import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
+import org.forester.archaeopteryx.util.TypomaticJButton;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
final class ControlPanel extends JPanel implements ActionListener {
enum NodeClickAction {
- ADD_NEW_NODE,
- BLAST,
- COLLAPSE,
- COLOR_SUBTREE,
- COPY_SUBTREE,
- CUT_SUBTREE,
- DELETE_NODE_OR_SUBTREE,
- EDIT_NODE_DATA,
- GET_EXT_DESC_DATA,
- OPEN_PDB_WEB,
- OPEN_SEQ_WEB,
- OPEN_TAX_WEB,
- PASTE_SUBTREE,
- REROOT,
- SELECT_NODES,
- SHOW_DATA,
- SORT_DESCENDENTS,
- SUBTREE,
- SWAP,
- CHANGE_NODE_FONT,
- COLOR_NODE_FONT,
- UNCOLLAPSE_ALL,
- ORDER_SUBTREE;
- }
- final static Font jcb_bold_font = new Font( Configuration.getDefaultFontFamilyName(),
- Font.BOLD,
- 9 );
- final static Font jcb_font = new Font( Configuration.getDefaultFontFamilyName(),
- Font.PLAIN,
- 9 );
- final static Font js_font = new Font( Configuration.getDefaultFontFamilyName(),
- Font.PLAIN,
- 9 );
+ ADD_NEW_NODE,
+ BLAST,
+ COLLAPSE,
+ COLOR_SUBTREE,
+ COPY_SUBTREE,
+ CUT_SUBTREE,
+ DELETE_NODE_OR_SUBTREE,
+ EDIT_NODE_DATA,
+ GET_EXT_DESC_DATA,
+ OPEN_PDB_WEB,
+ OPEN_SEQ_WEB,
+ OPEN_TAX_WEB,
+ PASTE_SUBTREE,
+ REROOT,
+ SELECT_NODES,
+ SHOW_DATA,
+ SORT_DESCENDENTS,
+ SUBTREE,
+ SWAP,
+ CHANGE_NODE_FONT,
+ COLOR_NODE_FONT,
+ UNCOLLAPSE_ALL,
+ ORDER_SUBTREE;
+ }
+ final static Font jcb_bold_font = new Font( Configuration
+ .getDefaultFontFamilyName(), Font.BOLD, 9 );
+ final static Font jcb_font = new Font( Configuration
+ .getDefaultFontFamilyName(), Font.PLAIN, 9 );
+ final static Font js_font = new Font( Configuration
+ .getDefaultFontFamilyName(), Font.PLAIN, 9 );
private static final String RETURN_TO_SUPER_TREE_TEXT = "Back to Super Tree";
private static final String SEARCH_TIP_TEXT = "Enter text to search for. Use ',' for logical OR and '+' for logical AND (not used in this manner for regular expression searches).";
private static final long serialVersionUID = -8463483932821545633L;
private int _collapse_cb_item;
private int _uncollapse_all_cb_item;
private int _order_subtree_cb_item;
-
-
private JCheckBox _color_acc_species;
private JCheckBox _color_acc_sequence;
private JCheckBox _color_according_to_annotation;
private JCheckBox _display_internal_data;
private JLabel _domain_display_label;
private JTextField _domain_structure_evalue_thr_tf;
+ private JTextField _depth_collapse_depth_tf;
+ private JTextField _rank_collapse_depth_tf;
private List<Boolean> _draw_phylogram;
private JCheckBox _dynamically_hide_data;
private int _edit_node_data_item;
private JButton _zoom_out_domain_structure;
private JButton _zoom_out_x;
private JButton _zoom_out_y;
+ private JButton _decr_depth_collapse_level;
+ private JButton _incr_depth_collapse_level;
+ private JLabel _depth_collapse_label;
+ private JButton _decr_rank_collapse_level;
+ private JButton _incr_rank_collapse_level;
+ private JLabel _rank_collapse_label;
ControlPanel( final MainPanel ap, final Configuration configuration ) {
init();
pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
}
PhylogenyMethods.orderAppearanceX( tp.getPhylogeny().getRoot(), true, pri );
-
tp.setNodeInPreorderToNull();
tp.getPhylogeny().externalNodesHaveChanged();
tp.getPhylogeny().clearHashIdToNodeMap();
setDynamicHidingIsOn( false );
displayedPhylogenyMightHaveChanged( true );
}
+ else if ( ( e.getSource() == _decr_depth_collapse_level )
+ || ( e.getSource() == _incr_depth_collapse_level ) ) {
+ if ( e.getSource() == _decr_depth_collapse_level ) {
+ _mainpanel.getCurrentTreePanel().decreaseDepthCollapseLevel();
+ }
+ else {
+ _mainpanel.getCurrentTreePanel().increaseDepthCollapseLevel();
+ }
