// 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;
private int _paste_subtree_item;
private int _add_new_node_item;
private int _edit_node_data_item;
+ private int _select_nodes_item;
private int _get_ext_desc_data;
private int _blast_item;
// zooming and quick tree manipulation buttons:
}
displayedPhylogenyMightHaveChanged( true );
}
- else if ( e.getSource() == _color_according_to_annotation ) {
- if ( ( _show_annotation != null ) && _color_according_to_annotation.isSelected() ) {
- _show_annotation.setSelected( true );
- }
- displayedPhylogenyMightHaveChanged( false );
- }
- else if ( e.getSource() == _show_annotation ) {
- if ( ( _color_according_to_annotation != null ) && !_show_annotation.isSelected() ) {
- _color_according_to_annotation.setSelected( false );
- }
- displayedPhylogenyMightHaveChanged( false );
- }
else if ( e.getSource() == _show_domain_architectures ) {
search();
displayedPhylogenyMightHaveChanged( false );
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() ) {
}
}
+ public JCheckBox getColorAccSpeciesCb() {
+ return _color_acc_species;
+ }
+
+ public JCheckBox getColorBranchesCb() {
+ return _color_branches_cb;
+ }
+
+ public JCheckBox getDisplayAsPhylogramCb() {
+ return _display_as_phylogram_cb;
+ }
+
+ public JCheckBox getDynamicallyHideData() {
+ return _dynamically_hide_data;
+ }
+
+ public JCheckBox getNodeDescPopupCb() {
+ return _node_desc_popup_cb;
+ }
+
+ public Sequence getSelectedQuerySequence() {
+ return _selected_query_seq;
+ }
+
+ public JComboBox getSequenceRelationBox() {
+ if ( _show_sequence_relations == null ) {
+ _show_sequence_relations = new JComboBox();
+ _show_sequence_relations.setFocusable( false );
+ _show_sequence_relations.setMaximumRowCount( 20 );
+ _show_sequence_relations.setFont( ControlPanel.js_font );
+ if ( !_configuration.isUseNativeUI() ) {
+ _show_sequence_relations.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
+ _show_sequence_relations.setForeground( getConfiguration().getGuiButtonTextColor() );
+ }
+ _show_sequence_relations.addItem( "-----" );
+ _show_sequence_relations.setToolTipText( "To display orthology information for selected query" );
+ }
+ return _show_sequence_relations;
+ }
+
+ /* GUILHEM_BEG */
+ public JComboBox getSequenceRelationTypeBox() {
+ if ( _sequence_relation_type_box == null ) {
+ _sequence_relation_type_box = new JComboBox();
+ for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : SequenceRelation.SEQUENCE_RELATION_TYPE.values() ) {
+ _sequence_relation_type_box.addItem( type );
+ }
+ _sequence_relation_type_box.addActionListener( new ActionListener() {
+
+ @Override
+ public void actionPerformed( final ActionEvent e ) {
+ if ( _mainpanel.getCurrentPhylogeny() != null ) {
+ setSequenceRelationQueries( getMainPanel().getCurrentPhylogeny().getSequenceRelationQueries() );
+ }
+ }
+ } );
+ }
+ return _sequence_relation_type_box;
+ }
+
+ public JCheckBox getShowEventsCb() {
+ return _show_events;
+ }
+
+ public JCheckBox getWriteConfidenceCb() {
+ return _write_confidence;
+ }
+
+ public boolean isShowProperties() {
+ return ( ( _show_properties_cb != null ) && _show_properties_cb.isSelected() );
+ }
+
+ public boolean isShowTaxonomyImages() {
+ return ( ( _show_taxo_images_cb != null ) && _show_taxo_images_cb.isSelected() );
+ }
+
+ public boolean isShowVectorData() {
+ return ( ( _show_vector_data_cb != null ) && _show_vector_data_cb.isSelected() );
+ }
+
+ public void setSequenceRelationQueries( final Collection<Sequence> sequenceRelationQueries ) {
+ final JComboBox box = getSequenceRelationBox();
+ while ( box.getItemCount() > 1 ) {
+ box.removeItemAt( 1 );
+ }
+ final HashMap<String, Sequence> sequencesByName = new HashMap<String, Sequence>();
+ final SequenceRelation.SEQUENCE_RELATION_TYPE relationType = ( SequenceRelation.SEQUENCE_RELATION_TYPE ) _sequence_relation_type_box
+ .getSelectedItem();
+ if ( relationType == null ) {
+ return;
+ }
+ final ArrayList<String> sequenceNamesToAdd = new ArrayList<String>();
+ for( final Sequence seq : sequenceRelationQueries ) {
+ if ( seq.hasSequenceRelations() ) {
+ boolean fFoundForCurrentType = false;
+ for( final SequenceRelation sq : seq.getSequenceRelations() ) {
+ if ( sq.getType().equals( relationType ) ) {
+ fFoundForCurrentType = true;
+ break;
+ }
+ }
+ if ( fFoundForCurrentType ) {
+ sequenceNamesToAdd.add( seq.getName() );
+ sequencesByName.put( seq.getName(), seq );
+ }
+ }
+ }
+ // sort sequences by name before adding them to the combo
+ final String[] sequenceNameArray = sequenceNamesToAdd.toArray( new String[ sequenceNamesToAdd.size() ] );
+ Arrays.sort( sequenceNameArray, String.CASE_INSENSITIVE_ORDER );
+ for( final String seqName : sequenceNameArray ) {
+ box.addItem( seqName );
+ }
+ for( final ItemListener oldItemListener : box.getItemListeners() ) {
+ box.removeItemListener( oldItemListener );
+ }
+ box.addItemListener( new ItemListener() {
+
+ @Override
+ public void itemStateChanged( final ItemEvent e ) {
+ _selected_query_seq = sequencesByName.get( e.getItem() );
+ _mainpanel.getCurrentTreePanel().repaint();
+ }
+ } );
+ }
+
void activateButtonToReturnToSuperTree( int index ) {
--index;
if ( index > 0 ) {
_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:
}
}// addCheckbox
- private void addClickToOption( final int which, final String title ) {
- _click_to_combobox.addItem( title );
- _click_to_names.add( title );
- _all_click_to_names.put( new Integer( which ), title );
- if ( !_configuration.isUseNativeUI() ) {
- _click_to_combobox.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
- _click_to_combobox.setForeground( getConfiguration().getGuiButtonTextColor() );
- }
- }
-
void addJButton( final JButton jb, final JPanel p ) {
jb.setFocusPainted( false );
jb.setFont( ControlPanel.jcb_font );
tf.addActionListener( this );
}
- /* GUILHEM_BEG */
- private void addSequenceRelationBlock() {
- final JLabel spacer = new JLabel( "" );
- spacer.setSize( 1, 1 );
- add( spacer );
- final JLabel mainLabel = new JLabel( "Sequence relations to display" );
- final JLabel typeLabel = customizeLabel( new JLabel( "(type) " ), getConfiguration() );
- typeLabel.setFont( ControlPanel.js_font.deriveFont( 7 ) );
- getSequenceRelationTypeBox().setFocusable( false );
- _sequence_relation_type_box.setFont( ControlPanel.js_font );
- if ( !_configuration.isUseNativeUI() ) {
