X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryxE.java;h=9146fe8c3765faaf38c03589bb5ade2036a19029;hb=790ebe51ea3e7fcafc91057f4842453a1c351b61;hp=d186d16d176b295ff39f185e29dde1b58c2cb073;hpb=a5c10503459aaada602af51a0169b568ada036b4;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index d186d16..9146fe8 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -72,7 +72,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { private JMenu _view_jmenu; private JMenuItem _view_as_XML_item; private JMenuItem _view_as_NH_item; - private JMenuItem _view_as_NHX_item; private JMenuItem _view_as_nexus_item; private JMenuItem _display_basic_information_item; private JMenu _type_menu; @@ -92,7 +91,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { private JMenuItem _phyloxml_ref_item; private JMenuItem _aptx_ref_item; private JMenuItem _remove_branch_color_item; - private JMenuItem _infer_common_sn_names_item; private JCheckBoxMenuItem _show_domain_labels; private JCheckBoxMenuItem _color_labels_same_as_parent_branch; private JCheckBoxMenuItem _abbreviate_scientific_names; @@ -115,7 +113,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { private JMenuItem _collapse_species_specific_subtrees; private JMenuItem _overview_placment_mi; private ButtonGroup _radio_group_1; - private JCheckBoxMenuItem _show_default_node_shapes_cbmi; + private JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi; + private JCheckBoxMenuItem _show_default_node_shapes_external_cbmi; private JMenuItem _cycle_node_shape_mi; private JMenuItem _cycle_node_fill_mi; private JMenuItem _choose_node_size_mi; @@ -154,9 +153,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { else if ( o == _view_as_NH_item ) { viewAsNH(); } - else if ( o == _view_as_NHX_item ) { - viewAsNHX(); - } else if ( o == _view_as_XML_item ) { viewAsXML(); } @@ -271,7 +267,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { else if ( o == _color_labels_same_as_parent_branch ) { updateOptions( getOptions() ); } - else if ( o == _show_default_node_shapes_cbmi ) { + else if ( o == _show_default_node_shapes_internal_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _show_default_node_shapes_external_cbmi ) { updateOptions( getOptions() ); } else if ( o == _taxonomy_colorize_node_shapes_cbmi ) { @@ -625,7 +624,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) ); _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) ); _options_jmenu - .add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) ); + .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); + _options_jmenu + .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.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 ) ); @@ -664,7 +665,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() ); customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() ); customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() ); - customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() ); + customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions() + .isShowDefaultNodeShapesExternal() ); + customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() + .isShowDefaultNodeShapesInternal() ); customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() ); customizeJMenuItem( _cycle_node_shape_mi ); customizeJMenuItem( _cycle_node_fill_mi ); @@ -699,9 +703,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _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 ); @@ -737,11 +738,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _view_jmenu.addSeparator(); _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) ); _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) ); - _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) ); _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) ); customizeJMenuItem( _display_basic_information_item ); customizeJMenuItem( _view_as_NH_item ); - customizeJMenuItem( _view_as_NHX_item ); customizeJMenuItem( _view_as_XML_item ); customizeJMenuItem( _view_as_nexus_item ); _jmenubar.add( _view_jmenu ); @@ -1027,8 +1026,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { && _abbreviate_scientific_names.isSelected() ); options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null ) && _color_labels_same_as_parent_branch.isSelected() ); - options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null ) - && _show_default_node_shapes_cbmi.isSelected() ); + options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null ) + && _show_default_node_shapes_internal_cbmi.isSelected() ); + options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null ) + && _show_default_node_shapes_external_cbmi.isSelected() ); options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null ) && _taxonomy_colorize_node_shapes_cbmi.isSelected() ); if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) { @@ -1118,16 +1119,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } - void viewAsNHX() { - if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { - String title = "NHX"; - if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { - title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; - } - showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshireX(), title ); - } - } - void viewAsXML() { if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { String title = "phyloXML";