// $Id: // FORESTER -- software libraries and applications // for evolutionary biology research and applications. // // Copyright (C) 2008-2009 Christian M. Zmasek // Copyright (C) 2008-2009 Burnham Institute for Medical Research // Copyright (C) 2000-2001 Washington University School of Medicine // 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 // version 2.1 of the License, or (at your option) any later version. // // This library is distributed in the hope that it will be useful, // 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 // // Contact: phylosoft @ gmail . com // WWW: www.phylosoft.org/forester package org.forester.archaeopteryx; import java.awt.Color; import java.io.BufferedReader; import java.io.File; import java.io.FileReader; import java.io.IOException; import java.io.InputStreamReader; import java.net.MalformedURLException; import java.net.URL; import java.util.Arrays; import java.util.Hashtable; import java.util.Map; import java.util.SortedMap; import java.util.StringTokenizer; import java.util.TreeMap; import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE; import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION; import org.forester.archaeopteryx.Options.NodeFill; import org.forester.archaeopteryx.Options.NodeShape; import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE; import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE; import org.forester.util.ForesterUtil; public final class Configuration { public enum UI { NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN } static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema"; private static final String WEB_LINK_KEY = "web_link"; private static final String DISPLAY_COLOR_KEY = "display_color"; private static final int DEPRECATED = -2; private UI _ui = UI.UNKNOWN; private boolean _use_tabbed_display = false; private boolean _hide_controls_and_menus = false; private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT; private SortedMap _weblinks = null; private SortedMap _display_colors = null; private boolean _antialias_screen = true; private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR; private String _base_font_family_name = ""; private int _base_font_size = -1; private int _graphics_export_x = -1; private int _graphics_export_y = -1; private short _ov_max_width = 80; private short _ov_max_height = 80; private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT; private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT; private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT; private boolean _show_scale = false; private boolean _show_branch_length_values = false; private boolean _show_overview = true; private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT; private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT; private boolean _editable = true; private boolean _nh_parsing_replace_underscores = false; private boolean _nh_parsing_extract_pfam_taxonomy_codes = false; private boolean _internal_number_are_confidence_for_nh_parsing = false; private boolean _display_sequence_relations = false; private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT; private boolean _background_color_gradient = false; private boolean _show_domain_labels = true; private boolean _abbreviate_scientific_names = false; private boolean _color_labels_same_as_parent_branch = false; private int _default_bootstrap_samples = -1; private boolean _show_default_node_shapes = false; private NodeShape _default_node_shape = NodeShape.NONE; private NodeFill _default_node_fill = NodeFill.GRADIENT; private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; private boolean _taxonomy_colorize_node_shapes = false; final static int display_as_phylogram = 0; final static int show_node_names = 1; final static int show_tax_code = 2; final static int show_annotation = 3; final static int write_confidence_values = 4; final static int write_events = 5; final static int color_according_to_species = 6; final static int color_branches = 7; final static int width_branches = 8; final static int show_custom_node_shapes = 9; final static int show_domain_architectures = 10; final static int show_binary_characters = 11; final static int show_binary_character_counts = 12; final static int show_gene_names = 13; final static int show_sequence_acc = 14; final static int display_internal_data = 15; final static int dynamically_hide_data = 16; final static int show_taxonomy_scientific_names = 17; final static int show_taxonomy_common_names = 18; final static int color_according_to_annotation = 19; final static int show_property = 20; final static int show_gene_symbols = 21; final static int node_data_popup = 22; final static int show_relation_confidence = 23; final static int show_vector_data = 24; final static int show_taxonomy_images = 25; // ------------------ // Click-to options // ------------------ final static int display_node_data = 0; final static int collapse_uncollapse = 1; final static int reroot = 2; final static int subtree = 3; final static int swap = 4; final static int color_subtree = 5; final static int open_seq_web = 6; final static int open_tax_web = 7; final static int cut_subtree = 8; final static int copy_subtree = 9; final static int paste_subtree = 10; final static int delete_subtree_or_node = 11; final static int add_new_node = 12; final static int edit_node_data = 13; final static int blast = 14; // --------------------------- // Display options for trees // --------------------------- // --------------------------------- // Pertaining to the config itself // --------------------------------- // Full path to config (may be URL) String config_filename; String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME; final static String display_options[][] = { { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" }, { "Annotation", "nodisplay", "no" }, { "Confidence Value", "display", "?" }, { "Event", "display", "?" }, { "Taxonomy Colorize", "display", "yes" }, { "Colorize Branches", "display", "no" }, { "Use Branch-Width", "nodisplay", "no" }, { "Show Custom Nodes", "display", "yes"}, { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" }, { "Prot/Gene Name", "display", "no" }, { "Prot/Gene Acc", "display", "no" }, { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" }, { "Property", "nodisplay", "no" }, { "Prot/Gene Symbol", "display", "no" }, { "Rollover", "display", "yes" }, { "Relation Confidence", "display", "no" }, { "Vector Data", "display", "no" }, { "Taxonomy Images", "display", "no" } }; final static String clickto_options[][] = { { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" }, { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" }, { "Open Sequence Web", "nodisplay" }, { "Open Taxonomy Web", "nodisplay" }, { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Blast", "display" } }; // This option is selected in the dropdown int default_clickto = Configuration.display_node_data; // -------------- // Color set // -------------- TreeColorSet tree_color_set; // ------- // Fonts // ------- TreeFontSet tree_font_set; // ---------------- // Species colors // ---------------- private static Hashtable _species_colors; // ---------------- // Domain colors // ---------------- private static Hashtable _domain_colors; // ---------------- // Function colors // ---------------- private static Hashtable _annotation_colors; boolean verbose = Constants.VERBOSE_DEFAULT; private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL; private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT; private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT; private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT; private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT; private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT; private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT; private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT; private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT; private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT; private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT; private static String DEFAULT_FONT_FAMILY = ""; static { for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) { if ( Arrays.binarySearch( Util.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) { DEFAULT_FONT_FAMILY = font_name; break; } } if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) { DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ]; } } Configuration( final String cf, final boolean is_url, final boolean is_applet ) { if ( ForesterUtil.isEmpty( cf ) ) { config_filename = default_config_filename; } else { config_filename = cf; } setWebLinks( new TreeMap() ); setDisplayColors( new TreeMap() ); config_filename = config_filename.trim(); URL u = null; if ( is_url ) { // If URL, open accordingly try { u = new URL( config_filename ); try { final InputStreamReader isr = new InputStreamReader( u.openStream() ); final BufferedReader bf = new BufferedReader( isr ); readConfig( bf ); bf.close(); ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url [" + config_filename + "]" ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from [" + config_filename + "]: " + e.getLocalizedMessage() ); } } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url [" + config_filename + "]" ); } } else { // Otherwise, open as a file File f = new File( config_filename ); if ( !f.exists() ) { f = new File( config_filename + ".txt" ); } if ( f.exists() && f.canRead() ) { try { final BufferedReader bf = new BufferedReader( new FileReader( f ) ); readConfig( bf ); bf.close(); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from [" + config_filename + "]: " + e ); } } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file [" + config_filename + "]" ); } } } private void createWebLink( final String url_str, final String desc, final String source_identifier ) { WebLink weblink = null; boolean ex = false; try { weblink = new WebLink( new URL( url_str.trim() ), desc.trim(), source_identifier.trim() ); } catch ( final MalformedURLException e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not create URL from [" + url_str + "]" ); ex = true; } if ( !ex && ( weblink != null ) ) { getWebLinks().put( weblink.getSourceIdentifier().toLowerCase(), weblink ); } } Color getGuiBackgroundColor() { return _gui_background_color; } Color getGuiCheckboxTextColor() { return _gui_checkbox_text_color; } Color getGuiCheckboxAndButtonActiveColor() { return _gui_checkbox_and_button_active_color; } Color getGuiButtonTextColor() { return _gui_button_text_color; } Color getGuiButtonBackgroundColor() { return _gui_button_background_color; } Color getGuiMenuBackgroundColor() { return _gui_menu_background_color; } Color getGuiMenuTextColor() { return _gui_menu_text_color; } Color getGuiButtonBorderColor() { return _gui_button_border_color; } boolean displaySequenceRelations() { return _display_sequence_relations; } boolean doCheckOption( final int which ) { return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) ) || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) ); } boolean doDisplayClickToOption( final int which ) { return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" ); } boolean doDisplayOption( final int which ) { return display_options[ which ][ 1 ].equalsIgnoreCase( "display" ); } /** * Will attempt to use the phylogeny to determine whether to check * this or not (e.g. phylogram) * */ boolean doGuessCheckOption( final int which ) { return display_options[ which ][ 2 ].equals( "?" ); } Map getAnnotationColors() { if ( _annotation_colors == null ) { _annotation_colors = new Hashtable(); } return _annotation_colors; } public String getBaseFontFamilyName() { return _base_font_family_name; } int getBaseFontSize() { return _base_font_size; } CLADOGRAM_TYPE getCladogramType() { return _cladogram_type; } private int getClickToIndex( final String name ) { int index = -1; if ( name.equals( "edit_info" ) ) { index = Configuration.display_node_data; ForesterUtil .printWarningMessage( Constants.PRG_NAME, "configuration key [edit_info] is deprecated, use [display node data] instead" ); } else if ( name.equals( "display_node_data" ) ) { index = Configuration.display_node_data; } else if ( name.equals( "collapse_uncollapse" ) ) { index = Configuration.collapse_uncollapse; } else if ( name.equals( "reroot" ) ) { index = Configuration.reroot; } else if ( name.equals( "subtree" ) ) { index = Configuration.subtree; } else if ( name.equals( "swap" ) ) { index = Configuration.swap; } else if ( name.equals( "display_sequences" ) ) { ForesterUtil .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" ); return DEPRECATED; } else if ( name.equals( "open_seq_web" ) ) { index = Configuration.open_seq_web; } else if ( name.equals( "open_tax_web" ) ) { index = Configuration.open_tax_web; } else if ( name.equals( "cut_subtree" ) ) { index = Configuration.cut_subtree; } else if ( name.equals( "copy_subtree" ) ) { index = Configuration.copy_subtree; } else if ( name.equals( "paste_subtree" ) ) { index = Configuration.paste_subtree; } else if ( name.equals( "delete" ) ) { index = Configuration.delete_subtree_or_node; } else if ( name.equals( "add_new_node" ) ) { index = Configuration.add_new_node; } else if ( name.equals( "edit_node_data" ) ) { index = Configuration.edit_node_data; } else if ( name.equals( "display_node_popup" ) ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [display_node_popup] is deprecated" ); return DEPRECATED; } else if ( name.equals( "custom_option" ) ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" ); return DEPRECATED; } else if ( name.equals( "color_subtree" ) ) { index = Configuration.color_subtree; } else if ( name.equals( "go_to_swiss_prot" ) ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" ); return DEPRECATED; } return index; } int getClickToOptionsCount() { return clickto_options.length; } String getClickToTitle( final int which ) { return clickto_options[ which ][ 0 ]; } int getDefaultDisplayClicktoOption() { return default_clickto; } SortedMap getDisplayColors() { return _display_colors; } String getDisplayTitle( final int which ) { return display_options[ which ][ 0 ]; } Map getDomainColors() { if ( _domain_colors == null ) { _domain_colors = new Hashtable(); } return _domain_colors; } int getGraphicsExportX() { return _graphics_export_x; } int getGraphicsExportY() { return _graphics_export_y; } public int getDefaultBootstrapSamples() { return _default_bootstrap_samples; } double getMinConfidenceValue() { return _min_confidence_value; } NODE_LABEL_DIRECTION getNodeLabelDirection() { return _node_label_direction; } short getNumberOfDigitsAfterCommaForBranchLengthValues() { return _number_of_digits_after_comma_for_branch_length_values; } short getNumberOfDigitsAfterCommaForConfidenceValues() { return _number_of_digits_after_comma_for_confidence_values; } short getOvMaxHeight() { return _ov_max_height; } short getOvMaxWidth() { return _ov_max_width; } OVERVIEW_PLACEMENT_TYPE getOvPlacement() { return _ov_placement; } PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() { return _phylogeny_graphics_type; } float getPrintLineWidth() { return _print_line_width; } Hashtable getSpeciesColors() { if ( _species_colors == null ) { _species_colors = new Hashtable(); } return _species_colors; } TreeColorSet getTreeColorSet() { return null; } TreeFontSet