+ search0();
+ search1();
+ _mainpanel.getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
+ _mainpanel.getCurrentTreePanel().getPhylogeny().recalculateNumberOfExternalDescendants( true );
+ _mainpanel.getCurrentTreePanel().resetNodeIdToDistToLeafMap();
+ _mainpanel.getCurrentTreePanel().calculateLongestExtNodeInfo();
+ _mainpanel.getCurrentTreePanel().setNodeInPreorderToNull();
+ displayedPhylogenyMightHaveChanged( true );
+ _mainpanel.getCurrentTreePanel().resetPreferredSize();
+ _mainpanel.getCurrentTreePanel().updateOvSizes();
+ _mainpanel.adjustJScrollPane();
+ showWhole();
+ repaint();
+ }
+ else if ( ( e.getSource() == _decr_rank_collapse_level )
+ || ( e.getSource() == _incr_rank_collapse_level ) ) {
+ if ( e.getSource() == _decr_rank_collapse_level ) {
+ _mainpanel.getCurrentTreePanel().decreaseRankCollapseLevel();
+ }
+ else {
+ _mainpanel.getCurrentTreePanel().increaseRankCollapseLevel();
+ }
+ search0();
+ search1();
+ _mainpanel.getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
+ _mainpanel.getCurrentTreePanel().getPhylogeny().recalculateNumberOfExternalDescendants( true );
+ _mainpanel.getCurrentTreePanel().resetNodeIdToDistToLeafMap();
+ _mainpanel.getCurrentTreePanel().calculateLongestExtNodeInfo();
+ _mainpanel.getCurrentTreePanel().setNodeInPreorderToNull();
+ displayedPhylogenyMightHaveChanged( true );
+ _mainpanel.getCurrentTreePanel().resetPreferredSize();
+ _mainpanel.getCurrentTreePanel().updateOvSizes();
+ _mainpanel.adjustJScrollPane();
+ showWhole();
+ repaint();
+ }
else {
displayedPhylogenyMightHaveChanged( true );
}
public JComboBox<SEQUENCE_RELATION_TYPE> getSequenceRelationTypeBox() {
if ( _sequence_relation_type_box == null ) {
_sequence_relation_type_box = new JComboBox<SEQUENCE_RELATION_TYPE>();
- for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : SequenceRelation.SEQUENCE_RELATION_TYPE.values() ) {
+ 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() {
final int index,
final boolean isSelected,
final boolean cellHasFocus ) {
- final Component component = new DefaultListCellRenderer().getListCellRendererComponent( list,
- value,
- index,
- isSelected,
- 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 ) );
}// addSequenceRelationBlock
/* GUILHEM_END */
-
private List<Boolean> getIsDrawPhylogramList() {
return _draw_phylogram;
}
getOptions().isSearchCaseSensitive(),
!getOptions().isMatchWholeTermsOnly(),
isShowDomainArchitectures(),
- tp != null ? Math.pow( 10,
- tp.getDomainStructureEvalueThresholdExp() )
- : 0 ) );
+ tp != null
+ ? Math.pow( 10,
+ tp.getDomainStructureEvalueThresholdExp() )
+ : 0 ) );
}
else {
- nodes.addAll( PhylogenyMethods.searchData( query,
- tree,
- getOptions().isSearchCaseSensitive(),
- !getOptions().isMatchWholeTermsOnly(),
- getOptions().isSearchWithRegex(),
- isShowDomainArchitectures(),
- tp != null ? Math.pow( 10, tp
- .getDomainStructureEvalueThresholdExp() ) : 0 ) );
+ nodes.addAll( PhylogenyMethods
+ .searchData( query,
+ tree,
+ getOptions().isSearchCaseSensitive(),
+ !getOptions().isMatchWholeTermsOnly(),
+ getOptions().isSearchWithRegex(),
+ isShowDomainArchitectures(),
+ tp != null ? Math.pow( 10, tp.getDomainStructureEvalueThresholdExp() ) : 0 ) );
}
}
if ( getOptions().isInverseSearchResult() ) {
final Set<Long> temp_nodes = nodes;
nodes = new HashSet<Long>();
for( final PhylogenyNode n : all ) {
- if ( (!temp_nodes.contains( n.getId() )) && n.isHasNodeData() ) {
+ if ( ( !temp_nodes.contains( n.getId() ) ) && n.isHasNodeData() ) {
nodes.add( n.getId() );
}
}
getOptions().isSearchCaseSensitive(),
!getOptions().isMatchWholeTermsOnly(),
isShowDomainArchitectures(),
