X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=3418951a898498a915f6126c6be3474c39caa9e4;hb=f6b29c53c14e1ef16e4cd614c7f9465e0073309e;hp=f8f530285759cc316ebf9a68c22340c85a626aa9;hpb=a59710c5067970e8c5b20c9de492088844210c57;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index f8f5302..3418951 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -47,7 +47,7 @@ import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION; import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE; import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE; import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; -import org.forester.phylogeny.data.NodeData.NODE_DATA; +import org.forester.phylogeny.data.NodeDataField; import org.forester.phylogeny.data.NodeVisualData; import org.forester.phylogeny.data.NodeVisualData.NodeFill; import org.forester.phylogeny.data.NodeVisualData.NodeShape; @@ -59,40 +59,40 @@ public final class Configuration { BUFFER_ONLY, CONSOLE, WINODW; } - static enum TRIPLET { - FALSE, TRUE, UNKNOWN - } - public enum UI { CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN } + + static enum TRIPLET { + FALSE, TRUE, UNKNOWN + } final static String clickto_options[][] = { - { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" }, - { "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "display" }, - { "Colorize Node(s)", "display" }, { "Change Node Font(s)", "display" }, - { "Colorize Subtree(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "display" }, - { "Open Taxonomy DB", "display" }, { "Launch BLAST", "display" }, { "Cut Subtree", "display" }, - { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" }, - { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Sort Descendants", "display" }, - { "Return", "display" }, { "Select Node(s)", "display" } }; + { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" }, + { "Go to Sub/Supertree", "display" }, { "Swap Descendants", "display" }, + { "Colorize Node(s)", "display" }, { "Change Node Font(s)", "display" }, + { "Colorize Subtree(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "display" }, + { "Open Taxonomy DB", "display" }, { "Launch BLAST", "display" }, { "Cut Subtree", "display" }, + { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" }, + { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Sort Descendants", "display" }, + { "List Node Data", "display" }, { "Select Node(s)", "display" } , { "Uncollapse All", "display" }, { "Order Subtree", "display" }, }; private final static String DEFAULT_SPECIES_COLORS[][] = { - { "BRAFL", "0x00FFFF" }, { "SPHGR", "0x9620F0" }, { "STRPU", "0x9620F0" }, { "CIOIN", "0xFF1CAE" }, - { "CIOSA", "0xFF2CAE" }, { "BOVIN", "0x5C3317" }, { "CANFA", "0x8B2323" }, { "HUMAN", "0xFF2400" }, - { "PANTR", "0xCC2400" }, { "MOUSE", "0xFF7F00" }, { "RAT", "0xFFEF00" }, { "MONDO", "0xEE9A49" }, - { "ORNAN", "0xCD853F" }, { "XENLA", "0x6BAA23" }, { "XENTR", "0x6BAA23" }, { "CHICK", "0xFFC125" }, - { "FUGRU", "0x0000FF" }, { "BRARE", "0x0000DD" }, { "DANRE", "0x0000BB" }, { "TETNG", "0x0000AA" }, - { "ORYLA", "0x000088" }, { "GASAC", "0x000066" }, { "CAEEL", "0x666699" }, { "CAEBR", "0xB0B0B0" }, - { "DROME", "0x663366" }, { "DROPS", "0x996699" }, { "APIME", "0x7A7700" }, { "AEDAE", "0x8C5900" }, - { "TRICA", "0x918E00" }, { "NEMVE", "0x0066CC" }, { "HYDVU", "0x3399FF" }, { "LUBBA", "0xF7B5CB" }, - { "GEOCY", "0xF5A0BD" }, { "AMPQE", "0x009966" }, { "SUBDO", "0xC790B9" }, { "MONBE", "0xFC0FC0" }, - { "DICPU", "0xFFCC33" }, { "DICDI", "0xFFCC00" }, { "ENTHI", "0x5959AB" }, { "ARATH", "0x00FF00" }, - { "POPTR", "0x006400" }, { "VITVI", "0x00CD00" }, { "GLYMA", "0x00FF7F" }, { "ORYSA", "0x008B00" }, - { "ORYSJ", "0x008C00" }, { "SORBI", "0x00EE76" }, { "SELMO", "0x238E23" }, { "PHYPA", "0x09F911" }, - { "OSTLU", "0x7FFF00" }, { "OSTTA", "0x7FFF00" }, { "OSTRC", "0x7FFF00" }, { "MICPU", "0x66CD00" }, - { "MIC99", "0x66CD00" }, { "CHLRE", "0xB3EE3A" }, { "VOLCA", "0xC0FF3E" }, { "CHLSP", "0x6B8E23" }, - { "CYAME", "0xD02090" }, { "YEAST", "0xAAAAAA" }, { "BACFR", "0xFF0000" }, { "BACTN", "0xFFFF00" }, - { "MYXXD", "0x0000FF" }, { "STIAU", "0x00FFFF" }, { "BACOV", "0x8C5900" }, { "BACUN", "0x66CD00" }, - { "PORGI", "0x918E00" } }; + { "BRAFL", "0x00FFFF" }, { "SPHGR", "0x9620F0" }, { "STRPU", "0x9620F0" }, { "CIOIN", "0xFF1CAE" }, + { "CIOSA", "0xFF2CAE" }, { "BOVIN", "0x5C3317" }, { "CANFA", "0x8B2323" }, { "HUMAN", "0xFF2400" }, + { "PANTR", "0xCC2400" }, { "MOUSE", "0xFF7F00" }, { "RAT", "0xFFEF00" }, { "MONDO", "0xEE9A49" }, + { "ORNAN", "0xCD853F" }, { "XENLA", "0x6BAA23" }, { "XENTR", "0x6BAA23" }, { "CHICK", "0xFFC125" }, + { "FUGRU", "0x0000FF" }, { "BRARE", "0x0000DD" }, { "DANRE", "0x0000BB" }, { "TETNG", "0x0000AA" }, + { "ORYLA", "0x000088" }, { "GASAC", "0x000066" }, { "CAEEL", "0x666699" }, { "CAEBR", "0xB0B0B0" }, + { "DROME", "0x663366" }, { "DROPS", "0x996699" }, { "APIME", "0x7A7700" }, { "AEDAE", "0x8C5900" }, + { "TRICA", "0x918E00" }, { "NEMVE", "0x0066CC" }, { "HYDVU", "0x3399FF" }, { "LUBBA", "0xF7B5CB" }, + { "GEOCY", "0xF5A0BD" }, { "AMPQE", "0x009966" }, { "SUBDO", "0xC790B9" }, { "MONBE", "0xFC0FC0" }, + { "DICPU", "0xFFCC33" }, { "DICDI", "0xFFCC00" }, { "ENTHI", "0x5959AB" }, { "ARATH", "0x00FF00" }, + { "POPTR", "0x006400" }, { "VITVI", "0x00CD00" }, { "GLYMA", "0x00FF7F" }, { "ORYSA", "0x008B00" }, + { "ORYSJ", "0x008C00" }, { "SORBI", "0x00EE76" }, { "SELMO", "0x238E23" }, { "PHYPA", "0x09F911" }, + { "OSTLU", "0x7FFF00" }, { "OSTTA", "0x7FFF00" }, { "OSTRC", "0x7FFF00" }, { "MICPU", "0x66CD00" }, + { "MIC99", "0x66CD00" }, { "CHLRE", "0xB3EE3A" }, { "VOLCA", "0xC0FF3E" }, { "CHLSP", "0x6B8E23" }, + { "CYAME", "0xD02090" }, { "YEAST", "0xAAAAAA" }, { "BACFR", "0xFF0000" }, { "BACTN", "0xFFFF00" }, + { "MYXXD", "0x0000FF" }, { "STIAU", "0x00FFFF" }, { "BACOV", "0x8C5900" }, { "BACUN", "0x66CD00" }, + { "PORGI", "0x918E00" } }; final static int display_node_data = 0; final static int collapse_uncollapse = 1; final static int reroot = 2; @@ -114,24 +114,28 @@ public final class Configuration { final static int sort_descendents = 18; final static int get_ext_desc_data = 19; final static int select_nodes = 20; + final static int uncollapse_all = 21; + final static int order_subtree = 22; + // ------------------ // Click-to options // ------------------ final static String display_options[][] = { - { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" }, - { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" }, - { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" }, - { "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" }, - { "Branch Widths", "display", "no" }, { "Domain Architectures", "display", "no" }, - { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" }, - { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" }, - { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" }, - { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" }, - { "Colorize by Annotation", "display", "no" }, { "Seq Symbol", "display", "yes" }, - { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" }, - { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" }, - { "Properties", "display", "no" }, { "Gene