// Indices for the click-to options in the combo box
private int _show_data_item;
private JCheckBox _show_domain_architectures;
+ private JCheckBox _show_mol_seqs;
+ private JCheckBox _write_branch_length_values;
private JCheckBox _show_events;
private JCheckBox _show_gene_names;
private JCheckBox _show_node_names;
private JCheckBox _width_branches;
private JCheckBox _write_confidence;
private JButton _zoom_in_domain_structure;
- // zooming and quick tree manipulation buttons:
private JButton _zoom_in_x;
private JButton _zoom_in_y;
private JLabel _zoom_label;
displayedPhylogenyMightHaveChanged( false );
}
else if ( e.getSource() == _show_whole ) {
+ displayedPhylogenyMightHaveChanged( true );
showWhole();
}
else if ( e.getSource() == _return_to_super_tree ) {
tp.getPhylogeny().recalculateNumberOfExternalDescendants( true );
tp.resetNodeIdToDistToLeafMap();
tp.setEdited( true );
- displayedPhylogenyMightHaveChanged( false );
+ displayedPhylogenyMightHaveChanged( true );
}
else if ( e.getSource() == _uncollapse_all ) {
uncollapseAll( tp );
addJCheckBox( _width_branches, ch_panel );
add( ch_panel );
break;
+ case Configuration.write_branch_length_values:
+ _write_branch_length_values = new JCheckBox( title );
+ addJCheckBox( _write_branch_length_values, ch_panel );
+ add( ch_panel );
+ break;
case Configuration.show_domain_architectures:
_show_domain_architectures = new JCheckBox( title );
addJCheckBox( _show_domain_architectures, ch_panel );
add( ch_panel );
break;
+ case Configuration.show_mol_seqs:
+ _show_mol_seqs = new JCheckBox( title );
+ addJCheckBox( _show_mol_seqs, ch_panel );
+ add( ch_panel );
+ break;
case Configuration.show_seq_names:
_show_seq_names = new JCheckBox( title );
addJCheckBox( _show_seq_names, ch_panel );
return ( ( getWriteConfidenceCb() != null ) && getWriteConfidenceCb().isSelected() );
}
+ boolean isWriteBranchLengthValues() {
+ return ( ( _write_branch_length_values != null ) && _write_branch_length_values.isSelected() );
+ }
+
boolean isShowDomainArchitectures() {
return ( ( _show_domain_architectures != null ) && _show_domain_architectures.isSelected() );
}
+ public boolean isShowMolSequences() {
+ return ( ( _show_mol_seqs != null ) && _show_mol_seqs.isSelected() );
+ }
+
boolean isShowGeneNames() {
return ( ( _show_gene_names != null ) && _show_gene_names.isSelected() );
}
_show_domain_architectures.setSelected( state );
}
break;
+ case Configuration.write_branch_length_values:
+ if ( _write_branch_length_values != null ) {
+ _write_branch_length_values.setSelected( state );
+ }
+ break;
+ case Configuration.show_mol_seqs:
+ if ( _show_mol_seqs != null ) {
+ _show_mol_seqs.setSelected( state );
+ }
+ break;
case Configuration.show_seq_names:
if ( _show_seq_names != null ) {
_show_seq_names.setSelected( state );
}
void setUpControlsForDomainStrucures() {
- _domain_display_label = new JLabel( "Domain Display:" );
+ _domain_display_label = new JLabel( "Domain Architectures:" );
add( customizeLabel( _domain_display_label, getConfiguration() ) );
add( _domain_display_label );
_zoom_in_domain_structure = new JButton( "d+" );
addCheckbox( Configuration.show_annotation, _configuration.getDisplayTitle( Configuration.show_annotation ) );
setCheckbox( Configuration.show_annotation, _configuration.doCheckOption( Configuration.show_annotation ) );
}
+ if ( _configuration.doDisplayOption( Configuration.write_confidence_values ) ) {
+ addCheckbox( Configuration.write_confidence_values,
+ _configuration.getDisplayTitle( Configuration.write_confidence_values ) );