- tp != null ? Math.pow( 10,
- tp.getDomainStructureEvalueThresholdExp() )
- : 0 ) );
+ tp != null
+ ? Math.pow( 10,
+ tp.getDomainStructureEvalueThresholdExp() )
+ : 0 ) );
}
else {
- nodes.addAll( PhylogenyMethods.searchData( query,
- tree,
- getOptions().isSearchCaseSensitive(),
- !getOptions().isMatchWholeTermsOnly(),
- getOptions().isSearchWithRegex(),
- isShowDomainArchitectures(),
- tp != null ? Math.pow( 10, tp
- .getDomainStructureEvalueThresholdExp() ) : 0 ) );
+ nodes.addAll( PhylogenyMethods
+ .searchData( query,
+ tree,
+ getOptions().isSearchCaseSensitive(),
+ !getOptions().isMatchWholeTermsOnly(),
+ getOptions().isSearchWithRegex(),
+ isShowDomainArchitectures(),
+ tp != null ? Math.pow( 10, tp.getDomainStructureEvalueThresholdExp() ) : 0 ) );
}
}
if ( getOptions().isInverseSearchResult() ) {
final Set<Long> temp_nodes = nodes;
nodes = new HashSet<Long>();
for( final PhylogenyNode n : all ) {
- if ( (!temp_nodes.contains( n.getId() )) && n.isHasNodeData() ) {
+ if ( ( !temp_nodes.contains( n.getId() ) ) && n.isHasNodeData() ) {
nodes.add( n.getId() );
}
}
searchReset1();
}
}
-
+
private void setDrawPhylogram( final int index, final boolean b ) {
getIsDrawPhylogramList().set( index, b );
}
}
cb_index++;
}
-if ( _configuration.doDisplayClickToOption( Configuration.uncollapse_all ) ) {
+ if ( _configuration.doDisplayClickToOption( Configuration.uncollapse_all ) ) {
_uncollapse_all_cb_item = cb_index;
addClickToOption( Configuration.uncollapse_all,
_configuration.getClickToTitle( Configuration.uncollapse_all ) );
selected_index = cb_index;
}
cb_index++;
-}
+ }
if ( _configuration.doDisplayClickToOption( Configuration.reroot ) ) {
_reroot_cb_item = cb_index;
addClickToOption( Configuration.reroot, _configuration.getClickToTitle( Configuration.reroot ) );
}
cb_index++;
}
-if ( _configuration.doDisplayClickToOption( Configuration.order_subtree ) ) {
+ if ( _configuration.doDisplayClickToOption( Configuration.order_subtree ) ) {
_order_subtree_cb_item = cb_index;
addClickToOption( Configuration.order_subtree,
_configuration.getClickToTitle( Configuration.order_subtree ) );
selected_index = cb_index;
}
cb_index++;
-}
-
+ }
if ( _configuration.doDisplayClickToOption( Configuration.sort_descendents ) ) {
_sort_descendents_item = cb_index;
addClickToOption( Configuration.sort_descendents,
}
if ( _configuration.doDisplayClickToOption( Configuration.color_subtree ) ) {
_color_subtree_cb_item = cb_index;
- addClickToOption( Configuration.color_subtree, _configuration.getClickToTitle( Configuration.color_subtree ) );
+ addClickToOption( Configuration.color_subtree,
+ _configuration.getClickToTitle( Configuration.color_subtree ) );
if ( default_option == Configuration.color_subtree ) {
selected_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 ) );
+ addClickToOption( Configuration.open_seq_web,
+ _configuration.getClickToTitle( Configuration.open_seq_web ) );
if ( default_option == Configuration.open_seq_web ) {
selected_index = cb_index;
}
}
if ( _configuration.doDisplayClickToOption( Configuration.open_pdb_web ) ) {
_open_pdb_item = cb_index;
- addClickToOption( Configuration.open_pdb_web, _configuration.getClickToTitle( Configuration.open_pdb_web ) );
+ addClickToOption( Configuration.open_pdb_web,
+ _configuration.getClickToTitle( Configuration.open_pdb_web ) );
if ( default_option == Configuration.open_pdb_web ) {
selected_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 ) );
+ addClickToOption( Configuration.open_tax_web,
+ _configuration.getClickToTitle( Configuration.open_tax_web ) );
if ( default_option == Configuration.open_tax_web ) {
selected_index = cb_index;