Name", "display", "yes" }, - { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" } }; + { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" }, + { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" }, + { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" }, + { "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" }, + { "Branch Widths", "display", "no" }, { "Domain Architectures", "display", "no" }, + { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" }, + { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" }, + { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" }, + { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" }, + { "Colorize by Annotation", "display", "no" }, { "Seq Symbol", "display", "yes" }, + { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" }, + { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" }, + { "Properties", "display", "no" }, { "Gene Name", "display", "yes" }, + { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" } + , { "Taxonomy Rank", "display", "no" }}; final static int display_as_phylogram = 0; final static int show_node_names = 1; final static int show_tax_code = 2; @@ -161,6 +165,8 @@ public final class Configuration { final static int show_gene_names = 26; final static int show_mol_seqs = 27; final static int write_branch_length_values = 28; + final static int show_tax_rank = 29; + static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema"; private static Hashtable _sequence_colors; private static Hashtable _annotation_colors; @@ -179,7 +185,7 @@ public final class Configuration { String config_filename; // This option is selected in the dropdown int default_clickto = Configuration.display_node_data; - String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME; + String default_config_filename = AptxConstants.DEFAULT_CONFIGURATION_FILE_NAME; // -------------- // Color set // -------------- @@ -188,35 +194,33 @@ public final class Configuration { // Fonts // ------- TreeFontSet tree_font_set; - boolean verbose = Constants.VERBOSE_DEFAULT; + boolean verbose = AptxConstants.VERBOSE_DEFAULT; private boolean _abbreviate_scientific_names = false; private boolean _antialias_screen = true; private boolean _background_color_gradient = false; private String _base_font_family_name = ""; private int _base_font_size = -1; - private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT; + private CLADOGRAM_TYPE _cladogram_type = AptxConstants.CLADOGRAM_TYPE_DEFAULT; private boolean _color_labels_same_as_parent_branch = false; private int _default_bootstrap_samples = -1; private NodeFill _default_node_fill = NodeFill.SOLID; private NodeShape _default_node_shape = NodeShape.RECTANGLE; - private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; + private short _default_node_shape_size = AptxConstants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; private SortedMap _display_colors = null; private boolean _display_sequence_relations = false; private boolean _editable = true; - private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN; + private NodeDataField _ext_desc_data_to_return = NodeDataField.UNKNOWN; private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW; private int _frame_x_size; private int _frame_y_size; - private int _graphics_export_x = -1; - private int _graphics_export_y = -1; - private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT; - private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT; - private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT; - private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT; - private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT; - private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_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_background_color = AptxConstants.GUI_BACKGROUND_DEFAULT; + private Color _gui_button_background_color = AptxConstants.BUTTON_BACKGROUND_COLOR_DEFAULT; + private Color _gui_button_border_color = AptxConstants.BUTTON_BORDER_COLOR_DEFAULT; + private Color _gui_button_text_color = AptxConstants.BUTTON_TEXT_COLOR_DEFAULT; + private Color _gui_checkbox_and_button_active_color = AptxConstants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT; + private Color _gui_checkbox_text_color = AptxConstants.CHECKBOX_TEXT_COLOR_DEFAULT; + private Color _gui_menu_background_color = AptxConstants.MENU_BACKGROUND_COLOR_DEFAULT; + private Color _gui_menu_text_color = AptxConstants.MENU_TEXT_COLOR_DEFAULT; private boolean _hide_controls_and_menus = false; private boolean _internal_number_are_confidence_for_nh_parsing = false; private String _label_for_get_ext_descendents_data = ""; @@ -226,8 +230,8 @@ public final class Configuration { private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT; private boolean _nh_parsing_replace_underscores = false; private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL; - private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT; - 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 = AptxConstants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT; + private short _number_of_digits_after_comma_for_confidence_values = AptxConstants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT; private short _ov_max_height = 80; private short _ov_max_width = 80; private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT; @@ -235,7 +239,7 @@ public final class Configuration { private File _path_to_local_mafft = null; private File _path_to_local_raxml = null; private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR; - private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT; + private float _print_line_width = AptxConstants.PDF_LINE_WIDTH_DEFAULT; private boolean _show_annotation_ref_source = true; private boolean _show_default_node_shapes_external = false; private boolean _show_default_node_shapes_for_marked_nodes = false; @@ -246,7 +250,7 @@ public final class Configuration { private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.NO; private UI _ui = UI.UNKNOWN; private boolean _use_tabbed_display = false; - private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT; + private boolean _validate_against_phyloxml_xsd_schema = AptxConstants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT; private Color _vector_data_min_color = Color.BLUE; private Color _vector_data_max_color = Color.YELLOW; private Color _vector_data_mean_color = Color.WHITE; @@ -255,22 +259,19 @@ public final class Configuration { private boolean _line_up_renderable_node_data = true; private boolean _right_align_domains = false; private boolean _allow_thick_strokes = false; + private boolean _could_read_config_file = false; static { - for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) { + for( final String font_name : AptxConstants.DEFAULT_FONT_CHOICES ) { if ( Arrays.binarySearch( AptxUtil.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 ]; + DEFAULT_FONT_FAMILY = AptxConstants.DEFAULT_FONT_CHOICES[ AptxConstants.DEFAULT_FONT_CHOICES.length - 1 ]; } } - static String getDefaultFontFamilyName() { - return DEFAULT_FONT_FAMILY; - } - public Configuration() { this( null, false, false, false ); } @@ -282,6 +283,7 @@ public final class Configuration { else { config_filename = cf; } + _could_read_config_file = false; setDisplayColors( new TreeMap() ); config_filename = config_filename.trim(); URL u = null; @@ -294,16 +296,17 @@ public final class Configuration { final BufferedReader bf = new BufferedReader( isr ); readConfig( bf ); bf.close(); - ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url [" + ForesterUtil.programMessage( AptxConstants.PRG_NAME, "successfully read from configuration url [" + config_filename + "]" ); + _could_read_config_file = true; } catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from [" + ForesterUtil.printWarningMessage( AptxConstants.