package org.forester.surfacing;
+import java.awt.Color;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import org.forester.util.CommandLineArguments;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
+import org.forester.util.TaxonomyColors;
public final class SurfacingUtil {
return 0;
}
}
- private final static NumberFormat FORMATTER_3 = new DecimalFormat( "0.000" );
- private static final Comparator<Domain> ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
-
- @Override
- public int compare( final Domain d1,
- final Domain d2 ) {
- if ( d1.getPerSequenceEvalue() < d2
- .getPerSequenceEvalue() ) {
- return -1;
- }
- else if ( d1
- .getPerSequenceEvalue() > d2
- .getPerSequenceEvalue() ) {
- return 1;
- }
- else {
- return d1.compareTo( d2 );
- }
- }
- };
- public final static Pattern PATTERN_SP_STYLE_TAXONOMY = Pattern.compile( "^[A-Z0-9]{3,5}$" );
+ private final static NumberFormat FORMATTER_3 = new DecimalFormat( "0.000" );
+ private static final Comparator<Domain> ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
+
+ @Override
+ public int compare( final Domain d1,
+ final Domain d2 ) {
+ if ( d1.getPerSequenceEvalue() < d2
+ .getPerSequenceEvalue() ) {
+ return -1;
+ }
+ else if ( d1
+ .getPerSequenceEvalue() > d2
+ .getPerSequenceEvalue() ) {
+ return 1;
+ }
+ else {
+ return d1.compareTo( d2 );
+ }
+ }
+ };
+ public final static Pattern PATTERN_SP_STYLE_TAXONOMY = Pattern.compile( "^[A-Z0-9]{3,5}$" );
+ private final static Map<String, String> _TAXCODE_HEXCOLORSTRING_MAP = new HashMap<String, String>();
public static void addAllBinaryDomainCombinationToSet( final GenomeWideCombinableDomains genome,
final SortedSet<BinaryDomainCombination> binary_domain_combinations ) {
}
}
- public static void addHtmlHead( final Writer w, final String title ) throws IOException {
+ public static void writeHtmlHead( final Writer w, final String title ) throws IOException {
w.write( SurfacingConstants.NL );
w.write( "<head>" );
w.write( "<title>" );
w.write( SurfacingConstants.NL );
w.write( "<style>" );
w.write( SurfacingConstants.NL );
- w.write( "a:visited { color : #6633FF; text-decoration : none; }" );
+ w.write( "a:visited { color : #000066; text-decoration : none; }" );
w.write( SurfacingConstants.NL );
- w.write( "a:link { color : #6633FF; text-decoration : none; }" );
+ w.write( "a:link { color : #000066; text-decoration : none; }" );
w.write( SurfacingConstants.NL );
- w.write( "a:active { color : #99FF00; text-decoration : none; }" );
+ w.write( "a:active { color : ##000066; text-decoration : none; }" );
w.write( SurfacingConstants.NL );
- w.write( "a:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; }" );
+ w.write( "a:hover { color : #FFFFFF; background-color : #000000; text-decoration : none; }" );
w.write( SurfacingConstants.NL );
//
- w.write( "a.pl:visited { color : #505050; text-decoration : none; font-size: 7pt;}" );
+ w.write( "a.pl:visited { color : #505050; text-decoration : none; font-size: 7px;}" );
w.write( SurfacingConstants.NL );
- w.write( "a.pl:link { color : #505050; text-decoration : none; font-size: 7pt;}" );
+ w.write( "a.pl:link { color : #505050; text-decoration : none; font-size: 7px;}" );
w.write( SurfacingConstants.NL );
- w.write( "a.pl:active { color : #505050; text-decoration : none; font-size: 7pt;}" );
+ w.write( "a.pl:active { color : #505050; text-decoration : none; font-size: 7px;}" );
w.write( SurfacingConstants.NL );
