// and Howard Hughes Medical Institute
// Copyright (C) 2003-2007 Ethalinda K.S. Cannon
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
catch ( final Exception e ) {
ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, e.toString() );
e.printStackTrace();
- JOptionPane
- .showMessageDialog( this,
- ArchaeopteryxA.NAME + ": Could not create URL from: \""
- + _applet.getUrlString() + "\"\nError: " + e,
- "Failed to create URL",
- JOptionPane.ERROR_MESSAGE );
+ JOptionPane.showMessageDialog( this,
+ ArchaeopteryxA.NAME + ": Could not create URL from: \""
+ + _applet.getUrlString() + "\"\nError: " + e,
+ "Failed to create URL",
+ JOptionPane.ERROR_MESSAGE );
close();
}
}
// Load the tree from URL
if ( url != null ) {
try {
- phys = Util.readPhylogeniesFromUrl( url, getConfiguration().isValidatePhyloXmlAgainstSchema() );
+ phys = AptxUtil.readPhylogeniesFromUrl( url, getConfiguration().isValidatePhyloXmlAgainstSchema() );
}
catch ( final Exception e ) {
ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, e.toString() );
+ "] are null or empty", "Failed to read phylogenies", JOptionPane.ERROR_MESSAGE );
}
else {
- Util.printAppletMessage( ArchaeopteryxA.NAME, "loaded " + phys.length + " phylogenies from: " + url );
+ AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "loaded " + phys.length + " phylogenies from: " + url );
}
_mainpanel = new MainPanelApplets( _configuration, this );
// build the menu bar
setFocusable( true );
requestFocus();
requestFocusInWindow();
- // All done: hello, world!
setVisible( true );
System.gc();
}
@Override
public void stateChanged( final ChangeEvent e ) {
- MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getCurrentTreePanel() );
+ MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
MainFrame
.setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
_uniform_cladograms_rbmi,
_ext_node_dependent_cladogram_rbmi,
_label_direction_cbmi );
+ MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
+ MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
+ MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
}
} );
_options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
_radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
_radio_group_1.add( _uniform_cladograms_rbmi );
_radio_group_1.add( _non_lined_up_cladograms_rbmi );
- _options_jmenu.add( _show_node_boxes_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) );
+ _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
_options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
_options_jmenu
.add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
- _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
+ _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
+ _options_jmenu.add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL ) );
+ _options_jmenu
+ .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
+ _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
+ _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
+ _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
_options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
_label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
_options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
customizeJMenuItem( _switch_colors_mi );
customizeJMenuItem( _choose_minimal_confidence_mi );
customizeJMenuItem( _overview_placment_mi );
- customizeCheckBoxMenuItem( _show_node_boxes_cbmi, getOptions().isShowNodeBoxes() );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
+ customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
+ customizeJMenuItem( _cycle_node_shape_mi );
+ customizeJMenuItem( _cycle_node_fill_mi );
+ customizeJMenuItem( _choose_node_size_mi );
customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
+ customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
_jmenubar.add( _options_jmenu );
}
}
@Override
- MainPanel getMainPanel() {
+ public MainPanel getMainPanel() {
return _mainpanel;
}