}
}
if ( _configuration.doDisplayClickToOption( Configuration.select_nodes ) ) {
_select_nodes_item = cb_index;
- addClickToOption( Configuration.select_nodes, _configuration.getClickToTitle( Configuration.select_nodes ) );
+ addClickToOption( Configuration.select_nodes,
+ _configuration.getClickToTitle( Configuration.select_nodes ) );
if ( default_option == Configuration.select_nodes ) {
selected_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() );
+ addClickToOption( Configuration.get_ext_desc_data,
+ getConfiguration().getLabelForGetExtDescendentsData() );
}
else {
addClickToOption( Configuration.get_ext_desc_data,
if ( getOptions().isEditable() ) {
if ( _configuration.doDisplayClickToOption( Configuration.cut_subtree ) ) {
_cut_subtree_item = cb_index;
- addClickToOption( Configuration.cut_subtree, _configuration.getClickToTitle( Configuration.cut_subtree ) );
+ addClickToOption( Configuration.cut_subtree,
+ _configuration.getClickToTitle( Configuration.cut_subtree ) );
if ( default_option == Configuration.cut_subtree ) {
selected_index = cb_index;
}
_configuration.doCheckOption( Configuration.dynamically_hide_data ) );
}
if ( _configuration.doDisplayOption( Configuration.node_data_popup ) ) {
- addCheckbox( Configuration.node_data_popup, _configuration.getDisplayTitle( 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 ) ) {
}
add( label );
if ( _configuration.doDisplayOption( Configuration.show_node_names ) ) {
- addCheckbox( Configuration.show_node_names, _configuration.getDisplayTitle( 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 ) ) {
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 ) );
+ 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 ) );
+ setCheckbox( Configuration.show_seq_symbols,
+ _configuration.doCheckOption( Configuration.show_seq_symbols ) );
}
if ( _configuration.doDisplayOption( Configuration.show_sequence_acc ) ) {
addCheckbox( 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 ) );
+ 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 ) ) {
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 ) );
+ 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 ) );
+ 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 ) ) {
add( y_panel );
add( z_panel );
if ( getConfiguration().isUseNativeUI() ) {
- _zoom_in_x = new JButton( "+" );
- _zoom_out_x = new JButton( "-" );
+ _zoom_in_x = new TypomaticJButton( "+" );
+ _zoom_out_x = new TypomaticJButton( "-" );
}
else {
- _zoom_in_x = new JButton( "X+" );
- _zoom_out_x = new JButton( "X-" );
+ _zoom_in_x = new TypomaticJButton( "X+" );
+ _zoom_out_x = new TypomaticJButton( "X-" );
}
- _zoom_in_y = new JButton( "Y+" );
- _zoom_out_y = new JButton( "Y-" );
+ _zoom_in_y = new TypomaticJButton( "Y+" );
+ _zoom_out_y = new TypomaticJButton( "Y-" );
_show_whole = new JButton( "F" );
_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]" );
_return_to_super_tree.setEnabled( false );
_order = new JButton( "Order Tree" );
_uncollapse_all = new JButton( "Uncollapse All" );
-
addJButton( _zoom_in_y, x_panel );
addJButton( _zoom_out_x, y_panel );
addJButton( _show_whole, y_panel );
if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
setUpControlsForDomainStrucures();
}
+ if ( true ) {
+ setUpControlsForDepthCollapse();
+ }
+ if ( true ) {
+ setUpControlsForRankCollapse();
+ }
final JLabel spacer2 = new JLabel( "" );
add( spacer2 );
addJButton( _return_to_super_tree, this );
_show_taxo_rank = new JCheckBox( title );
addJCheckBox( _show_taxo_rank, ch_panel );
add( ch_panel );
- break;
+ break;
case Configuration.show_taxonomy_images:
_show_taxo_images_cb = new JCheckBox( title );