- _sequence_relation_type_box.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
- _sequence_relation_type_box.setForeground( getConfiguration().getGuiButtonTextColor() );
- }
- _sequence_relation_type_box.setRenderer( new ListCellRenderer() {
-
- @Override
- public Component getListCellRendererComponent( final JList list,
- final Object value,
- final int index,
- final boolean isSelected,
- final boolean cellHasFocus ) {
- final Component component = new DefaultListCellRenderer().getListCellRendererComponent( list,
- value,
- index,
- isSelected,
- cellHasFocus );
- if ( ( value != null ) && ( value instanceof SequenceRelation.SEQUENCE_RELATION_TYPE ) ) {
- ( ( DefaultListCellRenderer ) component ).setText( SequenceRelation
- .getPrintableNameByType( ( SequenceRelation.SEQUENCE_RELATION_TYPE ) value ) );
- }
- return component;
- }
- } );
- final GridBagLayout gbl = new GridBagLayout();
- _sequence_relation_type_box.setMinimumSize( new Dimension( 115, 17 ) );
- _sequence_relation_type_box.setPreferredSize( new Dimension( 115, 20 ) );
- final JPanel horizGrid = new JPanel( gbl );
- horizGrid.setBackground( getBackground() );
- horizGrid.add( typeLabel );
- horizGrid.add( _sequence_relation_type_box );
- add( customizeLabel( mainLabel, getConfiguration() ) );
- add( horizGrid );
- add( getSequenceRelationBox() );
- if ( _configuration.doDisplayOption( Configuration.show_relation_confidence ) ) {
- addCheckbox( Configuration.show_relation_confidence,
- _configuration.getDisplayTitle( Configuration.show_relation_confidence ) );
- setCheckbox( Configuration.show_relation_confidence,
- _configuration.doCheckOption( Configuration.show_relation_confidence ) );
- }
- }// addSequenceRelationBlock
-
void deactivateButtonToReturnToSuperTree() {
_return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT );
_return_to_super_tree.setForeground( getConfiguration().getGuiButtonTextColor() );
return _annotation_colors;
}
- public JCheckBox getColorBranchesCb() {
- return _color_branches_cb;
- }
-
- public JCheckBox getColorAccSpeciesCb() {
- return _color_acc_species;
- }
-
Configuration getConfiguration() {
return _configuration;
}
return getMainPanel().getCurrentTreePanel();
}
- public JCheckBox getDisplayAsPhylogramCb() {
- return _display_as_phylogram_cb;
+ MainPanel getMainPanel() {
+ return _mainpanel;
}
- public JCheckBox getDynamicallyHideData() {
- return _dynamically_hide_data;
+ Options getOptions() {
+ return getMainPanel().getOptions();
}
- /* GUILHEM_END */
- private List<Boolean> getIsDrawPhylogramList() {
- return _draw_phylogram;
+ JTextField getSearchTextField() {
+ return _search_tf;
}
- MainPanel getMainPanel() {
- return _mainpanel;
+ List<String> getSingleClickToNames() {
+ return _click_to_names;
}
- public JCheckBox getNodeDescPopupCb() {
- return _node_desc_popup_cb;
+ Map<String, Color> getSpeciesColors() {
+ return _species_colors;
}
- Options getOptions() {
- return getMainPanel().getOptions();
+ boolean isAntialiasScreenText() {
+ return true;
}
- private JLabel getSearchFoundCountsLabel() {
- return _search_found_label;
+ boolean isColorAccordingToAnnotation() {
+ return ( ( _color_according_to_annotation != null ) && _color_according_to_annotation.isSelected() );
}
- private JButton getSearchResetButton() {
- return _search_reset_button;
+ boolean isColorAccordingToTaxonomy() {
+ return ( ( _color_acc_species != null ) && _color_acc_species.isSelected() );
}
- JTextField getSearchTextField() {
- return _search_tf;
+ boolean isColorBranches() {
+ return ( ( ( getColorBranchesCb() != null ) && getColorBranchesCb().isSelected() ) || ( ( getColorBranchesCb() == null ) && _color_branches ) );
}
- public Sequence getSelectedQuerySequence() {
- return _selected_query_seq;
- }
-
- public JComboBox getSequenceRelationBox() {
- if ( _show_sequence_relations == null ) {
- _show_sequence_relations = new JComboBox();
- _show_sequence_relations.setFocusable( false );
- _show_sequence_relations.setMaximumRowCount( 20 );
- _show_sequence_relations.setFont( ControlPanel.js_font );
- if ( !_configuration.isUseNativeUI() ) {
- _show_sequence_relations.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
- _show_sequence_relations.setForeground( getConfiguration().getGuiButtonTextColor() );
- }
- _show_sequence_relations.addItem( "-----" );
- _show_sequence_relations.setToolTipText( "To display orthology information for selected query" );
- }
- return _show_sequence_relations;
- }
-
- /* GUILHEM_BEG */
- public JComboBox getSequenceRelationTypeBox() {
- if ( _sequence_relation_type_box == null ) {
- _sequence_relation_type_box = new JComboBox();
- for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : SequenceRelation.SEQUENCE_RELATION_TYPE.values() ) {
- _sequence_relation_type_box.addItem( type );
- }
- _sequence_relation_type_box.addActionListener( new ActionListener() {
-
- @Override
- public void actionPerformed( final ActionEvent e ) {
- if ( _mainpanel.getCurrentPhylogeny() != null ) {
- setSequenceRelationQueries( getMainPanel().getCurrentPhylogeny().getSequenceRelationQueries() );
- }
- }
- } );
- }
- return _sequence_relation_type_box;
- }
-
- public JCheckBox getShowEventsCb() {
- return _show_events;
- }
-
- List<String> getSingleClickToNames() {
- return _click_to_names;
- }
-
- Map<String, Color> getSpeciesColors() {
- return _species_colors;
- }
-
- public JCheckBox getWriteConfidenceCb() {
- return _write_confidence;
- }
-
- private void init() {
- _draw_phylogram = new ArrayList<Boolean>();
- setSpeciesColors( new HashMap<String, Color>() );
- setAnnotationColors( new HashMap<String, Color>() );
- }
-
- boolean isAntialiasScreenText() {
- return true;
- }
-
- boolean isColorAccordingToAnnotation() {
- return ( ( _color_according_to_annotation != null ) && _color_according_to_annotation.isSelected() );
- }
-
- boolean isColorAccordingToTaxonomy() {
- return ( ( _color_acc_species != null ) && _color_acc_species.isSelected() );
- }
-
- boolean isColorBranches() {
- return ( ( ( getColorBranchesCb() != null ) && getColorBranchesCb().isSelected() ) || ( ( getColorBranchesCb() == null ) && _color_branches ) );
- }
-
- boolean isDrawPhylogram() {
- return isDrawPhylogram( getMainPanel().getCurrentTabIndex() );
- }
-
- private boolean isDrawPhylogram( final int index ) {
- return getIsDrawPhylogramList().get( index );
+ boolean isDrawPhylogram() {
+ return isDrawPhylogram( getMainPanel().getCurrentTabIndex() );
