// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.archaeopteryx;
_save_filechooser.setCurrentDirectory( new File( "." ) );
_save_filechooser.setMultiSelectionEnabled( false );
_save_filechooser.setFileFilter( MainFrameApplication.xmlfilter );
- _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );
_save_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
_save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
_save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
_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_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_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 ) );
customizeJMenuItem( _print_size_mi );
customizeJMenuItem( _choose_pdf_width_mi );
customizeJMenuItem( _overview_placment_mi );
- customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
+ .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 );
.setToolTipText( "To collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );
_tools_menu.addSeparator();
_tools_menu
- .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Codes or Ids from Node Names" ) );
+ .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
_extract_tax_code_from_node_names_jmi
- .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', or Uniprot/NCBI identifiers from nodes names in the form of 'xyz_6239'" );
+ .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );
_tools_menu
.add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
else {
JOptionPane
.showMessageDialog( this,
- "Could not extract any taxonomic data. Maybe node names are empty\n"
- + "or not in the forms \"XYZ_CAEEL\", \"XYZ_CAEEL/12-394\", or \"XYZ_6239\",\n"
+ "Could not extract any taxonomic data.\nMaybe node names are empty\n"
+ + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
+ "or nodes already have taxonomic data?\n",
"No Taxonomic Data Extracted",
JOptionPane.ERROR_MESSAGE );
return exception;
}
- private boolean writeAsNHX( final Phylogeny t, boolean exception, final File file ) {
- try {
- final PhylogenyWriter writer = new PhylogenyWriter();
- writer.toNewHampshireX( t, file );
- }
- catch ( final Exception e ) {
- exception = true;
- exceptionOccuredDuringSaveAs( e );
- }
- return exception;
- }
-
private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {
try {
final PhylogenyWriter writer = new PhylogenyWriter();
if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {
exception = writeAsNewHampshire( t, exception, file );
}
- else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) {
- exception = writeAsNHX( t, exception, file );
- }
else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
exception = writeAsPhyloXml( t, exception, file );
}
|| file_name.endsWith( ".tree" ) ) {
exception = writeAsNewHampshire( t, exception, file );
}
- else if ( file_name.endsWith( ".nhx" ) ) {
- exception = writeAsNHX( t, exception, file );
- }
else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
exception = writeAsNexus( t, exception, file );
}
@Override
public String getDescription() {
- return "NHX files (*.nhx)";
+ return "NHX files (*.nhx) [deprecated]";
}
}