addJCheckBox( _show_node_names, ch_panel );
add( ch_panel );
break;
- case Configuration.show_tax_code:
- _show_taxo_code = new JCheckBox( title );
- addJCheckBox( _show_taxo_code, ch_panel );
- add( ch_panel );
- break;
case Configuration.show_taxonomy_scientific_names:
_show_taxo_scientific_names = new JCheckBox( title );
addJCheckBox( _show_taxo_scientific_names, ch_panel );
addJCheckBox( _show_taxo_common_names, ch_panel );
add( ch_panel );
break;
+ case Configuration.show_tax_code:
+ _show_taxo_code = new JCheckBox( title );
+ addJCheckBox( _show_taxo_code, ch_panel );
+ add( ch_panel );
+ break;
case Configuration.show_taxonomy_images:
_show_taxo_images_cb = new JCheckBox( title );
addJCheckBox( _show_taxo_images_cb, ch_panel );
return _color_branches_cb;
}
+ public JCheckBox getColorAccSpeciesCb() {
+ return _color_acc_species;
+ }
+
Configuration getConfiguration() {
return _configuration;
}
_show_node_names.setSelected( state );
}
break;
- case Configuration.show_tax_code:
- if ( _show_taxo_code != null ) {
- _show_taxo_code.setSelected( state );
- }
- break;
case Configuration.show_taxonomy_scientific_names:
if ( _show_taxo_scientific_names != null ) {
_show_taxo_scientific_names.setSelected( state );
_show_taxo_common_names.setSelected( state );
}
break;
+ case Configuration.show_tax_code:
+ if ( _show_taxo_code != null ) {
+ _show_taxo_code.setSelected( state );
+ }
+ break;
case Configuration.show_taxonomy_images:
if ( _show_taxo_images_cb != null ) {
_show_taxo_images_cb.setSelected( state );
void colorRank() {
if ( _mainpanel.getCurrentTreePanel() != null ) {
- final String[] ranks = Util.getAllRanks( _mainpanel.getCurrentTreePanel().getPhylogeny() );
- if ( ranks.length < 1 ) {
- JOptionPane.showMessageDialog( this,
- "No rank information was found",
- "No Rank Information",
- JOptionPane.WARNING_MESSAGE );
- return;
- }
+ final String[] ranks = Util.getAllPossibleRanks();
final String rank = ( String ) JOptionPane
.showInputDialog( this,
"What rank should the colorization be based on",
public final class MainFrameApplication extends MainFrame {
- private final static int FRAME_X_SIZE = 800;
- private final static int FRAME_Y_SIZE = 800;
+ static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";
+ static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";
+ private final static int FRAME_X_SIZE = 800;
+ private final static int FRAME_Y_SIZE = 800;
// Filters for the file-open dialog (classes defined in this file)
- private final static NHFilter nhfilter = new NHFilter();
- private final static NHXFilter nhxfilter = new NHXFilter();
- private final static XMLFilter xmlfilter = new XMLFilter();
- private final static TolFilter tolfilter = new TolFilter();
- private final static NexusFilter nexusfilter = new NexusFilter();
- private final static PdfFilter pdffilter = new PdfFilter();
- private final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
- private final static MsaFileFilter msafilter = new MsaFileFilter();
- private final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
- private final static DefaultFilter defaultfilter = new DefaultFilter();
- private static final long serialVersionUID = -799735726778865234L;
+ private final static NHFilter nhfilter = new NHFilter();
+ private final static NHXFilter nhxfilter = new NHXFilter();
+ private final static XMLFilter xmlfilter = new XMLFilter();
+ private final static TolFilter tolfilter = new TolFilter();
+ private final static NexusFilter nexusfilter = new NexusFilter();
+ private final static PdfFilter pdffilter = new PdfFilter();