}
boolean isDynamicallyHideData() {
return ( ( _show_domain_architectures != null ) && _show_domain_architectures.isSelected() );
}
- boolean isShowGeneNames() {
- return ( ( _show_gene_names != null ) && _show_gene_names.isSelected() );
- }
-
- public boolean isShowVectorData() {
- return ( ( _show_vector_data_cb != null ) && _show_vector_data_cb.isSelected() );
- }
-
- public boolean isShowProperties() {
- return ( ( _show_properties_cb != null ) && _show_properties_cb.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() ) );
}
return ( ( _show_taxo_code != null ) && _show_taxo_code.isSelected() );
}
- public boolean isShowTaxonomyImages() {
- return ( ( _show_taxo_images_cb != null ) && _show_taxo_images_cb.isSelected() );
- }
-
boolean isShowTaxonomyCommonNames() {
return ( ( _show_taxo_common_names != null ) && _show_taxo_common_names.isSelected() );
}
}
}
- private void search( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
- getSearchFoundCountsLabel().setVisible( true );
- getSearchResetButton().setEnabled( true );
- getSearchResetButton().setVisible( true );
- String[] queries = null;
- List<PhylogenyNode> nodes = null;
- if ( query_str.indexOf( ',' ) >= 0 ) {
- queries = query_str.split( ",+" );
- }
- else {
- queries = new String[ 1 ];
- queries[ 0 ] = query_str.trim();
- }
- if ( ( queries != null ) && ( queries.length > 0 ) ) {
- nodes = new ArrayList<PhylogenyNode>();
- for( String query : queries ) {
- if ( ForesterUtil.isEmpty( query ) ) {
- continue;
- }
- query = query.trim();
- if ( query.indexOf( '+' ) >= 0 ) {
- nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ),
- tree,
- getOptions().isSearchCaseSensitive(),
- !getOptions().isMatchWholeTermsOnly(),
- isShowDomainArchitectures() ) );
- }
- else {
- nodes.addAll( PhylogenyMethods.searchData( query,
- tree,
- getOptions().isSearchCaseSensitive(),
- !getOptions().isMatchWholeTermsOnly(),
- isShowDomainArchitectures() ) );
- }
- }
- if ( getOptions().isInverseSearchResult() ) {
- final List<PhylogenyNode> all = PhylogenyMethods.obtainAllNodesAsList( tree );
- all.removeAll( nodes );
- nodes = all;
- }
- }
- if ( ( nodes != null ) && ( nodes.size() > 0 ) ) {
- main_panel.getCurrentTreePanel().setFoundNodes( new HashSet<Integer>() );
- for( final PhylogenyNode node : nodes ) {
- main_panel.getCurrentTreePanel().getFoundNodes().add( node.getId() );
- }
- setSearchFoundCountsOnLabel( nodes.size() );
- }
- else {
- setSearchFoundCountsOnLabel( 0 );
- searchReset();
- }
- }
-
- private void searchReset() {
- if ( getMainPanel().getCurrentTreePanel() != null ) {
- getMainPanel().getCurrentTreePanel().setFoundNodes( null );
- }
- }
-
void setActionWhenNodeClicked( final NodeClickAction action ) {
_action_when_node_clicked = action;
}
_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:
else if ( action == _edit_node_data_item ) {
setActionWhenNodeClicked( NodeClickAction.EDIT_NODE_DATA );
}
+ else if ( action == _select_nodes_item ) {
+ setActionWhenNodeClicked( NodeClickAction.SELECT_NODES );
+ }
else if ( action == _get_ext_desc_data ) {
setActionWhenNodeClicked( NodeClickAction.GET_EXT_DESC_DATA );
}
setDrawPhylogram( getMainPanel().getCurrentTabIndex(), b );
}
- private void setDrawPhylogram( final int index, final boolean b ) {
- getIsDrawPhylogramList().set( index, b );
- }
-
void setDrawPhylogramEnabled( final boolean b ) {
getDisplayAsPhylogramCb().setEnabled( b );
}
// }
}
- private void setSearchFoundCountsOnLabel( final int counts ) {
- getSearchFoundCountsLabel().setText( "Found: " + counts );
- }
-
- public void setSequenceRelationQueries( final Collection<Sequence> sequenceRelationQueries ) {
- final JComboBox box = getSequenceRelationBox();
- while ( box.getItemCount() > 1 ) {
- box.removeItemAt( 1 );
- }
- final HashMap<String, Sequence> sequencesByName = new HashMap<String, Sequence>();
- final SequenceRelation.SEQUENCE_RELATION_TYPE relationType = ( SequenceRelation.SEQUENCE_RELATION_TYPE ) _sequence_relation_type_box
- .getSelectedItem();
- if ( relationType == null ) {
- return;
- }
- final ArrayList<String> sequenceNamesToAdd = new ArrayList<String>();
- for( final Sequence seq : sequenceRelationQueries ) {
- if ( seq.hasSequenceRelations() ) {
- boolean fFoundForCurrentType = false;
- for( final SequenceRelation sq : seq.getSequenceRelations() ) {
- if ( sq.getType().equals( relationType ) ) {
- fFoundForCurrentType = true;
- break;
- }
- }
- if ( fFoundForCurrentType ) {
- sequenceNamesToAdd.add( seq.getName() );
- sequencesByName.put( seq.getName(), seq );
- }
- }
- }
- // sort sequences by name before adding them to the combo
- final String[] sequenceNameArray = sequenceNamesToAdd.toArray( new String[ sequenceNamesToAdd.size() ] );
- Arrays.sort( sequenceNameArray, String.CASE_INSENSITIVE_ORDER );
- for( final String seqName : sequenceNameArray ) {
- box.addItem( seqName );
- }
- for( final ItemListener oldItemListener : box.getItemListeners() ) {
- box.removeItemListener( oldItemListener );
- }
- box.addItemListener( new ItemListener() {
-
- @Override
- public void itemStateChanged( final ItemEvent e ) {
- _selected_query_seq = sequencesByName.get( e.getItem() );
- _mainpanel.getCurrentTreePanel().repaint();
- }
- } );
- }
-
void setShowEvents( final boolean show_events ) {
if ( getShowEventsCb() == null ) {
_show_events = new JCheckBox( "" );
_species_colors = species_colors;
}
- private void setupClickToOptions() {
- final int default_option = _configuration.getDefaultDisplayClicktoOption();
- int selected_index = 0;
- int cb_index = 0;
- if ( _configuration.doDisplayClickToOption( Configuration.display_node_data ) ) {
- _show_data_item = cb_index;
- addClickToOption( Configuration.display_node_data,
- _configuration.getClickToTitle( Configuration.display_node_data ) );
- if ( default_option == Configuration.display_node_data ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.collapse_uncollapse ) ) {
- _collapse_cb_item = cb_index;
- addClickToOption( Configuration.collapse_uncollapse,
- _configuration.getClickToTitle( Configuration.collapse_uncollapse ) );
- if ( default_option == Configuration.collapse_uncollapse ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.reroot ) ) {
- _reroot_cb_item = cb_index;
- addClickToOption( Configuration.reroot, _configuration.getClickToTitle( Configuration.reroot ) );
