import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
-import org.forester.phylogeny.data.NodeData;
-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;
private NodeVisualData.NodeShape _default_node_shape;
private short _default_node_shape_size;
private boolean _editable;
- private NODE_DATA _ext_desc_data_to_return;
+ private NodeDataField _ext_desc_data_to_return;
private boolean _graphics_export_using_actual_size;
private boolean _graphics_export_visible_only;
private boolean _internal_number_are_confidence_for_nh_parsing;
private boolean _inverse_search_result;
private boolean _match_whole_terms_only;
+ private boolean _search_with_regex;
private double _min_confidence_value;
private NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style;
private boolean _nh_parsing_replace_underscores;
private double _scale_bar_length;
private boolean _search_case_sensitive;
private boolean _show_annotation_ref_source;
- private boolean _show_branch_length_values;
private boolean _show_confidence_stddev;
+ private boolean _show_default_node_shapes_for_marked_nodes;
private boolean _show_default_node_shapes_external;
private boolean _show_default_node_shapes_internal;
private boolean _show_domain_labels;
private boolean _show_overview;
private boolean _show_scale;
private TAXONOMY_EXTRACTION _taxonomy_extraction;
+ private boolean _line_up_renderable_node_data;
+ private boolean _right_align_domains;
private Options() {
init();
}
- public NodeData.NODE_DATA getExtDescNodeDataToReturn() {
+ public NodeDataField getExtDescNodeDataToReturn() {
return _ext_desc_data_to_return;
}
return _allow_errors_in_distance_to_parent;
}
- public boolean isAllowFontSizeChange() {
- return true;
- }
-
public final boolean isShowAnnotationRefSource() {
return _show_annotation_ref_source;
}
_color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
}
- public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
+ public void setExtDescNodeDataToReturn( final NodeDataField ext_desc_data_to_return ) {
_ext_desc_data_to_return = ext_desc_data_to_return;
}
return _match_whole_terms_only;
}
+ final boolean isSearchWithRegex() {
+ return _search_with_regex;
+ }
+
final boolean isPrintBlackAndWhite() {
return _print_black_and_white;
}
return _search_case_sensitive;
}
- final boolean isShowBranchLengthValues() {
- return _show_branch_length_values;
- }
-
boolean isShowConfidenceStddev() {
return _show_confidence_stddev;
}
return _show_default_node_shapes_external;
}
+ boolean isShowDefaultNodeShapesForMarkedNodes() {
+ return _show_default_node_shapes_for_marked_nodes;
+ }
+
boolean isShowDefaultNodeShapesInternal() {
return _show_default_node_shapes_internal;
}
_match_whole_terms_only = search_whole_words_only;
}
+ final void setSearchWithRegex( final boolean search_with_regex ) {
+ _search_with_regex = search_with_regex;
+ }
+
final void setMinConfidenceValue( final double min_confidence_value ) {
_min_confidence_value = min_confidence_value;
}
_search_case_sensitive = search_case_sensitive;
}
- final void setShowBranchLengthValues( final boolean show_branch_length_values ) {
- _show_branch_length_values = show_branch_length_values;
- }
-
void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
_show_confidence_stddev = show_confidence_stddev;
}
_show_default_node_shapes_internal = show_default_node_shapes_internal;
}
+ 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;
+ }
+
final void setShowOverview( final boolean show_overview ) {
_show_overview = show_overview;
}
_default_node_shape = NodeShape.CIRCLE;
_default_node_fill = NodeFill.GRADIENT;
_default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
- _show_branch_length_values = false;
_internal_number_are_confidence_for_nh_parsing = false;
_show_scale = false;
_antialias_screen = true;
_background_color_gradient = false;
_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;
_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;
_show_overview = true;
_show_annotation_ref_source = true;
setAbbreviateScientificTaxonNames( false );
_color_labels_same_as_parent_branch = false;
- _show_confidence_stddev = true;
+ _show_confidence_stddev = false;
_nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
- _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
+ _ext_desc_data_to_return = NodeDataField.UNKNOWN;
+ _line_up_renderable_node_data = true;
+ _right_align_domains = false;
}
final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) {
if ( configuration != null ) {
instance.setAntialiasScreen( configuration.isAntialiasScreen() );
instance.setShowScale( configuration.isShowScale() );
- instance.setShowBranchLengthValues( configuration.isShowBranchLengthValues() );
instance.setShowOverview( configuration.isShowOverview() );
instance.setColorByTaxonomicGroup( configuration.isColorByTaxonomicGroup() );
instance.setCladogramType( configuration.getCladogramType() );
}
instance.setShowDefaultNodeShapesInternal( configuration.isShowDefaultNodeShapesInternal() );
instance.setShowDefaultNodeShapesExternal( configuration.isShowDefaultNodeShapesExternal() );
+ instance.setShowDefaultNodeShapesForMarkedNodes( configuration.isShowDefaultNodeShapesForMarkedNodes() );
if ( configuration.getExtDescNodeDataToReturn() != null ) {
instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() );
}
+ instance.setRightLineUpDomains( configuration.isRightLineUpDomains() );
+ instance.setLineUpRendarableNodeData( configuration.isLineUpRendarableNodeData() );
instance.setAllowErrorsInDistanceToParent( false );
}
return instance;
return toString().replaceAll( " ", "_" );
}
}
+
+ final public boolean isLineUpRendarableNodeData() {
+ return _line_up_renderable_node_data;
+ }
+
+ final public boolean isRightLineUpDomains() {
+ return _right_align_domains;
+ }
+
+ final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) {
+ _line_up_renderable_node_data = line_up_renderable_node_data;
+ }
+
+ final public void setRightLineUpDomains( final boolean right_align_domains ) {
+ _right_align_domains = right_align_domains;
+ }
}