private JCheckBox _show_annotation;
private JCheckBox _show_binary_characters;
private JCheckBox _show_binary_character_counts;
+ private JCheckBox _show_seq_names;
+ private JCheckBox _show_seq_symbols;
private JCheckBox _show_gene_names;
- private JCheckBox _show_gene_symbols;
private JCheckBox _show_sequence_acc;
private JCheckBox _node_desc_popup_cb;
private JCheckBox _dynamically_hide_data;
else if ( e.getSource() == _order ) {
DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
if ( ( !isShowTaxonomyScientificNames() && !isShowTaxonomyCode() && !isShowTaxonomyCommonNames() ) ) {
- if ( ( isShowSequenceAcc() || isShowGeneNames() || isShowGeneSymbols() ) ) {
+ if ( ( isShowSequenceAcc() || isShowSeqNames() || isShowSeqSymbols() ) ) {
pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
}
else if ( isShowNodeNames() ) {
}
void showAnnotations() {
- _show_annotation.setSelected( true );
- _color_according_to_annotation.setSelected( true );
- _color_acc_species.setSelected( false );
+ if ( _show_annotation != null ) {
+ _show_annotation.setSelected( true );
+ }
+ if ( _color_according_to_annotation != null ) {
+ _color_according_to_annotation.setSelected( true );
+ }
+ if ( _color_acc_species != null ) {
+ _color_acc_species.setSelected( false );
+ }
_mainpanel.getCurrentTreePanel().repaint();
}
addJCheckBox( _show_domain_architectures, ch_panel );
add( ch_panel );
break;
+ case Configuration.show_seq_names:
+ _show_seq_names = new JCheckBox( title );
+ addJCheckBox( _show_seq_names, ch_panel );
+ add( ch_panel );
+ break;
case Configuration.show_gene_names:
_show_gene_names = new JCheckBox( title );
addJCheckBox( _show_gene_names, ch_panel );
add( ch_panel );
break;
- case Configuration.show_gene_symbols:
- _show_gene_symbols = new JCheckBox( title );
- addJCheckBox( _show_gene_symbols, ch_panel );
+ case Configuration.show_seq_symbols:
+ _show_seq_symbols = new JCheckBox( title );
+ addJCheckBox( _show_seq_symbols, ch_panel );
add( ch_panel );
break;
case Configuration.show_sequence_acc:
return ( ( _show_domain_architectures != null ) && _show_domain_architectures.isSelected() );
}
- boolean isShowGeneNames() {
- return ( ( _show_gene_names != null ) && _show_gene_names.isSelected() );
+ boolean isShowSeqNames() {
+ return ( ( _show_seq_names != null ) && _show_seq_names.isSelected() );
}
- boolean isShowGeneSymbols() {
- return ( ( _show_gene_symbols != null ) && _show_gene_symbols.isSelected() );
+ boolean isShowSeqSymbols() {
+ return ( ( _show_seq_symbols != null ) && _show_seq_symbols.isSelected() );
}
boolean isShowInternalData() {
return ( ( _show_sequence_acc != null ) && _show_sequence_acc.isSelected() );
}
+ boolean isShowGeneNames() {
+ return ( ( _show_gene_names != null ) && _show_gene_names.isSelected() );
+ }
+
boolean isShowSequenceRelationConfidence() {
return ( ( _seq_relation_confidence_switch != null ) && ( _seq_relation_confidence_switch.isSelected() ) );
}
_show_domain_architectures.setSelected( state );
}
break;
+ case Configuration.show_seq_names:
+ if ( _show_seq_names != null ) {
+ _show_seq_names.setSelected( state );
+ }
+ break;
case Configuration.show_gene_names:
if ( _show_gene_names != null ) {
_show_gene_names.setSelected( state );
}
break;
- case Configuration.show_gene_symbols:
- if ( _show_gene_symbols != null ) {
- _show_gene_symbols.setSelected( state );
+ case Configuration.show_seq_symbols:
+ if ( _show_seq_symbols != null ) {
+ _show_seq_symbols.setSelected( state );
}
break;
case Configuration.show_vector_data:
}
cb_index++;
}
