X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=adb0f402486c57dfa4cee9a4cd0ccb38dd76204c;hb=a32f4076b5b309b4dcc0852d6283a2bd18785f28;hp=342fcdb7ac73242c40ce8ce50e6dbcf77a517fe0;hpb=724bd2bd4cbc5b3ea5ec856d156fa37b93b3d0fb;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 342fcdb..adb0f40 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -24,7 +24,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; @@ -34,7 +34,6 @@ 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; @@ -45,58 +44,94 @@ 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.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; +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; import org.forester.util.ForesterUtil; public final class Configuration { + public enum EXT_NODE_DATA_RETURN_ON { + BUFFER_ONLY, CONSOLE, WINODW; + } + + static enum TRIPLET { + FALSE, TRUE, UNKNOWN + } + public enum UI { - NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN + CROSSPLATFORM, NATIVE, 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 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_instead_of_labels = false; + 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" }, + { "List Node Data", "display" }, { "Select Node(s)", "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" } }; + 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_node_font = 5; + final static int change_node_font = 6; + final static int color_subtree = 7; + final static int open_seq_web = 8; + final static int open_pdb_web = 9; + final static int open_tax_web = 10; + final static int blast = 11; + final static int cut_subtree = 12; + final static int copy_subtree = 13; + final static int paste_subtree = 14; + final static int delete_subtree_or_node = 15; + final static int add_new_node = 16; + final static int edit_node_data = 17; + final static int sort_descendents = 18; + final static int get_ext_desc_data = 19; + final static int select_nodes = 20; + // ------------------ + // 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" } }; final static int display_as_phylogram = 0; final static int show_node_names = 1; final static int show_tax_code = 2; @@ -104,42 +139,36 @@ public final class Configuration { 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_domain_architectures = 9; - final static int show_binary_characters = 10; - final static int show_binary_character_counts = 11; - final static int show_gene_names = 12; - final static int show_sequence_acc = 13; - final static int display_internal_data = 14; - final static int dynamically_hide_data = 15; - final static int show_taxonomy_scientific_names = 16; - final static int show_taxonomy_common_names = 17; - final static int color_according_to_annotation = 18; - final static int show_property = 19; - final static int show_gene_symbols = 20; + final static int color_according_to_sequence = 7; + final static int use_style = 8; + final static int width_branches = 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_seq_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_seq_symbols = 20; final static int node_data_popup = 21; final static int show_relation_confidence = 22; final static int show_vector_data = 23; final static int show_taxonomy_images = 24; - // ------------------ - // 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; + final static int show_properties = 25; + final static int show_gene_names = 26; + final static int show_mol_seqs = 27; + final static int write_branch_length_values = 28; + static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema"; + private static Hashtable _sequence_colors; + private static Hashtable _annotation_colors; + private static Hashtable _domain_colors; + private static Hashtable _species_colors; + private static String DEFAULT_FONT_FAMILY = ""; + private static final int DEPRECATED = -2; + private static final String DISPLAY_COLOR_KEY = "display_color"; // --------------------------- // Display options for trees // --------------------------- @@ -148,28 +177,9 @@ public final class Configuration { // --------------------------------- // 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" }, { "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; + String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME; // -------------- // Color set // -------------- @@ -178,34 +188,76 @@ public final class Configuration { // 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 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 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 SortedMap _display_colors = null; + private boolean _display_sequence_relations = false; + private boolean _editable = true; + 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_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_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_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 = ""; + 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 = ""; + private int _max_base_font_size = 20; + private boolean _midpoint_root = false; + private int _min_base_font_size = 2; + 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 _ov_max_height = 