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" },
- { "List Node Data", "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 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 ];
}
}
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 + "]" );
}
}
public void setDisplayInternalData( final boolean b ) {
display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
}
+
+ public void setDisplayExternalData( final boolean b ) {
+ display_options[ display_external_data ][ 2 ] = b ? "yes" : "no";
+ }
public void setDisplayMultipleSequenceAlignment( final boolean b ) {
display_options[ show_mol_seqs ][ 2 ] = b ? "yes" : "no";
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 void setDisplayTaxonomyCommonNames( final boolean b ) {
display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
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( 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( "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( "display_sequences" ) ) {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
+ .printWarningMessage( AptxConstants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
return DEPRECATED;
}
else if ( name.equals( "open_seq_web" ) ) {
index = Configuration.select_nodes;
}
else if ( name.equals( "display_node_popup" ) ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "configuration key [display_node_popup] is deprecated" );
+ ForesterUtil.printWarningMessage( AptxConstants.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" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "configuration key [custom_option] is deprecated" );
return DEPRECATED;
}
else if ( name.equals( "color_subtree" ) ) {
return false;
}
else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
return false;
}
}
d = Double.parseDouble( str.trim() );
}
catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse double from [" + str + "]" );
d = 0.0;
}
return d;
f = Float.parseFloat( str.trim() );
}
catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse float from [" + str + "]" );
f = 0.0f;
}
return f;
i = Integer.parseInt( str.trim() );
}
catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse integer from [" + str + "]" );
i = -1;
}
return i;
i = Short.parseShort( str.trim() );
}
catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse short from [" + str + "]" );
i = -1;
}
return i;
_ext_node_data_return_on = ext_node_data_return_on;
}
- private void setGraphicsExportX( final int graphics_export_x ) {
- _graphics_export_x = graphics_export_x;
- }
+ //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" ) ) {
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( "list_node_data_custom_label" ) || key.equals( "label_for_get_ext_descendents_data" ) ) {
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: "
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown configuration key [" + key + "] in: "
+ config_filename );
}
}
return _domain_colors;
}
- int getGraphicsExportX() {
- return _graphics_export_x;
- }
-
- int getGraphicsExportY() {
- return _graphics_export_y;
- }
-
+
Color getGuiBackgroundColor() {
return _gui_background_color;
}
return _gui_menu_text_color;
}
+ static int getGuiFontSize() {
+ return 11;
+ }
+
int getMaxBaseFontSize() {
return _max_base_font_size;
}
return _species_colors;
}
- final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+ public final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
return _taxonomy_extraction;
}
return _hide_controls_and_menus;
}
- boolean isInternalNumberAreConfidenceForNhParsing() {
+ public boolean isInternalNumberAreConfidenceForNhParsing() {
return _internal_number_are_confidence_for_nh_parsing;
}
- boolean isReplaceUnderscoresInNhParsing() {
+ public boolean isReplaceUnderscoresInNhParsing() {
return _nh_parsing_replace_underscores;
}
return _use_tabbed_display;
}
- boolean isValidatePhyloXmlAgainstSchema() {
+ public boolean isValidatePhyloXmlAgainstSchema() {
return _validate_against_phyloxml_xsd_schema;
}
static String getDefaultFontFamilyName() {
return DEFAULT_FONT_FAMILY;
}
+
+ public boolean isCouldReadConfigFile() {
+ return _could_read_config_file;
+ }
+
+
+ public String getConfigFilename() {
+ return config_filename;
+ }
+
+
+
}
git://source.jalview.org / jalview.git / blobdiff