package org.forester.surfacing;
+import java.awt.Color;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
import java.util.SortedMap;
import java.util.SortedSet;
+import java.util.TreeMap;
+import java.util.TreeSet;
+import org.forester.phylogeny.Phylogeny;
import org.forester.species.Species;
-import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
+import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
+import org.forester.util.ForesterUtil;
-/*
- * This is to represent a measure of similarity between two or more domains from
- * different genomes.
- */
-public interface DomainSimilarity extends Comparable<DomainSimilarity> {
+public class DomainSimilarity implements Comparable<DomainSimilarity> {
- static public enum DomainSimilarityScoring {
- DOMAINS, PROTEINS, COMBINATIONS;
+ final public static String SPECIES_SEPARATOR = " ";
+ final private static int EQUAL = 0;
+ final private static String NO_SPECIES = " ";
+ private static final boolean OUTPUT_TAXCODES_PER_DOMAIN = false;
+ final private CombinableDomains _combinable_domains;
+ private DomainSimilarityCalculator.Detailedness _detailedness;
+ final private double _max;
+ private final int _max_difference;
+ private final int _max_difference_in_counts;
+ final private double _mean;
+ final private double _min;
+ final private int _n;
+ final private double _sd;
+ final private SortedMap<Species, SpeciesSpecificDcData> _species_data;
+ private List<Species> _species_order;
+ private final boolean _treat_as_binary_comparison;
+
+ public DomainSimilarity( final CombinableDomains combinable_domains,
+ final double min,
+ final double max,
+ final double mean,
+ final double median,
+ final double sd,
+ final int n,
+ final int max_difference_in_counts,
+ final int max_difference,
+ final SortedMap<Species, SpeciesSpecificDcData> species_data,
+ final boolean sort_by_species_count_first,
+ final boolean treat_as_binary_comparison ) {
+ if ( combinable_domains == null ) {
+ throw new IllegalArgumentException( "attempt to use null combinable domains" );
+ }
+ if ( species_data == null ) {
+ throw new IllegalArgumentException( "attempt to use null species data" );
+ }
+ if ( species_data.size() < 1 ) {
+ throw new IllegalArgumentException( "attempt to use empty species data" );
+ }
+ if ( n < 0 ) {
+ throw new IllegalArgumentException( "attempt to use N less than 0" );
+ }
+ if ( ( species_data.size() > 1 ) && ( n < 1 ) ) {
+ throw new IllegalArgumentException( "attempt to use N less than 1" );
+ }
+ if ( sd < 0.0 ) {
+ throw new IllegalArgumentException( "attempt to use negative SD" );
+ }
+ if ( max < min ) {
+ throw new IllegalArgumentException( "attempt to use max smaller than min" );
+ }
+ init();
+ _combinable_domains = combinable_domains;
+ _min = min;
+ _max = max;
+ _mean = mean;
+ _sd = sd;
+ _n = n;
+ _max_difference_in_counts = max_difference_in_counts;
+ _max_difference = max_difference;
+ _species_data = species_data;
+ _treat_as_binary_comparison = treat_as_binary_comparison;
+ final int s = species_data.size();
+ if ( ( ( s * s ) - s ) != ( getN() * 2 ) ) {
+ throw new IllegalArgumentException( "illegal species count and n: species count:" + s + ", n:" + _n
+ + " for domain " + combinable_domains.getKeyDomain() );
+ }
+ if ( s > 2 ) {
