scoring,
true,
tax_code_to_id_map,
- intree_0_orig );
+ intree_0_orig,
+ positive_filter_file != null ? filter : null );
simple_tab_writer.close();
ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote main output (includes domain similarities) to: \""
+ ( out_dir == null ? my_outfile : out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) + "\"" );
}
public boolean isColorByTaxonomicGroup() {
-
return false;
}
}
static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values";
- static final String COLOR_BY_TAXONOMIC_GROUP = "Color by Taxonomic Group";
+ static final String COLOR_BY_TAXONOMIC_GROUP = "Color by Taxonomic Group";
static final String DISPLAY_SCALE_LABEL = "Display Scale";
static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
JCheckBoxMenuItem _show_branch_length_values_cbmi;
JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;
-
JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
JCheckBoxMenuItem _show_overview_cbmi;
JCheckBoxMenuItem _show_domain_labels;
else if ( o == _color_by_taxonomic_group_cbmi ) {
updateOptions( getOptions() );
}
-
else if ( o == _show_confidence_stddev_cbmi ) {
updateOptions( getOptions() );
}
if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
}
-
- if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
- options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
+ if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
+ options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
}
-
-
options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
&& ( _print_using_actual_size_cbmi.isSelected() ) );
options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
_options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
_options_jmenu
.add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
-
-
_options_jmenu
.add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
_options_jmenu
.add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
-
- _options_jmenu
- .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );
-
+ _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );
_options_jmenu
.add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
_options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
-
_options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
_options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
_options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
customizeJMenuItem( _choose_node_size_mi );
customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
-
- customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
+ customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
final boolean isColorByTaxonomicGroup() {
return _color_by_taxonomic_group;
}
-
-
+
boolean isShowConfidenceStddev() {
return _show_confidence_stddev;
}
final void setColorByTaxonomicGroup( final boolean color_by_taxonomic_group ) {
_color_by_taxonomic_group = color_by_taxonomic_group;
}
-
+
void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
_show_confidence_stddev = show_confidence_stddev;
}
final class TaxonomyUtil {
- static String getTaxGroupByTaxCode( String code ) {
+ static String getTaxGroupByTaxCode( final String code ) {
return _default_taxcode_taxgroup_map.get( code );
}
-
-
private final static Map<String, String> _default_taxcode_taxgroup_map = new HashMap<String, String>();
static {
_default_taxcode_taxgroup_map.put( "HUMAN", "deuterostomia" );
_default_taxcode_taxgroup_map.put( "HOMSA", "deuterostomia" );
-
_default_taxcode_taxgroup_map.put( "PANTR", "deuterostomia" );
_default_taxcode_taxgroup_map.put( "GORGO", "deuterostomia" );
_default_taxcode_taxgroup_map.put( "PONAB", "deuterostomia" );