addJCheckBox( _show_taxo_images_cb, ch_panel );
void displayedPhylogenyMightHaveChanged( final boolean recalc_longest_ext_node_info ) {
if ( ( _mainpanel != null )
&& ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
-
if ( recalc_longest_ext_node_info ) {
_mainpanel.getCurrentTreePanel().initNodeData();
_mainpanel.getCurrentTreePanel().calculateLongestExtNodeInfo();
_mainpanel.getCurrentTreePanel().recalculateMaxDistanceToRoot();
setVisibilityOfDomainStrucureControls();
updateDomainStructureEvaluethresholdDisplay();
+ updateDepthCollapseDepthDisplay();
+ updateRankCollapseRankDisplay();
+ getMainPanel().getControlPanel();
_mainpanel.getCurrentTreePanel().calculateScaleDistance();
_mainpanel.getCurrentTreePanel().calcMaxDepth();
_mainpanel.adjustJScrollPane();
-
_mainpanel.getCurrentTreePanel().repaint();
// _mainpanel.getCurrentTreePanel().setUpUrtFactor();
}
boolean isShowTaxonomyCode() {
return ( ( _show_taxo_code != null ) && _show_taxo_code.isSelected() );
}
-
+
boolean isShowTaxonomyRank() {
return ( ( _show_taxo_rank != null ) && _show_taxo_rank.isSelected() );
}
}
boolean isUseVisualStyles() {
- return ( ( ( getUseVisualStylesCb() != null ) && getUseVisualStylesCb().isSelected() ) || ( ( getUseVisualStylesCb() == null ) && _color_branches ) );
+ return ( ( ( getUseVisualStylesCb() != null ) && getUseVisualStylesCb().isSelected() )
+ || ( ( getUseVisualStylesCb() == null ) && _color_branches ) );
}
boolean isWidthBranches() {
_domain_display_label = new JLabel( "Domain Architectures:" );
add( customizeLabel( _domain_display_label, getConfiguration() ) );
add( _domain_display_label );
- _zoom_in_domain_structure = new JButton( "d+" );
- _zoom_out_domain_structure = new JButton( "d-" );
+ _zoom_in_domain_structure = new TypomaticJButton( "d+" );
+ _zoom_out_domain_structure = new TypomaticJButton( "d-" );
_decr_domain_structure_evalue_thr = new JButton( "-" );
_incr_domain_structure_evalue_thr = new JButton( "+" );
_zoom_in_domain_structure.setPreferredSize( new Dimension( 10, 10 ) );
addJButton( _incr_domain_structure_evalue_thr, d2_panel );
}
+ void setUpControlsForDepthCollapse() {
+ _depth_collapse_label = new JLabel( "Collapse by Node Depth:" );
+ _depth_collapse_label
+ .setToolTipText( "to automaticall collapse nodes with a depth equal or larger than a threshold" );
+ add( customizeLabel( _depth_collapse_label, getConfiguration() ) );
+ add( _depth_collapse_label );
+ _decr_depth_collapse_level = new TypomaticJButton( "-" );
+ _incr_depth_collapse_level = new TypomaticJButton( "+" );
+ _decr_depth_collapse_level.setPreferredSize( new Dimension( 10, 10 ) );
+ _incr_depth_collapse_level.setPreferredSize( new Dimension( 10, 10 ) );
+ _decr_depth_collapse_level.setToolTipText( "to decrease the depth threshold (wraps around)" );
+ _incr_depth_collapse_level.setToolTipText( "to increase the depth threshold (wraps around)" );
+ _depth_collapse_depth_tf = new JTextField( 3 );
+ _depth_collapse_depth_tf.setToolTipText( "the current depth threshold" );
+ _depth_collapse_depth_tf.setEditable( false );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ _depth_collapse_depth_tf.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
+ _depth_collapse_depth_tf.setBackground( getConfiguration().getGuiCheckboxTextColor() );
+ _depth_collapse_depth_tf.setBorder( null );
+ }
+ final JPanel panel = new JPanel( new GridLayout( 1, 3, 0, 0 ) );
+ if ( !_configuration.isUseNativeUI() ) {
+ panel.setBackground( getBackground() );
+ }
+ add( panel );
+ addJButton( _decr_depth_collapse_level, panel );
+ addJTextField( _depth_collapse_depth_tf, panel );
