// 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 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', 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 );
_move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
_tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
customizeJMenuItem( _move_node_names_to_seq_names_jmi );
_move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
- _tools_menu
- .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Codes or Ids from Node Names" ) );
- customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
- _extract_tax_code_from_node_names_jmi
- .setToolTipText( "To extract taxonomic codes (mnemonics) from nodes names in the form of 'xyz_ECOLI', or Uniprot identifiers from nodes names in the form of 'xyz_1234567'" );
_tools_menu.addSeparator();
_tools_menu
.add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
if ( counter_failed < 15 ) {
sb_failed.append( name + "\n" );
}
- else if ( counter_failed == 15 ) {
+ else if ( counter_failed == 15 ) {
sb_failed.append( "...\n" );
}
counter_failed++;
}
if ( counter > 0 ) {
String failed = "";
+ String all = "all ";
if ( counter_failed > 0 ) {
- failed = "\nDid not extract taxonomic data for " + counter_failed + " (named) external nodes:\n" + sb_failed;
-
+ all = "";
+ failed = "\nCould not extract taxonomic data for " + counter_failed
+ + " named external nodes:\n" + sb_failed;
}
JOptionPane.showMessageDialog( this,
- "Successfully extracted taxonomic data from " + counter
- + " external nodes:\n" + sb.toString() + failed,
- "Taxonomic Data Extraction Successfully Completed",
- JOptionPane.INFORMATION_MESSAGE );
+ "Extracted taxonomic data from " + all + counter
+ + " named external nodes:\n" + sb.toString() + failed,
+ "Taxonomic Data Extraction Completed",
+ counter_failed > 0 ? JOptionPane.WARNING_MESSAGE
+ : JOptionPane.INFORMATION_MESSAGE );
}
else {
JOptionPane
.showMessageDialog( this,
- "Could not extract any taxonomic data, maybe node names are empty\nor not in the form \"XYZ_CAEEL\", \"XYZ_CAEEL/12-394\", or \"XYZ_1234567\"?",
+ "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.WARNING_MESSAGE );
+ 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]";
}
}
git://source.jalview.org / jalview.git / blobdiff