_default_taxcode_taxgroup_map.put( "NEMVE", "cnidaria" );
_default_taxcode_taxgroup_map.put( "HMAXX", "cnidaria" );
_default_taxcode_taxgroup_map.put( "HYDMA", "cnidaria" ); //TODO
-
_default_taxcode_taxgroup_map.put( "TRIAD", "placozoa" );
_default_taxcode_taxgroup_map.put( "MNELE", "ctenophora" );
_default_taxcode_taxgroup_map.put( "AMPQE", "porifera" );
_default_taxcode_taxgroup_map.put( "AMPQU", "porifera" ); //TODO
-
_default_taxcode_taxgroup_map.put( "MONBE", "choanoflagellida" );
_default_taxcode_taxgroup_map.put( "SALS5", "choanoflagellida" );
_default_taxcode_taxgroup_map.put( "AMOPA", "ichthyophonida & filasterea" );
_default_taxcode_taxgroup_map.put( "SARXX", "ichthyophonida & filasterea" );
_default_taxcode_taxgroup_map.put( "SPHAR", "ichthyophonida & filasterea" ); //TODO
-
_default_taxcode_taxgroup_map.put( "CAPO3", "ichthyophonida & filasterea" );
_default_taxcode_taxgroup_map.put( "CAPOW", "ichthyophonida & filasterea" ); //TODO
-
_default_taxcode_taxgroup_map.put( "AALXX", "dikarya" );
_default_taxcode_taxgroup_map.put( "GIBZE", "dikarya" );
_default_taxcode_taxgroup_map.put( "HYPVG", "dikarya" );
_default_taxcode_taxgroup_map.put( "COPC7", "dikarya" );
_default_taxcode_taxgroup_map.put( "LACBS", "dikarya" );
_default_taxcode_taxgroup_map.put( "LACBI", "dikarya" ); //TODO
-
_default_taxcode_taxgroup_map.put( "PLEOS", "dikarya" );
_default_taxcode_taxgroup_map.put( "CPUXX", "dikarya" );
_default_taxcode_taxgroup_map.put( "SERL9", "dikarya" );
_default_taxcode_taxgroup_map.put( "NAEGR", "excavata" );
_default_taxcode_taxgroup_map.put( "GIAIC", "excavata" );
_default_taxcode_taxgroup_map.put( "GIALA", "excavata" ); //TODO
-
_default_taxcode_taxgroup_map.put( "TRIVA", "excavata" );
_default_taxcode_taxgroup_map.put( "TTRXX", "apusozoa" );
_default_taxcode_taxgroup_map.put( "THETR", "apusozoa" ); //TODO //FIXME
-
-
_default_taxcode_taxgroup_map.put( "METAC", "archaea" );
_default_taxcode_taxgroup_map.put( "METBF", "archaea" );
_default_taxcode_taxgroup_map.put( "METMA", "archaea" );
boolean ex = false;
String group = null;
try {
- group =TaxonomyUtil.getTaxGroupByTaxCode( tax.getTaxonomyCode() );
+ group = TaxonomyUtil.getTaxGroupByTaxCode( tax.getTaxonomyCode() );
}
- catch ( Exception e ) {
+ catch ( final Exception e ) {
ex = true;
}
if ( !ex && !ForesterUtil.isEmpty( group ) ) {
- Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group );
+ final Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group );
if ( c != null ) {
return c;
}
scoring,
false,
tax_code_to_id_map,
- phy );
+ phy,
+ null );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( command_line_prg_name, "Failed to write similarites to: \""
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;
return sb;
}
- private StringBuffer getTaxonomyGroupDistribution( Phylogeny tol ) {
+ private StringBuffer getTaxonomyGroupDistribution( final Phylogeny tol ) {
//TODO work on me
final SortedMap<String, Set<String>> domain_to_species_set_map = new TreeMap<String, Set<String>>();
for( final Species species : getSpeciesData().keySet() ) {
}
}
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> countz = new HashMap<String, Integer>();
- final ValueComparator bvc = new ValueComparator( countz );
- final SortedMap<String, Integer> sorted_countz = new TreeMap<String, Integer>( bvc );
+ final Map<String, Integer> counts = new HashMap<String, Integer>();
+ // final ValueComparator bvc = new ValueComparator( counts );
+ // final SortedMap<String, Integer> sorted_counts = new TreeMap<String, Integer>( bvc );
for( final String tax_code : domain_to_species_set.getValue() ) {