80; + private short _ov_max_width = 80; + private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT; + private File _path_to_local_fastme = null; + 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 boolean _show_annotation_ref_source = true; + private boolean _show_default_node_shapes_external = false; + private boolean _show_default_node_shapes_for_marked_nodes = false; + private boolean _show_default_node_shapes_internal = false; + private boolean _show_domain_labels = true; + private boolean _show_overview = true; + private boolean _show_scale = false; + 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 Color _vector_data_min_color = Color.BLUE; + private Color _vector_data_max_color = Color.YELLOW; + private Color _vector_data_mean_color = Color.WHITE; + private double _vector_data_height = 12; + private int _vector_data_width = 120; + private boolean _line_up_renderable_node_data = true; + private boolean _right_align_domains = false; + private boolean _allow_thick_strokes = false; static { for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) { - if ( Arrays.binarySearch( Util.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) { + if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) { DEFAULT_FONT_FAMILY = font_name; break; } @@ -215,14 +267,21 @@ public final class Configuration { } } - Configuration( final String cf, final boolean is_url, final boolean is_applet ) { + static String getDefaultFontFamilyName() { + return DEFAULT_FONT_FAMILY; + } + + public Configuration() { + this( null, false, false, false ); + } + + public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) { 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; @@ -261,64 +320,21 @@ public final class Configuration { bf.close(); } catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from [" - + config_filename + "]: " + e ); + if ( verbose ) { + 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 + "]" ); + if ( verbose ) { + 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; } @@ -339,7 +355,7 @@ public final class Configuration { /** * 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( "?" ); @@ -369,8 +385,8 @@ public final class Configuration { 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" ); + .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; @@ -387,17 +403,29 @@ public final class Configuration { 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" ); + .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; } @@ -416,9 +444,12 @@ public final class Configuration { 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" ); + "configuration key [display_node_popup] is deprecated" ); return DEPRECATED; } else if ( name.equals( "custom_option" ) ) { @@ -428,9 +459,14 @@ public final class Configuration { 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; + 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; } @@ -443,10 +479,26 @@ public final class Configuration { return clickto_options[ which ][ 0 ]; } + public int getDefaultBootstrapSamples() { + return _default_bootstrap_samples; + } + int getDefaultDisplayClicktoOption() { return default_clickto; } + public NodeFill getDefaultNodeFill() { + return _default_node_fill; + } + + public NodeShape getDefaultNodeShape() { + return _default_node_shape; + } + + public short getDefaultNodeShapeSize() { + return _default_node_shape_size; + } + SortedMap getDisplayColors() { return _display_colors; } @@ -462,6 +514,22 @@ public final class Configuration { return _domain_colors; } + public NodeDataField getExtDescNodeDataToReturn() { + return _ext_desc_data_to_return; + } + + public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() { + return _ext_node_data_return_on; + } + + public int getFrameXSize() { + return _frame_x_size; + } + + public int getFrameYSize() { + return _frame_y_size; + } + int getGraphicsExportX() { return _graphics_export_x; } @@ -470,8 +538,48 @@ public final class Configuration { return _graphics_export_y; } - public int getDefaultBootstrapSamples() { - return _default_bootstrap_samples; + Color getGuiBackgroundColor() { + return _gui_background_color; + } + + Color getGuiButtonBackgroundColor() { + return _gui_button_background_color; + } + + Color getGuiButtonBorderColor() { + return _gui_button_border_color; + } + + Color getGuiButtonTextColor() { + return _gui_button_text_color; + } + + Color getGuiCheckboxAndButtonActiveColor() { + return _gui_checkbox_and_button_active_color; + } + + Color getGuiCheckboxTextColor() { + return _gui_checkbox_text_color; + } + + Color getGuiMenuBackgroundColor() { + return _gui_menu_background_color; + } + + Color getGuiMenuTextColor() { + return _gui_menu_text_color; + } + + public String getLabelForGetExtDescendentsData() { + return _label_for_get_ext_descendents_data; + } + + int getMaxBaseFontSize() { + return _max_base_font_size; + } + + int getMinBaseFontSize() { + return _min_base_font_size; } double getMinConfidenceValue() { @@ -502,6 +610,18 @@ public final class Configuration { return _ov_placement; } + public File getPathToLocalFastme() { + return _path_to_local_fastme; + } + + public File