+ private final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
+ private final static MsaFileFilter msafilter = new MsaFileFilter();
+ private final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
+ private final static DefaultFilter defaultfilter = new DefaultFilter();
+ private static final long serialVersionUID = -799735726778865234L;
private final JFileChooser _values_filechooser;
private final JFileChooser _open_filechooser;
private final JFileChooser _msa_filechooser;
private File _current_dir;
private ButtonGroup _radio_group_1;
// Others:
- double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;
+ double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;
// Phylogeny Inference menu
private JMenu _inference_menu;
private JMenuItem _inference_from_msa_item;
private JMenuItem _inference_from_seqs_item;
// Phylogeny Inference
- private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;
- private Msa _msa = null;
- private File _msa_file = null;
- private List<Sequence> _seqs = null;
- private File _seqs_file = null;
+ private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;
+ private Msa _msa = null;
+ private File _msa_file = null;
+ private List<Sequence> _seqs = null;
+ private File _seqs_file = null;
// expression values menu:
JMenuItem _read_values_jmi;
customizeJMenuItem( _root_min_cost_l_item );
customizeJMenuItem( _load_species_tree_item );
_analysis_menu.addSeparator();
- _analysis_menu.add( _lineage_inference = new JMenuItem( "Infer Ancestor Taxonomies" ) );
+ _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
customizeJMenuItem( _lineage_inference );
_lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
_jmenubar.add( _analysis_menu );
customizeJMenuItem( _infer_common_sn_names_item );
_tools_menu.addSeparator();
_tools_menu
- .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information" ) );
+ .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
_obtain_detailed_taxonomic_information_jmi
.setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
import java.awt.event.ComponentListener;
import java.awt.image.BufferedImage;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
import java.util.Set;
import javax.swing.JPanel;
private Phylogeny _cut_or_copied_tree;
private Set<Integer> _copied_and_pasted_nodes;
private Hashtable<String, BufferedImage> _image_map;
+ private static Map<String, String> _lineage_to_rank_map;
MainPanel() {
}
synchronized Hashtable<String, BufferedImage> getImageMap() {
return _image_map;
}
+
+ public synchronized static Map<String, String> getLineageToRankMap() {
+ if ( _lineage_to_rank_map == null ) {
+ _lineage_to_rank_map = new HashMap<String, String>();
+ }
+ return _lineage_to_rank_map;
+ }
}
}
setWaitCursor();
Util.removeBranchColors( _phylogeny );
- Util.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
- _control_panel.setColorBranches( true );
- if ( _control_panel.getColorBranchesCb() != null ) {
- _control_panel.getColorBranchesCb().setSelected( true );
+ final int colorizations = Util.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
+ if ( colorizations > 0 ) {
+ _control_panel.setColorBranches( true );
+ if ( _control_panel.getColorBranchesCb() != null ) {
+ _control_panel.getColorBranchesCb().setSelected( true );
+ }
+ if ( _control_panel.getColorAccSpeciesCb() != null ) {
+ _control_panel.getColorAccSpeciesCb().setSelected( false );
+ }
+ _options.setColorLabelsSameAsParentBranch( true );
+ _control_panel.repaint();
}
setArrowCursor();
repaint();
+ if ( colorizations > 0 ) {
