_mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()\r
.getWidth(),\r
_mainpanel.getCurrentTreePanel()\r
- .getHeight(),\r
- getOptions().isAllowFontSizeChange() );\r
+ .getHeight() );\r
}\r
}\r
} );\r
setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );\r
MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );\r
MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );\r
+ \r
+ MainFrame.setCycleDataReturnMenuItem( _cycle_data_return, getOptions() );\r
MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );\r
try {\r
getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();\r
_radio_group_1.add( _ext_node_dependent_cladogram_rbmi );\r
_radio_group_1.add( _uniform_cladograms_rbmi );\r
_radio_group_1.add( _non_lined_up_cladograms_rbmi );\r
- ///////\r
_options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );\r
_options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );\r
_options_jmenu\r
.add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );\r
_options_jmenu\r
.add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );\r
+ _options_jmenu\r
+ .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );\r
_options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );\r
if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {\r
_options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );\r
_options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );\r
_options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );\r
_options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );\r
- ///////\r
+ _options_jmenu.addSeparator();\r
+ _options_jmenu.add( _cycle_data_return = new JMenuItem( "Cycle Data Return" ) );\r
_options_jmenu.addSeparator();\r
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );\r
_options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );\r
_options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );\r
+ _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );\r
+ _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );\r
_options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );\r
_options_jmenu.addSeparator();\r
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),\r
_options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );\r
_options_jmenu\r
.add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );\r
- //\r
_options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );\r
_options_jmenu\r
.add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );\r
_radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );\r
_radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );\r
_radio_group_2.add( _extract_taxonomy_agressive_rbmi );\r
- // \r
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );\r
_options_jmenu\r
.add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );\r
.isShowDefaultNodeShapesExternal() );\r
customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()\r
.isShowDefaultNodeShapesInternal() );\r
+ customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()\r
+ .isShowDefaultNodeShapesForMarkedNodes() );\r
customizeJMenuItem( _cycle_node_shape_mi );\r
customizeJMenuItem( _cycle_node_fill_mi );\r
customizeJMenuItem( _choose_node_size_mi );\r
+ customizeJMenuItem( _cycle_data_return);\r
+ \r
customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );\r
customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );\r
customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );\r
customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );\r
customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()\r
.isReplaceUnderscoresInNhParsing() );\r
+ customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );\r
customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );\r
customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );\r
customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );\r
\r
void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {\r
_mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),\r
- _mainpanel.getCurrentTreePanel().getHeight(),\r
- true );\r
+ _mainpanel.getCurrentTreePanel().getHeight() );\r
String file_written_to = "";\r
boolean error = false;\r
try {\r
}\r
if ( !getOptions().isPrintUsingActualSize() ) {\r
getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX() - 80,\r
- getOptions().getPrintSizeY() - 140,\r
- true );\r
+ getOptions().getPrintSizeY() - 140 );\r
getCurrentTreePanel().resetPreferredSize();\r
getCurrentTreePanel().repaint();\r
}\r
\r
private void printPhylogenyToPdf( final String file_name ) {\r
if ( !getOptions().isPrintUsingActualSize() ) {\r
- getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX(),\r
- getOptions().getPrintSizeY(),\r
- true );\r
+ getCurrentTreePanel()\r
+ .calcParametersForPainting( getOptions().getPrintSizeX(), getOptions().getPrintSizeY() );\r
getCurrentTreePanel().resetPreferredSize();\r
getCurrentTreePanel().repaint();\r
}\r