- if ( default_option == Configuration.reroot ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.subtree ) ) {
- _subtree_cb_item = cb_index;
- addClickToOption( Configuration.subtree, _configuration.getClickToTitle( Configuration.subtree ) );
- if ( default_option == Configuration.subtree ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.swap ) ) {
- _swap_cb_item = cb_index;
- addClickToOption( Configuration.swap, _configuration.getClickToTitle( Configuration.swap ) );
- if ( default_option == Configuration.swap ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.sort_descendents ) ) {
- _sort_descendents_item = cb_index;
- addClickToOption( Configuration.sort_descendents,
- _configuration.getClickToTitle( Configuration.sort_descendents ) );
- if ( default_option == Configuration.sort_descendents ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.color_subtree ) ) {
- _color_subtree_cb_item = cb_index;
- addClickToOption( Configuration.color_subtree, _configuration.getClickToTitle( Configuration.color_subtree ) );
- if ( default_option == Configuration.color_subtree ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.open_seq_web ) ) {
- _open_seq_web_item = cb_index;
- addClickToOption( Configuration.open_seq_web, _configuration.getClickToTitle( Configuration.open_seq_web ) );
- if ( default_option == Configuration.open_seq_web ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.open_tax_web ) ) {
- _open_tax_web_item = cb_index;
- addClickToOption( Configuration.open_tax_web, _configuration.getClickToTitle( Configuration.open_tax_web ) );
- if ( default_option == Configuration.open_tax_web ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.blast ) ) {
- _blast_item = cb_index;
- addClickToOption( Configuration.blast, _configuration.getClickToTitle( Configuration.blast ) );
- if ( default_option == Configuration.blast ) {
- 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() ) ) {
- addClickToOption( Configuration.get_ext_desc_data, getConfiguration()
- .getLabelForGetExtDescendentsData() );
- }
- else {
- String s = ";";
- switch ( getConfiguration().getExtDescNodeDataToReturn() ) {
- case NODE_NAME:
- s = "Node Names";
- break;
- case SEQUENCE_ACC:
- s = "Sequence Accessors";
- break;
- case SEQUENCE_MOL_SEQ:
- s = "Molecular Sequence";
- break;
- case SEQUENCE_NAME:
- s = "Sequence Names";
- break;
- case SEQUENCE_SYMBOL:
- s = "Sequence Symbols";
- break;
- case TAXONOMY_CODE:
- s = "Taxonomy Codes";
- break;
- case TAXONOMY_SCIENTIFIC_NAME:
- s = "Scientific names";
- break;
- }
- final String label = _configuration.getClickToTitle( Configuration.get_ext_desc_data ) + " " + s;
- addClickToOption( Configuration.get_ext_desc_data, label );
- }
- if ( default_option == Configuration.get_ext_desc_data ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( getOptions().isEditable() ) {
- if ( _configuration.doDisplayClickToOption( Configuration.cut_subtree ) ) {
- _cut_subtree_item = cb_index;
- addClickToOption( Configuration.cut_subtree, _configuration.getClickToTitle( Configuration.cut_subtree ) );
- if ( default_option == Configuration.cut_subtree ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.copy_subtree ) ) {
- _copy_subtree_item = cb_index;
- addClickToOption( Configuration.copy_subtree,
- _configuration.getClickToTitle( Configuration.copy_subtree ) );
- if ( default_option == Configuration.copy_subtree ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.paste_subtree ) ) {
- _paste_subtree_item = cb_index;
- addClickToOption( Configuration.paste_subtree,
- _configuration.getClickToTitle( Configuration.paste_subtree ) );
- if ( default_option == Configuration.paste_subtree ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.delete_subtree_or_node ) ) {
- _delete_node_or_subtree_item = cb_index;
- addClickToOption( Configuration.delete_subtree_or_node,
- _configuration.getClickToTitle( Configuration.delete_subtree_or_node ) );
- if ( default_option == Configuration.delete_subtree_or_node ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.add_new_node ) ) {
- _add_new_node_item = cb_index;
- addClickToOption( Configuration.add_new_node,
- _configuration.getClickToTitle( Configuration.add_new_node ) );
- if ( default_option == Configuration.add_new_node ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.edit_node_data ) ) {
- _edit_node_data_item = cb_index;
- addClickToOption( Configuration.edit_node_data,
- _configuration.getClickToTitle( Configuration.edit_node_data ) );
- if ( default_option == Configuration.edit_node_data ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- }
- // Set default selection and its action
- _click_to_combobox.setSelectedIndex( selected_index );
- setClickToAction( selected_index );
- }
-
- /* GUILHEM_END */
- /*
- * Set up the controls from the config settings. 11/26/05
- */
- void setupControls() {
- // The tree display options:
- setupDisplayCheckboxes();
- /* GUILHEM_BEG */
- // The sequence relation query selection combo-box
- if ( _configuration.displaySequenceRelations() ) {
- addSequenceRelationBlock();
+ /* GUILHEM_END */
+ /*
+ * Set up the controls from the config settings. 11/26/05
+ */
+ void setupControls() {
+ // The tree display options:
+ setupDisplayCheckboxes();
+ /* GUILHEM_BEG */
+ // The sequence relation query selection combo-box
+ if ( _configuration.displaySequenceRelations() ) {
+ addSequenceRelationBlock();
}
/* GUILHEM_END */
// Click-to options
addJButton( _incr_domain_structure_evalue_thr, d2_panel );
}
- private void setupDisplayCheckboxes() {
- if ( _configuration.doDisplayOption( Configuration.display_as_phylogram ) ) {
- addCheckbox( Configuration.display_as_phylogram,
- _configuration.getDisplayTitle( Configuration.display_as_phylogram ) );
- setCheckbox( Configuration.display_as_phylogram,
- _configuration.doCheckOption( Configuration.display_as_phylogram ) );
- }
- if ( _configuration.doDisplayOption( Configuration.dynamically_hide_data ) ) {
- addCheckbox( Configuration.dynamically_hide_data,
- _configuration.getDisplayTitle( Configuration.dynamically_hide_data ) );
- setCheckbox( Configuration.dynamically_hide_data,
- _configuration.doCheckOption( Configuration.dynamically_hide_data ) );
- }
- if ( _configuration.doDisplayOption( Configuration.node_data_popup ) ) {
- addCheckbox( Configuration.node_data_popup, _configuration.getDisplayTitle( Configuration.node_data_popup ) );