getPathToLocalMafft() { + return _path_to_local_mafft; + } + + public File getPathToLocalRaxml() { + return _path_to_local_raxml; + } + PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() { return _phylogeny_graphics_type; } @@ -510,30 +630,60 @@ public final class Configuration { return _print_line_width; } + Hashtable getSequenceColors() { + if ( _sequence_colors == null ) { + _sequence_colors = new Hashtable(); + } + return _sequence_colors; + } + Hashtable getSpeciesColors() { if ( _species_colors == null ) { - _species_colors = new Hashtable(); + initSpeciesColors(); } return _species_colors; } - TreeColorSet getTreeColorSet() { - return null; + final TAXONOMY_EXTRACTION getTaxonomyExtraction() { + return _taxonomy_extraction; + } + + public double getVectorDataHeight() { + return _vector_data_height; + } + + public Color getVectorDataMaxColor() { + return _vector_data_max_color; + } + + public Color getVectorDataMeanColor() { + return _vector_data_mean_color; + } + + public Color getVectorDataMinColor() { + return _vector_data_min_color; } - TreeFontSet getTreeFontSet() { - return null; + public int getVectorDataWidth() { + return _vector_data_width; } - WebLink getWebLink( final String source ) { - return getWebLinks().get( source ); + private final void initSpeciesColors() { + _species_colors = new Hashtable(); + for( final String[] s : DEFAULT_SPECIES_COLORS ) { + _species_colors.put( s[ 0 ], Color.decode( s[ 1 ] ) ); + } } - Map getWebLinks() { - return _weblinks; + public boolean isAbbreviateScientificTaxonNames() { + return _abbreviate_scientific_names; } boolean isAntialiasScreen() { + if ( ForesterUtil.isMac() ) { + //Apple Macintosh graphics are slow, turn off anti-alias. + return false; + } return _antialias_screen; } @@ -541,9 +691,17 @@ public final class Configuration { return _background_color_gradient; } + public boolean isColorByTaxonomicGroup() { + return false; + } + + public boolean isColorLabelsSameAsParentBranch() { + return _color_labels_same_as_parent_branch; + } + /** * Convenience method. - * + * * @return true if value in configuration file was 'yes' */ boolean isDrawAsPhylogram() { @@ -554,14 +712,6 @@ public final class Configuration { return _editable; } - boolean isExtractPfamTaxonomyCodesInNhParsing() { - return _nh_parsing_extract_pfam_taxonomy_codes; - } - - boolean isHasWebLink( final String source ) { - return getWebLinks().containsKey( source ); - } - /** * Only used by ArchaeoptryxE. * @@ -574,12 +724,40 @@ public final class Configuration { return _internal_number_are_confidence_for_nh_parsing; } + final public boolean isLineUpRendarableNodeData() { + return _line_up_renderable_node_data; + } + + public boolean isMidpointReroot() { + return _midpoint_root; + } + boolean isReplaceUnderscoresInNhParsing() { return _nh_parsing_replace_underscores; } - boolean isShowBranchLengthValues() { - return _show_branch_length_values; + final public boolean isRightLineUpDomains() { + return _right_align_domains; + } + + public boolean isShowAnnotationRefSource() { + return _show_annotation_ref_source; + } + + public boolean isShowDefaultNodeShapesExternal() { + return _show_default_node_shapes_external; + } + + public boolean isShowDefaultNodeShapesForMarkedNodes() { + return _show_default_node_shapes_for_marked_nodes; + } + + public boolean isShowDefaultNodeShapesInternal() { + return _show_default_node_shapes_internal; + } + + public boolean isShowDomainLabels() { + return _show_domain_labels; } boolean isShowOverview() { @@ -591,7 +769,7 @@ public final class Configuration { } final boolean isUseNativeUI() { - if ( ( _ui == UI.UNKNOWN ) && Util.isMac() && Util.isJava15() ) { + if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) { _ui = UI.NATIVE; } return _ui == UI.NATIVE; @@ -626,7 +804,7 @@ public final class Configuration { private double parseDouble( final String str ) { double d = 0.0; try { - d = Double.parseDouble( str ); + d = Double.parseDouble( str.trim() ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" ); @@ -638,7 +816,7 @@ public final class Configuration { private float parseFloat( final String str ) { float f = 0.0f; try { - f = Float.parseFloat( str ); + f = Float.parseFloat( str.trim() ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" ); @@ -650,7 +828,7 @@ public final class Configuration { private int parseInt( final String str ) { int i = -1; try { - i = Integer.parseInt( str ); + i = Integer.parseInt( str.trim() ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" ); @@ -662,7 +840,7 @@ public final class Configuration { private short parseShort( final String str ) { short i = -1; try { - i = Short.parseShort( str ); + i = Short.parseShort( str.trim() ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" ); @@ -677,16 +855,20 @@ public final class Configuration { final String[] fonts = font_str.split( ",+" ); for( String font : fonts ) { font = font.replace( '_', ' ' ).trim(); - if ( Arrays.binarySearch( Util.getAvailableFontFamiliesSorted(), font ) >= 0 ) { + if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) { setBaseFontFamilyName( font ); break; } } } + public void putDisplayColors( final