+ if ( getMaximalDifferenceInCounts() < 0 ) {
+ throw new IllegalArgumentException( "attempt to use negative max difference in counts with more than two species" );
+ }
+ if ( getMaximalDifference() < 0 ) {
+ throw new IllegalArgumentException( "attempt to use negative max difference with more than two species" );
+ }
+ }
}
- public static enum DomainSimilaritySortField {
- MIN, MAX, SD, MEAN, ABS_MAX_COUNTS_DIFFERENCE, MAX_COUNTS_DIFFERENCE, MAX_DIFFERENCE, SPECIES_COUNT, DOMAIN_ID,
+ public DomainSimilarity( final CombinableDomains combinable_domains,
+ final int max_difference_in_counts,
+ final int max_difference,
+ final SortedMap<Species, SpeciesSpecificDcData> species_data,
+ final boolean sort_by_species_count_first,
+ final boolean treat_as_binary_comparison ) {
+ if ( combinable_domains == null ) {
+ throw new IllegalArgumentException( "attempt to use null combinable domains" );
+ }
+ if ( species_data == null ) {
+ throw new IllegalArgumentException( "attempt to use null species data" );
+ }
+ if ( species_data.size() < 1 ) {
+ throw new IllegalArgumentException( "attempt to use empty species data" );
+ }
+ init();
+ _combinable_domains = combinable_domains;
+ _min = -1;
+ _max = -1;
+ _mean = -1;
+ _sd = -1;
+ _n = -1;
+ _max_difference_in_counts = max_difference_in_counts;
+ _max_difference = max_difference;
+ _species_data = species_data;
+ _treat_as_binary_comparison = treat_as_binary_comparison;
+ final int s = species_data.size();
+ if ( s > 2 ) {
+ if ( getMaximalDifferenceInCounts() < 0 ) {
+ throw new IllegalArgumentException( "attempt to use negative max difference in counts with more than two species" );
+ }
+ if ( getMaximalDifference() < 0 ) {
+ throw new IllegalArgumentException( "attempt to use negative max difference with more than two species" );
+ }
+ }
+ }
+
+ @Override
+ public int compareTo( final DomainSimilarity domain_similarity ) {
+ if ( this == domain_similarity ) {
+ return EQUAL;
+ }
+ else if ( domain_similarity == null ) {
+ throw new IllegalArgumentException( "attempt to compare " + this.getClass() + " to null" );
+ }
+ else if ( domain_similarity.getClass() != this.getClass() ) {
+ throw new IllegalArgumentException( "attempt to compare " + this.getClass() + " to "
+ + domain_similarity.getClass() );
+ }
+ return compareByDomainId( domain_similarity );
}
- public SortedSet<String> getCombinableDomainIds( final Species species_of_combinable_domain );
+ public SortedSet<String> getCombinableDomainIds( final Species species_of_combinable_domain ) {
+ final SortedSet<String> sorted_ids = new TreeSet<String>();
+ if ( getSpeciesData().containsKey( species_of_combinable_domain ) ) {
+ for( final String id : getSpeciesData().get( species_of_combinable_domain )
+ .getCombinableDomainIdToCountsMap().keySet() ) {
+ sorted_ids.add( id );
+ }
+ }
+ return sorted_ids;
+ }
- public String getDomainId();
+ public String getDomainId() {
+ return getCombinableDomains().getKeyDomain();
+ }
/**
* For pairwise similarities, this should return the "difference"; for example the difference in counts
* for copy number based features (the same as getMaximalDifferenceInCounts(), or the number
- * of actually different domain combinations.
+ * of actually different domain combinations.