+ String msg = "Taxonomy colorization via " + rank + " completed:\n";
+ if ( colorizations > 1 ) {
+ msg += "colorized " + colorizations + " subtrees";
+ }
+ else {
+ msg += "colorized one subtree";
+ }
+ JOptionPane.showMessageDialog( this,
+ msg,
+ "Taxonomy Colorization Completed (" + rank + ")",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ else {
+ String msg = "Could not taxonomy colorize any subtree via " + rank + ".\n";
+ msg += "Possible solutions (given that suitable taxonomic information is present):\n";
+ msg += "select a different rank (e.g. phylum, genus, ...)\n";
+ msg += " and/or\n";
+ msg += "execute:\n";
+ msg += "1. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
+ msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
+ JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Failed", JOptionPane.WARNING_MESSAGE );
+ }
}
final private void copySubtree( final PhylogenyNode node ) {
import org.forester.analysis.AncestralTaxonomyInference;
import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.io.parsers.tol.TolParser;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
if ( n.getBranchData().isHasConfidences() ) {
final double conf = PhylogenyMethods.getConfidenceValue( n );
final BranchColor c = new BranchColor( ForesterUtil.calcColor( conf, 0.0, max_conf, bg, br ) );
- n.getBranchData().setBranchColor( c );
- final List<PhylogenyNode> descs = PhylogenyMethods.getAllDescendants( n );
- for( final PhylogenyNode desc : descs ) {
- desc.getBranchData().setBranchColor( c );
- }
+ colorizeSubtree( n, c );
}
}
}
}
- final static void colorPhylogenyAccordingToRanks( final Phylogeny tree,
- final String rank,
- final TreePanel tree_panel ) {
+ final static int colorPhylogenyAccordingToRanks( final Phylogeny tree, final String rank, final TreePanel tree_panel ) {
final Map<String, Color> true_lineage_to_color_map = new HashMap<String, Color>();
+ int colorizations = 0;
for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) {
final PhylogenyNode n = it.next();
if ( n.getNodeData().isHasTaxonomy()
&& n.getNodeData().getTaxonomy().getRank().equalsIgnoreCase( rank ) ) {
final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( n.getNodeData()
.getTaxonomy() ) );
- n.getBranchData().setBranchColor( c );
- final List<PhylogenyNode> descs = PhylogenyMethods.getAllDescendants( n );
- for( final PhylogenyNode desc : descs ) {
- desc.getBranchData().setBranchColor( c );
- }
+ colorizeSubtree( n, c );
+ ++colorizations;
if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
true_lineage_to_color_map.put( n.getNodeData().getTaxonomy().getScientificName(), c.getValue() );
}
if ( !true_lineage_to_color_map.isEmpty() ) {
for( final String lin : node.getNodeData().getTaxonomy().getLineage() ) {
if ( true_lineage_to_color_map.containsKey( lin ) ) {
- final BranchColor c = new BranchColor( true_lineage_to_color_map.get( lin ) );
- node.getBranchData().setBranchColor( c );
- final List<PhylogenyNode> descs = PhylogenyMethods.getAllDescendants( node );
- for( final PhylogenyNode desc : descs ) {
- desc.getBranchData().setBranchColor( c );
- }
+ colorizeSubtree( node, new BranchColor( true_lineage_to_color_map.get( lin ) ) );
+ ++colorizations;
success = true;
break;
}
}
}
- //TODO refactor refactor refactor refactor refactor refactor
if ( !success ) {
+ final Map<String, String> lineage_to_rank_map = MainPanel.getLineageToRankMap();
for( final String lin : node.getNodeData().getTaxonomy().getLineage() ) {
final Taxonomy temp_tax = new Taxonomy();
temp_tax.setScientificName( lin );