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 [" + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "cannot find or open configuration url [" + config_filename + "]" ); } } @@ -318,175 +321,32 @@ public final class Configuration { final BufferedReader bf = new BufferedReader( new FileReader( f ) ); readConfig( bf ); bf.close(); + _could_read_config_file = true; } catch ( final Exception e ) { if ( verbose ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from [" + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "failed to read configuration from [" + config_filename + "]: " + e ); } } } else { if ( verbose ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file [" + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "cannot find or open configuration file [" + config_filename + "]" ); } } } } - 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( "sort_descendants" ) ) { - index = Configuration.sort_descendents; - } - else if ( name.equals( "get_ext_descendents_data" ) ) { - index = Configuration.get_ext_desc_data; - } - 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_pdb_web" ) ) { - index = Configuration.open_pdb_web; - } - else if ( name.equals( "open_tax_web" ) ) { - index = Configuration.open_tax_web; - } - else if ( name.equals( "blast" ) ) { - index = Configuration.blast; - } - 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( "select_nodes" ) ) { - index = Configuration.select_nodes; - } - 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( "change_node_font" ) ) { - index = Configuration.change_node_font; - } - else if ( name.equals( "color_node_font" ) ) { - index = Configuration.color_node_font; - } - else if ( name.equals( "color_subtree" ) ) { - index = Configuration.color_subtree; - } - return index; - } - - int getClickToOptionsCount() { - return clickto_options.length; - } - - String getClickToTitle( final int which ) { - return clickto_options[ which ][ 0 ]; - } - public int getDefaultBootstrapSamples() { return _default_bootstrap_samples; } - int getDefaultDisplayClicktoOption() { - return default_clickto; - } - public NodeFill getDefaultNodeFill() { return _default_node_fill; } @@ -499,22 +359,7 @@ public final class Configuration { return _default_node_shape_size; } - 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; - } - - public NODE_DATA getExtDescNodeDataToReturn() { + public NodeDataField getExtDescNodeDataToReturn() { return _ext_desc_data_to_return; } @@ -530,502 +375,509 @@ public final class Configuration { return _frame_y_size; } - int getGraphicsExportX() { - return _graphics_export_x; + public String getLabelForGetExtDescendentsData() { + return _label_for_get_ext_descendents_data; } - int getGraphicsExportY() { - return _graphics_export_y; + public File getPathToLocalFastme() { + return _path_to_local_fastme; } - Color getGuiBackgroundColor() { - return _gui_background_color; + public File getPathToLocalMafft() { + return _path_to_local_mafft; } - Color getGuiButtonBackgroundColor() { - return _gui_button_background_color; + public File getPathToLocalRaxml() { + return _path_to_local_raxml; } - Color getGuiButtonBorderColor() { - return _gui_button_border_color; + public double getVectorDataHeight() { + return _vector_data_height; } - Color getGuiButtonTextColor() { - return _gui_button_text_color; + public Color getVectorDataMaxColor() { + return _vector_data_max_color; } - Color getGuiCheckboxAndButtonActiveColor() { - return _gui_checkbox_and_button_active_color; + public Color getVectorDataMeanColor() { + return _vector_data_mean_color; } - Color getGuiCheckboxTextColor() { - return _gui_checkbox_text_color; + public Color getVectorDataMinColor() { + return _vector_data_min_color; } - Color getGuiMenuBackgroundColor() { - return _gui_menu_background_color; + public int getVectorDataWidth() { + return _vector_data_width; } - Color getGuiMenuTextColor() { - return _gui_menu_text_color; + public boolean isAbbreviateScientificTaxonNames() { + return _abbreviate_scientific_names; } - public String getLabelForGetExtDescendentsData() { - return _label_for_get_ext_descendents_data; + public boolean isAllowThickStrokes() { + return _allow_thick_strokes; } - int getMaxBaseFontSize() { - return _max_base_font_size; + public boolean isBackgroundColorGradient() { + return _background_color_gradient; } - int getMinBaseFontSize() { - return _min_base_font_size; + public boolean isColorByTaxonomicGroup() { + return false; } - double getMinConfidenceValue() { - return _min_confidence_value; + public boolean isColorLabelsSameAsParentBranch() { + return _color_labels_same_as_parent_branch; } - NODE_LABEL_DIRECTION getNodeLabelDirection() { - return _node_label_direction; + final public boolean isLineUpRendarableNodeData() { + return _line_up_renderable_node_data; } - short getNumberOfDigitsAfterCommaForBranchLengthValues() { - return _number_of_digits_after_comma_for_branch_length_values; + public boolean isMidpointReroot() { + return _midpoint_root; } - short getNumberOfDigitsAfterCommaForConfidenceValues() { - return _number_of_digits_after_comma_for_confidence_values; + final public boolean isRightLineUpDomains() { + return _right_align_domains; } - short getOvMaxHeight() { - return _ov_max_height; + public boolean isShowAnnotationRefSource() { + return _show_annotation_ref_source; } - short getOvMaxWidth() { - return _ov_max_width; + public boolean isShowDefaultNodeShapesExternal() { + return _show_default_node_shapes_external; } - OVERVIEW_PLACEMENT_TYPE getOvPlacement() { - return _ov_placement; + public boolean isShowDefaultNodeShapesForMarkedNodes() { + return _show_default_node_shapes_for_marked_nodes; } - public File getPathToLocalFastme() { - return _path_to_local_fastme; + public boolean isShowDefaultNodeShapesInternal() { + return _show_default_node_shapes_internal; } - public File getPathToLocalMafft() { - return _path_to_local_mafft; + public boolean isShowDomainLabels() { + return _show_domain_labels; } - public File getPathToLocalRaxml() { - return _path_to_local_raxml; + public void putDisplayColors( final String key, final Color color ) { + getDisplayColors().put( key, color ); } - PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() { - return _phylogeny_graphics_type; - } - - float getPrintLineWidth() { - return _print_line_width; + public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) { + _abbreviate_scientific_names = abbreviate_scientific_names; } - Hashtable getSequenceColors() { - if ( _sequence_colors == null ) { - _sequence_colors = new Hashtable(); - } - return _sequence_colors; + public void setAddTaxonomyImagesCB( final boolean b ) { + display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no"; } - Hashtable getSpeciesColors() { - if ( _species_colors == null ) { - initSpeciesColors(); - } - return _species_colors; + public void setBackgroundColorGradient( final boolean