- setCheckbox( Configuration.node_data_popup, _configuration.doCheckOption( Configuration.node_data_popup ) );
- }
- if ( _configuration.doDisplayOption( Configuration.display_internal_data ) ) {
- addCheckbox( Configuration.display_internal_data,
- _configuration.getDisplayTitle( Configuration.display_internal_data ) );
- setCheckbox( Configuration.display_internal_data,
- _configuration.doCheckOption( Configuration.display_internal_data ) );
- }
- if ( _configuration.doDisplayOption( Configuration.color_according_to_species ) ) {
- addCheckbox( Configuration.color_according_to_species,
- _configuration.getDisplayTitle( Configuration.color_according_to_species ) );
- setCheckbox( Configuration.color_according_to_species,
- _configuration.doCheckOption( Configuration.color_according_to_species ) );
- }
- if ( _configuration.doDisplayOption( Configuration.color_according_to_annotation ) ) {
- addCheckbox( Configuration.color_according_to_annotation,
- _configuration.getDisplayTitle( Configuration.color_according_to_annotation ) );
- setCheckbox( Configuration.color_according_to_annotation,
- _configuration.doCheckOption( Configuration.color_according_to_annotation ) );
- }
- if ( _configuration.doDisplayOption( Configuration.color_branches ) ) {
- addCheckbox( Configuration.color_branches, _configuration.getDisplayTitle( Configuration.color_branches ) );
- setCheckbox( Configuration.color_branches, _configuration.doCheckOption( Configuration.color_branches ) );
- }
- if ( _configuration.doDisplayOption( Configuration.width_branches ) ) {
- addCheckbox( Configuration.width_branches, _configuration.getDisplayTitle( Configuration.width_branches ) );
- setCheckbox( Configuration.width_branches, _configuration.doCheckOption( Configuration.width_branches ) );
- }
- final JLabel label = new JLabel( "Display Data:" );
- label.setFont( ControlPanel.jcb_bold_font );
+ void setupSearchTools() {
+ final String tip = "Enter text to search for. Use ',' for multiple searches (logical OR) and '+' for logical AND.";
+ final JLabel search_label = new JLabel( "Search:" );
+ search_label.setFont( ControlPanel.jcb_bold_font );
if ( !getConfiguration().isUseNativeUI() ) {
- label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
- }
- add( label );
- if ( _configuration.doDisplayOption( Configuration.show_node_names ) ) {
- addCheckbox( Configuration.show_node_names, _configuration.getDisplayTitle( Configuration.show_node_names ) );
- setCheckbox( Configuration.show_node_names, _configuration.doCheckOption( Configuration.show_node_names ) );
- }
- if ( _configuration.doDisplayOption( Configuration.show_tax_code ) ) {
- addCheckbox( Configuration.show_tax_code, _configuration.getDisplayTitle( Configuration.show_tax_code ) );
- setCheckbox( Configuration.show_tax_code, _configuration.doCheckOption( Configuration.show_tax_code ) );
- }
- if ( _configuration.doDisplayOption( Configuration.show_taxonomy_scientific_names ) ) {
- addCheckbox( Configuration.show_taxonomy_scientific_names,
- _configuration.getDisplayTitle( Configuration.show_taxonomy_scientific_names ) );
- setCheckbox( Configuration.show_taxonomy_scientific_names,
- _configuration.doCheckOption( Configuration.show_taxonomy_scientific_names ) );
- }
- if ( _configuration.doDisplayOption( Configuration.show_taxonomy_common_names ) ) {
- addCheckbox( Configuration.show_taxonomy_common_names,
- _configuration.getDisplayTitle( Configuration.show_taxonomy_common_names ) );
- 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 ) );
+ search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
}
- 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 ) );
+ add( search_label );
+ search_label.setToolTipText( tip );
+ _search_found_label = new JLabel();
+ getSearchFoundCountsLabel().setVisible( false );
+ _search_found_label.setFont( ControlPanel.jcb_bold_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ _search_found_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
}
- 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_sequence_acc ) ) {
- addCheckbox( Configuration.show_sequence_acc,
- _configuration.getDisplayTitle( Configuration.show_sequence_acc ) );
- setCheckbox( Configuration.show_sequence_acc,
- _configuration.doCheckOption( Configuration.show_sequence_acc ) );
- }
- if ( _configuration.doDisplayOption( Configuration.show_annotation ) ) {
- addCheckbox( Configuration.show_annotation, _configuration.getDisplayTitle( Configuration.show_annotation ) );
- setCheckbox( Configuration.show_annotation, _configuration.doCheckOption( Configuration.show_annotation ) );
- }
- if ( _configuration.doDisplayOption( Configuration.show_binary_characters ) ) {
- addCheckbox( Configuration.show_binary_characters,
- _configuration.getDisplayTitle( Configuration.show_binary_characters ) );
- setCheckbox( Configuration.show_binary_characters,
- _configuration.doCheckOption( Configuration.show_binary_characters ) );
- }
- if ( _configuration.doDisplayOption( Configuration.show_binary_character_counts ) ) {
- addCheckbox( Configuration.show_binary_character_counts,
- _configuration.getDisplayTitle( Configuration.show_binary_character_counts ) );
- setCheckbox( Configuration.show_binary_character_counts,
- _configuration.doCheckOption( Configuration.show_binary_character_counts ) );
- }
- if ( _configuration.doDisplayOption( Configuration.show_domain_architectures ) ) {
- addCheckbox( Configuration.show_domain_architectures,
- _configuration.getDisplayTitle( Configuration.show_domain_architectures ) );
- 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.write_events ) ) {
- addCheckbox( Configuration.write_events, _configuration.getDisplayTitle( Configuration.write_events ) );
- setCheckbox( Configuration.write_events, _configuration.doCheckOption( Configuration.write_events ) );
- }
- if ( _configuration.doDisplayOption( Configuration.show_vector_data ) ) {
- addCheckbox( Configuration.show_vector_data,
- _configuration.getDisplayTitle( Configuration.show_vector_data ) );
- setCheckbox( Configuration.show_vector_data, _configuration.doCheckOption( Configuration.show_vector_data ) );
- }
- if ( _configuration.doDisplayOption( Configuration.show_properties ) ) {
- addCheckbox( Configuration.show_properties, _configuration.getDisplayTitle( Configuration.show_properties ) );
- setCheckbox( Configuration.show_properties, _configuration.doCheckOption( Configuration.show_properties ) );