String key, final Color color ) { + getDisplayColors().put( key, color ); + } + /** * read each line of config file, process non-comment lines - * @throws IOException + * @throws IOException */ private void readConfig( final BufferedReader conf_in ) throws IOException { String line; @@ -705,6 +887,14 @@ public final class Configuration { } while ( line != null ); } + public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) { + _abbreviate_scientific_names = abbreviate_scientific_names; + } + + 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; } @@ -713,44 +903,120 @@ public final class Configuration { _background_color_gradient = background_color_gradient; } - private void setBaseFontFamilyName( final String base_font_family_name ) { + public void setBaseFontFamilyName( final String base_font_family_name ) { _base_font_family_name = base_font_family_name; } - private void setBaseFontSize( final int base_font_size ) { + public 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 setCladogramType( final CLADOGRAM_TYPE cladogram_type ) { + _cladogram_type = cladogram_type; } - private void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) { - _abbreviate_scientific_names = abbreviate_scientific_names; + public void setColorizeBranches( final boolean b ) { + display_options[ use_style ][ 2 ] = b ? "yes" : "no"; } - private void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) { + 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 setCladogramType( final CLADOGRAM_TYPE cladogram_type ) { - _cladogram_type = cladogram_type; + private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) { + _default_bootstrap_samples = default_bootstrap_samples; } - void setDisplayColors( final SortedMap display_colors ) { + 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; } - private void setDisplaySequenceRelations( final boolean display_sequence_relations ) { + 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"; + } + + public void setDisplayInternalData( final boolean b ) { + display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayNodeNames( final boolean b ) { + display_options[ show_node_names ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplaySequenceAcc( final boolean b ) { + display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplaySequenceNames( final boolean b ) { + display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplaySequenceRelations( final boolean display_sequence_relations ) { _display_sequence_relations = display_sequence_relations; } + public void setDisplaySequenceSymbols( final boolean b ) { + display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayTaxonomyCode( final boolean b ) { + display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayTaxonomyCommonNames( final boolean b ) { + display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayTaxonomyImages( final boolean b ) { + display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayTaxonomyScientificNames( final boolean b ) { + display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no"; + } + + public void setDynamicallyHideData( final boolean b ) { + display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no"; + } + 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; + public void setExtDescNodeDataToReturn( final NodeDataField 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; + } + + public void setFrameYSize( final int frame_y_size ) { + _frame_y_size = frame_y_size; } private void setGraphicsExportX( final int graphics_export_x ) { @@ -761,10 +1027,6 @@ public final class Configuration { _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; } @@ -773,17 +1035,17 @@ public final class Configuration { * 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(); + final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase(); + if ( !st.hasMoreElements() ) { + return; + } // 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]" ); + + "] for [default_click_to]" ); default_clickto = 0; } else if ( default_clickto == DEPRECATED ) { @@ -803,7 +1065,7 @@ public final class Configuration { } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str - + "]" ); + + "]" ); _ui = UI.UNKNOWN; } } @@ -842,7 +1104,7 @@ public final class Configuration { else { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str - + "] for [phylogeny_graphics_type]" ); + + "] for [phylogeny_graphics_type]" ); } } else if ( key.equals( "min_confidence_value" ) ) { @@ -856,17 +1118,37 @@ public final class Configuration { else if ( key.equals( "font_size" ) ) { final String size_str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( size_str ); - setBaseFontSize( i ); + if ( i > 0 ) { + setBaseFontSize( i ); + } + } + else if ( key.equals( "font_size_min" ) ) { + final String size_str = ( ( String ) st.nextElement() ).trim(); + final int i = parseInt( size_str ); + if ( i > 0 ) { + setMinBaseFontSize( i ); + } + } + else if ( key.equals( "font_size_max" ) ) { + final String size_str = ( ( String ) st.nextElement() ).trim(); + final int i = parseInt( size_str ); + if ( i > 1 ) { + setMaxBaseFontSize( i ); + } } else if ( key.equals( "graphics_export_x" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( str ); - setGraphicsExportX( i ); + if ( i > 0 ) { + setGraphicsExportX( i ); + } } else if ( key.equals( "graphics_export_y" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( str ); - setGraphicsExportY( i ); + if ( i > 0 ) { + setGraphicsExportY( i ); + } } else if ( key.equals( "pdf_export_line_width" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); @@ -876,7 +1158,21 @@ public final class Configuration { } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "value for [pdf_export_line_width] cannot be zero or negative" ); + "value for [pdf_export_line_width] cannot be zero or negative" ); + } + } + else if ( key.equals( "window_initial_size_x" ) ) { + final String str = ( ( String ) st.nextElement() ).trim(); + final int i = parseInt( str ); + if ( i > 0 ) { + setFrameXSize( i ); + } + } + else if ( key.equals( "window_initial_size_y" ) ) { + final String str = ( ( String ) st.nextElement() ).trim(); + final int i = parseInt( str ); + if ( i > 0 ) { + setFrameYSize( i ); } } else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) { @@ -887,8 +1183,26 @@ public final class Configuration { } else { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "value for [default_number_of_bootstrap_resamples] cannot be negative" ); + .printWarningMessage( Constants.PRG_NAME, + "value for [default_number_of_bootstrap_resamples] cannot be negative" ); + } + } + else if ( key.equals( "mafft_local" ) ) { + final String str = ( ( String ) st.nextElement() ).trim(); + if ( !ForesterUtil.isEmpty( str ) ) { + setPathToLocalMafft( new File( str ) ); + } + } + else if ( key.equals( "fastme_local" ) ) { + final String str = ( ( String ) st.nextElement() ).trim(); + if ( !ForesterUtil.isEmpty( str ) ) { + setPathToLocalFastme( new File( str ) ); + } + } + else if ( key.equals( "raxml_local" ) ) { + final String str = ( ( String ) st.nextElement() ).trim(); + if ( !ForesterUtil.isEmpty( str ) ) { + setPathToLocalRaxml( new File( str ) ); } } else if ( key.equals( "show_scale" ) ) { @@ -897,9 +1211,6 @@ public final class Configuration { 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() ) ); } @@ -909,6 +1220,9 @@ public final class Configuration { else if ( key.equals( "show_domain_labels" ) ) { setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) ); } + else if ( key.equals( "show_seq_annotation_ref_sources" ) ) { + setShowAnnotationRefSource( parseBoolean( ( String ) st.nextElement() ) ); + } else if ( key.equals( "abbreviate_scientific_names" ) ) { setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) ); } @@ -925,13 +1239,13 @@ public final class Configuration { } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str - + "] for [cladogram_type]" ); + + "] 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" ); + .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() ); @@ -940,11 +1254,11 @@ public final class Configuration { _use_tabbed_display = parseBoolean( ( String ) st.nextElement() ); } else if ( key.equals( "overview_width" ) ) { - final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); + final short i = parseShort( ( ( String ) st.nextElement() ) ); setOvMaxWidth( i ); } else if ( key.equals( "overview_height" ) ) { - final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); + final short i = parseShort( ( ( String ) st.nextElement() ) ); setOvMaxHeight( i ); } else if ( key.equals( "overview_placement_type" ) ) { @@ -964,7 +1278,7 @@ public final class Configuration { else { setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT ); ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str - + "] for [overview_placement_type]" ); + + "] for [overview_placement_type]" ); } } else if ( key.equals( "node_label_direction" ) ) { @@ -978,7 +1292,7 @@ public final class Configuration { else { setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL ); ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str - + "] for [node_label_direction]" ); + + "] for [node_label_direction]" ); } } else if ( key.equals( "branch_length_value_digits" ) ) { @@ -988,7 +1302,7 @@ public final class Configuration { } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i - + "] for [branch_length_value_digits]" ); + + "] for [branch_length_value_digits]" ); } } else if ( key.equals( "confidence_value_digits" ) ) { @@ -998,7 +1312,7 @@ public final class Configuration { } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i - + "] for [confidence_value_digits]" ); + + "] for [confidence_value_digits]" ); } } else if ( key.equals( "allow_editing" ) ) { @@ -1009,24 +1323,40 @@ public final class Configuration { } else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) { final boolean r = parseBoolean( ( String ) st.nextElement() ); - if ( r && isExtractPfamTaxonomyCodesInNhParsing() ) { + if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "attempt to extract taxonomies and replace underscores at the same time" ); + .