_domain_confidence_descriptive_statistics;
  77     }
  78
  79     private int getKeyDomainDomainsCount() {
  80         return _key_domain_domains_count;
  81     }
  82
  83     private int getKeyDomainProteinsCount() {
  84         return _key_domain_proteins_count;
  85     }
  86
  87     @Override
  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" );
  91         }
  92         return getCombinableDomainIdToCountsMap().get( domain_id );
  93     }
  94
  95     @Override
  96     public String toString() {
  97         return toStringBuffer( DomainSimilarityCalculator.Detailedness.LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES, false )
  98                 .toString();
  99     }
 100
 101     @Override
 102     public StringBuffer toStringBuffer( final DomainSimilarityCalculator.Detailedness detailedness, final boolean html ) {
 103         final StringBuffer sb = new StringBuffer();
 104         if ( detailedness == DomainSimilarityCalculator.Detailedness.PUNCTILIOUS ) {
 105             sb.append( " " );
 106             sb.append( getKeyDomainDomainsCount() );
 107             sb.append( ", " );
 108             sb.append( getKeyDomainProteinsCount() );
 109             sb.append( ", " );
 110             sb.append( getCombinableDomainsCount() );
 111             sb.append( ", " );
 112             if ( html ) {
 113                 sb.append( "<i>" );
 114             }
 115             sb.append( FORMATTER.format( getKeyDomainConfidenceDescriptiveStatistics().arithmeticMean() ) );
 116             if ( html ) {
 117                 sb.append( "</i>" );
 118             }
 119             if ( !getCombinableDomainIdToCountsMap().isEmpty() ) {
 120                 sb.append( ":" );
 121             }
 122         }
 123         final Set<DomainId> ids = getCombinableDomainIdToCountsMap().keySet();
 124         int i = 0;
 125         for( final DomainId domain_id : ids ) {
 126             ++i;
 127             sb.append( " " );
 128             if ( html ) {
 129                 sb.append( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_id.getId() + "\">"
 130                         + domain_id.getId() + "</a>" );
 131             }
 132             else {
 133                 sb.append( domain_id.getId() );
 134             }
 135             if ( detailedness == DomainSimilarityCalculator.Detailedness.PUNCTILIOUS ) {
 136                 sb.append( ":" );
 137                 sb.append( getCombinableDomainIdToCountsMap().get( domain_id ) );
 138             }
 139             if ( i < ids.size() - 1 ) {
 140                 sb.append( "," );
 141             }
 142         }
 143         return sb;
 144     }
 145 }