- }
- }
-
- void setupSearchTools() {
- final String tip = "Enter text to search for. Use ',' for multiple searches (logical OR) and '+' for logical AND.";
- final JLabel search_label = new JLabel( "Search:" );
- search_label.setFont( ControlPanel.jcb_bold_font );
- if ( !getConfiguration().isUseNativeUI() ) {
- search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
- }
- add( search_label );
- search_label.setToolTipText( tip );
- _search_found_label = new JLabel();
- getSearchFoundCountsLabel().setVisible( false );
- _search_found_label.setFont( ControlPanel.jcb_bold_font );
- if ( !getConfiguration().isUseNativeUI() ) {
- _search_found_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
- }
- _search_tf = new JTextField( 3 );
- _search_tf.setToolTipText( tip );
- _search_tf.setEditable( true );
- if ( !getConfiguration().isUseNativeUI() ) {
- _search_tf.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
- _search_tf.setBackground( getConfiguration().getGuiCheckboxTextColor() );
- _search_tf.setBorder( null );
+ _search_tf = new JTextField( 3 );
+ _search_tf.setToolTipText( tip );
+ _search_tf.setEditable( true );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ _search_tf.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
+ _search_tf.setBackground( getConfiguration().getGuiCheckboxTextColor() );
+ _search_tf.setBorder( null );
}
_search_reset_button = new JButton();
getSearchResetButton().setText( "Reset" );
addJButton( _search_reset_button, s_panel_2 );
}
- 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 );
- }
- 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 );
- }
- }
- }
-
/**
* Fit entire tree into window.
*/
_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();
}
}
}
+ private void addClickToOption( final int which, final String title ) {
+ _click_to_combobox.addItem( title );
+ _click_to_names.add( title );
+ _all_click_to_names.put( new Integer( which ), title );
+ if ( !_configuration.isUseNativeUI() ) {
+ _click_to_combobox.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
+ _click_to_combobox.setForeground( getConfiguration().getGuiButtonTextColor() );
+ }
+ }
+
+ /* GUILHEM_BEG */
+ private void addSequenceRelationBlock() {
+ final JLabel spacer = new JLabel( "" );
+ spacer.setSize( 1, 1 );
+ add( spacer );
+ final JLabel mainLabel = new JLabel( "Sequence relations to display" );
+ final JLabel typeLabel = customizeLabel( new JLabel( "(type) " ), getConfiguration() );
+ typeLabel.setFont( ControlPanel.js_font.deriveFont( 7 ) );
+ getSequenceRelationTypeBox().setFocusable( false );
+ _sequence_relation_type_box.setFont( ControlPanel.js_font );
+ if ( !_configuration.isUseNativeUI() ) {
+ _sequence_relation_type_box.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
+ _sequence_relation_type_box.setForeground( getConfiguration().getGuiButtonTextColor() );
+ }
+ _sequence_relation_type_box.setRenderer( new ListCellRenderer() {
+
+ @Override
+ public Component getListCellRendererComponent( final JList list,
+ final Object value,
+ final int index,
+ final boolean isSelected,
+ final boolean cellHasFocus ) {
+ final Component component = new DefaultListCellRenderer().getListCellRendererComponent( list,
+ value,
+ index,
+ isSelected,
+ cellHasFocus );
+ if ( ( value != null ) && ( value instanceof SequenceRelation.SEQUENCE_RELATION_TYPE ) ) {
+ ( ( DefaultListCellRenderer ) component ).setText( SequenceRelation
+ .getPrintableNameByType( ( SequenceRelation.SEQUENCE_RELATION_TYPE ) value ) );
+ }
+ return component;
+ }
+ } );
+ final GridBagLayout gbl = new GridBagLayout();
+ _sequence_relation_type_box.setMinimumSize( new Dimension( 115, 17 ) );
+ _sequence_relation_type_box.setPreferredSize( new Dimension( 115, 20 ) );
+ final JPanel horizGrid = new JPanel( gbl );
+ horizGrid.setBackground( getBackground() );
+ horizGrid.add( typeLabel );
+ horizGrid.add( _sequence_relation_type_box );
+ add( customizeLabel( mainLabel, getConfiguration() ) );
+ add( horizGrid );
+ add( getSequenceRelationBox() );
+ if ( _configuration.doDisplayOption( Configuration.show_relation_confidence ) ) {
+ addCheckbox( Configuration.show_relation_confidence,
+ _configuration.getDisplayTitle( Configuration.show_relation_confidence ) );
+ setCheckbox( Configuration.show_relation_confidence,
+ _configuration.doCheckOption( Configuration.show_relation_confidence ) );
+ }
+ }// addSequenceRelationBlock
+
+ /* GUILHEM_END */
+ private List<Boolean> getIsDrawPhylogramList() {
+ return _draw_phylogram;
+ }
+
+ JLabel getSearchFoundCountsLabel() {
+ return _search_found_label;
+ }
+
+ JButton getSearchResetButton() {
+ return _search_reset_button;
+ }
+
+ private void init() {
+ _draw_phylogram = new ArrayList<Boolean>();
+ setSpeciesColors( new HashMap<String, Color>() );
+ setAnnotationColors( new HashMap<String, Color>() );
+ }
+
+ private boolean isDrawPhylogram( final int index ) {
+ return getIsDrawPhylogramList().get( index );
+ }
+
+ private void search( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
+ getSearchFoundCountsLabel().setVisible( true );
+ getSearchResetButton().setEnabled( true );
+ getSearchResetButton().setVisible( true );
+ String[] queries = null;
+ List<PhylogenyNode> nodes = null;
+ if ( query_str.indexOf( ',' ) >= 0 ) {
+ queries = query_str.split( ",+" );
+ }
+ else {
+ queries = new String[ 1 ];
+ queries[ 0 ] = query_str.trim();
+ }
+ if ( ( queries != null ) && ( queries.length > 0 ) ) {
+ nodes = new ArrayList<PhylogenyNode>();
+ for( String query : queries ) {
+ if ( ForesterUtil.isEmpty( query ) ) {
+ continue;
+ }
+ query = query.trim();
+ if ( query.indexOf( '+' ) >= 0 ) {
+ nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ),
+ tree,
+ getOptions().isSearchCaseSensitive(),
+ !getOptions().isMatchWholeTermsOnly(),
+ isShowDomainArchitectures() ) );
+ }
+ else {
+ nodes.addAll( PhylogenyMethods.searchData( query,
+ tree,
+ getOptions().isSearchCaseSensitive(),
+ !getOptions().isMatchWholeTermsOnly(),
+ isShowDomainArchitectures() ) );
+ }
+ }
+ if ( getOptions().isInverseSearchResult() ) {
+ final List<PhylogenyNode> all = PhylogenyMethods.obtainAllNodesAsList( tree );
+ all.removeAll( nodes );
+ nodes = all;
+ }
+ }
+ if ( ( nodes != null ) && ( nodes.size() > 0 ) ) {
+ main_panel.getCurrentTreePanel().setFoundNodes( new HashSet<Long>() );
+ for( final PhylogenyNode node : nodes ) {