getTreeFontSet() { return null; } WebLink getWebLink( final String source ) { return getWebLinks().get( source ); } Map getWebLinks() { return _weblinks; } boolean isAntialiasScreen() { return _antialias_screen; } public boolean isBackgroundColorGradient() { return _background_color_gradient; } /** * Convenience method. * * @return true if value in configuration file was 'yes' */ boolean isDrawAsPhylogram() { return doCheckOption( display_as_phylogram ); } boolean isEditable() { return _editable; } boolean isExtractPfamTaxonomyCodesInNhParsing() { return _nh_parsing_extract_pfam_taxonomy_codes; } boolean isHasWebLink( final String source ) { return getWebLinks().containsKey( source ); } /** * Only used by ArchaeoptryxE. * */ boolean isHideControlPanelAndMenubar() { return _hide_controls_and_menus; } boolean isInternalNumberAreConfidenceForNhParsing() { return _internal_number_are_confidence_for_nh_parsing; } boolean isReplaceUnderscoresInNhParsing() { return _nh_parsing_replace_underscores; } boolean isShowBranchLengthValues() { return _show_branch_length_values; } boolean isShowOverview() { return _show_overview; } boolean isShowScale() { return _show_scale; } final boolean isUseNativeUI() { if ( ( _ui == UI.UNKNOWN ) && Util.isMac() && Util.isJava15() ) { _ui = UI.NATIVE; } return _ui == UI.NATIVE; } /** * Only used by ArchaeoptryxE. * */ boolean isUseTabbedDisplay() { return _use_tabbed_display; } boolean isValidatePhyloXmlAgainstSchema() { return _validate_against_phyloxml_xsd_schema; } private boolean parseBoolean( final String str ) { final String my_str = str.trim().toLowerCase(); if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) { return true; } else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) { return false; } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" ); return false; } } private double parseDouble( final String str ) { double d = 0.0; try { d = Double.parseDouble( str ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" ); d = 0.0; } return d; } private float parseFloat( final String str ) { float f = 0.0f; try { f = Float.parseFloat( str ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" ); f = 0.0f; } return f; } private int parseInt( final String str ) { int i = -1; try { i = Integer.parseInt( str ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" ); i = -1; } return i; } private short parseShort( final String str ) { short i = -1; try { i = Short.parseShort( str ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" ); i = -1; } return i; } private void processFontFamily( final StringTokenizer st ) { setBaseFontFamilyName( "" ); final String font_str = ( ( String ) st.nextElement() ).trim(); final String[] fonts = font_str.split( ",+" ); for( String font : fonts ) { font = font.replace( '_', ' ' ).trim(); if ( Arrays.binarySearch( Util.getAvailableFontFamiliesSorted(), font ) >= 0 ) { setBaseFontFamilyName( font ); break; } } } /** * read each line of config file, process non-comment lines * @throws IOException */ private void readConfig( final BufferedReader conf_in ) throws IOException { String line; do { line = conf_in.readLine(); if ( line != null ) { line = line.trim(); // skip comments and blank lines if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) { // convert runs of spaces to tabs line = line.replaceAll( "\\s+", "\t" ); final StringTokenizer st = new StringTokenizer( line, "\t" ); setKeyValue( st ); } } } while ( line != null ); } private void setAntialiasScreen( final boolean antialias_screen ) { _antialias_screen = antialias_screen; } public void setBackgroundColorGradient( final boolean background_color_gradient ) { _background_color_gradient = background_color_gradient; } private void setBaseFontFamilyName( final String base_font_family_name ) { _base_font_family_name = base_font_family_name; } private void setBaseFontSize( final int base_font_size ) { _base_font_size = base_font_size; } private void setShowDomainLabels( final boolean show_domain_labels ) { _show_domain_labels = show_domain_labels; } private void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) { _abbreviate_scientific_names = abbreviate_scientific_names; } private void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) { _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch; } private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) { _cladogram_type = cladogram_type; } void setDisplayColors( final SortedMap display_colors ) { _display_colors = display_colors; } private void setDisplaySequenceRelations( final boolean display_sequence_relations ) { _display_sequence_relations = display_sequence_relations; } private void setEditable( final boolean editable ) { _editable = editable; } private void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) { _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes; } private void setGraphicsExportX( final int graphics_export_x ) { _graphics_export_x = graphics_export_x; } private void setGraphicsExportY( final int graphics_export_y ) { _graphics_export_y = graphics_export_y; } private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) { _default_bootstrap_samples = default_bootstrap_samples; } private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) { _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing; } /** * Set a key-value(s) tuple */ private void setKeyValue( final StringTokenizer st ) { String key = ( String ) st.nextElement(); key = key.replace( ':', ' ' ); key = key.trim(); key = key.toLowerCase(); // Handle single value settings first: if ( key.equals( "default_click_to" ) ) { final String clickto_name = ( String ) st.nextElement(); default_clickto = getClickToIndex( clickto_name ); if ( default_clickto == -1 ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name + "] for [default_click_to]" ); default_clickto = 0; } else if ( default_clickto == DEPRECATED ) { // Deprecated. } } else if ( key.equals( "native_ui" ) ) { final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase(); if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) { _ui = UI.NATIVE; } else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) { _ui = UI.CROSSPLATFORM; } else if ( my_str.equals( "?" ) ) { _ui = UI.UNKNOWN; } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str + "]" ); _ui = UI.UNKNOWN; } } else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) { setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "antialias_screen" ) ) { setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "phylogeny_graphics_type" ) ) { final String type_str = ( ( String ) st.nextElement() ).trim(); if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX ); } else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED ); } else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ); } else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED ); } else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); } else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ); } else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); } else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ); } else { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str + "] for [phylogeny_graphics_type]" ); } } else if ( key.equals( "min_confidence_value" ) ) { final String mcv_str = ( ( String ) st.nextElement() ).trim(); final double d = parseDouble( mcv_str ); setMinConfidenceValue( d ); } else if ( key.equals( "font_family" ) ) { processFontFamily( st ); } else if ( key.equals( "font_size" ) ) { final String size_str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( size_str ); setBaseFontSize( i ); } else if ( key.equals( "graphics_export_x" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( str ); setGraphicsExportX( i ); } else if ( key.equals( "graphics_export_y" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( str ); setGraphicsExportY( i ); } else if ( key.equals( "pdf_export_line_width" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final float f = parseFloat( str ); if ( f > 0 ) { setPrintLineWidth( f ); } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "value for [pdf_export_line_width] cannot be zero or negative" ); } } else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( str ); if ( i >= 0 ) { setDefaultBootstrapSamples( i ); } else { ForesterUtil .printWarningMessage( Constants.PRG_NAME, "value for [default_number_of_bootstrap_resamples] cannot be negative" ); } } else if ( key.equals( "show_scale" ) ) { setShowScale( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "show_overview" ) ) { setShowOverview( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "show_branch_length_values" ) ) { setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "background_gradient" ) ) { setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) { setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "show_domain_labels" ) ) { setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "abbreviate_scientific_names" ) ) { setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "cladogram_type" ) ) { final String type_str = ( ( String ) st.nextElement() ).trim(); if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) { setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP ); } else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) { setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP ); } else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) { setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP ); } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str + "] for [cladogram_type]" ); } } else if ( key.equals( "non_lined_up_cladogram" ) ) { ForesterUtil .printWarningMessage( Constants.PRG_NAME, "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" ); } else if ( key.equals( "hide_controls_and_menus" ) ) { _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() ); } else if ( key.equals( "use_tabbed_display" ) ) { _use_tabbed_display = parseBoolean( ( String ) st.nextElement() ); } else if ( key.equals( "overview_width" ) ) { final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); setOvMaxWidth( i ); } else if ( key.equals( "overview_height" ) ) { final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); setOvMaxHeight( i ); } else if ( key.equals( "overview_placement_type" ) ) { final