background_color_gradient ) { + _background_color_gradient = background_color_gradient; } - final TAXONOMY_EXTRACTION getTaxonomyExtraction() { - return _taxonomy_extraction; + public void setBaseFontFamilyName( final String base_font_family_name ) { + _base_font_family_name = base_font_family_name; } - public double getVectorDataHeight() { - return _vector_data_height; + public void setBaseFontSize( final int base_font_size ) { + _base_font_size = base_font_size; } - public Color getVectorDataMaxColor() { - return _vector_data_max_color; + public void setColorizeBranches( final boolean b ) { + display_options[ use_style ][ 2 ] = b ? "yes" : "no"; } - public Color getVectorDataMeanColor() { - return _vector_data_mean_color; + public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) { + _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch; } - public Color getVectorDataMinColor() { - return _vector_data_min_color; + public void setDefaultNodeFill( final NodeFill default_node_fill ) { + _default_node_fill = default_node_fill; } - public int getVectorDataWidth() { - return _vector_data_width; + public void setDefaultNodeShape( final NodeShape default_node_shape ) { + _default_node_shape = default_node_shape; } - private final void initSpeciesColors() { - _species_colors = new Hashtable(); - for( final String[] s : DEFAULT_SPECIES_COLORS ) { - _species_colors.put( s[ 0 ], Color.decode( s[ 1 ] ) ); - } + public void setDefaultNodeShapeSize( final short default_node_shape_size ) { + _default_node_shape_size = default_node_shape_size; } - public boolean isAbbreviateScientificTaxonNames() { - return _abbreviate_scientific_names; + public void setDisplayAsPhylogram( final boolean b ) { + display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no"; } - boolean isAntialiasScreen() { - if ( ForesterUtil.isMac() ) { - //Apple Macintosh graphics are slow, turn off anti-alias. - return false; - } - return _antialias_screen; + public void setDisplayColors( final SortedMap display_colors ) { + _display_colors = display_colors; } - public boolean isBackgroundColorGradient() { - return _background_color_gradient; + public void setDisplayConfidenceValues( final boolean b ) { + display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no"; } - public boolean isColorByTaxonomicGroup() { - return false; + public void setDisplayGeneNames( final boolean b ) { + display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no"; } - public boolean isColorLabelsSameAsParentBranch() { - return _color_labels_same_as_parent_branch; + public void setDisplayInternalData( final boolean b ) { + display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no"; } - /** - * Convenience method. - * - * @return true if value in configuration file was 'yes' - */ - boolean isDrawAsPhylogram() { - return doCheckOption( display_as_phylogram ); + public void setDisplayMultipleSequenceAlignment( final boolean b ) { + display_options[ show_mol_seqs ][ 2 ] = b ? "yes" : "no"; } - boolean isEditable() { - return _editable; + public void setDisplayNodeNames( final boolean b ) { + display_options[ show_node_names ][ 2 ] = b ? "yes" : "no"; } - /** - * Only used by ArchaeoptryxE. - * - */ - boolean isHideControlPanelAndMenubar() { - return _hide_controls_and_menus; + public void setDisplaySequenceAcc( final boolean b ) { + display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no"; } - boolean isInternalNumberAreConfidenceForNhParsing() { - return _internal_number_are_confidence_for_nh_parsing; + public void setDisplaySequenceNames( final boolean b ) { + display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no"; } - final public boolean isLineUpRendarableNodeData() { - return _line_up_renderable_node_data; + public void setDisplaySequenceRelations( final boolean display_sequence_relations ) { + _display_sequence_relations = display_sequence_relations; } - public boolean isMidpointReroot() { - return _midpoint_root; + public void setDisplaySequenceSymbols( final boolean b ) { + display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no"; } - boolean isReplaceUnderscoresInNhParsing() { - return _nh_parsing_replace_underscores; + public void setDisplayTaxonomyCode( final boolean b ) { + display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no"; } - - final public boolean isRightLineUpDomains() { - return _right_align_domains; + + public void setDisplayTaxonomyRank( final boolean b ) { + display_options[ show_tax_rank ][ 2 ] = b ? "yes" : "no"; } - public boolean isShowAnnotationRefSource() { - return _show_annotation_ref_source; + public void setDisplayTaxonomyCommonNames( final boolean b ) { + display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no"; } - public boolean isShowDefaultNodeShapesExternal() { - return _show_default_node_shapes_external; + public void setDisplayTaxonomyImages( final boolean b ) { + display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no"; } - public boolean isShowDefaultNodeShapesForMarkedNodes() { - return _show_default_node_shapes_for_marked_nodes; + public void setDisplayTaxonomyScientificNames( final boolean b ) { + display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no"; } - public boolean isShowDefaultNodeShapesInternal() { - return _show_default_node_shapes_internal; + public void setDynamicallyHideData( final boolean b ) { + display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no"; } - public boolean isShowDomainLabels() { - return _show_domain_labels; + public void setExtDescNodeDataToReturn( final NodeDataField ext_desc_data_to_return ) { + _ext_desc_data_to_return = ext_desc_data_to_return; } - boolean isShowOverview() { - return _show_overview; + public void setFrameXSize( final int frame_x_size ) { + _frame_x_size = frame_x_size; } - boolean isShowScale() { - return _show_scale; + public void setFrameYSize( final int frame_y_size ) { + _frame_y_size = frame_y_size; } - final boolean isUseNativeUI() { - if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) { - _ui = UI.NATIVE; - } - return _ui == UI.NATIVE; + final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) { + _line_up_renderable_node_data = line_up_renderable_node_data; } - /** - * Only used by ArchaeoptryxE. - * - */ - boolean isUseTabbedDisplay() { - return _use_tabbed_display; + public void setMidpointReroot( final boolean midpoint_root ) { + _midpoint_root = midpoint_root; } - boolean isValidatePhyloXmlAgainstSchema() { - return _validate_against_phyloxml_xsd_schema; + public void setMinConfidenceValue( final double min_confidence_value ) { + _min_confidence_value = min_confidence_value; } - 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; - } + public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) { + _node_label_direction = node_label_direction; } - private double parseDouble( final String str ) { - double d = 0.0; - try { - d = Double.parseDouble( str.trim() ); - } - catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" ); - d = 0.0; - } - return d; + public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) { + _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values; } - private float parseFloat( final String str ) { - float f = 0.0f; - try { - f = Float.parseFloat( str.trim() ); - } - catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" ); - f = 0.0f; - } - return f; + public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) { + _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values; } - private int parseInt( final String str ) { - int i = -1; - try { - i = Integer.parseInt( str.trim() ); - } - catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" ); - i = -1; - } - return i; + public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) { + _phylogeny_graphics_type = phylogeny_graphics_type; } - private short parseShort( final String str ) { - short i = -1; - try { - i = Short.parseShort( str.trim() ); - } - catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" ); - i = -1; - } - return i; + public void setPrintLineWidth( final float print_line_width ) { + _print_line_width = print_line_width; } - 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( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) { - setBaseFontFamilyName( font ); - break; - } - } + public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) { + _nh_parsing_replace_underscores = nh_parsing_replace_underscores; } - public void putDisplayColors( final String key, final Color color ) { - getDisplayColors().put( key, color ); + final public void setRightLineUpDomains( final boolean right_align_domains ) { + _right_align_domains = right_align_domains; } - /** - * 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 ); + public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) { + _show_default_node_shapes_external = show_default_node_shapes_external; } - public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) { - _abbreviate_scientific_names = abbreviate_scientific_names; + public void setShowDefaultNodeShapesForMarkedNodes( final boolean show_default_node_shapes_for_marked_nodes ) { + _show_default_node_shapes_for_marked_nodes = show_default_node_shapes_for_marked_nodes; } - public void setAddTaxonomyImagesCB( final boolean b ) { - display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no"; - } - - 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; - } - - public void setBaseFontFamilyName( final String base_font_family_name ) { - _base_font_family_name = base_font_family_name; + public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) { + _show_default_node_shapes_internal = show_default_node_shapes_internal; } - public void setBaseFontSize( final int base_font_size ) { - _base_font_size = base_font_size; + public void setShowDomainLabels( final boolean show_domain_labels ) { + _show_domain_labels = show_domain_labels; } - private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) { - _cladogram_type = cladogram_type; + public void setShowScale( final boolean show_scale ) { + _show_scale = show_scale; } - public void setColorizeBranches( final boolean b ) { + public void setUseStyle( final boolean b ) { display_options[ use_style ][ 2 ] = b ? "yes" : "no"; } - public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) { - _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch; - } - - private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) { - _default_bootstrap_samples = default_bootstrap_samples; - } - - public void setDefaultNodeFill( final NodeFill default_node_fill ) { - _default_node_fill = default_node_fill; - } - - public void setDefaultNodeShape( final NodeShape default_node_shape ) { - _default_node_shape = default_node_shape; - } - - public void setDefaultNodeShapeSize( final short default_node_shape_size ) { - _default_node_shape_size = default_node_shape_size; - } - - public void setDisplayAsPhylogram( final boolean b ) { - display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplayColors( final SortedMap display_colors ) { - _display_colors = display_colors; - } - - public void setDisplayConfidenceValues( final boolean b ) { - display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplayGeneNames( final boolean b ) { - display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no"; + private int getClickToIndex( final String name ) { + int index = -1; + if ( name.equals( "edit_info" ) ) { + index = Configuration.display_node_data; + ForesterUtil + .printWarningMessage( AptxConstants.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( "uncollapse_all" ) ) { + index = Configuration.uncollapse_all; + } + 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( "order_subtree" ) ) { + index = Configuration.order_subtree; + } + else if ( name.equals( "sort_descendants" ) ) { + index = Configuration.sort_descendents; + } + else if ( name.equals( "get_ext_descendents_data" ) ) { + index = Configuration.get_ext_desc_data; + } + else if ( name.equals( "display_sequences" ) ) { + ForesterUtil + .printWarningMessage( AptxConstants.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_pdb_web" ) ) { + index = Configuration.open_pdb_web; + } + else if ( name.equals( "open_tax_web" ) ) { + index = Configuration.open_tax_web; + } + else if ( name.equals( "blast" ) ) { + index = Configuration.blast; + } + 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( "select_nodes" ) ) { + index = Configuration.select_nodes; + } + else if ( name.equals( "display_node_popup" ) ) { + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, + "configuration key [display_node_popup] is deprecated" ); + return DEPRECATED; + } + else if ( name.equals( "custom_option" ) ) { + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "configuration key [custom_option] is deprecated" ); + return DEPRECATED; + } + else if ( name.equals( "color_subtree" ) ) { + index = Configuration.color_subtree; + } + else if ( name.equals( "change_node_font" ) ) { + index = Configuration.change_node_font; + } + else if ( name.equals( "color_node_font" ) ) { + index = Configuration.color_node_font; + } + else if ( name.equals( "color_subtree" ) ) { + index = Configuration.color_subtree; + } + return index; } - public void setDisplayInternalData( final boolean b ) { - display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no"; + private final void initSpeciesColors() { + _species_colors = new Hashtable(); + for( final String[] s : DEFAULT_SPECIES_COLORS ) { + _species_colors.put( s[ 0 ], Color.decode( s[ 1 ] ) ); + } } - public void setDisplayNodeNames( final boolean b ) { - display_options[ show_node_names ][ 2 ] = b ? "yes" : "no"; + 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( AptxConstants.PRG_NAME, "could not parse boolean value from [" + str + "]" ); + return false; + } } - public void setDisplaySequenceAcc( final boolean b ) { - display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no"; + private double parseDouble( final String str ) { + double d = 0.0; + try { + d = Double.parseDouble( str.trim() ); + } + catch ( final Exception e ) { + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse double from [" + str + "]" ); + d = 0.0; + } + return d; } - public void setDisplaySequenceNames( final boolean b ) { - display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no"; + private float parseFloat( final String str ) { + float f = 0.0f; + try { + f = Float.parseFloat( str.trim() ); + } + catch ( final Exception e ) { + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse float from [" + str + "]" ); + f = 0.0f; + } + return f; } - public void setDisplaySequenceRelations( final