* For pairwise similarities, this should return the difference,
* while for comparisons of more than two domains, this should return the maximal difference
- *
- *
- *
- * @return
+ *
*/
- public int getMaximalDifference();
+ public int getMaximalDifference() {
+ return _max_difference;
+ }
/**
* For pairwise similarities, this should return the difference in counts,
* while for comparisons of more than two domains, this should return the maximal difference
* in counts
- *
- *
+ *
+ *
* @return the (maximal) difference in counts
*/
- public int getMaximalDifferenceInCounts();
+ public int getMaximalDifferenceInCounts() {
+ return _max_difference_in_counts;
+ }
- public double getMaximalSimilarityScore();
+ public double getMaximalSimilarityScore() {
+ return _max;
+ }
- public double getMeanSimilarityScore();
+ public double getMeanSimilarityScore() {
+ return _mean;
+ }
- public double getMinimalSimilarityScore();
+ public double getMinimalSimilarityScore() {
+ return _min;
+ }
/**
* This should return the number of pairwise distances used to calculate
* this similarity score
- *
+ *
* @return the number of pairwise distances
*/
- public int getN();
+ public int getN() {
+ return _n;
+ }
+
+ public SortedSet<Species> getSpecies() {
+ final SortedSet<Species> species = new TreeSet<Species>();
+ for( final Species s : getSpeciesData().keySet() ) {
+ species.add( s );
+ }
+ return species;
+ }
- public SortedSet<Species> getSpecies();
+ public List<Species> getSpeciesCustomOrder() {
+ return _species_order;
+ }
/**
* This should return a map, which maps species names to
* SpeciesSpecificDomainSimilariyData
- *
- *
+ *
+ *
* @return SortedMap<String, SpeciesSpecificDomainSimilariyData>
*/
- public SortedMap<Species, SpeciesSpecificDomainSimilariyData> getSpeciesData();
+ public SortedMap<Species, SpeciesSpecificDcData> getSpeciesData() {
+ return _species_data;
+ }
+
+ public double getStandardDeviationOfSimilarityScore() {
+ return _sd;
+ }
+
+ public void setDetailedness( final Detailedness detailedness ) {
+ _detailedness = detailedness;
+ }
+
+ public void setSpeciesOrder( final List<Species> species_order ) {
+ if ( !species_order.containsAll( getSpeciesData().keySet() ) ) {
+ throw new IllegalArgumentException( "list to order species must contain all species of multiple combinable domains similarity" );
+ }
+ _species_order = species_order;
+ }
+
+ public StringBuffer toStringBuffer( final DomainSimilarity.PRINT_OPTION print_option,
+ final Map<String, Integer> tax_code_to_id_map,
+ final Phylogeny phy ) {
+ switch ( print_option ) {
+ case SIMPLE_TAB_DELIMITED:
+ return toStringBufferSimpleTabDelimited();
+ case HTML:
+ return toStringBufferDetailedHTML( tax_code_to_id_map, phy, OUTPUT_TAXCODES_PER_DOMAIN );
+ default:
+ throw new AssertionError( "Unknown print option: " + print_option );
+ }
+ }
+
+ private void addSpeciesSpecificDomainData( final StringBuffer sb,
+ final Species species,
+ final boolean html,
+ final Map<String, Integer> tax_code_to_id_map,
+ final Phylogeny phy ) {
+ if ( html ) {
+ sb.append( "<tr>" );
+ sb.append( "<td>" );
+ addTaxWithLink( sb, species.getSpeciesId(), tax_code_to_id_map, phy );
+ sb.append( "</td>" );
+ }
+ else {
+ sb.append( species.getSpeciesId() );
+ }
+ if ( getDetaildness() != DomainSimilarityCalculator.Detailedness.BASIC ) {
+ if ( html ) {
+ //sb.append( ":" );
+ }
+ else {
+ sb.append( "\t" );
+ }
+ sb.append( getSpeciesData().get( species ).toStringBuffer( getDetaildness(), html ) );
+ }
+ if ( html ) {
