import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
-import java.net.MalformedURLException;
-import java.net.URL;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Taxonomy;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.sequence.Sequence;
import org.forester.util.BasicDescriptiveStatistics;
}
updateOptions( getOptions() );
}
+ else if ( o == _allow_errors_in_distance_to_parent_cbmi ) {
+ updateOptions( getOptions() );
+ }
else if ( o == _collapse_below_threshold ) {
if ( isSubtreeDisplayed() ) {
return;
_file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
_file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
_file_jmenu.addSeparator();
- _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
- _file_jmenu.addSeparator();
final WebservicesManager webservices_manager = WebservicesManager.getInstance();
_load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
.getAvailablePhylogeniesWebserviceClients().size() ];
customizeJMenuItem( _open_item );
_open_item
.setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
- customizeJMenuItem( _open_url_item );
for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
}
_radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
_radio_group_1.add( _uniform_cladograms_rbmi );
_radio_group_1.add( _non_lined_up_cladograms_rbmi );
+ ///////
_options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
_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_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_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( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_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 ) );
- _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
- _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
+ if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
+ _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
+ }
+ _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );
+ _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
+ _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );
_options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
_color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
_options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
+ _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
+ _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
_options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
_options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
- if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
- _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
- }
- _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_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 ) );
_options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
_options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
_options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
_options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
+ ///////
_options_jmenu.addSeparator();
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
_options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
_options_jmenu
.add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
_options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
+ _options_jmenu
+ .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );
//
_options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
_options_jmenu
.isShowDefaultNodeShapesExternal() );
customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
.isShowDefaultNodeShapesInternal() );
- customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
customizeJMenuItem( _cycle_node_shape_mi );
customizeJMenuItem( _cycle_node_fill_mi );
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( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,
getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );
customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
+ customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()
+ .isReplaceUnderscoresInNhParsing() );
customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
_color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
_tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
customizeJMenuItem( _taxcolor_item );
- _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
- _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny" );
+ _tools_menu.addSeparator();
+ _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
+ _remove_visual_styles_item
+ .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
+ customizeJMenuItem( _remove_visual_styles_item );
+ _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
+ _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
customizeJMenuItem( _remove_branch_color_item );
_tools_menu.addSeparator();
_tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );
System.exit( 0 );
}
- @Override
- void readPhylogeniesFromURL() {
- URL url = null;
- Phylogeny[] phys = null;
- final String message = "Please enter a complete URL, for example \"http://www.phyloxml.org/examples/apaf.xml\"";
- final String url_string = JOptionPane.showInputDialog( this,
- message,
- "Use URL/webservice to obtain a phylogeny",
- JOptionPane.QUESTION_MESSAGE );
- boolean nhx_or_nexus = false;
- if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
- try {
- url = new URL( url_string );
- PhylogenyParser parser = null;
- if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
- parser = new TolParser();
- }
- else {
- parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
- .isValidatePhyloXmlAgainstSchema() );
- }
- if ( parser instanceof NexusPhylogeniesParser ) {
- nhx_or_nexus = true;
- }
- else if ( parser instanceof NHXParser ) {
- nhx_or_nexus = true;
- }
- if ( _mainpanel.getCurrentTreePanel() != null ) {
- _mainpanel.getCurrentTreePanel().setWaitCursor();
- }
- else {
- _mainpanel.setWaitCursor();
- }
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- phys = factory.create( url.openStream(), parser );
- }
- catch ( final MalformedURLException e ) {
- JOptionPane.showMessageDialog( this,
- "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
- "Malformed URL",
- JOptionPane.ERROR_MESSAGE );
- }
- catch ( final IOException e ) {
- JOptionPane.showMessageDialog( this,
- "Could not read from " + url + "\n"
- + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
- "Failed to read URL",
- JOptionPane.ERROR_MESSAGE );
- }
- catch ( final Exception e ) {
- JOptionPane.showMessageDialog( this,
- ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
- "Unexpected Exception",
- JOptionPane.ERROR_MESSAGE );
- }
- finally {
- if ( _mainpanel.getCurrentTreePanel() != null ) {
- _mainpanel.getCurrentTreePanel().setArrowCursor();
- }
- else {
- _mainpanel.setArrowCursor();
- }
- }
- if ( ( phys != null ) && ( phys.length > 0 ) ) {
- if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
- for( final Phylogeny phy : phys ) {
- PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
- }
- }
- AptxUtil.addPhylogeniesToTabs( phys,
- new File( url.getFile() ).getName(),
- new File( url.getFile() ).toString(),
- getConfiguration(),
- getMainPanel() );
- _mainpanel.getControlPanel().showWhole();
- }
- }
- activateSaveAllIfNeeded();
- System.gc();
- }
-
void setMsa( final Msa msa ) {
_msa = msa;
}
}
}
if ( xml_parser == null ) {
- xml_parser = new PhyloXmlParser();
+ xml_parser = PhyloXmlParser.createPhyloXmlParser();
}
return xml_parser;
}
if ( nhx_or_nexus ) {
for( final Phylogeny phy : phys ) {
if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
- PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
}
if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
one_desc = true;
if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
try {
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
+ .createPhyloXmlParserXsdValidating(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
// "*.*":
else {
try {
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
+ .createPhyloXmlParserXsdValidating(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
+ nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() );
}
private void writeAllToFile() {
private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
try {
final PhylogenyWriter writer = new PhylogenyWriter();
- writer.toNewHampshire( t, false, true, getOptions().getNhConversionSupportValueStyle(), file );
+ writer.toNewHampshire( t, true, getOptions().getNhConversionSupportValueStyle(), file );
}
catch ( final Exception e ) {
exception = true;
git://source.jalview.org / jalview.git / blobdiff