package org.forester.archaeopteryx;
+import java.awt.Component;
import java.awt.Container;
import java.awt.Font;
import java.awt.event.ActionEvent;
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.data.NodeVisualization.NodeFill;
+import org.forester.phylogeny.data.NodeVisualization.NodeShape;
import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
JMenuItem _collapse_species_specific_subtrees;
JMenuItem _collapse_below_threshold; //TODO implememt me
JMenuItem _obtain_detailed_taxonomic_information_jmi;
+ JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
JMenuItem _obtain_uniprot_seq_information_jmi;
JMenuItem _move_node_names_to_tax_sn_jmi;
JMenuItem _move_node_names_to_seq_names_jmi;
else if ( o == _choose_minimal_confidence_mi ) {
chooseMinimalConfidence();
}
+ else if ( o == _choose_node_size_mi ) {
+ chooseNodeSize( getOptions(), this );
+ }
else if ( o == _overview_placment_mi ) {
MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
}
+ else if ( o == _cycle_node_fill_mi ) {
+ MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
+ }
+ else if ( o == _cycle_node_shape_mi ) {
+ MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
+ }
else if ( o == _screen_antialias_cbmi ) {
updateOptions( getOptions() );
updateScreenTextAntialias( getMainPanel().getTreePanels() );
}
}
+ static void chooseNodeSize( final Options options, final Component parent ) {
+ final String s = ( String ) JOptionPane.showInputDialog( parent,
+ "Please enter the default size for node shapes.\n"
+ + "[current value: "
+ + options.getDefaultNodeShapeSize() + "]\n",
+ "Node Shape Size",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ options.getDefaultNodeShapeSize() );
+ if ( !ForesterUtil.isEmpty( s ) ) {
+ boolean success = true;
+ double m = 0.0;
+ final String m_str = s.trim();
+ if ( !ForesterUtil.isEmpty( m_str ) ) {
+ try {
+ m = Double.parseDouble( m_str );
+ }
+ catch ( final Exception ex ) {
+ success = false;
+ }
+ }
+ else {
+ success = false;
+ }
+ if ( success && ( m >= 0.0 ) ) {
+ final short size = ForesterUtil.roundToShort( m );
+ if ( size >= 0.0 ) {
+ options.setDefaultNodeShapeSize( size );
+ }
+ }
+ }
+ }
+
void close() {
removeTextFrame();
if ( _mainpanel != null ) {
&& _abbreviate_scientific_names.isSelected() );
options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
&& _color_labels_same_as_parent_branch.isSelected() );
- //TODO FIXME ~~
options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
&& _show_default_node_shapes_cbmi.isSelected() );
options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
&& _taxonomy_colorize_node_shapes_cbmi.isSelected() );
- //TODO FIXME ~~
if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
}
default:
throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
}
- tree_panel.updateOvSettings();
+ if ( tree_panel != null ) {
+ tree_panel.updateOvSettings();
+ }
+ }
+
+ static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {
+ switch ( op.getDefaultNodeFill() ) {
+ case GRADIENT:
+ op.setDefaultNodeFill( NodeFill.SOLID );
+ break;
+ case NONE:
+ op.setDefaultNodeFill( NodeFill.GRADIENT );
+ break;
+ case SOLID:
+ op.setDefaultNodeFill( NodeFill.NONE );
+ break;
+ default:
+ throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
+ }
+ }
+
+ static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {
+ switch ( op.getDefaultNodeShape() ) {
+ case CIRCLE:
+ op.setDefaultNodeShape( NodeShape.RECTANGLE );
+ break;
+ case RECTANGLE:
+ op.setDefaultNodeShape( NodeShape.CIRCLE );
+ break;
+ default:
+ throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
+ }
}
static void help( final Map<String, WebLink> weblinks ) {
TextFrame.instantiate( sb.toString() );
}
- static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
- if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
- mi.setText( "Overview Placement... (current: " + tree_panel.getOptions().getOvPlacement() + ")" );
+ static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
+ if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
+ mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
}
else {
- mi.setText( "Overview Placement..." );
+ mi.setText( "Cycle Overview Placement..." );
+ }
+ }
+
+ static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
+ if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
+ mi.setText( "Cycle Node Shape Fill Type... (current: "
+ + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
+ }
+ else {
+ mi.setText( "Cycle Node Shape Fill Type..." );
+ }
+ }
+
+ static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
+ if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
+ mi.setText( "Cycle Node Shape Fill Type... (current: "
+ + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
+ }
+ else {
+ mi.setText( "Cycle Node Shape Fill Type..." );
}
}
mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
}
+ static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
+ mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
+ }
+
static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
final JCheckBoxMenuItem scale,
final JCheckBoxMenuItem branch_lengths,
git://source.jalview.org / jalview.git / blobdiff