- w.write( "a.pl:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; font-size: 7pt;}" );
+ w.write( "a.pl:hover { color : #FFFFFF; background-color : #000000; text-decoration : none; font-size: 7px;}" );
w.write( SurfacingConstants.NL );
//
- w.write( "a.ps:visited { color : #707070; text-decoration : none; font-size: 7pt;}" );
+ w.write( "a.ps:visited { color : #707070; text-decoration : none; font-size: 7px;}" );
w.write( SurfacingConstants.NL );
- w.write( "a.ps:link { color : #707070; text-decoration : none; font-size: 7pt;}" );
+ w.write( "a.ps:link { color : #707070; text-decoration : none; font-size: 7px;}" );
w.write( SurfacingConstants.NL );
- w.write( "a.ps:active { color : #707070; text-decoration : none; font-size: 7pt;}" );
+ w.write( "a.ps:active { color : #707070; text-decoration : none; font-size: 7px;}" );
w.write( SurfacingConstants.NL );
- w.write( "a.ps:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; font-size: 7pt;}" );
+ w.write( "a.ps:hover { color : #FFFFFF; background-color : #000000; text-decoration : none; font-size: 7px;}" );
w.write( SurfacingConstants.NL );
//
w.write( "td { text-align: left; vertical-align: top; font-family: Verdana, Arial, Helvetica; font-size: 8pt}" );
}
}
+ public static String obtainHexColorStringDependingOnTaxonomyGroup( final String tax_code, final Phylogeny phy )
+ throws IllegalArgumentException {
+ if ( !_TAXCODE_HEXCOLORSTRING_MAP.containsKey( tax_code ) ) {
+ if ( phy != null && !phy.isEmpty() ) {
+ List<PhylogenyNode> nodes = phy.getNodesViaTaxonomyCode( tax_code );
+ Color c = null;
+ if ( nodes == null || nodes.isEmpty() ) {
+ throw new IllegalArgumentException( "code " + tax_code + " is not found" );
+ }
+ if ( nodes.size() != 1 ) {
+ throw new IllegalArgumentException( "code " + tax_code + " is not unique" );
+ }
+ PhylogenyNode n = nodes.get( 0 );
+ while ( n != null ) {
+ if ( n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+ c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( n.getNodeData().getTaxonomy()
+ .getScientificName(), tax_code );
+ }
+ if ( c == null && !ForesterUtil.isEmpty( n.getName() ) ) {
+ c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( n.getName(), tax_code );
+ }
+ if ( c != null ) {
+ break;
+ }
+ n = n.getParent();
+ }
+ if ( c == null ) {
+ throw new IllegalArgumentException( "no color found for taxonomy code \"" + tax_code + "\"" );
+ }
+ final String hex = String.format( "#%02x%02x%02x", c.getRed(), c.getGreen(), c.getBlue() );
+ _TAXCODE_HEXCOLORSTRING_MAP.put( tax_code, hex );
+ }
+ else {
+ throw new IllegalArgumentException( "unable to obtain color for code " + tax_code
+ + " (tree is null or empty and code is not in map)" );
+ }
+ }
+ return _TAXCODE_HEXCOLORSTRING_MAP.get( tax_code );
+ }
+
public static Phylogeny[] obtainAndPreProcessIntrees( final File[] intree_files,
final int number_of_genomes,
final String[][] input_file_properties ) {
int per_node_counter = 0;
out.write( "<html>" );
out.write( SurfacingConstants.NL );
- addHtmlHead( out, title_for_html );
+ writeHtmlHead( out, title_for_html );
out.write( SurfacingConstants.NL );
out.write( "<body>" );
out.write( SurfacingConstants.NL );
out.write( "</td>" );
}
+ private final static void writeColorLabels( String l, Color c, Writer w ) throws IOException {
+ w.write( "<tr><td><b><span style=\"color:" );
+ w.write( String.format( "#%02x%02x%02x", c.getRed(), c.getGreen(), c.getBlue() ) );
+ w.write( "\">" );
+ w.write( l );
+ w.write( "</span></b></td></tr>" );