- UniProtTaxonomy up = null;
- try {
- up = AncestralTaxonomyInference.obtainUniProtTaxonomy( temp_tax, null, null );
- }
- catch ( final Exception e ) {
- e.printStackTrace();
- }
- if ( ( up != null ) && !ForesterUtil.isEmpty( up.getRank() )
- && up.getRank().equalsIgnoreCase( rank ) ) {
+ if ( lineage_to_rank_map.containsKey( lin )
+ && !ForesterUtil.isEmpty( lineage_to_rank_map.get( lin ) )
+ && lineage_to_rank_map.get( lin ).equalsIgnoreCase( rank ) ) {
final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( temp_tax ) );
- node.getBranchData().setBranchColor( c );
- final List<PhylogenyNode> descs = PhylogenyMethods.getAllDescendants( node );
- for( final PhylogenyNode desc : descs ) {
- desc.getBranchData().setBranchColor( c );
- }
+ colorizeSubtree( node, c );
+ ++colorizations;
true_lineage_to_color_map.put( lin, c.getValue() );
break;
}
+ else {
+ UniProtTaxonomy up = null;
+ try {
+ up = AncestralTaxonomyInference.obtainUniProtTaxonomy( temp_tax, null, null );
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ }
+ if ( ( up != null ) && !ForesterUtil.isEmpty( up.getRank() ) ) {
+ lineage_to_rank_map.put( lin, up.getRank() );
+ if ( up.getRank().equalsIgnoreCase( rank ) ) {
+ final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( temp_tax ) );
+ colorizeSubtree( node, c );
+ ++colorizations;
+ true_lineage_to_color_map.put( lin, c.getValue() );
+ break;
+ }
+ }
+ }
}
}
}
}
+ return colorizations;
+ }
+
+ private static void colorizeSubtree( final PhylogenyNode node, final BranchColor c ) {
+ node.getBranchData().setBranchColor( c );
+ final List<PhylogenyNode> descs = PhylogenyMethods.getAllDescendants( node );
+ for( final PhylogenyNode desc : descs ) {
+ desc.getBranchData().setBranchColor( c );
+ }
}
final static String[] getAllRanks( final Phylogeny tree ) {
return ForesterUtil.stringSetToArray( ranks );
}
+ public static String[] getAllPossibleRanks() {
+ final String[] str_array = new String[ PhyloXmlUtil.TAXONOMY_RANKS_LIST.size() - 2 ];
+ int i = 0;
+ for( final String e : PhyloXmlUtil.TAXONOMY_RANKS_LIST ) {
+ if ( !e.equals( PhyloXmlUtil.UNKNOWN ) && !e.equals( PhyloXmlUtil.OTHER ) ) {
+ str_array[ i++ ] = e;
+ }
+ }
+ return str_array;
+ }
+
final static void colorPhylogenyAccordingToExternalTaxonomy( final Phylogeny tree, final TreePanel tree_panel ) {
for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
it.next().getBranchData().setBranchColor( null );
package org.forester.io.parsers.phyloxml;
+import java.util.ArrayList;
import java.util.HashSet;
+import java.util.List;
import java.util.Set;
import java.util.regex.Pattern;
public final class PhyloXmlUtil {
- public final static Pattern SEQUENCE_SYMBOL_PATTERN = Pattern.compile( "\\S{1,20}" );
- public final static Pattern TAXOMONY_CODE_PATTERN = Pattern.compile( "[a-zA-Z0-9_]{1,10}" );
- public final static Pattern LIT_REF_DOI_PATTERN = Pattern
- .compile( "[a-zA-Z0-9_\\.]+\\S+" );
- public final static Set<String> SEQUENCE_TYPES = new HashSet<String>();
- public final static Set<String> TAXONOMY_RANKS = new HashSet<String>();
- public static final int ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT = 9;
- public static final String VECTOR_PROPERTY_REF = "vector:index=";
- public static final String VECTOR_PROPERTY_TYPE = "xsd:decimal";
- public static final String UNIPROT_TAX_PROVIDER = "uniprot";
+ public static final String OTHER = "other";
+ public static final String UNKNOWN = "unknown";
+ public final static Pattern SEQUENCE_SYMBOL_PATTERN = Pattern.compile( "\\S{1,20}" );
