}
final static String clickto_options[][] = {
{ "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
- { "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "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" } };
+ { "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" },
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
// ------------------
{ "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" } };
+ { "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,
+ .printWarningMessage( AptxConstants.PRG_NAME,
"configuration key [edit_info] is deprecated, use [display node data] instead" );
}
else if ( name.equals( "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,
+ 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
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "invalid value [" + clickto_name
+ "] for [default_click_to]" );
default_clickto = 0;
}
_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
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str
+ "] for [phylogeny_graphics_type]" );
}
}
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,
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME,
"value for [pdf_export_line_width] cannot be zero or negative" );
}
}
}
else {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
+ .printWarningMessage( AptxConstants.PRG_NAME,
"value for [default_number_of_bootstrap_resamples] cannot be negative" );
}
}
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
+ 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
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str
+ "] for [overview_placement_type]" );
}
}
}
else {
setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str
+ "] for [node_label_direction]" );
}
}
setNumberOfDigitsAfterCommaForBranchLengthValue( i );
}
else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "illegal value [" + i
+ "] for [branch_length_value_digits]" );
}
}
setNumberOfDigitsAfterCommaForConfidenceValues( i );
}
else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "illegal value [" + i
+ "] for [confidence_value_digits]" );
}
}
final boolean r = parseBoolean( ( String ) st.nextElement() );
if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
+ .printWarningMessage( AptxConstants.PRG_NAME,
"attempt to extract taxonomies and replace underscores at the same time" );
}
else {
}
else {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
+ .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,
+ .printWarningMessage( AptxConstants.PRG_NAME,
"attempt to extract taxonomies and replace underscores at the same time" );
}
}
setDefaultNodeFill( NodeFill.SOLID );
}
else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + fill_str
+ "] for [default_node_fill]" );
}
}
setDefaultNodeShape( NodeShape.RECTANGLE );
}
else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + shape_str
+ "] for [default_node_shape]" );
}
}
setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );
}
else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + s
+ "] for [ext_descendents_data_to_return]" );
}
}
setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
}
else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + s
+ "] for [ext_descendents_data_to_return_on]" );
}
}
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,
+ .printWarningMessage( AptxConstants.PRG_NAME,
"configuration key [color_branches] is deprecated, use [use_visual_styles] instead" );
}
else if ( key.equals( "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 );
}
}
.put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
}
else if ( key.equals( "function_color" ) ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME,
+ 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
+ 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;
+ }
+
+
+
}