final String group = SurfacingUtil.obtainTaxonomyGroup( tax_code, tol );
if ( !ForesterUtil.isEmpty( group ) ) {
- if ( !countz.containsKey( group ) ) {
- countz.put( group, 1 );
+ if ( !counts.containsKey( group ) ) {
+ counts.put( group, 1 );
}
else {
- countz.put( group, countz.get( group ) + 1 );
+ counts.put( group, counts.get( group ) + 1 );
}
}
else {
return null;
}
}
- sorted_countz.putAll( countz );
- sb.append( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_to_species_set.getKey() + "\">" + domain_to_species_set.getKey() + "</a>" );
+ 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() );
+ }
+ // sorted_counts.putAll( counts );
+ 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( "<span style=\"font-size:8px\">" );
- for( final Map.Entry<String, Integer> group_to_counts : sorted_countz.entrySet() ) {
- final String group = group_to_counts.getKey();
- final Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group );
- if ( c == null ) {
- throw new IllegalArgumentException( "no color found for taxonomy group\"" + group + "\"" );
- }
- final String hex = String.format( "#%02x%02x%02x", c.getRed(), c.getGreen(), c.getBlue() );
-
- sb.append( "<span style=\"color:" );
- sb.append( hex );
- sb.append( "\">" );
- sb.append( group );
- sb.append( ": " );
- sb.append( group_to_counts.getValue() );
- sb.append( "</span>" );
- sb.append( " " );
- sb.append( "<br>\n" );
+ sb.append( "</td>" );
+ // sb.append( "<span style=\"font-size:9px\">" );
+ 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( "</span>" );
-
+ // sb.append( "</span>" );
+ sb.append( ForesterUtil.getLineSeparator() );
}
+ sb.append( "</table>" );
// 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( getSpeciesDataInCustomOrder( true, tax_code_to_id_map, phy ) );
sb.append( getDomainDataInAlphabeticalOrder() );
sb.append( getTaxonomyGroupDistribution( phy ) );
-
sb.append( "</td>" );
}
sb.append( "</tr>" );
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>();
-
-
- private final static Map<String, String> _TAXCODE_TAXGROUP_MAP = new HashMap<String, String>();
-
-
+ private final static Map<String, String> _TAXCODE_TAXGROUP_MAP = new HashMap<String, String>();
private static final Comparator<Domain> ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
@Override
throws IllegalArgumentException {
if ( !_TAXCODE_HEXCOLORSTRING_MAP.containsKey( tax_code ) ) {
if ( ( phy != null ) && !phy.isEmpty() ) {
-// final 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();
-// }
+ // final 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();
+ // }
final String group = obtainTaxonomyGroup( tax_code, phy );
- Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group );
+ final Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group );
if ( c == null ) {
- throw new IllegalArgumentException( "no color found for taxonomy code \"" + tax_code + "\"" );
- }
+ throw new IllegalArgumentException( "no color found for taxonomy group \"" + group
+ + "\" for code \"" + tax_code + "\"" );
+ }
final String hex = String.format( "#%02x%02x%02x", c.getRed(), c.getGreen(), c.getBlue() );
_TAXCODE_HEXCOLORSTRING_MAP.put( tax_code, hex );
}
}
return _TAXCODE_HEXCOLORSTRING_MAP.get( tax_code );
}
-
-
+
public static String obtainTaxonomyGroup( final String tax_code, final Phylogeny species_tree )
throws IllegalArgumentException {
if ( !_TAXCODE_TAXGROUP_MAP.containsKey( tax_code ) ) {
if ( ( species_tree != null ) && !species_tree.isEmpty() ) {
final List<PhylogenyNode> nodes = species_tree.getNodesViaTaxonomyCode( tax_code );
-
if ( ( nodes == null ) || nodes.isEmpty() ) {
throw new IllegalArgumentException( "code " + tax_code + " is not found" );