+ setCheckbox( Configuration.write_confidence_values,
+ _configuration.doCheckOption( Configuration.write_confidence_values ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.write_branch_length_values ) ) {
+ addCheckbox( Configuration.write_branch_length_values,
+ _configuration.getDisplayTitle( Configuration.write_branch_length_values ) );
+ setCheckbox( Configuration.write_branch_length_values,
+ _configuration.doCheckOption( Configuration.write_branch_length_values ) );
+ }
if ( _configuration.doDisplayOption( Configuration.show_binary_characters ) ) {
addCheckbox( Configuration.show_binary_characters,
_configuration.getDisplayTitle( Configuration.show_binary_characters ) );
setCheckbox( Configuration.show_domain_architectures,
_configuration.doCheckOption( Configuration.show_domain_architectures ) );
}
- if ( _configuration.doDisplayOption( Configuration.write_confidence_values ) ) {
- addCheckbox( Configuration.write_confidence_values,
- _configuration.getDisplayTitle( Configuration.write_confidence_values ) );
- setCheckbox( Configuration.write_confidence_values,
- _configuration.doCheckOption( Configuration.write_confidence_values ) );
+ if ( _configuration.doDisplayOption( Configuration.show_mol_seqs ) ) {
+ addCheckbox( Configuration.show_mol_seqs, _configuration.getDisplayTitle( Configuration.show_mol_seqs ) );
+ setCheckbox( Configuration.show_mol_seqs, _configuration.doCheckOption( Configuration.show_mol_seqs ) );
}
if ( _configuration.doDisplayOption( Configuration.write_events ) ) {
addCheckbox( Configuration.write_events, _configuration.getDisplayTitle( Configuration.write_events ) );
private void setVisibilityOfDomainStrucureControls() {
if ( _zoom_in_domain_structure != null ) {
- if ( isShowDomainArchitectures() ) {
- _domain_display_label.setVisible( true );
- _zoom_in_domain_structure.setVisible( true );
- _zoom_out_domain_structure.setVisible( true );
- _decr_domain_structure_evalue_thr.setVisible( true );
- _incr_domain_structure_evalue_thr.setVisible( true );
- _domain_structure_evalue_thr_tf.setVisible( true );
+ final MainFrame mf = getMainFrame();
+ if ( mf != null ) {
+ if ( isShowDomainArchitectures() ) {
+ _domain_display_label.setVisible( true );
+ _zoom_in_domain_structure.setVisible( true );
+ _zoom_out_domain_structure.setVisible( true );
+ _decr_domain_structure_evalue_thr.setVisible( true );
+ _incr_domain_structure_evalue_thr.setVisible( true );
+ _domain_structure_evalue_thr_tf.setVisible( true );
+ if ( mf._right_line_up_domains_cbmi != null ) {
+ mf._right_line_up_domains_cbmi.setVisible( true );
+ }
+ if ( mf._show_domain_labels != null ) {
+ mf._show_domain_labels.setVisible( true );
+ }
+ }
+ else {
+ _domain_display_label.setVisible( false );
+ _zoom_in_domain_structure.setVisible( false );
+ _zoom_out_domain_structure.setVisible( false );
+ _decr_domain_structure_evalue_thr.setVisible( false );
+ _incr_domain_structure_evalue_thr.setVisible( false );
+ _domain_structure_evalue_thr_tf.setVisible( false );
+ if ( mf._right_line_up_domains_cbmi != null ) {
+ mf._right_line_up_domains_cbmi.setVisible( false );
+ }
+ if ( mf._show_domain_labels != null ) {
+ mf._show_domain_labels.setVisible( false );
+ }
+ }
+ }
+ }
+ }
+
+ // This takes care of ArchaeopteryxE-issue.
+ // Can, and will, return null prior to ArchaeopteryxE initialization completion.
+ final private MainFrame getMainFrame() {
+ MainFrame mf = getMainPanel().getMainFrame();
+ if ( mf == null ) {
+ // Must be "E" applet version.
