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 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();
}
_show_default_node_shapes_external = false;
_show_default_node_shapes_for_marked_nodes = false;
_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;
_phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
_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 ) {
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;
+ }
+
+
+
}