+ addJButton( _incr_depth_collapse_level, panel );
+ }
+
+ void setUpControlsForRankCollapse() {
+ _rank_collapse_label = new JLabel( "Collapse by Node Rank:" );
+ _rank_collapse_label
+ .setToolTipText( "to automatically collapse nodes with a taxonomic rank equal or lower than a threshold" );
+ add( customizeLabel( _rank_collapse_label, getConfiguration() ) );
+ add( _rank_collapse_label );
+ _decr_rank_collapse_level = new TypomaticJButton( "-" );
+ _incr_rank_collapse_level = new TypomaticJButton( "+" );
+ _decr_rank_collapse_level.setPreferredSize( new Dimension( 10, 10 ) );
+ _incr_rank_collapse_level.setPreferredSize( new Dimension( 10, 10 ) );
+ _decr_rank_collapse_level.setToolTipText( "to decrease the taxonomic rank threshold (wraps around)" );
+ _incr_rank_collapse_level.setToolTipText( "to increase the taxonomic rank threshold (wraps around)" );
+ _rank_collapse_depth_tf = new JTextField( 3 );
+ _rank_collapse_depth_tf.setToolTipText( "the current taxonomic rank threshold" );
+ _rank_collapse_depth_tf.setEditable( false );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ _rank_collapse_depth_tf.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
+ _rank_collapse_depth_tf.setBackground( getConfiguration().getGuiCheckboxTextColor() );
+ _rank_collapse_depth_tf.setBorder( null );
+ }
+ final JPanel panel = new JPanel( new GridLayout( 1, 3, 0, 0 ) );
+ if ( !_configuration.isUseNativeUI() ) {
+ panel.setBackground( getBackground() );
+ }
+ add( panel );
+ addJButton( _decr_rank_collapse_level, panel );
+ addJTextField( _rank_collapse_depth_tf, panel );
+ addJButton( _incr_rank_collapse_level, panel );
+ }
+
void setupSearchTools0() {
final JLabel search_label = new JLabel( "Search (A):" );
search_label.setFont( ControlPanel.jcb_bold_font );
void setVisibilityOfDomainStrucureCB() {
try {
- if ( ( getCurrentTreePanel() != null )
- && ( ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( getCurrentTreePanel()
- .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
+ 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 ( isDrawPhylogram()
- || ( ( getCurrentTreePanel() != null ) && ( ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( getCurrentTreePanel()
- .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) ) {
+ 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 );
}
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 );
}
* Fit entire tree into window.
*/
void showWhole() {
- if ( ( _mainpanel.getCurrentScrollPane() == null ) || _mainpanel.getCurrentTreePanel().getPhylogeny().isEmpty() ) {
+ if ( ( _mainpanel.getCurrentScrollPane() == null )
+ || _mainpanel.getCurrentTreePanel().getPhylogeny().isEmpty() ) {
return;
}
getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
e.setSelectedTypeInTypeMenu( e.getCurrentTreePanel().getPhylogenyGraphicsType() );
}
else {
- getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getMainPanel().getCurrentTreePanel()
- .getPhylogenyGraphicsType() );
+ getMainPanel().getMainFrame()
+ .setSelectedTypeInTypeMenu( getMainPanel().getCurrentTreePanel().getPhylogenyGraphicsType() );
}
getMainPanel().getCurrentTreePanel().updateSubSuperTreeButton();
getMainPanel().getControlPanel().search0();
getMainPanel().getControlPanel().search1();
getMainPanel().getControlPanel().updateDomainStructureEvaluethresholdDisplay();
+ getMainPanel().getControlPanel().updateDepthCollapseDepthDisplay();
+ getMainPanel().getControlPanel().updateRankCollapseRankDisplay();
getSequenceRelationTypeBox().removeAllItems();
for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
.getRelevantSequenceRelationTypes() ) {
/**
* Uncollapse all nodes.