+ final ArchaeopteryxE e = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
+ if ( e.getMainPanel() == null ) {
+ return null;
+ }
+ mf = e.getMainPanel().getMainFrame();
+ }
+ return mf;
+ }
+
+ void setVisibilityOfX() {
+ final MainFrame mf = getMainFrame();
+ if ( mf != null ) {
+ if ( ( getCurrentTreePanel() != null ) && ( getCurrentTreePanel().getPhylogeny() != null ) ) {
+ if ( AptxUtil.isHasAtLeastOneBranchWithSupportSD( getCurrentTreePanel().getPhylogeny() ) ) {
+ if ( mf._show_confidence_stddev_cbmi != null ) {
+ mf._show_confidence_stddev_cbmi.setVisible( true );
+ }
+ }
+ else {
+ if ( mf._show_confidence_stddev_cbmi != null ) {
+ mf._show_confidence_stddev_cbmi.setVisible( false );
+ }
+ }
+ if ( AptxUtil.isHasAtLeastOneNodeWithScientificName( getCurrentTreePanel().getPhylogeny() ) ) {
+ if ( mf._abbreviate_scientific_names != null ) {
+ mf._abbreviate_scientific_names.setVisible( true );
+ }
+ }
+ else {
+ if ( mf._abbreviate_scientific_names != null ) {
+ mf._abbreviate_scientific_names.setVisible( false );
+ }
+ }
+ if ( AptxUtil.isHasAtLeastOneNodeWithSequenceAnnotation( getCurrentTreePanel().getPhylogeny() ) ) {
+ if ( mf._show_annotation_ref_source != null ) {
+ mf._show_annotation_ref_source.setVisible( true );
+ }
+ }
+ else {
+ if ( mf._show_annotation_ref_source != null ) {
+ mf._show_annotation_ref_source.setVisible( false );
+ }
+ }
+ }
+ if ( isDrawPhylogram()
+ || ( ( getCurrentTreePanel() != null ) && ( ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( getCurrentTreePanel()
+ .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) ) {
+ if ( mf._non_lined_up_cladograms_rbmi != null ) {
+ mf._non_lined_up_cladograms_rbmi.setVisible( false );
+ }
+ if ( mf._uniform_cladograms_rbmi != null ) {
+ mf._uniform_cladograms_rbmi.setVisible( false );
+ }
+ if ( mf._ext_node_dependent_cladogram_rbmi != null ) {
+ mf._ext_node_dependent_cladogram_rbmi.setVisible( false );
+ }
}
else {
- _domain_display_label.setVisible( false );
- _zoom_in_domain_structure.setVisible( false );
- _zoom_out_domain_structure.setVisible( false );
- _decr_domain_structure_evalue_thr.setVisible( false );
- _incr_domain_structure_evalue_thr.setVisible( false );
- _domain_structure_evalue_thr_tf.setVisible( false );
+ if ( mf._non_lined_up_cladograms_rbmi != null ) {
+ mf._non_lined_up_cladograms_rbmi.setVisible( true );
+ }
+ if ( mf._uniform_cladograms_rbmi != null ) {
+ mf._uniform_cladograms_rbmi.setVisible( true );
+ }
+ if ( mf._ext_node_dependent_cladogram_rbmi != null ) {
+ mf._ext_node_dependent_cladogram_rbmi.setVisible( true );
+ }
+ }
+ if ( isDrawPhylogram() ) {
+ if ( mf._show_scale_cbmi != null ) {
+ mf._show_scale_cbmi.setVisible( true );
+ }
}
+ else {
+ if ( mf._show_scale_cbmi != null ) {
+ mf._show_scale_cbmi.setVisible( false );
+ }
+ }
+ if ( getCurrentTreePanel() != null ) {
+ if ( ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
+ || ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
+ if ( mf._label_direction_cbmi != null ) {
+ mf._label_direction_cbmi.setVisible( true );
+ }
+ }
+ else {
+ if ( mf._label_direction_cbmi != null ) {
+ mf._label_direction_cbmi.setVisible( false );
+ }
+ }
+ }
+ }
+ }
+
+ void setVisibilityOfDomainStrucureCB() {
+ try {
+ if ( ( getCurrentTreePanel() != null )
+ && ( ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( getCurrentTreePanel()
+ .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
+ if ( getMainPanel().getMainFrame()._right_line_up_domains_cbmi != null ) {
+ getMainPanel().getMainFrame()._right_line_up_domains_cbmi.setVisible( false );
+ }
+ if ( getMainPanel().getMainFrame()._show_domain_labels != null ) {
+ getMainPanel().getMainFrame()._show_domain_labels.setVisible( false );
+ }
+ }
+ else if ( isShowDomainArchitectures() ) {
+ if ( getMainPanel().getMainFrame()._right_line_up_domains_cbmi != null ) {
+ getMainPanel().getMainFrame()._right_line_up_domains_cbmi.setVisible( true );
+ }
+ if ( getMainPanel().getMainFrame()._show_domain_labels != null ) {
+ getMainPanel().getMainFrame()._show_domain_labels.setVisible( true );
+ }
+ }
+ else {
+ if ( getMainPanel().getMainFrame()._right_line_up_domains_cbmi != null ) {
+ getMainPanel().getMainFrame()._right_line_up_domains_cbmi.setVisible( false );
+ }
+ if ( getMainPanel().getMainFrame()._show_domain_labels != null ) {
+ getMainPanel().getMainFrame()._show_domain_labels.setVisible( false );
+ }
+ }
+ }
+ catch ( final Exception ignore ) {
+ //not important...
}
}
git://source.jalview.org / jalview.git / blobdiff