boolean display_sequence_relations ) { - _display_sequence_relations = display_sequence_relations; + private int parseInt( final String str ) { + int i = -1; + try { + i = Integer.parseInt( str.trim() ); + } + catch ( final Exception e ) { + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse integer from [" + str + "]" ); + i = -1; + } + return i; } - public void setDisplaySequenceSymbols( final boolean b ) { - display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no"; + private short parseShort( final String str ) { + short i = -1; + try { + i = Short.parseShort( str.trim() ); + } + catch ( final Exception e ) { + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse short from [" + str + "]" ); + i = -1; + } + return i; } - public void setDisplayTaxonomyCode( final boolean b ) { - display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no"; + 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( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) { + setBaseFontFamilyName( font ); + break; + } + } } - public void setDisplayTaxonomyCommonNames( final boolean b ) { - display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no"; + /** + * 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 ); } - public void setDisplayTaxonomyImages( final boolean b ) { - display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no"; + private void setAntialiasScreen( final boolean antialias_screen ) { + _antialias_screen = antialias_screen; } - public void setDisplayTaxonomyScientificNames( final boolean b ) { - display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no"; + private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) { + _cladogram_type = cladogram_type; } - public void setDynamicallyHideData( final boolean b ) { - display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no"; + private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) { + _default_bootstrap_samples = default_bootstrap_samples; } private void setEditable( final boolean editable ) { _editable = editable; } - public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) { - _ext_desc_data_to_return = ext_desc_data_to_return; - } - private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) { _ext_node_data_return_on = ext_node_data_return_on; } - public void setFrameXSize( final int frame_x_size ) { - _frame_x_size = frame_x_size; - } + //private void setGraphicsExportX( final int graphics_export_x ) { + // _graphics_export_x = graphics_export_x; + //} - public void setFrameYSize( final int frame_y_size ) { - _frame_y_size = frame_y_size; - } - - 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 setGraphicsExportY( final int graphics_export_y ) { + // _graphics_export_y = graphics_export_y; + //} 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; @@ -1044,8 +896,8 @@ public final class Configuration { 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]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "invalid value [" + clickto_name + + "] for [default_click_to]" ); default_clickto = 0; } else if ( default_clickto == DEPRECATED ) { @@ -1064,8 +916,8 @@ public final class Configuration { _ui = UI.UNKNOWN; } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str - + "]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse yes/no/? value from [" + my_str + + "]" ); _ui = UI.UNKNOWN; } } @@ -1103,8 +955,8 @@ public final class Configuration { } else { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str - + "] for [phylogeny_graphics_type]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str + + "] for [phylogeny_graphics_type]" ); } } else if ( key.equals( "min_confidence_value" ) ) { @@ -1136,20 +988,6 @@ public final class Configuration { setMaxBaseFontSize( i ); } } - else if ( key.equals( "graphics_export_x" ) ) { - final String str = ( ( String ) st.nextElement() ).trim(); - final int i = parseInt( str ); - if ( i > 0 ) { - setGraphicsExportX( i ); - } - } - else if ( key.equals( "graphics_export_y" ) ) { - final String str = ( ( String ) st.nextElement() ).trim(); - final int i = parseInt( str ); - if ( i > 0 ) { - setGraphicsExportY( i ); - } - } else if ( key.equals( "pdf_export_line_width" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final float f = parseFloat( str ); @@ -1157,8 +995,8 @@ public final class Configuration { setPrintLineWidth( f ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "value for [pdf_export_line_width] cannot be zero or negative" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, + "value for [pdf_export_line_width] cannot be zero or negative" ); } } else if ( key.equals( "window_initial_size_x" ) ) { @@ -1183,8 +1021,8 @@ public final class Configuration { } else { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "value for [default_number_of_bootstrap_resamples] cannot be negative" ); + .printWarningMessage( AptxConstants.PRG_NAME, + "value for [default_number_of_bootstrap_resamples] cannot be negative" ); } } else if ( key.equals( "mafft_local" ) ) { @@ -1231,22 +1069,14 @@ public final class Configuration { 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 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.LINED_UP.toString() ) ) { + setCladogramType( Options.CLADOGRAM_TYPE.LINED_UP ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str - + "] for [cladogram_type]" ); + ForesterUtil.printWarningMessage( AptxConstants.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() ); } @@ -1277,8 +1107,8 @@ public final class Configuration { } else { setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT ); - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str - + "] for [overview_placement_type]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str + + "] for [overview_placement_type]" ); } } else if ( key.equals( "node_label_direction" ) ) { @@ -1291,8 +1121,8 @@ public final class Configuration { } else { setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL ); - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str - + "] for [node_label_direction]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str + + "] for [node_label_direction]" ); } } else if ( key.equals( "branch_length_value_digits" ) ) { @@ -1301,8 +1131,8 @@ public final class Configuration { setNumberOfDigitsAfterCommaForBranchLengthValue( i ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i - + "] for [branch_length_value_digits]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "illegal value [" + i + + "] for [branch_length_value_digits]" ); } } else if ( key.equals( "confidence_value_digits" ) ) { @@ -1311,8 +1141,8 @@ public final class Configuration { setNumberOfDigitsAfterCommaForConfidenceValues( i ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i - + "] for [confidence_value_digits]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "illegal value [" + i + + "] for [confidence_value_digits]" ); } } else if ( key.equals( "allow_editing" ) ) { @@ -1325,8 +1155,8 @@ public final class Configuration { final boolean r = parseBoolean( ( String ) st.nextElement() ); if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "attempt to extract taxonomies and replace underscores at the same time" ); + .printWarningMessage( AptxConstants.PRG_NAME, + "attempt to extract taxonomies and replace underscores at