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 if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) { + final String s = ( String ) st.nextElement(); + if ( s.equalsIgnoreCase( "no" ) ) { + setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO ); + } + else if ( s.equalsIgnoreCase( "pfam_relaxed" ) ) { + setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + } + else if ( s.equalsIgnoreCase( "pfam_strict" ) ) { + setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + } + else if ( s.equalsIgnoreCase( "aggressive" ) ) { + setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE ); } else { - setExtractPfamTaxonomyCodesInNhParsing( e ); + ForesterUtil + .printWarningMessage( Constants.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" ); } } else if ( key.equals( "internal_labels_are_confidence_values" ) ) { @@ -1056,62 +1386,154 @@ public final class Configuration { 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( "show_default_node_shapes_internal" ) ) { + setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) ); + } + else if ( key.equals( "show_default_node_shapes_external" ) ) { + setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) ); } - else if ( key.equals( "domain_structure_base_color" ) ) { - _domain_structure_base_color = Color.decode( ( String ) st.nextElement() ); + else if ( key.equals( "show_node_shapes_for_nodes_with_vis_data" ) ) { + setShowDefaultNodeShapesForMarkedNodes( 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() ) ) { + if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.NONE.toString() ) ) { setDefaultNodeFill( NodeFill.NONE ); } - else if ( fill_str.equalsIgnoreCase( Options.NodeFill.GRADIENT.toString() ) ) { + else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.GRADIENT.toString() ) ) { setDefaultNodeFill( NodeFill.GRADIENT ); } - else if ( fill_str.equalsIgnoreCase( Options.NodeFill.SOLID.toString() ) ) { + else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.SOLID.toString() ) ) { setDefaultNodeFill( NodeFill.SOLID ); } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str - + "] for [default_node_fill]" ); + + "] 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() ) ) { + if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.CIRCLE.toString() ) ) { setDefaultNodeShape( NodeShape.CIRCLE ); } - else if ( shape_str.equalsIgnoreCase( Options.NodeShape.RECTANGLE.toString() ) ) { + else if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.RECTANGLE.toString() ) ) { setDefaultNodeShape( NodeShape.RECTANGLE ); } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str - + "] for [default_node_shape]" ); + + "] for [default_node_shape]" ); + } + } + else if ( key.equals( "midpoint_reroot" ) ) { + setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) ); + } + 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( NodeDataField.NODE_NAME ); + } + else if ( s.equalsIgnoreCase( "sequence_acc" ) ) { + setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_ACC ); + } + else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) { + setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA ); + } + else if ( s.equalsIgnoreCase( "sequence_name" ) ) { + setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_NAME ); + } + else if ( s.equalsIgnoreCase( "gene_name" ) ) { + setExtDescNodeDataToReturn( NodeDataField.GENE_NAME ); + } + else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) { + setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_SYMBOL ); + } + else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) { + setExtDescNodeDataToReturn( NodeDataField.TAXONOMY_SCIENTIFIC_NAME ); + } + else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) { + setExtDescNodeDataToReturn( NodeDataField.TAXONOMY_CODE ); + } + else if ( s.equalsIgnoreCase( "user_selected" ) ) { + setExtDescNodeDataToReturn( NodeDataField.UNKNOWN ); + } + else if ( s.equalsIgnoreCase( "domains" ) ) { + setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL ); + } + else if ( s.equalsIgnoreCase( "domains_collapsed" ) ) { + setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ); + } + else if ( s.equalsIgnoreCase( "seq_annotations" ) ) { + setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS ); + } + else if ( s.equalsIgnoreCase( "go_term_ids" ) ) { + setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS ); + } + else { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s + + "] for [ext_descendents_data_to_return]" ); } } - else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) { - setTaxonomyColorizeNodeShapesInsteadOfLabels( parseBoolean( ( String ) st.nextElement() ) ); + 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() > 1 ) ) { + setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) ); + } + } + 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 ); + } + else if ( s.equals( "window" ) ) { + setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW ); + } + else if ( s.equals( "buffer_only" ) ) { + setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ); + } + else { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s + + "] for [ext_descendents_data_to_return_on]" ); + } + } + else if ( key.equals( "vector_data_min_color" ) ) { + _vector_data_min_color = Color.decode( ( String ) st.nextElement() ); + } + else if ( key.equals( "vector_data_max_color" ) ) { + _vector_data_max_color = Color.decode( ( String ) st.nextElement() ); + } + else if ( key.equals( "vector_data_mean_color" ) ) { + _vector_data_mean_color = Color.decode( ( String ) st.nextElement() ); + } + else if ( key.equals( "vector_data_width" ) ) { + _vector_data_width = parseShort( ( String ) st.nextElement() ); + if ( _vector_data_width < 1 ) { + _vector_data_width = 120; + } + } + else if ( key.equals( "vector_data_height" ) ) { + _vector_data_height = parseShort( ( String ) st.nextElement() ); + if ( _vector_data_height < 1 ) { + _vector_data_height = 12; + } + } + else if ( key.equals( "line_up_renderable_data" ) ) { + setLineUpRendarableNodeData( parseBoolean( ( String ) st.nextElement() ) ); + } + else if ( key.equals( "right_align_domain_architectures" ) ) { + setRightLineUpDomains( parseBoolean( ( String ) st.nextElement() ) ); + } + else if ( key.equals( "allow_thick_strokes" ) ) { + _allow_thick_strokes = 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" ) ) { + if ( 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; @@ -1119,64 +1541,42 @@ public final class Configuration { else if ( key.equals( "color_according_to_species" ) ) { key_index = Configuration.color_according_to_species; } + else if ( key.equals( "color_according_to_sequence" ) ) { + key_index = Configuration.color_according_to_sequence; + } else if ( key.equals( "show_node_names" ) ) { key_index = Configuration.show_node_names; } - else if ( key.equals( "show_taxonomy" ) || key.equals( "show_taxonomy_code" ) ) { + else if ( 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" ) ) { + else if ( 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" ) ) { + else if ( key.equals( "write_branch_length_values" ) ) { + key_index = Configuration.write_branch_length_values; + } + else if ( key.equals( "write_events" ) ) { 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( "use_visual_styles" ) ) { + key_index = Configuration.use_style; } else if ( key.equals( "color_branches" ) ) { - key_index = Configuration.color_branches; + key_index = Configuration.use_style; + ForesterUtil + .printWarningMessage( Constants.PRG_NAME, + "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" ); } 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_msa" ) ) { + key_index = Configuration.show_mol_seqs; + } else if ( key.equals( "show_annotations" ) ) { key_index = Configuration.show_annotation; } @@ -1186,31 +1586,24 @@ public final class Configuration { else if ( key.equals( "show_binary_character_counts" ) ) { key_index = Configuration.show_binary_character_counts; } + else if ( key.equals( "show_seq_names" ) ) { + key_index = Configuration.show_seq_names; + } 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_seq_symbols" ) ) { + key_index = Configuration.show_seq_symbols; } - else if ( key.equals( "show_sequence_acc" ) ) { + else if ( key.equals( "show_seq_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; } @@ -1223,12 +1616,12 @@ public final class Configuration { 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_properties" ) ) { + key_index = Configuration.show_properties; + } else if ( key.equals( "show_relation_confidence" ) ) { key_index = Configuration.show_relation_confidence; } @@ -1257,36 +1650,30 @@ public final class Configuration { } } else if ( key.equals( "species_color" ) ) { - getSpeciesColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); + getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ), + Color.decode( ( String ) st.nextElement() ) ); + } + else if ( key.equals( "sequence_color" ) ) { + getSequenceColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ), + 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() ) ); + .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" ); + "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 + "]" ); - } + putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key - + "] in: " + config_filename ); + + "] in: " + config_filename ); } } } @@ -1296,123 +1683,123 @@ public final class Configuration { } } - private void setMinConfidenceValue( final double min_confidence_value ) { - _min_confidence_value = min_confidence_value; + private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) { + _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data; } - void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) { - _node_label_direction = node_label_direction; + final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) { + _line_up_renderable_node_data = line_up_renderable_node_data; } - 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 setMaxBaseFontSize( final int max_base_font_size ) { + _max_base_font_size = max_base_font_size; } - 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; + public void setMidpointReroot( final boolean midpoint_root ) { + _midpoint_root = midpoint_root; } - private void setOvMaxHeight( final short ov_max_height ) { - _ov_max_height = ov_max_height; + private void setMinBaseFontSize( final int min_base_font_size ) { + _min_base_font_size = min_base_font_size; } - private void