+ main_panel.getCurrentTreePanel().getFoundNodes().add( node.getId() );
+ }
+ setSearchFoundCountsOnLabel( nodes.size() );
+ }
+ else {
+ setSearchFoundCountsOnLabel( 0 );
+ searchReset();
+ }
+ }
+
+ void searchReset() {
+ if ( getMainPanel().getCurrentTreePanel() != null ) {
+ getMainPanel().getCurrentTreePanel().setFoundNodes( null );
+ }
+ }
+
+ private void setDrawPhylogram( final int index, final boolean b ) {
+ getIsDrawPhylogramList().set( index, b );
+ }
+
+ void setSearchFoundCountsOnLabel( final int counts ) {
+ getSearchFoundCountsLabel().setText( "Found: " + counts );
+ }
+
+ private void setupClickToOptions() {
+ final int default_option = _configuration.getDefaultDisplayClicktoOption();
+ int selected_index = 0;
+ int cb_index = 0;
+ if ( _configuration.doDisplayClickToOption( Configuration.display_node_data ) ) {
+ _show_data_item = cb_index;
+ addClickToOption( Configuration.display_node_data,
+ _configuration.getClickToTitle( Configuration.display_node_data ) );
+ if ( default_option == Configuration.display_node_data ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.collapse_uncollapse ) ) {
+ _collapse_cb_item = cb_index;
+ addClickToOption( Configuration.collapse_uncollapse,
+ _configuration.getClickToTitle( Configuration.collapse_uncollapse ) );
+ if ( default_option == Configuration.collapse_uncollapse ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.reroot ) ) {
+ _reroot_cb_item = cb_index;
+ addClickToOption( Configuration.reroot, _configuration.getClickToTitle( Configuration.reroot ) );
+ if ( default_option == Configuration.reroot ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.subtree ) ) {
+ _subtree_cb_item = cb_index;
+ addClickToOption( Configuration.subtree, _configuration.getClickToTitle( Configuration.subtree ) );
+ if ( default_option == Configuration.subtree ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.swap ) ) {
+ _swap_cb_item = cb_index;
+ addClickToOption( Configuration.swap, _configuration.getClickToTitle( Configuration.swap ) );
+ if ( default_option == Configuration.swap ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.sort_descendents ) ) {
+ _sort_descendents_item = cb_index;
+ addClickToOption( Configuration.sort_descendents,
+ _configuration.getClickToTitle( Configuration.sort_descendents ) );
+ if ( default_option == Configuration.sort_descendents ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.color_subtree ) ) {
+ _color_subtree_cb_item = cb_index;
+ addClickToOption( Configuration.color_subtree, _configuration.getClickToTitle( Configuration.color_subtree ) );
+ if ( default_option == Configuration.color_subtree ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.open_seq_web ) ) {
+ _open_seq_web_item = cb_index;
+ addClickToOption( Configuration.open_seq_web, _configuration.getClickToTitle( Configuration.open_seq_web ) );
+ if ( default_option == Configuration.open_seq_web ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.open_tax_web ) ) {
+ _open_tax_web_item = cb_index;
+ addClickToOption( Configuration.open_tax_web, _configuration.getClickToTitle( Configuration.open_tax_web ) );
+ if ( default_option == Configuration.open_tax_web ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.blast ) ) {
+ _blast_item = cb_index;
+ addClickToOption( Configuration.blast, _configuration.getClickToTitle( Configuration.blast ) );
+ if ( default_option == Configuration.blast ) {
+ selected_index = cb_index;
+ }
+ 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() ) ) {
+ addClickToOption( Configuration.get_ext_desc_data, getConfiguration()
+ .getLabelForGetExtDescendentsData() );
+ }
+ else {
+ String s = ";";
+ switch ( getConfiguration().getExtDescNodeDataToReturn() ) {
+ case NODE_NAME:
+ s = "Node Names";
+ break;
+ case SEQUENCE_ACC:
+ s = "Sequence Accessors";
+ break;
+ 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;
+ case UNKNOWN:
+ s = "User Selected Data";
+ break;
+ }
+ final String label = _configuration.getClickToTitle( Configuration.get_ext_desc_data ) + " " + s;
+ addClickToOption( Configuration.get_ext_desc_data, label );
+ }
+ if ( default_option == Configuration.get_ext_desc_data ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( getOptions().isEditable() ) {
+ if ( _configuration.doDisplayClickToOption( Configuration.cut_subtree ) ) {
+ _cut_subtree_item = cb_index;
+ addClickToOption( Configuration.cut_subtree, _configuration.getClickToTitle( Configuration.cut_subtree ) );
+ if ( default_option == Configuration.cut_subtree ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.copy_subtree ) ) {
+ _copy_subtree_item = cb_index;
+ addClickToOption( Configuration.copy_subtree,
+ _configuration.getClickToTitle( Configuration.copy_subtree ) );
+ if ( default_option == Configuration.copy_subtree ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.paste_subtree ) ) {
+ _paste_subtree_item = cb_index;
+ addClickToOption( Configuration.paste_subtree,
+ _configuration.getClickToTitle( Configuration.paste_subtree ) );
+ if ( default_option == Configuration.paste_subtree ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.delete_subtree_or_node ) ) {
+ _delete_node_or_subtree_item = cb_index;
+ addClickToOption( Configuration.delete_subtree_or_node,
+ _configuration.getClickToTitle( Configuration.delete_subtree_or_node ) );
+ if ( default_option == Configuration.delete_subtree_or_node ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.add_new_node ) ) {
+ _add_new_node_item = cb_index;
+ addClickToOption( Configuration.add_new_node,
+ _configuration.getClickToTitle( Configuration.add_new_node ) );
+ if ( default_option == Configuration.add_new_node ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.edit_node_data ) ) {
+ _edit_node_data_item = cb_index;
+ addClickToOption( Configuration.edit_node_data,
+ _configuration.getClickToTitle( Configuration.edit_node_data ) );
+ if ( default_option == Configuration.edit_node_data ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ }
+ // Set default selection and its action
+ _click_to_combobox.setSelectedIndex( selected_index );
+ setClickToAction( selected_index );
+ }
+
+ private void setupDisplayCheckboxes() {
+ if ( _configuration.doDisplayOption( Configuration.display_as_phylogram ) ) {
+ addCheckbox( Configuration.display_as_phylogram,
+ _configuration.getDisplayTitle( Configuration.display_as_phylogram ) );