the same time" ); } else { setReplaceUnderscoresInNhParsing( r ); @@ -1348,15 +1178,15 @@ public final class Configuration { } else { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "unknown value for \"taxonomy_extraction_in_nh_parsing\": " - + s - + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" ); + .printWarningMessage( AptxConstants.PRG_NAME, + "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + + s + + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" ); } if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "attempt to extract taxonomies and replace underscores at the same time" ); + .printWarningMessage( AptxConstants.PRG_NAME, + "attempt to extract taxonomies and replace underscores at the same time" ); } } else if ( key.equals( "internal_labels_are_confidence_values" ) ) { @@ -1411,8 +1241,8 @@ public final class Configuration { setDefaultNodeFill( NodeFill.SOLID ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str - + "] for [default_node_fill]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + fill_str + + "] for [default_node_fill]" ); } } else if ( key.equals( "default_node_shape" ) ) { @@ -1424,76 +1254,66 @@ public final class Configuration { setDefaultNodeShape( NodeShape.RECTANGLE ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str - + "] for [default_node_shape]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + shape_str + + "] for [default_node_shape]" ); } } else if ( key.equals( "midpoint_reroot" ) ) { setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) ); } - else if ( key.equals( "ext_descendents_data_to_return" ) ) { + else if ( key.equals( "list_node_data_field" ) || key.equals( "ext_descendents_data_to_return" ) ) { final String s = ( ( String ) st.nextElement() ).trim(); if ( s.equalsIgnoreCase( "node_name" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME ); + setExtDescNodeDataToReturn( NodeDataField.NODE_NAME ); } else if ( s.equalsIgnoreCase( "sequence_acc" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC ); + setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_ACC ); } else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ); - } - else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ ); + setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA ); } else if ( s.equalsIgnoreCase( "sequence_name" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME ); + setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_NAME ); } else if ( s.equalsIgnoreCase( "gene_name" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.GENE_NAME ); + setExtDescNodeDataToReturn( NodeDataField.GENE_NAME ); } else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL ); + setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_SYMBOL ); } else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME ); + setExtDescNodeDataToReturn( NodeDataField.TAXONOMY_SCIENTIFIC_NAME ); } else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE ); - } - else if ( s.equalsIgnoreCase( "taxonomy_common_name" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_COMM0N_NAME ); + setExtDescNodeDataToReturn( NodeDataField.TAXONOMY_CODE ); } else if ( s.equalsIgnoreCase( "user_selected" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN ); + setExtDescNodeDataToReturn( NodeDataField.UNKNOWN ); } else if ( s.equalsIgnoreCase( "domains" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.DOMAINS_ALL ); + setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL ); } else if ( s.equalsIgnoreCase( "domains_collapsed" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.DOMAINS_COLLAPSED_PER_PROTEIN ); + setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ); } else if ( s.equalsIgnoreCase( "seq_annotations" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.SEQ_ANNOTATIONS ); + setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS ); } else if ( s.equalsIgnoreCase( "go_term_ids" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.GO_TERM_IDS ); + setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s - + "] for [ext_descendents_data_to_return]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + s + + "] for [ext_descendents_data_to_return]" ); } } - else if ( key.equals( "label_for_get_ext_descendents_data" ) ) { + else if ( key.equals( "list_node_data_custom_label" ) || key.equals( "label_for_get_ext_descendents_data" ) ) { final String s = ( ( String ) st.nextElement() ).trim(); - if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s - + "] for [label_for_get_ext_descendents_data]" ); - } - else { + if ( !ForesterUtil.isEmpty( s ) && ( s.length() > 1 ) ) { setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) ); } } - else if ( key.equals( "ext_descendents_data_to_return_on" ) ) { + else if ( key.equals( "list_node_data_in" ) || key.equals( "ext_descendents_data_to_return_on" ) ) { final String s = ( ( String ) st.nextElement() ).trim().toLowerCase(); if ( s.equals( "console" ) ) { setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE ); @@ -1505,8 +1325,8 @@ public final class Configuration { setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s - + "] for [ext_descendents_data_to_return_on]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + s + + "] for [ext_descendents_data_to_return_on]" ); } } else if ( key.equals( "vector_data_min_color" ) ) { @@ -1560,6 +1380,9 @@ public final class Configuration { else if ( key.equals( "show_taxonomy_code" ) ) { key_index = Configuration.show_tax_code; } + else if ( key.equals( "show_taxonomy_rank" ) ) { + key_index = Configuration.show_tax_rank; + } else if ( key.equals( "write_confidence_values" ) ) { key_index = Configuration.write_confidence_values; } @@ -1575,8 +1398,8 @@ public final class Configuration { else if ( key.equals( "color_branches" ) ) { key_index = Configuration.use_style; ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" ); + .printWarningMessage( AptxConstants.PRG_NAME, + "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" ); } else if ( key.equals( "width_branches" ) ) { key_index = Configuration.width_branches; @@ -1655,7 +1478,7 @@ public final class Configuration { // Deprecated. } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: " + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown click-to option: " + click_to_name ); } } @@ -1672,144 +1495,309 @@ public final class Configuration { } else if ( key.equals( "annotation_color" ) ) { getAnnotationColors() - .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); + .