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;
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;
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" }, { "Show External Data", "display", "yes" }};
final static int display_as_phylogram = 0;
final static int show_node_names = 1;
final static int show_tax_code = 2;
final static int show_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;
+ final static int display_external_data = 30;
+
static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
private static Hashtable<String, Color> _sequence_colors;
private static Hashtable<String, Color> _annotation_colors;
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
// --------------
// 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<String, Color> _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 = "";
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;
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;
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;
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 );
}
else {
config_filename = cf;
}
+ _could_read_config_file = false;
setDisplayColors( new TreeMap<String, Color>() );
config_filename = config_filename.trim();
URL u = null;
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 + "]" );
}
}
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<String, Color> getAnnotationColors() {
- if ( _annotation_colors == null ) {
- _annotation_colors = new Hashtable<String, Color>();
- }
- 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;
}
return _default_node_shape_size;
}
- SortedMap<String, Color> getDisplayColors() {
- return _display_colors;
- }
-
- String getDisplayTitle( final int which ) {
- return display_options[ which ][ 0 ];
- }
-
- Map<String, Color> getDomainColors() {
- if ( _domain_colors == null ) {
- _domain_colors = new Hashtable<String, Color>();
- }
- return _domain_colors;
- }
-
- public NODE_DATA getExtDescNodeDataToReturn() {
+ public NodeDataField getExtDescNodeDataToReturn() {
return _ext_desc_data_to_return;
}
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<String, Color> getSequenceColors() {
- if ( _sequence_colors == null ) {
- _sequence_colors = new Hashtable<String, Color>();
- }
- return _sequence_colors;
+ public void setAddTaxonomyImagesCB( final boolean b ) {
+ display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no";
}
- Hashtable<String, Color> 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<String, Color>();
- 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<String, Color> 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 setDisplayExternalData( final boolean b ) {
+ display_options[ display_external_data ][ 2 ] = b ? "yes" : "no";
}
- boolean isEditable() {
- return _editable;
+ public void setDisplayMultipleSequenceAlignment( final boolean b ) {
+ display_options[ show_mol_seqs ][ 2 ] = b ? "yes" : "no";
}
- /**
- * Only used by ArchaeoptryxE.
- *
- */
- boolean isHideControlPanelAndMenubar() {
- return _hide_controls_and_menus;
+ public void setDisplayNodeNames( final boolean b ) {
+ display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
}
- boolean isInternalNumberAreConfidenceForNhParsing() {
- return _internal_number_are_confidence_for_nh_parsing;
+ public void setDisplaySequenceAcc( final boolean b ) {
+ display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
}
- final public boolean isLineUpRendarableNodeData() {
- return _line_up_renderable_node_data;
+ public void setDisplaySequenceNames( final boolean b ) {
+ display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no";
}
- public boolean isMidpointReroot() {
- return _midpoint_root;
+ public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
+ _display_sequence_relations = display_sequence_relations;
}
- boolean isReplaceUnderscoresInNhParsing() {
- return _nh_parsing_replace_underscores;
+ public void setDisplaySequenceSymbols( final boolean b ) {
+ display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no";
}
- final public boolean isRightLineUpDomains() {
- return _right_align_domains;
+ public void setDisplayTaxonomyCode( final boolean b ) {
+ display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
+ }
+
+ 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";
+ public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
+ _show_default_node_shapes_internal = show_default_node_shapes_internal;
}
- 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 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<String, Color> 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<String, Color>();
+ 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;
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 ) {
_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;
}
}
}
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" ) ) {
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 );
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" ) ) {
}
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" ) ) {
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() );
}
}
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" ) ) {
}
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" ) ) {
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" ) ) {
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" ) ) {
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 );
}
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" ) ) {
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" ) ) {
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 );
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" ) ) {
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;
}
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;
else if ( key.equals( "display_internal_data" ) ) {
key_index = Configuration.display_internal_data;
}
+ else if ( key.equals( "display_external_data" ) ) {
+ key_index = Configuration.display_external_data;
+ }
else if ( key.equals( "dynamically_hide_data" ) ) {
key_index = Configuration.dynamically_hide_data;
}
// Deprecated.
}
else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown click-to option: "
+ click_to_name );
}
}
}
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<String, Color> getAnnotationColors() {
+ if ( _annotation_colors == null ) {
+ _annotation_colors = new Hashtable<String, Color>();
+ }
+ 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<String, Color> getDisplayColors() {
+ return _display_colors;
+ }
+
+ String getDisplayTitle( final int which ) {
+ return display_options[ which ][ 0 ];
+ }
+
+ Map<String, Color> getDomainColors() {
+ if ( _domain_colors == null ) {
+ _domain_colors = new Hashtable<String, Color>();
}
+ 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;
+ static int getGuiFontSize() {
+ return 11;
+ }
+
+ 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<String, Color> getSequenceColors() {
+ if ( _sequence_colors == null ) {
+ _sequence_colors = new Hashtable<String, Color>();
+ }
+ return _sequence_colors;
}
- public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
- _show_default_node_shapes_external = show_default_node_shapes_external;
+ Hashtable<String, Color> 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;
+ public 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;
+ }
+
+ public boolean isInternalNumberAreConfidenceForNhParsing() {
+ return _internal_number_are_confidence_for_nh_parsing;
+ }
+
+ public 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;
+ }
+
+ public 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;
- }
+
}