final public class Options {
public static enum CLADOGRAM_TYPE {
- EXT_NODE_SUM_DEP, NON_LINED_UP, TOTAL_NODE_SUM_DEP;
+ LINED_UP, NON_LINED_UP;
}
public static enum NODE_LABEL_DIRECTION {
public static enum PHYLOGENY_GRAPHICS_TYPE {
CIRCULAR, CONVEX, CURVED, EURO_STYLE, RECTANGULAR, ROUNDED, TRIANGULAR, UNROOTED;
}
+
+ static enum PHYLOGENY_DISPLAY_TYPE {
+ CLADOGRAM,
+ ALIGNED_PHYLOGRAM,
+ UNALIGNED_PHYLOGRAM
+ }
static enum OVERVIEW_PLACEMENT_TYPE {
LOWER_LEFT( "lower left" ),
return toString().replaceAll( " ", "_" );
}
}
+
static final double MIN_CONFIDENCE_DEFAULT = 0.0;
private boolean _abbreviate_scientific_names;
private boolean _allow_errors_in_distance_to_parent;
private short _default_node_shape_size;
private boolean _editable;
private NodeDataField _ext_desc_data_to_return;
- private boolean _graphics_export_using_actual_size;
+ private final boolean _graphics_export_using_actual_size = true;
private boolean _graphics_export_visible_only;
private boolean _internal_number_are_confidence_for_nh_parsing;
private boolean _inverse_search_result;
private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type;
private boolean _print_black_and_white;
private float _print_line_width;
- private int _print_size_x;
- private int _print_size_y;
- private boolean _print_using_actual_size;
+ private final boolean _print_using_actual_size = true;
private double _scale_bar_length;
private boolean _search_case_sensitive;
private boolean _show_annotation_ref_source;
private TAXONOMY_EXTRACTION _taxonomy_extraction;
private boolean _line_up_renderable_node_data;
private boolean _right_align_domains;
-
+ private boolean _color_all_found_nodes_when_coloring_subtree;
+ private boolean _parse_beast_style_extended_nexus_tags;
+ private boolean _collapsed_with_average_height;
+ private boolean _show_abbreviated_labels_for_collapsed_nodes;
+
private Options() {
init();
}
final private void init() {
_default_node_shape = NodeShape.CIRCLE;
_default_node_fill = NodeFill.GRADIENT;
- _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
+ _default_node_shape_size = AptxConstants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
_internal_number_are_confidence_for_nh_parsing = false;
_show_scale = false;
_antialias_screen = true;
_show_default_node_shapes_internal = false;
_show_default_node_shapes_external = false;
_show_default_node_shapes_for_marked_nodes = false;
- if ( AptxUtil.isUsOrCanada() ) {
- _print_size_x = Constants.US_LETTER_SIZE_X;
- _print_size_y = Constants.US_LETTER_SIZE_Y;
- }
- else {
- _print_size_x = Constants.A4_SIZE_X;
- _print_size_y = Constants.A4_SIZE_Y;
- }
+ _color_all_found_nodes_when_coloring_subtree = false;
+ _parse_beast_style_extended_nexus_tags= true;
_min_confidence_value = MIN_CONFIDENCE_DEFAULT;
_print_black_and_white = false;
- _print_using_actual_size = true;
- _graphics_export_using_actual_size = true;
_phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
_base_font = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 10 );
_match_whole_terms_only = false;
_search_with_regex = false;
_search_case_sensitive = false;
- _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
+ _print_line_width = AptxConstants.PDF_LINE_WIDTH_DEFAULT;
_show_overview = true;
_ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
_node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
_inverse_search_result = false;
_scale_bar_length = 0.0;
- _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
- _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
+ _number_of_digits_after_comma_for_branch_length_values = AptxConstants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
+ _number_of_digits_after_comma_for_confidence_values = AptxConstants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
_nh_parsing_replace_underscores = false;
_taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
- _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
+ _cladogram_type = AptxConstants.CLADOGRAM_TYPE_DEFAULT;
_show_domain_labels = true;
_show_annotation_ref_source = true;
setAbbreviateScientificTaxonNames( false );
_ext_desc_data_to_return = NodeDataField.UNKNOWN;
_line_up_renderable_node_data = true;
_right_align_domains = false;
+ _collapsed_with_average_height = true;
+ _show_abbreviated_labels_for_collapsed_nodes = true;
}
final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) {
return _print_line_width;
}
- final int getPrintSizeX() {
- return _print_size_x;
- }
-
- final int getPrintSizeY() {
- return _print_size_y;
- }
-
final double getScaleBarLength() {
return _scale_bar_length;
}
_editable = editable;
}
- final void setGraphicsExportUsingActualSize( final boolean graphics_export_using_actual_size ) {
- _graphics_export_using_actual_size = graphics_export_using_actual_size;
- if ( !graphics_export_using_actual_size ) {
- setGraphicsExportVisibleOnly( false );
- }
- }
-
final void setGraphicsExportVisibleOnly( final boolean graphics_export_visible_only ) {
_graphics_export_visible_only = graphics_export_visible_only;
- if ( graphics_export_visible_only ) {
- setGraphicsExportUsingActualSize( true );
- }
}
final void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
final void setPrintLineWidth( final float print_line_width ) {
_print_line_width = print_line_width;
}
-
- final void setPrintSizeX( final int print_size_x ) {
- _print_size_x = print_size_x;
- }
-
- final void setPrintSizeY( final int print_size_y ) {
- _print_size_y = print_size_y;
- }
-
- final void setPrintUsingActualSize( final boolean print_using_actual_size ) {
- _print_using_actual_size = print_using_actual_size;
- }
-
+
final void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
_nh_parsing_replace_underscores = nh_parsing_replace_underscores;
}
if ( configuration.getMinConfidenceValue() != MIN_CONFIDENCE_DEFAULT ) {
instance.setMinConfidenceValue( configuration.getMinConfidenceValue() );
}
- if ( configuration.getGraphicsExportX() > 0 ) {
- instance.setPrintSizeX( configuration.getGraphicsExportX() );
- }
- if ( configuration.getGraphicsExportY() > 0 ) {
- instance.setPrintSizeY( configuration.getGraphicsExportY() );
- }
if ( configuration.getBaseFontSize() > 0 ) {
instance.setBaseFont( instance.getBaseFont().deriveFont( ( float ) configuration.getBaseFontSize() ) );
}
final static Options createDefaultInstance() {
return new Options();
}
+
+ final boolean isColorAllFoundNodesWhenColoringSubtree() {
+ return _color_all_found_nodes_when_coloring_subtree;
+ }
+
+ final void setColorAllFoundNodesWhenColoringSubtree( final boolean color_all_found_nodes_when_coloring_subtree ) {
+ _color_all_found_nodes_when_coloring_subtree = color_all_found_nodes_when_coloring_subtree;
+ }
+
+ final boolean isParseBeastStyleExtendedNexusTags() {
+ return _parse_beast_style_extended_nexus_tags;
+ }
+
+ final void setParseBeastStyleExtendedNexusTags( final boolean parse_beast_style_extended_nexus_tags ) {
+ _parse_beast_style_extended_nexus_tags = parse_beast_style_extended_nexus_tags;
+ }
+
+ final boolean isCollapsedWithAverageHeigh() {
+ return _collapsed_with_average_height;
+ }
+
+ final void setCollapsedWithAverageHeigh( final boolean collapsed_with_average_height ) {
+ _collapsed_with_average_height = collapsed_with_average_height;
+ }
+
+ final boolean isShowAbbreviatedLabelsForCollapsedNodes() {
+ return _show_abbreviated_labels_for_collapsed_nodes;
+ }
+
+ final void setShowAbbreviatedLabelsForCollapsedNodes(final boolean show_abbreviated_labels_for_collapsed_nodes) {
+ _show_abbreviated_labels_for_collapsed_nodes = show_abbreviated_labels_for_collapsed_nodes;
+ }
+
+
+
}
git://source.jalview.org / jalview.git / blobdiff