}
}
PhylogenyNode n = nodes.get( 0 );
String group = null;
-
while ( n != null ) {
if ( n.getNodeData().isHasTaxonomy()
&& !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
group = ForesterUtil.obtainNormalizedTaxonomyGroup( n.getNodeData().getTaxonomy()
.getScientificName() );
-
}
- if ( ForesterUtil.isEmpty( group ) && !ForesterUtil.isEmpty( n.getName() ) ) {
+ if ( ForesterUtil.isEmpty( group ) && !ForesterUtil.isEmpty( n.getName() ) ) {
group = ForesterUtil.obtainNormalizedTaxonomyGroup( n.getName() );
-
}
- if ( !ForesterUtil.isEmpty( group ) ) {
+ if ( !ForesterUtil.isEmpty( group ) ) {
break;
}
-
n = n.getParent();
}
- if ( ForesterUtil.isEmpty( group ) ) {
+ if ( ForesterUtil.isEmpty( group ) ) {
throw new IllegalArgumentException( "no group found for taxonomy code \"" + tax_code + "\"" );
}
-
_TAXCODE_TAXGROUP_MAP.put( tax_code, group );
}
else {
}
return _TAXCODE_TAXGROUP_MAP.get( tax_code );
}
-
-
-
public static void performDomainArchitectureAnalysis( final SortedMap<String, Set<String>> domain_architecutures,
final SortedMap<String, Integer> domain_architecuture_counts,
final DomainSimilarity.DomainSimilarityScoring scoring,
final boolean verbose,
final Map<String, Integer> tax_code_to_id_map,
- final Phylogeny phy ) throws IOException {
+ final Phylogeny phy,
+ final Set<String> pos_filter_doms ) throws IOException {
if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
split_writers = new HashMap<Character, Writer>();
split_writers.put( '_', single_writer );
( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
}
if ( single_writer != null ) {
- single_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
- + similarity.getDomainId() + "</a></b></td></tr>" );
+ if ( !ForesterUtil.isEmpty( pos_filter_doms ) && pos_filter_doms.contains( similarity.getDomainId() ) ) {
+ single_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId()
+ + "\"><span style=\"color:#00ff00\">" + similarity.getDomainId()
+ + "</span></a></b></td></tr>" );
+ }
+ else {
+ single_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
+ + similarity.getDomainId() + "</a></b></td></tr>" );
+ }
single_writer.write( SurfacingConstants.NL );
}
else {
if ( local_writer == null ) {
local_writer = split_writers.get( '0' );
}
- local_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
- + similarity.getDomainId() + "</a></b></td></tr>" );
+ if ( !ForesterUtil.isEmpty( pos_filter_doms ) && pos_filter_doms.contains( similarity.getDomainId() ) ) {
+ local_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId()
+ + "\"><span style=\"color:#00ff00\">" + similarity.getDomainId()
+ + "</span></a></b></td></tr>" );
+ }
+ else {
+ local_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
+ + similarity.getDomainId() + "</a></b></td></tr>" );
+ }
local_writer.write( SurfacingConstants.NL );
}
}
public final static Color obtainColorDependingOnTaxonomyGroup( final String tax_group ) {
if ( !ForesterUtil.isEmpty( tax_group ) ) {
- if ( tax_group.equals( "deuterostomia" ) ) {
+ if ( tax_group.equals( TaxonomyGroups.DEUTEROSTOMIA ) ) {
return TaxonomyColors.DEUTEROSTOMIA_COLOR;
}
- else if ( tax_group.equals( "protostomia" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.PROTOSTOMIA ) ) {
return TaxonomyColors.PROTOSTOMIA_COLOR;
}
- else if ( tax_group.equals( "cnidaria" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.CNIDARIA ) ) {
return TaxonomyColors.CNIDARIA_COLOR;
}
- else if ( tax_group.equals( "placozoa" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.PLACOZOA ) ) {
return TaxonomyColors.PLACOZOA_COLOR;
}