+ if ( _configuration.doDisplayClickToOption( Configuration.select_nodes ) ) {
+ _select_nodes_item = cb_index;
+ addClickToOption( Configuration.select_nodes, _configuration.getClickToTitle( Configuration.select_nodes ) );
+ if ( default_option == Configuration.select_nodes ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
if ( _configuration.doDisplayClickToOption( Configuration.get_ext_desc_data ) ) {
_get_ext_desc_data = cb_index;
if ( !ForesterUtil.isEmpty( getConfiguration().getLabelForGetExtDescendentsData() ) ) {
case SEQUENCE_NAME:
s = "Sequence Names";
break;
+ case GENE_NAME:
+ s = "Gene Names";
+ break;
case SEQUENCE_SYMBOL:
s = "Sequence Symbols";
break;
}
cb_index++;
}
- if ( _configuration.doDisplayClickToOption( Configuration.select_nodes ) ) {
- _select_nodes_item = cb_index;
- addClickToOption( Configuration.select_nodes,
- _configuration.getClickToTitle( Configuration.select_nodes ) );
- if ( default_option == Configuration.select_nodes ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
}
// Set default selection and its action
_click_to_combobox.setSelectedIndex( selected_index );
setCheckbox( Configuration.show_taxonomy_common_names,
_configuration.doCheckOption( Configuration.show_taxonomy_common_names ) );
}
- if ( _configuration.doDisplayOption( Configuration.show_taxonomy_images ) ) {
- addCheckbox( Configuration.show_taxonomy_images,
- _configuration.getDisplayTitle( Configuration.show_taxonomy_images ) );
- setCheckbox( Configuration.show_taxonomy_images,
- _configuration.doCheckOption( Configuration.show_taxonomy_images ) );
- }
- if ( _configuration.doDisplayOption( Configuration.show_gene_symbols ) ) {
- addCheckbox( Configuration.show_gene_symbols,
- _configuration.getDisplayTitle( Configuration.show_gene_symbols ) );
- setCheckbox( Configuration.show_gene_symbols,
- _configuration.doCheckOption( Configuration.show_gene_symbols ) );
+ if ( _configuration.doDisplayOption( Configuration.show_seq_names ) ) {
+ addCheckbox( Configuration.show_seq_names, _configuration.getDisplayTitle( Configuration.show_seq_names ) );
+ setCheckbox( Configuration.show_seq_names, _configuration.doCheckOption( Configuration.show_seq_names ) );
}
if ( _configuration.doDisplayOption( Configuration.show_gene_names ) ) {
addCheckbox( Configuration.show_gene_names, _configuration.getDisplayTitle( Configuration.show_gene_names ) );
setCheckbox( Configuration.show_gene_names, _configuration.doCheckOption( Configuration.show_gene_names ) );
}
+ if ( _configuration.doDisplayOption( Configuration.show_seq_symbols ) ) {
+ addCheckbox( Configuration.show_seq_symbols,
+ _configuration.getDisplayTitle( Configuration.show_seq_symbols ) );
+ setCheckbox( Configuration.show_seq_symbols, _configuration.doCheckOption( Configuration.show_seq_symbols ) );
+ }
if ( _configuration.doDisplayOption( Configuration.show_sequence_acc ) ) {
addCheckbox( Configuration.show_sequence_acc,
_configuration.getDisplayTitle( Configuration.show_sequence_acc ) );
addCheckbox( Configuration.show_properties, _configuration.getDisplayTitle( Configuration.show_properties ) );
setCheckbox( Configuration.show_properties, _configuration.doCheckOption( Configuration.show_properties ) );
}
+ if ( _configuration.doDisplayOption( Configuration.show_taxonomy_images ) ) {
+ addCheckbox( Configuration.show_taxonomy_images,
+ _configuration.getDisplayTitle( Configuration.show_taxonomy_images ) );
+ setCheckbox( Configuration.show_taxonomy_images,
+ _configuration.doCheckOption( Configuration.show_taxonomy_images ) );
+ }
}
private void setVisibilityOfDomainStrucureControls() {