*/
- void uncollapseAll( final TreePanel tp ) {
+ final void uncollapseAll( final TreePanel tp ) {
final Phylogeny t = tp.getPhylogeny();
if ( ( t != null ) && !t.isEmpty() ) {
for( final PhylogenyNodeIterator iter = t.iteratorPreorder(); iter.hasNext(); ) {
t.recalculateNumberOfExternalDescendants( false );
tp.setNodeInPreorderToNull();
t.clearHashIdToNodeMap();
+ tp.resetDepthCollapseDepthValue();
+ tp.resetRankCollapseRankValue();
showWhole();
}
}
- void updateDomainStructureEvaluethresholdDisplay() {
+ final void updateDomainStructureEvaluethresholdDisplay() {
if ( _domain_structure_evalue_thr_tf != null ) {
- _domain_structure_evalue_thr_tf.setText( "10^"
- + getMainPanel().getCurrentTreePanel().getDomainStructureEvalueThresholdExp() );
+ _domain_structure_evalue_thr_tf
+ .setText( "10^" + getMainPanel().getCurrentTreePanel().getDomainStructureEvalueThresholdExp() );
+ }
+ }
+
+ private final String obtainDepthCollapseDepthValue() {
+ if ( getMainPanel().getCurrentTreePanel() == null ) {
+ return "";
+ }
+ final TreePanel tp = getMainPanel().getCurrentTreePanel();
+ final Phylogeny p = tp.getPhylogeny();
+ if ( ( p == null ) || ( p.getNumberOfExternalNodes() < 3 ) ) {
+ return "off";
+ }
+ else if ( tp.getDepthCollapseDepthValue() < 0 ) {
+ tp.setDepthCollapseDepthValue( PhylogenyMethods.calculateMaxDepth( p ) );
+ return "off";
+ }
+ else if ( tp.getDepthCollapseDepthValue() == PhylogenyMethods.calculateMaxDepth( p ) ) {
+ return "off";
+ }
+ return String.valueOf( tp.getDepthCollapseDepthValue() );
+ }
+
+ private final String obtainRankCollapseDepthValue() {
+ if ( getMainPanel().getCurrentTreePanel() == null ) {
+ return "";
+ }
+ final TreePanel tp = getMainPanel().getCurrentTreePanel();
+ final Phylogeny p = tp.getPhylogeny();
+ if ( ( p == null ) || ( p.getNumberOfExternalNodes() < 3 ) ) {
+ return "off";
+ }
+ else {
+ final String ranks[] = PhylogenyMethods.obtainPresentRanksSorted( p );
+ if ( ranks.length < 1 ) {
+ return "off";
+ }
+ else if ( tp.getRankCollapseRankValue() < 0 ) {
+ tp.setRankCollapseRankValue( ranks.length - 1 );
+ return "off";
+ }
+ else if ( tp.getRankCollapseRankValue() == ( ranks.length - 1 ) ) {
+ return "off";
+ }
+ }
+ return String.valueOf( tp.getRankCollapseRankValue() );
+ }
+
+ final void updateDepthCollapseDepthDisplay() {
+ if ( _depth_collapse_depth_tf != null ) {
+ _depth_collapse_depth_tf.setText( " " + obtainDepthCollapseDepthValue() );
+ }
+ }
+
+ final void updateRankCollapseRankDisplay() {
+ if ( _rank_collapse_depth_tf != null ) {
+ final String r = obtainRankCollapseDepthValue();
+ if ( r.equals( "off" ) ) {
+ _rank_collapse_depth_tf.setText( " off" );
+ _rank_collapse_depth_tf.setToolTipText( "the current taxonomic rank threshold" );
+ }
+ else {
+ final String ranks[] = PhylogenyMethods
+ .obtainPresentRanksSorted( getMainPanel().getCurrentTreePanel().getPhylogeny() );
+ final int rr = Integer.parseInt( r );
+ _rank_collapse_depth_tf.setText( ranks[ rr ] );
+ _rank_collapse_depth_tf.setToolTipText( ( rr + 1 ) + "/" + ( ranks.length - 1 ) + ": "
+ + ranks[ Integer.parseInt( r ) ] );
+ }
}
}
- void zoomInX( final float factor, final float x_correction_factor ) {
+ final void zoomInX( final float factor, final float x_correction_factor ) {
final JScrollBar sb = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar();
final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