+ setCheckbox( Configuration.display_as_phylogram,
+ _configuration.doCheckOption( Configuration.display_as_phylogram ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.dynamically_hide_data ) ) {
+ addCheckbox( Configuration.dynamically_hide_data,
+ _configuration.getDisplayTitle( Configuration.dynamically_hide_data ) );
+ setCheckbox( Configuration.dynamically_hide_data,
+ _configuration.doCheckOption( Configuration.dynamically_hide_data ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.node_data_popup ) ) {
+ addCheckbox( Configuration.node_data_popup, _configuration.getDisplayTitle( Configuration.node_data_popup ) );
+ setCheckbox( Configuration.node_data_popup, _configuration.doCheckOption( Configuration.node_data_popup ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.display_internal_data ) ) {
+ addCheckbox( Configuration.display_internal_data,
+ _configuration.getDisplayTitle( Configuration.display_internal_data ) );
+ setCheckbox( Configuration.display_internal_data,
+ _configuration.doCheckOption( Configuration.display_internal_data ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.color_according_to_species ) ) {
+ addCheckbox( Configuration.color_according_to_species,
+ _configuration.getDisplayTitle( Configuration.color_according_to_species ) );
+ setCheckbox( Configuration.color_according_to_species,
+ _configuration.doCheckOption( Configuration.color_according_to_species ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.color_according_to_annotation ) ) {
+ addCheckbox( Configuration.color_according_to_annotation,
+ _configuration.getDisplayTitle( Configuration.color_according_to_annotation ) );
+ setCheckbox( Configuration.color_according_to_annotation,
+ _configuration.doCheckOption( Configuration.color_according_to_annotation ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.color_branches ) ) {
+ addCheckbox( Configuration.color_branches, _configuration.getDisplayTitle( Configuration.color_branches ) );
+ setCheckbox( Configuration.color_branches, _configuration.doCheckOption( Configuration.color_branches ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.width_branches ) ) {
+ addCheckbox( Configuration.width_branches, _configuration.getDisplayTitle( Configuration.width_branches ) );
+ setCheckbox( Configuration.width_branches, _configuration.doCheckOption( Configuration.width_branches ) );
+ }
+ final JLabel label = new JLabel( "Display Data:" );
+ label.setFont( ControlPanel.jcb_bold_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
+ }
+ add( label );
+ if ( _configuration.doDisplayOption( Configuration.show_node_names ) ) {
+ addCheckbox( Configuration.show_node_names, _configuration.getDisplayTitle( Configuration.show_node_names ) );
+ setCheckbox( Configuration.show_node_names, _configuration.doCheckOption( Configuration.show_node_names ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_tax_code ) ) {
+ addCheckbox( Configuration.show_tax_code, _configuration.getDisplayTitle( Configuration.show_tax_code ) );
+ setCheckbox( Configuration.show_tax_code, _configuration.doCheckOption( Configuration.show_tax_code ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_taxonomy_scientific_names ) ) {
+ addCheckbox( Configuration.show_taxonomy_scientific_names,
+ _configuration.getDisplayTitle( Configuration.show_taxonomy_scientific_names ) );
+ setCheckbox( Configuration.show_taxonomy_scientific_names,
+ _configuration.doCheckOption( Configuration.show_taxonomy_scientific_names ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_taxonomy_common_names ) ) {
+ addCheckbox( Configuration.show_taxonomy_common_names,
+ _configuration.getDisplayTitle( Configuration.show_taxonomy_common_names ) );
+ setCheckbox( Configuration.show_taxonomy_common_names,
+ _configuration.doCheckOption( Configuration.show_taxonomy_common_names ) );
+ }
+ 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 ) );
+ setCheckbox( Configuration.show_sequence_acc,
+ _configuration.doCheckOption( Configuration.show_sequence_acc ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_annotation ) ) {
+ addCheckbox( Configuration.show_annotation, _configuration.getDisplayTitle( Configuration.show_annotation ) );
+ setCheckbox( Configuration.show_annotation, _configuration.doCheckOption( Configuration.show_annotation ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_binary_characters ) ) {
+ addCheckbox( Configuration.show_binary_characters,
+ _configuration.getDisplayTitle( Configuration.show_binary_characters ) );
+ setCheckbox( Configuration.show_binary_characters,
+ _configuration.doCheckOption( Configuration.show_binary_characters ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_binary_character_counts ) ) {
+ addCheckbox( Configuration.show_binary_character_counts,
+ _configuration.getDisplayTitle( Configuration.show_binary_character_counts ) );
+ setCheckbox( Configuration.show_binary_character_counts,
+ _configuration.doCheckOption( Configuration.show_binary_character_counts ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_domain_architectures ) ) {
+ addCheckbox( Configuration.show_domain_architectures,
+ _configuration.getDisplayTitle( Configuration.show_domain_architectures ) );
+ 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.write_events ) ) {
+ addCheckbox( Configuration.write_events, _configuration.getDisplayTitle( Configuration.write_events ) );
+ setCheckbox( Configuration.write_events, _configuration.doCheckOption( Configuration.write_events ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_vector_data ) ) {
+ addCheckbox( Configuration.show_vector_data,
+ _configuration.getDisplayTitle( Configuration.show_vector_data ) );
+ setCheckbox( Configuration.show_vector_data, _configuration.doCheckOption( Configuration.show_vector_data ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_properties ) ) {
+ 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() {
+ 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 );
+ }
+ 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 );
+ }
+ }
+ }
+
static JLabel customizeLabel( final JLabel label, final Configuration configuration ) {
label.setFont( ControlPanel.jcb_bold_font );
if ( !configuration.isUseNativeUI() ) {
PASTE_SUBTREE,
ADD_NEW_NODE,
EDIT_NODE_DATA,
+ SELECT_NODES,
SORT_DESCENDENTS,
GET_EXT_DESC_DATA,
BLAST;
git://source.jalview.org / jalview.git / blobdiff