- else if ( tax_group.equals( "ctenophora" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.CTENOPHORA ) ) {
return TaxonomyColors.CTENOPHORA_COLOR;
}
- else if ( tax_group.equals( "porifera" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.PORIFERA ) ) {
return TaxonomyColors.PORIFERA_COLOR;
}
- else if ( tax_group.equals( "choanoflagellida" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.CHOANOFLAGELLIDA ) ) {
return TaxonomyColors.CHOANOFLAGELLIDA;
}
- else if ( tax_group.equals( "ichthyophonida & filasterea" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.ICHTHYOPHONIDA_FILASTEREA ) ) {
return TaxonomyColors.ICHTHYOSPOREA_AND_FILASTEREA;
}
- else if ( tax_group.equals( "dikarya" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.DIKARYA ) ) {
return TaxonomyColors.DIKARYA_COLOR;
}
- else if ( tax_group.equalsIgnoreCase( "fungi" ) || tax_group.equalsIgnoreCase( "other fungi" ) ) {
+ else if ( tax_group.equalsIgnoreCase( TaxonomyGroups.FUNGI )
+ || tax_group.equalsIgnoreCase( TaxonomyGroups.OTHER_FUNGI ) ) {
return TaxonomyColors.OTHER_FUNGI_COLOR;
}
- else if ( tax_group.equals( "nucleariidae and fonticula" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.NUCLEARIIDAE_AND_FONTICULA_GROUP ) ) {
return TaxonomyColors.NUCLEARIIDAE_AND_FONTICULA_GROUP_COLOR;
}
- else if ( tax_group.equals( "amoebozoa" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.AMOEBOZOA ) ) {
return TaxonomyColors.AMOEBOZOA_COLOR;
}
- else if ( tax_group.equals( "embryophyta" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.EMBRYOPHYTA ) ) {
return TaxonomyColors.EMBRYOPHYTA_COLOR;
}
- else if ( tax_group.equals( "chlorophyta" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.CHLOROPHYTA ) ) {
return TaxonomyColors.CHLOROPHYTA_COLOR;
}
- else if ( tax_group.equals( "rhodophyta" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.RHODOPHYTA ) ) {
return TaxonomyColors.RHODOPHYTA_COLOR;
}
- else if ( tax_group.equals( "hacrobia" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.HACROBIA ) ) {
return TaxonomyColors.HACROBIA_COLOR;
}
- else if ( tax_group.equals( "glaucocystophyceae" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.GLAUCOCYSTOPHYCEAE ) ) {
return TaxonomyColors.GLAUCOPHYTA_COLOR;
}
- else if ( tax_group.equals( "stramenopiles" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.STRAMENOPILES ) ) {
return TaxonomyColors.STRAMENOPILES_COLOR;
}
- else if ( tax_group.equals( "alveolata" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.ALVEOLATA ) ) {
return TaxonomyColors.ALVEOLATA_COLOR;
}
- else if ( tax_group.equals( "rhizaria" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.RHIZARIA ) ) {
return TaxonomyColors.RHIZARIA_COLOR;
}
- else if ( tax_group.equals( "excavata" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.EXCAVATA ) ) {
return TaxonomyColors.EXCAVATA_COLOR;
}
- else if ( tax_group.equals( "apusozoa" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.APUSOZOA ) ) {
return TaxonomyColors.APUSOZOA_COLOR;
}
- else if ( tax_group.equals( "archaea" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.ARCHAEA ) ) {
return TaxonomyColors.ARCHAEA_COLOR;
}
- else if ( tax_group.equals( "bacteria" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.BACTERIA ) ) {
return TaxonomyColors.BACTERIA_COLOR;
}
}
}
public final static String obtainNormalizedTaxonomyGroup( final String tax ) {
- if ( tax.equalsIgnoreCase( "deuterostomia" ) ) {
- return "deuterostomia";
+ if ( tax.equalsIgnoreCase( TaxonomyGroups.DEUTEROSTOMIA ) ) {
+ return TaxonomyGroups.DEUTEROSTOMIA;
}
- else if ( tax.equalsIgnoreCase( "protostomia" ) ) {
- return "protostomia";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.PROTOSTOMIA ) ) {