+ //sb.append( "<br>" );
+ sb.append( "</tr>" );
+ }
+ else {
+ sb.append( "\n\t" );
+ }
+ }
+
+ private void addTaxWithLink( final StringBuffer sb,
+ final String tax_code,
+ final Map<String, Integer> tax_code_to_id_map,
+ final Phylogeny phy ) {
+ String hex = null;
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ hex = SurfacingUtil.obtainHexColorStringDependingOnTaxonomyGroup( tax_code, phy );
+ }
+ sb.append( "<b>" );
+ if ( !ForesterUtil.isEmpty( tax_code )
+ && ( ( tax_code_to_id_map != null ) && tax_code_to_id_map.containsKey( tax_code ) ) ) {
+ if ( !ForesterUtil.isEmpty( hex ) ) {
+ sb.append( "<a href=\"" );
+ sb.append( SurfacingConstants.UNIPROT_TAXONOMY_ID_LINK );
+ sb.append( tax_code_to_id_map.get( tax_code ) );
+ sb.append( "\" target=\"tw\"><span style=\"color:" );
+ sb.append( hex );
+ sb.append( "\">" );
+ sb.append( tax_code );
+ sb.append( "</span></a>" );
+ }
+ else {
+ sb.append( "<a href=\"" );
+ sb.append( SurfacingConstants.UNIPROT_TAXONOMY_ID_LINK );
+ sb.append( tax_code_to_id_map.get( tax_code ) );
+ sb.append( "\" target=\"tw\">" );
+ sb.append( tax_code );
+ sb.append( "</a>" );
+ }
+ }
+ else {
+ sb.append( tax_code );
+ }
+ sb.append( "</b>" );
+ }
+
+ private int compareByDomainId( final DomainSimilarity other ) {
+ return getDomainId().compareToIgnoreCase( other.getDomainId() );
+ }
- public double getStandardDeviationOfSimilarityScore();
+ private CombinableDomains getCombinableDomains() {
+ return _combinable_domains;
+ }
- public StringBuffer toStringBuffer( PRINT_OPTION print_option, Map<String, Integer> tax_code_to_id_map );
+ private DomainSimilarityCalculator.Detailedness getDetaildness() {
+ return _detailedness;
+ }
+
+ private StringBuffer getDomainDataInAlphabeticalOrder() {
+ final SortedMap<String, SortedSet<String>> m = new TreeMap<String, SortedSet<String>>();
+ final StringBuffer sb = new StringBuffer();
+ for( final Species species : getSpeciesData().keySet() ) {
+ for( final String combable_dom : getCombinableDomainIds( species ) ) {
+ if ( !m.containsKey( combable_dom ) ) {
+ m.put( combable_dom, new TreeSet<String>() );
+ }
+ m.get( combable_dom ).add( species.getSpeciesId() );
+ }
+ }
+ for( final Map.Entry<String, SortedSet<String>> e : m.entrySet() ) {
+ sb.append( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + e.getKey() + "\">" + e.getKey() + "</a>" );
+ sb.append( " " );
+ sb.append( "<span style=\"font-size:7px\">" );
+ for( final String tax : e.getValue() ) {
+ final String hex = SurfacingUtil.obtainHexColorStringDependingOnTaxonomyGroup( tax, null );
+ if ( !ForesterUtil.isEmpty( hex ) ) {
+ sb.append( "<span style=\"color:" );
+ sb.append( hex );
+ sb.append( "\">" );
+ sb.append( tax );
+ sb.append( "</span>" );
+ }
+ else {
+ sb.append( tax );
+ }
+ sb.append( " " );
+ }
+ sb.append( "</span>" );
+ sb.append( "<br>\n" );
+ }
+ return sb;
+ }
+
+ private StringBuffer getSpeciesDataInAlphabeticalOrder( final boolean html,
+ final Map<String, Integer> tax_code_to_id_map,
+ final Phylogeny phy ) {
+ final StringBuffer sb = new StringBuffer();
+ sb.append( "<table>" );
+ for( final Species species : getSpeciesData().keySet() ) {
+ addSpeciesSpecificDomainData( sb, species, html, tax_code_to_id_map, phy );
+ }
+ sb.append( "</table>" );
+ return sb;
+ }
+
+ private StringBuffer getSpeciesDataInCustomOrder( final boolean html,
+ final Map<String, Integer> tax_code_to_id_map,
+ final Phylogeny phy ) {
+ final StringBuffer sb = new StringBuffer();
+ for( final Species order_species : getSpeciesCustomOrder() ) {