+ public final static Pattern TAXOMONY_CODE_PATTERN = Pattern
+ .compile( "[a-zA-Z0-9_]{1,10}" );
+ public final static Pattern LIT_REF_DOI_PATTERN = Pattern
+ .compile( "[a-zA-Z0-9_\\.]+\\S+" );
+ public final static Set<String> SEQUENCE_TYPES = new HashSet<String>();
+ public final static List<String> TAXONOMY_RANKS_LIST = new ArrayList<String>();
+ public final static Set<String> TAXONOMY_RANKS_SET = new HashSet<String>();
+ public static final int ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT = 9;
+ public static final String VECTOR_PROPERTY_REF = "vector:index=";
+ public static final String VECTOR_PROPERTY_TYPE = "xsd:decimal";
+ public static final String UNIPROT_TAX_PROVIDER = "uniprot";
static {
SEQUENCE_TYPES.add( "rna" );
SEQUENCE_TYPES.add( "protein" );
SEQUENCE_TYPES.add( "dna" );
- TAXONOMY_RANKS.add( "domain" );
- TAXONOMY_RANKS.add( "superkingdom" );
- TAXONOMY_RANKS.add( "kingdom" );
- TAXONOMY_RANKS.add( "subkingdom" );
- TAXONOMY_RANKS.add( "branch" );
- TAXONOMY_RANKS.add( "infrakingdom" );
- TAXONOMY_RANKS.add( "superphylum" );
- TAXONOMY_RANKS.add( "phylum" );
- TAXONOMY_RANKS.add( "subphylum" );
- TAXONOMY_RANKS.add( "infraphylum" );
- TAXONOMY_RANKS.add( "microphylum" );
- TAXONOMY_RANKS.add( "superdivision" );
- TAXONOMY_RANKS.add( "division" );
- TAXONOMY_RANKS.add( "subdivision" );
- TAXONOMY_RANKS.add( "infradivision" );
- TAXONOMY_RANKS.add( "superclass" );
- TAXONOMY_RANKS.add( "class" );
- TAXONOMY_RANKS.add( "subclass" );
- TAXONOMY_RANKS.add( "infraclass" );
- TAXONOMY_RANKS.add( "superlegion" );
- TAXONOMY_RANKS.add( "legion" );
- TAXONOMY_RANKS.add( "sublegion" );
- TAXONOMY_RANKS.add( "infralegion" );
- TAXONOMY_RANKS.add( "supercohort" );
- TAXONOMY_RANKS.add( "cohort" );
- TAXONOMY_RANKS.add( "subcohort" );
- TAXONOMY_RANKS.add( "infracohort" );
- TAXONOMY_RANKS.add( "superorder" );
- TAXONOMY_RANKS.add( "order" );
- TAXONOMY_RANKS.add( "suborder" );
- TAXONOMY_RANKS.add( "superfamily" );
- TAXONOMY_RANKS.add( "family" );
- TAXONOMY_RANKS.add( "subfamily" );
- TAXONOMY_RANKS.add( "supertribe" );
- TAXONOMY_RANKS.add( "tribe" );
- TAXONOMY_RANKS.add( "subtribe" );
- TAXONOMY_RANKS.add( "infratribe" );
- TAXONOMY_RANKS.add( "genus" );
- TAXONOMY_RANKS.add( "subgenus" );
- TAXONOMY_RANKS.add( "superspecies" );
- TAXONOMY_RANKS.add( "species" );
- TAXONOMY_RANKS.add( "subspecies" );
- TAXONOMY_RANKS.add( "variety" );
- TAXONOMY_RANKS.add( "subvariety" );
- TAXONOMY_RANKS.add( "form" );
- TAXONOMY_RANKS.add( "subform" );
- TAXONOMY_RANKS.add( "cultivar" );
- TAXONOMY_RANKS.add( "strain" );
- TAXONOMY_RANKS.add( "unknown" );
- TAXONOMY_RANKS.add( "other" );
+ TAXONOMY_RANKS_LIST.add( "domain" );
+ TAXONOMY_RANKS_LIST.add( "superkingdom" );
+ TAXONOMY_RANKS_LIST.add( "kingdom" );
+ TAXONOMY_RANKS_LIST.add( "subkingdom" );
+ TAXONOMY_RANKS_LIST.add( "branch" );
+ TAXONOMY_RANKS_LIST.add( "infrakingdom" );
+ TAXONOMY_RANKS_LIST.add( "superphylum" );
+ TAXONOMY_RANKS_LIST.add( "phylum" );
+ TAXONOMY_RANKS_LIST.add( "subphylum" );
+ TAXONOMY_RANKS_LIST.add( "infraphylum" );
+ TAXONOMY_RANKS_LIST.add( "microphylum" );
+ TAXONOMY_RANKS_LIST.add( "superdivision" );
+ TAXONOMY_RANKS_LIST.add( "division" );
+ TAXONOMY_RANKS_LIST.add( "subdivision" );
+ TAXONOMY_RANKS_LIST.add( "infradivision" );
+ TAXONOMY_RANKS_LIST.add( "superclass" );
+ TAXONOMY_RANKS_LIST.add( "class" );
+ TAXONOMY_RANKS_LIST.add( "subclass" );
+ TAXONOMY_RANKS_LIST.add( "infraclass" );
+ TAXONOMY_RANKS_LIST.add( "superlegion" );
+ TAXONOMY_RANKS_LIST.add( "legion" );
+ TAXONOMY_RANKS_LIST.add( "sublegion" );