+ return TaxonomyGroups.PROTOSTOMIA;
}
- else if ( tax.equalsIgnoreCase( "cnidaria" ) ) {
- return "cnidaria";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.CNIDARIA ) ) {
+ return TaxonomyGroups.CNIDARIA;
}
- else if ( tax.toLowerCase().startsWith( "trichoplax" ) || tax.equalsIgnoreCase( "placozoa" ) ) {
- return "placozoa";
+ else if ( tax.toLowerCase().startsWith( "trichoplax" ) || tax.equalsIgnoreCase( TaxonomyGroups.PLACOZOA ) ) {
+ return TaxonomyGroups.PLACOZOA;
}
- else if ( tax.toLowerCase().startsWith( "mnemiopsis" ) || tax.equalsIgnoreCase( "ctenophora" ) ) {
- return "ctenophora";
+ else if ( tax.toLowerCase().startsWith( "mnemiopsis" ) || tax.equalsIgnoreCase( TaxonomyGroups.CTENOPHORA ) ) {
+ return TaxonomyGroups.CTENOPHORA;
}
- else if ( tax.toLowerCase().startsWith( "amphimedon" ) || tax.equalsIgnoreCase( "porifera" ) ) {
- return "porifera";
+ else if ( tax.toLowerCase().startsWith( "amphimedon" ) || tax.equalsIgnoreCase( TaxonomyGroups.PORIFERA ) ) {
+ return TaxonomyGroups.PORIFERA;
}
- else if ( tax.equalsIgnoreCase( "codonosigidae" ) || tax.equalsIgnoreCase( "choanoflagellida" ) ) {
- return "choanoflagellida";
+ else if ( tax.equalsIgnoreCase( "codonosigidae" ) || tax.equalsIgnoreCase( TaxonomyGroups.CHOANOFLAGELLIDA ) ) {
+ return TaxonomyGroups.CHOANOFLAGELLIDA;
}
- else if ( tax.toLowerCase().startsWith( "ichthyophonida & filasterea" )
+ else if ( tax.toLowerCase().startsWith( TaxonomyGroups.ICHTHYOPHONIDA_FILASTEREA )
|| tax.toLowerCase().startsWith( "ichthyophonida and filasterea" )
|| tax.toLowerCase().startsWith( "ichthyosporea & filasterea" )
|| tax.toLowerCase().startsWith( "ichthyosporea and filasterea" ) ) {
- return "ichthyophonida & filasterea";
+ return TaxonomyGroups.ICHTHYOPHONIDA_FILASTEREA;
}
- else if ( tax.equalsIgnoreCase( "dikarya" ) ) {
- return "dikarya";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.DIKARYA ) ) {
+ return TaxonomyGroups.DIKARYA;
}
- else if ( tax.equalsIgnoreCase( "other fungi" ) ) {
- return "other fungi";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.FUNGI ) || tax.equalsIgnoreCase( TaxonomyGroups.OTHER_FUNGI ) ) {
+ return TaxonomyGroups.OTHER_FUNGI;
}
else if ( tax.toLowerCase().startsWith( "nucleariidae and fonticula" ) ) {
- return "nucleariidae and fonticula group";
+ return TaxonomyGroups.NUCLEARIIDAE_AND_FONTICULA_GROUP;
}
- else if ( tax.equalsIgnoreCase( "amoebozoa" ) ) {
- return "amoebozoa";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.AMOEBOZOA ) ) {
+ return TaxonomyGroups.AMOEBOZOA;
}
- else if ( tax.equalsIgnoreCase( "embryophyta" ) ) {
- return "embryophyta";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.EMBRYOPHYTA ) ) {
+ return TaxonomyGroups.EMBRYOPHYTA;
}
- else if ( tax.equalsIgnoreCase( "chlorophyta" ) ) {
- return "chlorophyta";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.CHLOROPHYTA ) ) {
+ return TaxonomyGroups.CHLOROPHYTA;
}
- else if ( tax.equalsIgnoreCase( "rhodophyta" ) ) {
- return "rhodophyta";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.RHODOPHYTA ) ) {
+ return TaxonomyGroups.RHODOPHYTA;
}
- else if ( tax.toLowerCase().startsWith( "hacrobia" ) ) {
- return "hacrobia";
+ else if ( tax.toLowerCase().startsWith( TaxonomyGroups.HACROBIA ) ) {
+ return TaxonomyGroups.HACROBIA;
}
- else if ( tax.equalsIgnoreCase( "glaucocystophyceae" ) || tax.equalsIgnoreCase( "glaucophyta" ) ) {
- return "glaucocystophyceae";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.GLAUCOCYSTOPHYCEAE ) || tax.equalsIgnoreCase( "glaucophyta" ) ) {
+ return TaxonomyGroups.GLAUCOCYSTOPHYCEAE;
}