+ w.write( SurfacingConstants.NL );
+ }
+
public static void writeDomainSimilaritiesToFile( final StringBuilder html_desc,
final StringBuilder html_title,
final Writer simple_tab_writer,
final DomainSimilarity.DomainSimilarityScoring scoring,
final boolean verbose,
final Map<String, Integer> tax_code_to_id_map,
- final Phylogeny phy ) throws IOException {
+ Phylogeny phy ) throws IOException {
if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
split_writers = new HashMap<Character, Writer>();
split_writers.put( '_', single_writer );
w.write( "<html>" );
w.write( SurfacingConstants.NL );
if ( key != '_' ) {
- addHtmlHead( w, "DC analysis (" + html_title + ") " + key.toString().toUpperCase() );
+ writeHtmlHead( w, "DC analysis (" + html_title + ") " + key.toString().toUpperCase() );
}
else {
- addHtmlHead( w, "DC analysis (" + html_title + ")" );
+ writeHtmlHead( w, "DC analysis (" + html_title + ")" );
}
w.write( SurfacingConstants.NL );
w.write( "<body>" );
w.write( SurfacingConstants.NL );
w.write( "<hr>" );
w.write( SurfacingConstants.NL );
+ //
+ w.write( "<table>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<tr><td><b>" );
+ w.write( "Species group colors:" );
+ w.write( "</b></td></tr>" );
+ w.write( SurfacingConstants.NL );
+ writeColorLabels( "Deuterostomia", TaxonomyColors.DEUTEROSTOMIA_COLOR, w );
+ writeColorLabels( "Protostomia", TaxonomyColors.PROTOSTOMIA_COLOR, w );
+ writeColorLabels( "Cnidaria", TaxonomyColors.CNIDARIA_COLOR, w );
+ writeColorLabels( "Placozoa", TaxonomyColors.PLACOZOA_COLOR, w );
+ writeColorLabels( "Ctenophora (comb jellies)", TaxonomyColors.CTENOPHORA_COLOR, w );
+ writeColorLabels( "Porifera (sponges)", TaxonomyColors.PORIFERA_COLOR, w );
+ writeColorLabels( "Choanoflagellida", TaxonomyColors.CHOANOFLAGELLIDA, w );
+ writeColorLabels( "Ichthyosporea & Filasterea", TaxonomyColors.ICHTHYOSPOREA_AND_FILASTEREA, w );
+ writeColorLabels( "Fungi", TaxonomyColors.FUNGI_COLOR, w );
+ writeColorLabels( "Nucleariidae and Fonticula group",
+ TaxonomyColors.NUCLEARIIDAE_AND_FONTICULA_GROUP_COLOR,
+ w );
+ writeColorLabels( "Amoebozoa", TaxonomyColors.AMOEBOZOA_COLOR, w );
+ writeColorLabels( "Embryophyta (plants)", TaxonomyColors.EMBRYOPHYTA_COLOR, w );
+ writeColorLabels( "Chlorophyta (green algae)", TaxonomyColors.CHLOROPHYTA_COLOR, w );
+ writeColorLabels( "Rhodophyta (red algae)", TaxonomyColors.RHODOPHYTA_COLOR, w );
+ writeColorLabels( "Glaucocystophyce (Glaucophyta)", TaxonomyColors.GLAUCOPHYTA_COLOR, w );
+ writeColorLabels( "Hacrobia (Cryptophyta & Haptophyceae & Centroheliozoa)",
+ TaxonomyColors.HACROBIA_COLOR,
+ w );
+ writeColorLabels( "Stramenopiles (Chromophyta, heterokonts)", TaxonomyColors.STRAMENOPILES_COLOR, w );
+ writeColorLabels( "Alveolata", TaxonomyColors.ALVEOLATA_COLOR, w );
+ writeColorLabels( "Rhizaria", TaxonomyColors.RHIZARIA_COLOR, w );
+ writeColorLabels( "Excavata", TaxonomyColors.EXCAVATA_COLOR, w );
+ writeColorLabels( "Apusozoa", TaxonomyColors.APUSOZOA_COLOR, w );
+ writeColorLabels( "Archaea", TaxonomyColors.ARCHAEA_COLOR, w );
+ writeColorLabels( "Bacteria", TaxonomyColors.BACTERIA_COLOR, w );
+ w.write( "</table>" );
+ w.write( SurfacingConstants.NL );
+ //
+ w.write( "<hr>" );
+ w.write( SurfacingConstants.NL );
w.write( "<table>" );
w.write( SurfacingConstants.NL );
}
w.write( SurfacingConstants.NL );
}
break;
+ default:
+ break;
}
for( final Writer w : split_writers.values() ) {
w.close();
git://source.jalview.org / jalview.git / commitdiff