+ TAXONOMY_RANKS_LIST.add( "infralegion" );
+ TAXONOMY_RANKS_LIST.add( "supercohort" );
+ TAXONOMY_RANKS_LIST.add( "cohort" );
+ TAXONOMY_RANKS_LIST.add( "subcohort" );
+ TAXONOMY_RANKS_LIST.add( "infracohort" );
+ TAXONOMY_RANKS_LIST.add( "superorder" );
+ TAXONOMY_RANKS_LIST.add( "order" );
+ TAXONOMY_RANKS_LIST.add( "suborder" );
+ TAXONOMY_RANKS_LIST.add( "superfamily" );
+ TAXONOMY_RANKS_LIST.add( "family" );
+ TAXONOMY_RANKS_LIST.add( "subfamily" );
+ TAXONOMY_RANKS_LIST.add( "supertribe" );
+ TAXONOMY_RANKS_LIST.add( "tribe" );
+ TAXONOMY_RANKS_LIST.add( "subtribe" );
+ TAXONOMY_RANKS_LIST.add( "infratribe" );
+ TAXONOMY_RANKS_LIST.add( "genus" );
+ TAXONOMY_RANKS_LIST.add( "subgenus" );
+ TAXONOMY_RANKS_LIST.add( "superspecies" );
+ TAXONOMY_RANKS_LIST.add( "species" );
+ TAXONOMY_RANKS_LIST.add( "subspecies" );
+ TAXONOMY_RANKS_LIST.add( "variety" );
+ TAXONOMY_RANKS_LIST.add( "subvariety" );
+ TAXONOMY_RANKS_LIST.add( "form" );
+ TAXONOMY_RANKS_LIST.add( "subform" );
+ TAXONOMY_RANKS_LIST.add( "cultivar" );
+ TAXONOMY_RANKS_LIST.add( "strain" );
+ TAXONOMY_RANKS_LIST.add( UNKNOWN );
+ TAXONOMY_RANKS_LIST.add( OTHER );
+ // same thing as set:
+ TAXONOMY_RANKS_SET.add( "domain" );
+ TAXONOMY_RANKS_SET.add( "superkingdom" );
+ TAXONOMY_RANKS_SET.add( "kingdom" );
+ TAXONOMY_RANKS_SET.add( "subkingdom" );
+ TAXONOMY_RANKS_SET.add( "branch" );
+ TAXONOMY_RANKS_SET.add( "infrakingdom" );
+ TAXONOMY_RANKS_SET.add( "superphylum" );
+ TAXONOMY_RANKS_SET.add( "phylum" );
+ TAXONOMY_RANKS_SET.add( "subphylum" );
+ TAXONOMY_RANKS_SET.add( "infraphylum" );
+ TAXONOMY_RANKS_SET.add( "microphylum" );
+ TAXONOMY_RANKS_SET.add( "superdivision" );
+ TAXONOMY_RANKS_SET.add( "division" );
+ TAXONOMY_RANKS_SET.add( "subdivision" );
+ TAXONOMY_RANKS_SET.add( "infradivision" );
+ TAXONOMY_RANKS_SET.add( "superclass" );
+ TAXONOMY_RANKS_SET.add( "class" );
+ TAXONOMY_RANKS_SET.add( "subclass" );
+ TAXONOMY_RANKS_SET.add( "infraclass" );
+ TAXONOMY_RANKS_SET.add( "superlegion" );
+ TAXONOMY_RANKS_SET.add( "legion" );
+ TAXONOMY_RANKS_SET.add( "sublegion" );
+ TAXONOMY_RANKS_SET.add( "infralegion" );
+ TAXONOMY_RANKS_SET.add( "supercohort" );
+ TAXONOMY_RANKS_SET.add( "cohort" );
+ TAXONOMY_RANKS_SET.add( "subcohort" );
+ TAXONOMY_RANKS_SET.add( "infracohort" );
+ TAXONOMY_RANKS_SET.add( "superorder" );
+ TAXONOMY_RANKS_SET.add( "order" );
+ TAXONOMY_RANKS_SET.add( "suborder" );
+ TAXONOMY_RANKS_SET.add( "superfamily" );
+ TAXONOMY_RANKS_SET.add( "family" );
+ TAXONOMY_RANKS_SET.add( "subfamily" );
+ TAXONOMY_RANKS_SET.add( "supertribe" );
+ TAXONOMY_RANKS_SET.add( "tribe" );
+ TAXONOMY_RANKS_SET.add( "subtribe" );
+ TAXONOMY_RANKS_SET.add( "infratribe" );
+ TAXONOMY_RANKS_SET.add( "genus" );
+ TAXONOMY_RANKS_SET.add( "subgenus" );
+ TAXONOMY_RANKS_SET.add( "superspecies" );
+ TAXONOMY_RANKS_SET.add( "species" );
+ TAXONOMY_RANKS_SET.add( "subspecies" );
+ TAXONOMY_RANKS_SET.add( "variety" );
+ TAXONOMY_RANKS_SET.add( "subvariety" );
+ TAXONOMY_RANKS_SET.add( "form" );
+ TAXONOMY_RANKS_SET.add( "subform" );
+ TAXONOMY_RANKS_SET.add( "cultivar" );
+ TAXONOMY_RANKS_SET.add( "strain" );
+ TAXONOMY_RANKS_SET.add( UNKNOWN );
+ TAXONOMY_RANKS_SET.add( OTHER );
};
}
}
public void setRank( final String rank ) {
- if ( !ForesterUtil.isEmpty( rank ) && !PhyloXmlUtil.TAXONOMY_RANKS.contains( rank ) ) {
+ if ( !ForesterUtil.isEmpty( rank ) && !PhyloXmlUtil.TAXONOMY_RANKS_SET.contains( rank ) ) {
throw new PhyloXmlDataFormatException( "illegal rank: [" + rank + "]" );
}
_rank = rank;
git://source.jalview.org / jalview.git / commitdiff