+ if ( getSpeciesData().keySet().contains( order_species ) ) {
+ addSpeciesSpecificDomainData( sb, order_species, html, tax_code_to_id_map, phy );
+ }
+ else {
+ sb.append( DomainSimilarity.NO_SPECIES );
+ sb.append( DomainSimilarity.SPECIES_SEPARATOR );
+ }
+ }
+ return sb;
+ }
+
+ private StringBuffer getTaxonomyGroupDistribution( final Phylogeny tol ) {
+ final SortedMap<String, Set<String>> domain_to_species_set_map = new TreeMap<String, Set<String>>();
+ for( final Species species : getSpeciesData().keySet() ) {
+ for( final String combable_dom : getCombinableDomainIds( species ) ) {
+ if ( !domain_to_species_set_map.containsKey( combable_dom ) ) {
+ domain_to_species_set_map.put( combable_dom, new HashSet<String>() );
+ }
+ domain_to_species_set_map.get( combable_dom ).add( species.getSpeciesId() );
+ }
+ }
+ final StringBuffer sb = new StringBuffer();
+ sb.append( "<table>" );
+ for( final Map.Entry<String, Set<String>> domain_to_species_set : domain_to_species_set_map.entrySet() ) {
+ final Map<String, Integer> counts = new HashMap<String, Integer>();
+ for( final String tax_code : domain_to_species_set.getValue() ) {
+ final String group = SurfacingUtil.obtainTaxonomyGroup( tax_code, tol );
+ if ( !ForesterUtil.isEmpty( group ) ) {
+ if ( !counts.containsKey( group ) ) {
+ counts.put( group, 1 );
+ }
+ else {
+ counts.put( group, counts.get( group ) + 1 );
+ }
+ }
+ else {
+ return null;
+ }
+ }
+ final SortedMap<Integer, SortedSet<String>> counts_to_groups = new TreeMap<Integer, SortedSet<String>>( new Comparator<Integer>() {
+
+ @Override
+ public int compare( final Integer first, final Integer second ) {
+ return second.compareTo( first );
+ }
+ } );
+ for( final Map.Entry<String, Integer> group_to_counts : counts.entrySet() ) {
+ final int c = group_to_counts.getValue();
+ if ( !counts_to_groups.containsKey( c ) ) {
+ counts_to_groups.put( c, new TreeSet<String>() );
+ }
+ counts_to_groups.get( c ).add( group_to_counts.getKey() );
+ }
+ sb.append( "<tr>" );
+ sb.append( "<td>" );
+ sb.append( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_to_species_set.getKey() + "\">"
+ + domain_to_species_set.getKey() + "</a>" );
+ sb.append( " " );
+ sb.append( "</td>" );
+ boolean first = true;
+ for( final Entry<Integer, SortedSet<String>> count_to_groups : counts_to_groups.entrySet() ) {
+ if ( first ) {
+ first = false;
+ }
+ else {
+ sb.append( "<tr>" );
+ sb.append( "<td>" );
+ sb.append( "</td>" );
+ }
+ sb.append( "<td>" );
+ final SortedSet<String> groups = count_to_groups.getValue();
+ sb.append( count_to_groups.getKey() );
+ sb.append( " " );
+ for( final String group : groups ) {
+ final Color color = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group );
+ if ( color == null ) {
+ throw new IllegalArgumentException( "no color found for taxonomy group\"" + group + "\"" );
+ }
+ final String hex = String.format( "#%02x%02x%02x",
+ color.getRed(),
+ color.getGreen(),
+ color.getBlue() );
+ sb.append( "<span style=\"color:" );
+ sb.append( hex );
+ sb.append( "\">" );
+ sb.append( " " );
+ sb.append( group );
+ sb.append( "</span>" );
+ }
+ sb.append( "</td>" );
+ sb.append( "</tr>" );
+ }
+ sb.append( ForesterUtil.getLineSeparator() );
+ }
+ sb.append( "</table>" );
+ return sb;
+ }
+
+ private void init() {
+ _detailedness = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
+ }
+
+ private boolean isTreatAsBinaryComparison() {
+ return _treat_as_binary_comparison;
+ }
+
+ private StringBuffer toStringBufferDetailedHTML( final Map<String, Integer> tax_code_to_id_map,