setOvMaxWidth( final short ov_max_width ) { - _ov_max_width = ov_max_width; + public void setMinConfidenceValue( final double min_confidence_value ) { + _min_confidence_value = min_confidence_value; } - private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) { - _ov_placement = ov_placement; + public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) { + _node_label_direction = node_label_direction; } - void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) { - _phylogeny_graphics_type = phylogeny_graphics_type; + 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 void setPrintLineWidth( final float print_line_width ) { - _print_line_width = print_line_width; + 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 void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) { - _nh_parsing_replace_underscores = nh_parsing_replace_underscores; + private void setOvMaxHeight( final short ov_max_height ) { + _ov_max_height = ov_max_height; } - private void setShowBranchLengthValues( final boolean show_branch_length_values ) { - _show_branch_length_values = show_branch_length_values; + private void setOvMaxWidth( final short ov_max_width ) { + _ov_max_width = ov_max_width; } - private void setShowOverview( final boolean show_overview ) { - _show_overview = show_overview; + private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) { + _ov_placement = ov_placement; } - private void setShowScale( final boolean show_scale ) { - _show_scale = show_scale; + private void setPathToLocalFastme( final File path_to_local_fastme ) { + _path_to_local_fastme = path_to_local_fastme; } - private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) { - _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema; + private void setPathToLocalMafft( final File path_to_local_mafft ) { + _path_to_local_mafft = path_to_local_mafft; } - void setWebLinks( final SortedMap weblinks ) { - _weblinks = weblinks; + private void setPathToLocalRaxml( final File path_to_local_raxml ) { + _path_to_local_raxml = path_to_local_raxml; } - static String getDefaultFontFamilyName() { - return DEFAULT_FONT_FAMILY; + public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) { + _phylogeny_graphics_type = phylogeny_graphics_type; } - static enum TRIPLET { - TRUE, FALSE, UNKNOWN + public void setPrintLineWidth( final float print_line_width ) { + _print_line_width = print_line_width; } - public Color getDomainStructureFontColor() { - return _domain_structure_font_color; + public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) { + _nh_parsing_replace_underscores = nh_parsing_replace_underscores; } - public Color getDomainStructureBaseColor() { - return _domain_structure_base_color; + final public void setRightLineUpDomains( final boolean right_align_domains ) { + _right_align_domains = right_align_domains; } - public boolean isColorLabelsSameAsParentBranch() { - return _color_labels_same_as_parent_branch; + private void setShowAnnotationRefSource( final boolean b ) { + _show_annotation_ref_source = b; } - public boolean isShowDomainLabels() { - return _show_domain_labels; + public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) { + _show_default_node_shapes_external = show_default_node_shapes_external; } - public boolean isAbbreviateScientificTaxonNames() { - return _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 NodeShape getDefaultNodeShape() { - return _default_node_shape; + public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) { + _show_default_node_shapes_internal = show_default_node_shapes_internal; } - private void setDefaultNodeShape( final NodeShape default_node_shape ) { - _default_node_shape = default_node_shape; + public void setShowDomainLabels( final boolean show_domain_labels ) { + _show_domain_labels = show_domain_labels; } - private void setDefaultNodeFill( final NodeFill default_node_fill ) { - _default_node_fill = default_node_fill; + private void setShowOverview( final boolean show_overview ) { + _show_overview = show_overview; } - public NodeFill getDefaultNodeFill() { - return _default_node_fill; + public void setShowScale( final boolean show_scale ) { + _show_scale = show_scale; } - private void setDefaultNodeShapeSize( final short default_node_shape_size ) { - _default_node_shape_size = default_node_shape_size; + final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) { + _taxonomy_extraction = taxonomy_extraction; } - public short getDefaultNodeShapeSize() { - return _default_node_shape_size; + public void setUseStyle( final boolean b ) { + display_options[ use_style ][ 2 ] = b ? "yes" : "no"; } - private void setTaxonomyColorizeNodeShapesInsteadOfLabels( final boolean taxonomy_colorize_node_shapes_instead_of_labels ) { - _taxonomy_colorize_node_shapes_instead_of_labels = taxonomy_colorize_node_shapes_instead_of_labels; + private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) { + _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema; } - public boolean isTaxonomyColorizeNodeShapesInsteadOfLabels() { - return _taxonomy_colorize_node_shapes_instead_of_labels; + public boolean isAllowThickStrokes() { + return _allow_thick_strokes; } }