import java.awt.Font;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.io.File;
import java.io.IOException;
import java.util.LinkedList;
import java.util.List;
import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
import org.forester.phylogeny.data.Annotation;
-import org.forester.phylogeny.data.NodeVisualization.NodeFill;
-import org.forester.phylogeny.data.NodeVisualization.NodeShape;
+import org.forester.phylogeny.data.NodeVisualData.NodeFill;
+import org.forester.phylogeny.data.NodeVisualData.NodeShape;
import org.forester.sdi.GSDI;
import org.forester.sdi.GSDIR;
import org.forester.sdi.SDIException;
static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
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 DISPLAY_SCALE_LABEL = "Display Scale";
+ static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Branch Length Values";
+ static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group";
+ static final String DISPLAY_SCALE_LABEL = "Scale";
static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
static final String LABEL_DIRECTION_LABEL = "Radial Labels";
static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
static final String BG_GRAD_LABEL = "Background Color Gradient";
- static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Show External Node Shapes";
- static final String DISPLAY_NODE_BOXES_LABEL_INT = "Show Internal Node Shapes";
- static final String SHOW_OVERVIEW_LABEL = "Show Overview";
+ static final String DISPLAY_NODE_BOXES_LABEL_EXT = "External Node Shapes";
+ static final String DISPLAY_NODE_BOXES_LABEL_INT = "Internal Node Shapes";
+ static final String SHOW_OVERVIEW_LABEL = "Overview";
static final String FONT_SIZE_MENU_LABEL = "Font Size";
static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
- static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels";
+ static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels";
+ static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources";
static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";
static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
- static final String SHOW_CONF_STDDEV_LABEL = "Show Confidence Standard Deviations";
+ static final String SHOW_CONF_STDDEV_LABEL = "Confidence Standard Deviations";
static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
+ static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information";
JMenuBar _jmenubar;
JMenu _file_jmenu;
JMenu _tools_menu;
JMenuItem _gsdi_item;
JMenuItem _gsdir_item;
JMenuItem _lineage_inference;
- JMenuItem _function_analysis;
// file menu:
JMenuItem _open_item;
- JMenuItem _open_url_item;
JMenuItem _save_item;
JMenuItem _save_all_item;
JMenuItem _close_item;
JRadioButtonMenuItem _uniform_cladograms_rbmi;
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;
+ JCheckBoxMenuItem _show_annotation_ref_source;
JCheckBoxMenuItem _abbreviate_scientific_names;
JCheckBoxMenuItem _color_labels_same_as_parent_branch;
JMenuItem _overview_placment_mi;
JMenuItem _cycle_node_shape_mi;
JMenuItem _cycle_node_fill_mi;
JMenuItem _choose_node_size_mi;
- JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi;
JCheckBoxMenuItem _show_confidence_stddev_cbmi;
// _ print
JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
// _ parsing
JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
JRadioButtonMenuItem _extract_taxonomy_no_rbmi;
- JRadioButtonMenuItem _extract_taxonomy_yes_rbmi;
- JRadioButtonMenuItem _extract_taxonomy_pfam_rbmi;
+ JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;
+ JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;
+ JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;
JCheckBoxMenuItem _replace_underscores_cbmi;
+ JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi;
JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
// _ search
applet = getCurrentTreePanel().obtainApplet();
}
}
- if ( o == _open_url_item ) {
- readPhylogeniesFromURL();
- }
- else if ( o == _exit_item ) {
+ if ( o == _exit_item ) {
close();
}
else if ( o == _gsdi_item ) {
switchColors();
}
else if ( o == _display_basic_information_item ) {
- displayBasicInformation();
+ displayBasicInformation( getCurrentTreePanel().getTreeFile() );
}
else if ( o == _view_as_NH_item ) {
viewAsNH();
else if ( o == _show_domain_labels ) {
updateOptions( getOptions() );
}
+ else if ( o == _show_annotation_ref_source ) {
+ updateOptions( getOptions() );
+ }
else if ( o == _abbreviate_scientific_names ) {
updateOptions( getOptions() );
}
else if ( o == _show_default_node_shapes_external_cbmi ) {
updateOptions( getOptions() );
}
- else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
- updateOptions( getOptions() );
- }
else if ( o == _non_lined_up_cladograms_rbmi ) {
updateOptions( getOptions() );
showWhole();
}
else if ( o == _search_case_senstive_cbmi ) {
updateOptions( getOptions() );
- getMainPanel().getControlPanel().search();
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
}
else if ( o == _search_whole_words_only_cbmi ) {
updateOptions( getOptions() );
- getMainPanel().getControlPanel().search();
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
}
else if ( o == _inverse_search_result_cbmi ) {
updateOptions( getOptions() );
- getMainPanel().getControlPanel().search();
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
}
else if ( o == _show_scale_cbmi ) {
updateOptions( getOptions() );
else if ( o == _show_branch_length_values_cbmi ) {
updateOptions( getOptions() );
}
+ else if ( o == _color_by_taxonomic_group_cbmi ) {
+ updateOptions( getOptions() );
+ }
else if ( o == _show_confidence_stddev_cbmi ) {
updateOptions( getOptions() );
}
void buildFileMenu() {
_file_jmenu = createMenu( "File", getConfiguration() );