+ final Phylogeny phy,
+ final boolean output_tax_codes_per_domain ) {
+ final StringBuffer sb = new StringBuffer();
+ sb.append( "<tr>" );
+ sb.append( "<td>" );
+ sb.append( "<b>" );
+ sb.append( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + getDomainId() + "\" target=\"pfam_window\">"
+ + getDomainId() + "</a>" );
+ sb.append( "</b>" );
+ sb.append( "<a name=\"" + getDomainId() + "\">" );
+ sb.append( "</td>" );
+ sb.append( "<td>" );
+ sb.append( "<a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_SEARCH + getDomainId()
+ + "\" target=\"gs_window\">gs</a>" );
+ sb.append( "</td>" );
+ if ( getMaximalSimilarityScore() > 0 ) {
+ sb.append( "<td>" );
+ sb.append( ForesterUtil.round( getMeanSimilarityScore(), 3 ) );
+ sb.append( "</td>" );
+ if ( SurfacingConstants.PRINT_MORE_DOM_SIMILARITY_INFO ) {
+ if ( !isTreatAsBinaryComparison() ) {
+ sb.append( "<td>" );
+ sb.append( "(" );
+ sb.append( ForesterUtil.round( getStandardDeviationOfSimilarityScore(), 3 ) );
+ sb.append( ")" );
+ sb.append( "</td>" );
+ sb.append( "<td>" );
+ sb.append( "[" );
+ sb.append( ForesterUtil.round( getMinimalSimilarityScore(), 3 ) );
+ sb.append( "-" );
+ sb.append( ForesterUtil.round( getMaximalSimilarityScore(), 3 ) );
+ sb.append( "]" );
+ sb.append( "</td>" );
+ }
+ }
+ }
+ sb.append( "<td>" );
+ sb.append( getMaximalDifference() );
+ sb.append( "</td>" );
+ sb.append( "<td>" );
+ if ( isTreatAsBinaryComparison() ) {
+ sb.append( getMaximalDifferenceInCounts() );
+ }
+ else {
+ sb.append( Math.abs( getMaximalDifferenceInCounts() ) );
+ }
+ sb.append( "</td>" );
+ if ( !isTreatAsBinaryComparison() ) {
+ sb.append( "<td>" );
+ sb.append( "<b>" );
+ sb.append( getSpeciesData().size() );
+ sb.append( "</b>" );
+ sb.append( "</td>" );
+ }
+ if ( ( getSpeciesCustomOrder() == null ) || getSpeciesCustomOrder().isEmpty() ) {
+ sb.append( "<td>" );
+ sb.append( getSpeciesDataInAlphabeticalOrder( true, tax_code_to_id_map, phy ) );
+ if ( output_tax_codes_per_domain ) {
+ sb.append( getDomainDataInAlphabeticalOrder() );
+ }
+ sb.append( getTaxonomyGroupDistribution( phy ) );
+ sb.append( "</td>" );
+ }
+ else {
+ sb.append( "<td>" );
+ sb.append( getSpeciesDataInCustomOrder( true, tax_code_to_id_map, phy ) );
+ if ( output_tax_codes_per_domain ) {
+ sb.append( getDomainDataInAlphabeticalOrder() );
+ }
+ sb.append( getTaxonomyGroupDistribution( phy ) );
+ sb.append( "</td>" );
+ }
+ sb.append( "</tr>" );
+ return sb;
+ }
+
+ private StringBuffer toStringBufferSimpleTabDelimited() {
+ final StringBuffer sb = new StringBuffer();
+ sb.append( getDomainId() );
+ sb.append( "\t" );
+ sb.append( getSpeciesDataInAlphabeticalOrder( false, null, null ) );
+ sb.append( "\n" );
+ return sb;
+ }
+
+ static public enum DomainSimilarityScoring {
+ COMBINATIONS, DOMAINS, PROTEINS;
+ }
+
+ public static enum DomainSimilaritySortField {
+ ABS_MAX_COUNTS_DIFFERENCE, DOMAIN_ID, MAX, MAX_COUNTS_DIFFERENCE, MAX_DIFFERENCE, MEAN, MIN, SD, SPECIES_COUNT,
+ }
+
+ public static enum PRINT_OPTION {
+ HTML, SIMPLE_TAB_DELIMITED;
+ }
+
+ class ValueComparator implements Comparator<String> {
+
+ final private Map<String, Integer> _base;
+
+ public ValueComparator( final Map<String, Integer> base ) {
+ _base = base;
+ }
+
+ @Override
+ public int compare( final String a, final String b ) {
+ if ( _base.get( a ) >= _base.get( b ) ) {
+ return -1;
+ }
+ else {
+ return 1;
+ } // returning 0 would merge keys
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff