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;
_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 ] );
}
_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;
}
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;