// 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;
public final class MainFrameApplet extends MainFrame {
- private static final long serialVersionUID = 1941019292746717053L;
- private final static int FRAME_X_SIZE = 640, FRAME_Y_SIZE = 580;
+ private static final long serialVersionUID = 1941019292746717053L;
+ private final static int DEFAULT_FRAME_X_SIZE = 640;
+ private final static int DEFAULT_FRAME_Y_SIZE = 580;
private final ArchaeopteryxA _applet;
private ButtonGroup _radio_group_1;
_applet = parent_applet;
setConfiguration( configuration );
setOptions( Options.createInstance( configuration ) );
- _textframe = null;
+ //_textframes = null; //~~~~
URL url = null;
Phylogeny[] phys = null;
// Get URL to tree file
// Load the tree from URL
if ( url != null ) {
try {
- phys = Util.readPhylogeniesFromUrl( url, getConfiguration().isValidatePhyloXmlAgainstSchema() );
+ phys = AptxUtil.readPhylogeniesFromUrl( url,
+ configuration.isValidatePhyloXmlAgainstSchema(),
+ configuration.isReplaceUnderscoresInNhParsing(),
+ configuration.isInternalNumberAreConfidenceForNhParsing(),
+ configuration.getTaxonomyExtraction() );
}
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
_contentpane = getContentPane();
_contentpane.setLayout( new BorderLayout() );
_contentpane.add( _mainpanel, BorderLayout.CENTER );
- setSize( FRAME_X_SIZE, FRAME_Y_SIZE );
+ setSize( getConfiguration().getFrameXSize() > 40 ? getConfiguration().getFrameXSize() : DEFAULT_FRAME_X_SIZE,
+ getConfiguration().getFrameYSize() > 40 ? getConfiguration().getFrameYSize() : DEFAULT_FRAME_Y_SIZE );
addWindowListener( new WindowAdapter() {
@Override
@Override
public void componentResized( final ComponentEvent e ) {
if ( _mainpanel.getCurrentTreePanel() != null ) {
- _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel()
- .getWidth(),
- _mainpanel.getCurrentTreePanel()
- .getHeight(),
- false );
+ _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()
+ .getWidth(),
+ _mainpanel.getCurrentTreePanel()
+ .getHeight(),
+ getOptions().isAllowFontSizeChange() );
}
}
} );
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_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
+ _options_jmenu
+ .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
+ _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().getDefaultNodeShape() );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
+ .isShowDefaultNodeShapesInternal() );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
+ .isShowDefaultNodeShapesExternal() );
+ 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 );
}
_tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
customizeJMenuItem( _midpoint_root_item );
_tools_menu.addSeparator();
- _tools_menu
- .add( _infer_common_sn_names_item = new JMenuItem( "Infer Common Parts of Internal Scientific Names" ) );
- customizeJMenuItem( _infer_common_sn_names_item );
_tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
customizeJMenuItem( _collapse_species_specific_subtrees );
_jmenubar.add( _tools_menu );
}
@Override
- MainPanel getMainPanel() {
+ public MainPanel getMainPanel() {
return _mainpanel;
}