- _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
- _file_jmenu.addSeparator();
_file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
- customizeJMenuItem( _open_url_item );
customizeJMenuItem( _exit_item );
_jmenubar.add( _file_jmenu );
}
void buildViewMenu() {
_view_jmenu = createMenu( "View", getConfiguration() );
- _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
+ _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
_view_jmenu.addSeparator();
- _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
- _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
- _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
+ _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
+ _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
+ _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
customizeJMenuItem( _display_basic_information_item );
customizeJMenuItem( _view_as_NH_item );
customizeJMenuItem( _view_as_XML_item );
}
}
- void displayBasicInformation() {
+ void displayBasicInformation( final File treefile ) {
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
String title = "Basic Information";
if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
- title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
+ title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
}
- showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ), title );
+ showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );
}
}
GSDI gsdi = null;
final Phylogeny species_tree = getSpeciesTree().copy();
try {
- gsdi = new GSDI( gene_tree, species_tree, false, true, true );
+ gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
}
catch ( final SDIException e ) {
JOptionPane.showMessageDialog( this,
GSDIR gsdir = null;
final Phylogeny species_tree = getSpeciesTree().copy();
try {
- gsdir = new GSDIR( gene_tree, species_tree, true, true );
+ gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
}
catch ( final SDIException e ) {
JOptionPane.showMessageDialog( this,
result_gene_tree.setRerootable( false );
result_gene_tree.clearHashIdToNodeMap();
result_gene_tree.recalculateNumberOfExternalDescendants( true );
+ PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
_mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
getMainPanel().getControlPanel().setShowEvents( true );
showWhole();
}
}
- abstract void readPhylogeniesFromURL();
-
void readPhylogeniesFromWebservice( final int i ) {
final UrlTreeReader reader = new UrlTreeReader( this, i );
new Thread( reader ).start();
options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
&& _background_gradient_cbmi.isSelected() );
options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
+ options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
+ && _show_annotation_ref_source.isSelected() );
options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
&& _abbreviate_scientific_names.isSelected() );
options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
&& _show_default_node_shapes_internal_cbmi.isSelected() );
options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
&& _show_default_node_shapes_external_cbmi.isSelected() );
- options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
- && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
}
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() );
+ }
options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
&& ( _print_using_actual_size_cbmi.isSelected() ) );
options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
&& _print_black_and_white_cbmi.isSelected() );
options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
&& _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
- if ( ( _extract_taxonomy_yes_rbmi != null ) && _extract_taxonomy_yes_rbmi.isSelected() ) {
- options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.AGRESSIVE );
+ if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ }
+ else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
}
- else if ( ( _extract_taxonomy_pfam_rbmi != null ) && _extract_taxonomy_pfam_rbmi.isSelected() ) {
- options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
}
else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
- options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.NO );
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
}
options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
&& _replace_underscores_cbmi.isSelected() );
+ options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )
+ && _allow_errors_in_distance_to_parent_cbmi.isSelected() );
options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
&& _search_whole_words_only_cbmi.isSelected() );
options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
String title = "Nexus";
if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
- title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
}
showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
title );
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
String title = "New Hampshire";
if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
- title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
}
showTextFrame( _mainpanel.getCurrentPhylogeny()
.toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
String title = "phyloXML";
if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
- title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
}
showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
}
private void annotateSequences() {
if ( getCurrentTreePanel() != null ) {
- final Set<Long> nodes = getCurrentTreePanel().getFoundNodes();
+ final Set<Long> nodes = getCurrentTreePanel().getFoundNodes0();
if ( ( nodes == null ) || nodes.isEmpty() ) {
JOptionPane
.showMessageDialog( this,
git://source.jalview.org / jalview.git / blobdiff