package org.forester.surfacing;
-import java.awt.Color;
+import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.SortedMap;
import java.util.TreeSet;
import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyNode;
import org.forester.species.Species;
import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
import org.forester.util.ForesterUtil;
final public static String SPECIES_SEPARATOR = " ";
final private static int EQUAL = 0;
final private static String NO_SPECIES = " ";
- final private double _min;
+ 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 _sd;
+ final private double _min;
final private int _n;
- private final int _max_difference_in_counts;
- private final int _max_difference;
- final private CombinableDomains _combinable_domains;
+ final private double _sd;
final private SortedMap<Species, SpeciesSpecificDcData> _species_data;
private List<Species> _species_order;
- private DomainSimilarityCalculator.Detailedness _detailedness;
private final boolean _treat_as_binary_comparison;
public PrintableDomainSimilarity( final CombinableDomains combinable_domains,
}
}
- 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 ) {
- addTaxWithLink( sb, species.getSpeciesId(), tax_code_to_id_map, phy );
- }
- 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>" );
- }
- 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 ) {
- Color c = null;
- if ( phy != null && !phy.isEmpty() ) {
- c = getColorDependingOnTaxonomy( tax_code, phy );
- }
- if ( c == null ) {
- c = new Color( 0, 0, 0 );
- }
- final String hex = String.format( "#%02x%02x%02x", c.getRed(), c.getGreen(), c.getBlue() );
- sb.append( "<b>" );
- if ( !ForesterUtil.isEmpty( tax_code )
- && ( ( tax_code_to_id_map != null ) && tax_code_to_id_map.containsKey( tax_code ) ) ) {
- sb.append( "<a href=\"" + SurfacingConstants.UNIPROT_TAXONOMY_ID_LINK + tax_code_to_id_map.get( tax_code )
- + "\" target=\"taxonomy_window\" color=\"" + hex + "\">" + tax_code + "</a>" );
- }
- else {
- sb.append( tax_code );
- }
- sb.append( "</b>" );
- }
-
- private Color getColorDependingOnTaxonomy( final String tax_code, final Phylogeny phy ) {
- List<PhylogenyNode> nodes = phy.getNodesViaTaxonomyCode( tax_code );
- Color c = null;
- if ( nodes == null || nodes.isEmpty() ) {
- throw new RuntimeException( tax_code + " is not found" );
- }
- if ( nodes.size() != 1 ) {
- throw new RuntimeException( tax_code + " is not unique" );
- }
- PhylogenyNode n = nodes.get( 0 );
- while ( n != null ) {
- c = null;
- if ( n.getNodeData().isHasTaxonomy()
- && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
- c = SurfacingUtil.getColorForTaxCode( n.getNodeData().getTaxonomy().getScientificName() );
- }
- if ( c == null && !ForesterUtil.isEmpty( n.getName() ) ) {
- c = SurfacingUtil.getColorForTaxCode( n.getName() );
- }
- if ( c != null ) {
- break;
- }
- n = n.getParent();
- }
- return c;
- }
-
- private int compareByDomainId( final DomainSimilarity other ) {
- return getDomainId().compareToIgnoreCase( other.getDomainId() );
- }
-
@Override
public int compareTo( final DomainSimilarity domain_similarity ) {
if ( this == domain_similarity ) {
return sorted_ids;
}
- private CombinableDomains getCombinableDomains() {
- return _combinable_domains;
- }
-
- private DomainSimilarityCalculator.Detailedness getDetaildness() {
- return _detailedness;
- }
-
@Override
public String getDomainId() {
return getCombinableDomains().getKeyDomain();
return _species_data;
}
- private StringBuffer getSpeciesDataInAlphabeticalOrder( final boolean html,
- final Map<String, Integer> tax_code_to_id_map,
- final Phylogeny phy ) {
+ @Override
+ 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;
+ }
+
+ @Override
+ public StringBuffer toStringBuffer( final PrintableDomainSimilarity.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 );
+ 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 ) {
+ addTaxWithLink( sb, species.getSpeciesId(), tax_code_to_id_map, phy );
+ }
+ 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>" );
+ }
+ 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() );
+ }
+
+ private CombinableDomains getCombinableDomains() {
+ return _combinable_domains;
+ }
+
+ 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() ) {
- addSpeciesSpecificDomainData( sb, species, html, tax_code_to_id_map, phy );
+ 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 getDomainDataInAlphabeticalOrder() {
+
+
+ private StringBuffer getTaxonomyGroupDistribution( Phylogeny tol ) {
+ //TODO work on me
+
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.get( combable_dom ).add( species.getSpeciesId() );
}
}
+ Map<String,Integer> countz = new HashMap<String,Integer>();
+ for( final Map.Entry<String, SortedSet<String>> e : m.entrySet() ) {
+ for( final String tax_code : e.getValue() ) {
+ final String group = SurfacingUtil.obtainTaxonomyGroup( tax_code, tol );
+ if ( !ForesterUtil.isEmpty( group ) ) {
+ if ( !countz.containsKey( group ) ) {
+ countz.put( group, 1 );
+ }
+ else {
+ countz.put( group, countz.get( group) + 1 );
+ }
+
+ }
+ else {
+ return null;
+ }
+
+ }
+
+ }
+ final StringBuffer sb = new StringBuffer();
+
+ // i am just a template and need to be modified for "printout" TODO
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( ": " );
- for( final String s : e.getValue() ) {
- sb.append( s );
+ sb.append( "<span style=\"font-size:8px\">" );
+ 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( "<br>" );
+ 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();
+ for( final Species species : getSpeciesData().keySet() ) {
+ addSpeciesSpecificDomainData( sb, species, html, tax_code_to_id_map, phy );
}
return sb;
}
return sb;
}
- @Override
- public double getStandardDeviationOfSimilarityScore() {
- return _sd;
- }
-
private void init() {
_detailedness = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
}
return _treat_as_binary_comparison;
}
- 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;
- }
-
- @Override
- public StringBuffer toStringBuffer( final PrintableDomainSimilarity.PRINT_OPTION print_option,
- final Map<String, Integer> tax_code_to_id_map,
- Phylogeny phy ) {
- switch ( print_option ) {
- case SIMPLE_TAB_DELIMITED:
- return toStringBufferSimpleTabDelimited();
- case HTML:
- return toStringBufferDetailedHTML( tax_code_to_id_map, phy );
- default:
- throw new AssertionError( "Unknown print option: " + print_option );
- }
- }
-
- private StringBuffer toStringBufferDetailedHTML( final Map<String, Integer> tax_code_to_id_map, Phylogeny phy ) {
+ private StringBuffer toStringBufferDetailedHTML( final Map<String, Integer> tax_code_to_id_map, final Phylogeny phy ) {
final StringBuffer sb = new StringBuffer();
sb.append( "<tr>" );
sb.append( "<td>" );
}
public static enum PRINT_OPTION {
- SIMPLE_TAB_DELIMITED, HTML;
+ HTML, SIMPLE_TAB_DELIMITED;
}
}
git://source.jalview.org / jalview.git / blobdiff