String type_str = ( ( String ) st.nextElement() ).trim(); if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) { setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT ); } else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) { setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT ); } else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) { setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT ); } else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) { setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT ); } else { setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT ); ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str + "] for [overview_placement_type]" ); } } else if ( key.equals( "node_label_direction" ) ) { final String type_str = ( ( String ) st.nextElement() ).trim(); if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) { setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL ); } else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) { setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL ); } else { setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL ); ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str + "] for [node_label_direction]" ); } } else if ( key.equals( "branch_length_value_digits" ) ) { final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); if ( i >= 0 ) { setNumberOfDigitsAfterCommaForBranchLengthValue( i ); } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i + "] for [branch_length_value_digits]" ); } } else if ( key.equals( "confidence_value_digits" ) ) { final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); if ( i >= 0 ) { setNumberOfDigitsAfterCommaForConfidenceValues( i ); } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i + "] for [confidence_value_digits]" ); } } else if ( key.equals( "allow_editing" ) ) { setEditable( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "display_sequence_relations" ) ) { setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) { final boolean r = parseBoolean( ( String ) st.nextElement() ); if ( r && isExtractPfamTaxonomyCodesInNhParsing() ) { ForesterUtil .printWarningMessage( Constants.PRG_NAME, "attempt to extract taxonomies and replace underscores at the same time" ); } else { setReplaceUnderscoresInNhParsing( r ); } } else if ( key.equals( "extract_taxonomy_codes_in_nh_parsing" ) ) { final boolean e = parseBoolean( ( String ) st.nextElement() ); if ( e && isReplaceUnderscoresInNhParsing() ) { ForesterUtil .printWarningMessage( Constants.PRG_NAME, "attempt to extract taxonomies and replace underscores at the same time" ); } else { setExtractPfamTaxonomyCodesInNhParsing( e ); } } else if ( key.equals( "internal_labels_are_confidence_values" ) ) { setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "gui_background_color" ) ) { _gui_background_color = Color.decode( ( String ) st.nextElement() ); } else if ( key.equals( "gui_checkbox_text_color" ) ) { _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() ); } else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) { _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() ); } else if ( key.equals( "gui_button_text_color" ) ) { _gui_button_text_color = Color.decode( ( String ) st.nextElement() ); } else if ( key.equals( "gui_button_background_color" ) ) { _gui_button_background_color = Color.decode( ( String ) st.nextElement() ); } else if ( key.equals( "gui_menu_background_color" ) ) { _gui_menu_background_color = Color.decode( ( String ) st.nextElement() ); } else if ( key.equals( "gui_menu_text_color" ) ) { _gui_menu_text_color = Color.decode( ( String ) st.nextElement() ); } else if ( key.equals( "gui_button_border_color" ) ) { _gui_button_border_color = Color.decode( ( String ) st.nextElement() ); } else if ( key.equals( "domain_structure_font_color" ) ) { _domain_structure_font_color = Color.decode( ( String ) st.nextElement() ); } else if ( key.equals( "domain_structure_base_color" ) ) { _domain_structure_base_color = Color.decode( ( String ) st.nextElement() ); } // else if ( key.equals( "show_default_node_shapes" ) ) { setShowDefaultNodeShapes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) ); } else if ( key.equals( "default_node_size" ) ) { final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); setDefaultNodeShapeSize( i ); } else if ( key.equals( "default_node_fill" ) ) { final String fill_str = ( ( String ) st.nextElement() ).trim(); if ( fill_str.equalsIgnoreCase( Options.NodeFill.NONE.toString() ) ) { setDefaultNodeFill( NodeFill.NONE ); } else if ( fill_str.equalsIgnoreCase( Options.NodeFill.GRADIENT.toString() ) ) { setDefaultNodeFill( NodeFill.GRADIENT ); } else if ( fill_str.equalsIgnoreCase( Options.NodeFill.SOLID.toString() ) ) { setDefaultNodeFill( NodeFill.SOLID ); } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str + "] for [default_node_fill]" ); } } else if ( key.equals( "default_node_shape" ) ) { final String shape_str = ( ( String ) st.nextElement() ).trim(); if ( shape_str.equalsIgnoreCase( Options.NodeShape.NONE.toString() ) ) { setDefaultNodeShape( NodeShape.NONE ); } else if ( shape_str.equalsIgnoreCase( Options.NodeShape.CIRCLE.toString() ) ) { setDefaultNodeShape( NodeShape.CIRCLE ); } else if ( shape_str.equalsIgnoreCase( Options.NodeShape.RECTANGLE.toString() ) ) { setDefaultNodeShape( NodeShape.RECTANGLE ); } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str + "] for [default_node_shape]" ); } } else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) { setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) ); } else if ( st.countTokens() >= 2 ) { // counts the tokens that are not // yet retrieved! int key_index = -1; if ( key.equals( "use_real_br_lengths" ) || key.equals( "phylogram" ) ) { key_index = Configuration.display_as_phylogram; if ( key.equals( "use_real_br_lengths" ) ) { ForesterUtil .printWarningMessage( Constants.PRG_NAME, "configuration key [use_real_br_lengths] is deprecated, use [phylogram] instead" ); } } else if ( key.equals( "rollover" ) ) { key_index = Configuration.node_data_popup; } else if ( key.equals( "color_according_to_species" ) ) { key_index = Configuration.color_according_to_species; } else if ( key.equals( "show_node_names" ) ) { key_index = Configuration.show_node_names; } else if ( key.equals( "show_taxonomy" ) || key.equals( "show_taxonomy_code" ) ) { key_index = Configuration.show_tax_code; if ( key.equals( "show_taxonomy" ) ) { ForesterUtil .printWarningMessage( Constants.PRG_NAME, "configuration key [show_taxonomy] is deprecated, use [show_taxonomy_code] instead" ); } } else if ( key.equals( "write_br_length_values" ) ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [write_br_length_values] is deprecated" ); key_index = DEPRECATED; } else if ( key.equals( "write_bootstrap_values" ) || key.equals( "write_confidence_values" ) ) { key_index = Configuration.write_confidence_values; if ( key.equals( "write_bootstrap_values" ) ) { ForesterUtil .printWarningMessage( Constants.PRG_NAME, "configuration key [write_bootstrap_values] is deprecated, use [write_confidence_values] instead" ); } } else if ( key.equals( "write_events" ) || key.equals( "write_dup_spec" ) ) { key_index = Configuration.write_events; if ( key.equals( "write_dup_spec" ) ) { ForesterUtil .printWarningMessage( Constants.PRG_NAME, "configuration key [write_dup_spec] is deprecated, use [write_events] instead" ); } } else if ( key.equals( "color_branches" ) ) { key_index = Configuration.color_branches; } else if ( key.equals( "width_branches" ) ) { key_index = Configuration.width_branches; } else if ( key.equals( "color_orthologous" ) ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [color_orthologous] is deprecated" ); } else if ( key.equals( "color_subtree_neighbors" ) ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [color_subtree_neighbors] is deprecated" ); } else if ( key.equals( "color_super_orthologous" ) ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [color_super_orthologous] is deprecated" ); } else if ( key.equals( "mark_nodes_with_box" ) ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [mark_nodes_with_box] is deprecated" ); key_index = DEPRECATED; } else if ( key.equals( "show_domain_architectures" ) ) { key_index = Configuration.show_domain_architectures; } else if ( key.equals( "show_annotations" ) ) { key_index = Configuration.show_annotation; } else if ( key.equals( "show_binary_characters" ) ) { key_index = Configuration.show_binary_characters; } else if ( key.equals( "show_binary_character_counts" ) ) { key_index = Configuration.show_binary_character_counts; } else if ( key.equals( "show_gene_names" ) ) { key_index = Configuration.show_gene_names; } else if ( key.equals( "show_gene_symbols" ) ) { key_index = Configuration.show_gene_symbols; } else if ( key.equals( "show_sequence_acc" ) ) { key_index = Configuration.show_sequence_acc; } else if ( key.equals( "show_node_ids" ) ) { ForesterUtil .printWarningMessage( Constants.PRG_NAME, "configuration key [show_node_ids] is deprecated" ); key_index = DEPRECATED; } else if ( key.equals( "display_internal_data" ) ) { key_index = Configuration.display_internal_data; } else if ( key.equals( "dynamically_hide_data" ) ) { key_index = Configuration.dynamically_hide_data; } else if ( key.equals( "show_taxonomy_names" ) ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [show_taxonomy_names] is deprecated" ); key_index = DEPRECATED; } else if ( key.equals( "show_taxonomy_scientific_names" ) ) { key_index = Configuration.show_taxonomy_scientific_names; } else if ( key.equals( "show_taxonomy_common_names" ) ) { key_index = Configuration.show_taxonomy_common_names; } else if ( key.equals( "show_taxonomy_images" ) ) { key_index = Configuration.show_taxonomy_images; } else if ( key.equals( "color_according_to_annotation" ) ) { key_index = Configuration.color_according_to_annotation; } else if ( key.equals( "show_property" ) ) { key_index = Configuration.show_property; } else if ( key.equals( "show_vector_data" ) ) { key_index = Configuration.show_vector_data; } else if ( key.equals( "show_relation_confidence" ) ) { key_index = Configuration.show_relation_confidence; } else if ( key.equals( "show_custom_node_shapes" ) ) { key_index = Configuration.show_custom_node_shapes; } // If we've found the key, set the values if ( key_index >= 0 ) { display_options[ key_index ][ 1 ] = ( String ) st.nextElement(); display_options[ key_index ][ 2 ] = ( String ) st.nextElement(); // otherwise, keep looking } else { if ( key_index == DEPRECATED ) { // Deprecated. } else if ( key.equals( "click_to" ) ) { final String click_to_name = ( String ) st.nextElement(); key_index = getClickToIndex( click_to_name ); if ( key_index >= 0 ) { clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement(); } else if ( key_index == DEPRECATED ) { // Deprecated. } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: " + click_to_name ); } } else if ( key.equals( "species_color" ) ) { getSpeciesColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); } else if ( key.equals( "domain_color" ) ) { getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); } else if ( key.equals( "annotation_color" ) ) { getAnnotationColors() .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); } else if ( key.equals( "function_color" ) ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [function_color] is deprecated" ); } else if ( key.equals( DISPLAY_COLOR_KEY ) ) { getDisplayColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); } else if ( key.equals( WEB_LINK_KEY ) ) { if ( st.countTokens() == 3 ) { createWebLink( ( String ) st.nextElement(), ( String ) st.nextElement(), ( String ) st.nextElement() ); } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal format in configuration file for key [" + key + "]" ); } } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: " + config_filename ); } } } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: " + config_filename ); } } private void setMinConfidenceValue( final double min_confidence_value ) { _min_confidence_value = min_confidence_value; } void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) { _node_label_direction = node_label_direction; } private void setNumberOfDigitsAfterCommaForBranchLengthValue( final short _number_of_digits_after_comma_for_branch_length_values ) { this._number_of_digits_after_comma_for_branch_length_values = _number_of_digits_after_comma_for_branch_length_values; } private void setNumberOfDigitsAfterCommaForConfidenceValues( final short _number_of_digits_after_comma_for_confidence_values ) { this._number_of_digits_after_comma_for_confidence_values = _number_of_digits_after_comma_for_confidence_values; } private void setOvMaxHeight( final short ov_max_height ) { _ov_max_height = ov_max_height; } private void setOvMaxWidth( final short ov_max_width ) { _ov_max_width = ov_max_width; } private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) { _ov_placement = ov_placement; } void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) { _phylogeny_graphics_type = phylogeny_graphics_type; } private void setPrintLineWidth( final float print_line_width ) { _print_line_width = print_line_width; } private void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) { _nh_parsing_replace_underscores = nh_parsing_replace_underscores; } private void setShowBranchLengthValues( final boolean show_branch_length_values ) { _show_branch_length_values = show_branch_length_values; } private void setShowOverview( final boolean show_overview ) { _show_overview = show_overview; } private void setShowScale( final boolean show_scale ) { _show_scale = show_scale; } private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) { _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema; } void setWebLinks( final SortedMap weblinks ) { _weblinks = weblinks; } static String getDefaultFontFamilyName() { return DEFAULT_FONT_FAMILY; } static enum TRIPLET { TRUE, FALSE, UNKNOWN } public Color getDomainStructureFontColor() { return _domain_structure_font_color; } public Color getDomainStructureBaseColor() { return _domain_structure_base_color; } public boolean isColorLabelsSameAsParentBranch() { return _color_labels_same_as_parent_branch; } public boolean isShowDomainLabels() { return _show_domain_labels; } public boolean isAbbreviateScientificTaxonNames() { return _abbreviate_scientific_names; } public NodeShape getDefaultNodeShape() { return _default_node_shape; } private void setDefaultNodeShape( final NodeShape default_node_shape ) { _default_node_shape = default_node_shape; } private void setDefaultNodeFill( final NodeFill default_node_fill ) { _default_node_fill = default_node_fill; } public NodeFill getDefaultNodeFill() { return _default_node_fill; } private void setDefaultNodeShapeSize( final short default_node_shape_size ) { _default_node_shape_size = default_node_shape_size; } public short getDefaultNodeShapeSize() { return _default_node_shape_size; } private void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) { _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes; } public boolean isTaxonomyColorizeNodeShapes() { return _taxonomy_colorize_node_shapes; } public boolean isShowDefaultNodeShapes() { return _show_default_node_shapes; } private void setShowDefaultNodeShapes(boolean show_default_node_shapes) { _show_default_node_shapes =show_default_node_shapes; } }