- else if ( tax.equalsIgnoreCase( "stramenopiles" ) ) {
- return "stramenopiles";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.STRAMENOPILES ) ) {
+ return TaxonomyGroups.STRAMENOPILES;
}
- else if ( tax.equalsIgnoreCase( "alveolata" ) ) {
- return "alveolata";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.ALVEOLATA ) ) {
+ return TaxonomyGroups.ALVEOLATA;
}
- else if ( tax.equalsIgnoreCase( "rhizaria" ) ) {
- return "rhizaria";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.RHIZARIA ) ) {
+ return TaxonomyGroups.RHIZARIA;
}
- else if ( tax.equalsIgnoreCase( "excavata" ) ) {
- return "excavata";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.EXCAVATA ) ) {
+ return TaxonomyGroups.EXCAVATA;
}
- else if ( tax.equalsIgnoreCase( "apusozoa" ) ) {
- return "apusozoa";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.APUSOZOA ) ) {
+ return TaxonomyGroups.APUSOZOA;
}
- else if ( tax.equalsIgnoreCase( "archaea" ) ) {
- return "archaea";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.ARCHAEA ) ) {
+ return TaxonomyGroups.ARCHAEA;
}
- else if ( tax.equalsIgnoreCase( "bacteria" ) ) {
- return "bacteria";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.BACTERIA ) ) {
+ return TaxonomyGroups.BACTERIA;
}
return null;
}
--- /dev/null
+
+package org.forester.util;
+
+final class TaxonomyGroups {
+
+ static final String ALVEOLATA = "alveolata";
+ static final String AMOEBOZOA = "amoebozoa";
+ static final String APUSOZOA = "apusozoa";
+ static final String ARCHAEA = "archaea";
+ static final String BACTERIA = "bacteria";
+ static final String CHLOROPHYTA = "chlorophyta";
+ static final String CHOANOFLAGELLIDA = "choanoflagellida";
+ static final String CNIDARIA = "cnidaria";
+ static final String CTENOPHORA = "ctenophora";
+ static final String DEUTEROSTOMIA = "deuterostomia";
+ static final String DIKARYA = "dikarya";
+ static final String EMBRYOPHYTA = "embryophyta";
+ static final String EXCAVATA = "excavata";
+ static final String FUNGI = "fungi";
+ static final String GLAUCOCYSTOPHYCEAE = "glaucocystophyceae";
+ static final String HACROBIA = "hacrobia";
+ static final String ICHTHYOPHONIDA_FILASTEREA = "ichthyophonida & filasterea";
+ static final String NUCLEARIIDAE_AND_FONTICULA_GROUP = "nucleariidae and fonticula group";
+ static final String OTHER_FUNGI = "other fungi";
+ static final String PLACOZOA = "placozoa";
+ static final String PORIFERA = "porifera";
+ static final String PROTOSTOMIA = "protostomia";
+ static final String RHIZARIA = "rhizaria";
+ static final String RHODOPHYTA = "rhodophyta";
+ static final String STRAMENOPILES = "stramenopiles";
+}
private String _map;
private String _chromosome;
- private void setMap( String map ) {
+ private void setMap( final String map ) {
_map = map;
-
}
- private void setChromosome( String chromosome ) {
+ private void setChromosome( final String chromosome ) {
_chromosome = chromosome;
-
}
@Override
- public String getMap( ) {
+ public String getMap() {
return _map;
-
}
+
@Override
- public String getChromosome() {
+ public String getChromosome() {
return _chromosome;
-
}
-
-
+
private static void x( final StringBuilder sb, final String s ) {
if ( sb.length() > 0 ) {
sb.append( " " );
public SortedSet<Accession> getCrossReferences();
- public String getMap( );
+ public String getMap();
- public String getChromosome( );
+ public String getChromosome();
}
\ No newline at end of file
}
@Override
- public String getMap( ) {
-
+ public String getMap() {
return null;
}
@Override
- public String getChromosome( ) {
-
+ public String getChromosome() {
return null;
}
}
git://source.jalview.org / jalview.git / commitdiff