// 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;
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() ) {
_return_to_super_tree.setEnabled( true );
}
+ void showAnnotations() {
+ 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();
+ }
+
/**
* Add zoom and quick edit buttons. (Last modified 8/9/04)
*/
_zoom_in_y = new JButton( "Y+" );
_zoom_out_y = new JButton( "Y-" );
_show_whole = new JButton( "F" );
- _show_whole.setToolTipText( "To fit the complete phylogeny to the current display size [Backspace]" );
- _zoom_in_x.setToolTipText( "To zoom in horizontally [Shift+Right]" );
- _zoom_in_y.setToolTipText( "To zoom in vertically [Shift+Up]" );
- _zoom_out_x.setToolTipText( "To zoom out horizontally [Shift+Left]" );
- _zoom_out_y.setToolTipText( "To zoom out vertically [Shift+Down]" );
- if ( getConfiguration().isUseNativeUI() && AptxUtil.isMac() ) {
+ _show_whole.setToolTipText( "To fit the complete phylogeny to the current display size [F or Home]" );
+ _zoom_in_x.setToolTipText( "To zoom in horizontally [Shift+cursor-right]" );
+ _zoom_in_y.setToolTipText( "To zoom in vertically [Shift+cursor-up]" );
+ _zoom_out_x.setToolTipText( "To zoom out horizontally [Shift+cursor-left]" );
+ _zoom_out_y.setToolTipText( "To zoom out vertically [Shift+cursor-down]" );
+ if ( getConfiguration().isUseNativeUI() && ForesterUtil.isMac() ) {
_zoom_out_x.setPreferredSize( new Dimension( 55, 10 ) );
_zoom_in_x.setPreferredSize( new Dimension( 55, 10 ) );
}
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:
_mainpanel.getCurrentTreePanel().updateOvSettings();
_mainpanel.getCurrentTreePanel().validate();
_mainpanel.validate();
- _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getSizeOfViewport().width,
- _mainpanel.getSizeOfViewport().height,
- true );
+ _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
+ _mainpanel.getSizeOfViewport().height,
+ true );
_mainpanel.getCurrentTreePanel().resetPreferredSize();
_mainpanel.adjustJScrollPane();
_mainpanel.getCurrentTreePanel().repaint();
_mainpanel.getCurrentTreePanel().validate();
_mainpanel.validate();
- _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getSizeOfViewport().width,
- _mainpanel.getSizeOfViewport().height,
- true );
+ _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
+ _mainpanel.getSizeOfViewport().height,
+ true );
_mainpanel.getCurrentTreePanel().resetPreferredSize();
_mainpanel.adjustJScrollPane();
_mainpanel.getCurrentTreePanel().repaint();
for( final TreePanel tree_panel : _mainpanel.getTreePanels() ) {
if ( tree_panel != null ) {
tree_panel.validate();
- tree_panel.setParametersForPainting( _mainpanel.getSizeOfViewport().width,
- _mainpanel.getSizeOfViewport().height,
- true );
+ tree_panel.calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
+ _mainpanel.getSizeOfViewport().height,
+ true );
tree_panel.resetPreferredSize();
tree_panel.repaint();
}
}
}
if ( ( nodes != null ) && ( nodes.size() > 0 ) ) {
- main_panel.getCurrentTreePanel().setFoundNodes( new HashSet<Integer>() );
+ main_panel.getCurrentTreePanel().setFoundNodes( new HashSet<Long>() );
for( final PhylogenyNode node : nodes ) {
main_panel.getCurrentTreePanel().getFoundNodes().add( node.getId() );
}
}
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_MOL_SEQ:
s = "Molecular Sequence";
break;
+ case SEQUENCE_MOL_SEQ_FASTA:
+ s = "Molecular Sequence (Fasta)";
+ break;
case SEQUENCE_NAME:
s = "Sequence Names";
break;
+ case GENE_NAME:
+ s = "Gene Names";
+ break;
case SEQUENCE_SYMBOL:
s = "Sequence Symbols";
break;
case TAXONOMY_CODE:
s = "Taxonomy Codes";
break;
+ case TAXONOMY_COMM0N_NAME:
+ s = "Taxonomy Common Names";
+ break;
case TAXONOMY_SCIENTIFIC_NAME:
s = "Scientific Names";
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() {