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" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, + "configuration key [function_color] is deprecated" ); } else if ( key.equals( DISPLAY_COLOR_KEY ) ) { putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key - + "] in: " + config_filename ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown configuration key [" + key + + "] in: " + config_filename ); } } } - else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: " - + config_filename ); + else { + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown configuration key [" + key + "] in: " + + config_filename ); + } + } + + private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) { + _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data; + } + + private void setMaxBaseFontSize( final int max_base_font_size ) { + _max_base_font_size = max_base_font_size; + } + + private void setMinBaseFontSize( final int min_base_font_size ) { + _min_base_font_size = min_base_font_size; + } + + 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; + } + + private void setPathToLocalFastme( final File path_to_local_fastme ) { + _path_to_local_fastme = path_to_local_fastme; + } + + private void setPathToLocalMafft( final File path_to_local_mafft ) { + _path_to_local_mafft = path_to_local_mafft; + } + + private void setPathToLocalRaxml( final File path_to_local_raxml ) { + _path_to_local_raxml = path_to_local_raxml; + } + + private void setShowAnnotationRefSource( final boolean b ) { + _show_annotation_ref_source = b; + } + + private void setShowOverview( final boolean show_overview ) { + _show_overview = show_overview; + } + + private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) { + _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema; + } + + 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; + } + + int getBaseFontSize() { + return _base_font_size; + } + + CLADOGRAM_TYPE getCladogramType() { + return _cladogram_type; + } + + 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; } - private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) { - _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data; + + Color getGuiBackgroundColor() { + return _gui_background_color; } - final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) { - _line_up_renderable_node_data = line_up_renderable_node_data; + Color getGuiButtonBackgroundColor() { + return _gui_button_background_color; } - private void setMaxBaseFontSize( final int max_base_font_size ) { - _max_base_font_size = max_base_font_size; + Color getGuiButtonBorderColor() { + return _gui_button_border_color; } - public void setMidpointReroot( final boolean midpoint_root ) { - _midpoint_root = midpoint_root; + Color getGuiButtonTextColor() { + return _gui_button_text_color; } - private void setMinBaseFontSize( final int min_base_font_size ) { - _min_base_font_size = min_base_font_size; + Color getGuiCheckboxAndButtonActiveColor() { + return _gui_checkbox_and_button_active_color; } - public void setMinConfidenceValue( final double min_confidence_value ) { - _min_confidence_value = min_confidence_value; + Color getGuiCheckboxTextColor() { + return _gui_checkbox_text_color; } - public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) { - _node_label_direction = node_label_direction; + Color getGuiMenuBackgroundColor() { + return _gui_menu_background_color; } - public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) { - _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values; + Color getGuiMenuTextColor() { + return _gui_menu_text_color; } - public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) { - _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values; + int getMaxBaseFontSize() { + return _max_base_font_size; } - private void setOvMaxHeight( final short ov_max_height ) { - _ov_max_height = ov_max_height; + int getMinBaseFontSize() { + return _min_base_font_size; } - private void setOvMaxWidth( final short ov_max_width ) { - _ov_max_width = ov_max_width; + double getMinConfidenceValue() { + return _min_confidence_value; } - private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) { - _ov_placement = ov_placement; + NODE_LABEL_DIRECTION getNodeLabelDirection() { + return _node_label_direction; } - private void setPathToLocalFastme( final File path_to_local_fastme ) { - _path_to_local_fastme = path_to_local_fastme; + short getNumberOfDigitsAfterCommaForBranchLengthValues() { + return _number_of_digits_after_comma_for_branch_length_values; } - private void setPathToLocalMafft( final File path_to_local_mafft ) { - _path_to_local_mafft = path_to_local_mafft; + short getNumberOfDigitsAfterCommaForConfidenceValues() { + return _number_of_digits_after_comma_for_confidence_values; } - private void setPathToLocalRaxml( final File path_to_local_raxml ) { - _path_to_local_raxml = path_to_local_raxml; + short getOvMaxHeight() { + return _ov_max_height; } - public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) { - _phylogeny_graphics_type = phylogeny_graphics_type; + short getOvMaxWidth() { + return _ov_max_width; } - public void setPrintLineWidth( final float print_line_width ) { - _print_line_width = print_line_width; + OVERVIEW_PLACEMENT_TYPE getOvPlacement() { + return _ov_placement; } - public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) { - _nh_parsing_replace_underscores = nh_parsing_replace_underscores; + PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() { + return _phylogeny_graphics_type; } - final public void setRightLineUpDomains( final boolean right_align_domains ) { - _right_align_domains = right_align_domains; + float getPrintLineWidth() { + return _print_line_width; } - private void setShowAnnotationRefSource( final boolean b ) { - _show_annotation_ref_source = b; + Hashtable getSequenceColors() { + if ( _sequence_colors == null ) { + _sequence_colors = new Hashtable(); + } + return _sequence_colors; } - public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) { - _show_default_node_shapes_external = show_default_node_shapes_external; + Hashtable getSpeciesColors() { + if ( _species_colors == null ) { + initSpeciesColors(); + } + return _species_colors; } - public void setShowDefaultNodeShapesForMarkedNodes( final boolean show_default_node_shapes_for_marked_nodes ) { - _show_default_node_shapes_for_marked_nodes = show_default_node_shapes_for_marked_nodes; + final TAXONOMY_EXTRACTION getTaxonomyExtraction() { + return _taxonomy_extraction; } - public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) { - _show_default_node_shapes_internal = show_default_node_shapes_internal; + boolean isAntialiasScreen() { + return _antialias_screen; } - public void setShowDomainLabels( final boolean show_domain_labels ) { - _show_domain_labels = show_domain_labels; + /** + * Convenience method. + * + * @return true if value in configuration file was 'yes' + */ + boolean isDrawAsPhylogram() { + return doCheckOption( display_as_phylogram ); } - private void setShowOverview( final boolean show_overview ) { - _show_overview = show_overview; + boolean isEditable() { + return _editable; } - public void setShowScale( final boolean show_scale ) { - _show_scale = show_scale; + /** + * 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 isShowOverview() { + return _show_overview; + } + + boolean isShowScale() { + return _show_scale; + } + + final boolean isUseNativeUI() { + if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) { + _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; } final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) { _taxonomy_extraction = taxonomy_extraction; } - public void setUseStyle( final boolean b ) { - display_options[ use_style ][ 2 ] = b ? "yes" : "no"; + static String getDefaultFontFamilyName() { + return DEFAULT_FONT_FAMILY; } - private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) { - _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema; + public boolean isCouldReadConfigFile() { + return _could_read_config_file; } - public boolean isAllowThickStrokes() { - return _allow_thick_strokes; - } + }