treepanel.multiplyUrtFactor( 1f );
|| ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
|| isDrawPhylogram( getMainPanel().getCurrentTabIndex() )
|| ( getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ) ) {
- final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
+ final double x = ( sb.getMaximum() - sb.getMinimum() )
+ / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
getMainPanel().adjustJScrollPane();
treepanel.resetPreferredSize();
getMainPanel().getCurrentScrollPane().getViewport().validate();
- sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
- - ( sb.getVisibleAmount() / 2.0 ) ) );
+ sb.setValue( ForesterUtil
+ .roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x ) - ( sb.getVisibleAmount() / 2.0 ) ) );
}
else {
final int x = sb.getMaximum() - sb.getMinimum() - sb.getVisibleAmount() - sb.getValue();
treepanel.updateOvSizes();
}
- void zoomInY( final float factor ) {
+ final void zoomInY( final float factor ) {
final JScrollBar sb = getMainPanel().getCurrentScrollPane().getVerticalScrollBar();
final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
treepanel.multiplyUrtFactor( 1.1f );
getMainPanel().adjustJScrollPane();
treepanel.resetPreferredSize();
getMainPanel().getCurrentScrollPane().getViewport().validate();
- sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
- - ( sb.getVisibleAmount() / 2.0 ) ) );
+ sb.setValue( ForesterUtil
+ .roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x ) - ( sb.getVisibleAmount() / 2.0 ) ) );
treepanel.resetPreferredSize();
treepanel.updateOvSizes();
}
- void zoomOutX( final float factor, final float x_correction_factor ) {
+ final void zoomOutX( final float factor, final float x_correction_factor ) {
final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
treepanel.multiplyUrtFactor( 1f );
if ( ( treepanel.getXdistance() * factor ) > 0.0 ) {
}
}
- void zoomOutY( final float factor ) {
+ final void zoomOutY( final float factor ) {
final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
treepanel.multiplyUrtFactor( 0.9f );
if ( ( treepanel.getYdistance() * factor ) > 0.0 ) {
final JScrollBar sb = getMainPanel().getCurrentScrollPane().getVerticalScrollBar();
- final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
+ final double x = ( sb.getMaximum() - sb.getMinimum() )
+ / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
treepanel.setYdistance( ( treepanel.getYdistance() * factor ) );
getMainPanel().adjustJScrollPane();
treepanel.resetPreferredSize();
getMainPanel().getCurrentScrollPane().getViewport().validate();
- sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
- - ( sb.getVisibleAmount() / 2.0 ) ) );
+ sb.setValue( ForesterUtil
+ .roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x ) - ( sb.getVisibleAmount() / 2.0 ) ) );
treepanel.resetPreferredSize();
treepanel.updateOvSizes();
}
}
- static JLabel customizeLabel( final JLabel label, final Configuration configuration ) {
+ final static JLabel customizeLabel( final JLabel label, final Configuration configuration ) {
label.setFont( ControlPanel.jcb_bold_font );
if ( !configuration.isUseNativeUI() ) {
label.setForeground( configuration.getGuiCheckboxTextColor() );
return label;
}
- public JCheckBox getUseBranchWidthsCb() {
+ final public JCheckBox getUseBranchWidthsCb() {
return _width_branches;
}
}
git://source.jalview.org / jalview.git / blobdiff