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     public void addProteinsExhibitingCombinationCount( final DomainId domain_id, final int count ) {
  59         if ( getCombinableDomainIdToCountsMap().containsKey( domain_id ) ) {
  60             throw new IllegalArgumentException( "Domain with id " + domain_id + " already exists" );
  61         }
  62         getCombinableDomainIdToCountsMap().put( domain_id, count );
  63     }
  64
  65     public SortedMap<DomainId, Integer> getCombinableDomainIdToCountsMap() {
  66         return _combinable_domain_id_to_count_map;
  67     }
  68
  69     private int getCombinableDomainsCount() {
  70         return _combinable_domains_count;
  71     }
  72
  73     private DescriptiveStatistics getKeyDomainConfidenceDescriptiveStatistics() {
  74         return _key_domain_confidence_descriptive_statistics;
  75     }
  76
  77     private int getKeyDomainDomainsCount() {
  78         return _key_domain_domains_count;
  79     }
  80
  81     private int getKeyDomainProteinsCount() {
  82         return _key_domain_proteins_count;
  83     }
  84
  85     public int getNumberOfProteinsExhibitingCombinationWith( final DomainId domain_id ) {
  86         if ( !getCombinableDomainIdToCountsMap().containsKey( domain_id ) ) {
  87             throw new IllegalArgumentException( "Domain with id " + domain_id + " not found" );
  88         }
  89         return getCombinableDomainIdToCountsMap().get( domain_id );
  90     }
  91
  92     @Override
  93     public String toString() {
  94         return toStringBuffer( DomainSimilarityCalculator.Detailedness.LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES, false )
  95                 .toString();
  96     }
  97
  98     public StringBuffer toStringBuffer( final DomainSimilarityCalculator.Detailedness detailedness, final boolean html ) {
  99         final StringBuffer sb = new StringBuffer();
 100         if ( detailedness == DomainSimilarityCalculator.Detailedness.PUNCTILIOUS ) {
 101             sb.append( " " );
 102             sb.append( getKeyDomainDomainsCount() );
 103             sb.append( ", " );
 104             sb.append( getKeyDomainProteinsCount() );
 105             sb.append( ", " );
 106             sb.append( getCombinableDomainsCount() );
 107             sb.append( ", " );
 108             if ( html ) {
 109                 sb.append( "<i>" );
 110             }
 111             sb.append( FORMATTER.format( getKeyDomainConfidenceDescriptiveStatistics().arithmeticMean() ) );
 112             if ( html ) {
 113                 sb.append( "</i>" );
 114             }
 115             if ( !getCombinableDomainIdToCountsMap().isEmpty() ) {
 116                 sb.append( ":" );
 117             }
 118         }
 119         final Set<DomainId> ids = getCombinableDomainIdToCountsMap().keySet();
 120         int i = 0;
 121         for( final DomainId domain_id : ids ) {
 122             ++i;
 123             sb.append( " " );
 124             if ( html ) {
 125                 sb.append( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_id.getId() + "\">"
 126                         + domain_id.getId() + "</a>" );
 127             }
 128             else {
 129                 sb.append( domain_id.getId() );
 130             }
 131             if ( detailedness == DomainSimilarityCalculator.Detailedness.PUNCTILIOUS ) {
 132                 sb.append( ":" );
 133                 sb.append( getCombinableDomainIdToCountsMap().get( domain_id ) );
 134             }
 135             if ( i < ids.size() - 1 ) {
 136                 sb.append( "," );
 137             }
 138         }
 139         return sb;
 140     }
 141 }