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;
*/
final public class Options {
+ public static enum CLADOGRAM_TYPE {
+ LINED_UP, NON_LINED_UP;
+ }
+
+ public static enum NODE_LABEL_DIRECTION {
+ HORIZONTAL, RADIAL;
+ }
+
+ 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" ),
+ LOWER_RIGHT( "lower right" ),
+ UPPER_LEFT( "upper left" ),
+ UPPER_RIGHT( "upper right" );
+
+ private final String _name;
+
+ private OVERVIEW_PLACEMENT_TYPE( final String name ) {
+ _name = name;
+ }
+
+ @Override
+ public String toString() {
+ return _name;
+ }
+
+ public String toTag() {
+ 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 NodeVisualData.NodeShape _default_node_shape;
private short _default_node_shape_size;
private boolean _editable;
- private NODE_DATA _ext_desc_data_to_return;
- private boolean _graphics_export_using_actual_size;
+ private NodeDataField _ext_desc_data_to_return;
+ 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 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 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 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 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();
}
- 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;
+ final public boolean isLineUpRendarableNodeData() {
+ return _line_up_renderable_node_data;
+ }
+
+ final public boolean isRightLineUpDomains() {
+ return _right_align_domains;
}
public final boolean isShowAnnotationRefSource() {
_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;
}
+ 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;
+ }
+
public final void setShowAnnotationRefSource( final boolean show_annotation_ref_source ) {
_show_annotation_ref_source = show_annotation_ref_source;
}
_show_domain_labels = show_domain_labels;
}
+ final private void init() {
+ _default_node_shape = NodeShape.CIRCLE;
+ _default_node_fill = NodeFill.GRADIENT;
+ _default_node_shape_size = AptxConstants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
+ _internal_number_are_confidence_for_nh_parsing = false;
+ _show_scale = false;
+ _antialias_screen = true;
+ _antialias_print = true;
+ _graphics_export_visible_only = false;
+ _editable = 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;
+ _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;
+ _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 = 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 = 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 = AptxConstants.CLADOGRAM_TYPE_DEFAULT;
+ _show_domain_labels = true;
+ _show_annotation_ref_source = true;
+ setAbbreviateScientificTaxonNames( false );
+ _color_labels_same_as_parent_branch = false;
+ _show_confidence_stddev = false;
+ _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
+ _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 ) {
+ _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
+ }
+
+ final private void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
+ _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
+ }
+
final Font getBaseFont() {
return _base_font;
}
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;
}
return _search_case_sensitive;
}
- final boolean isShowBranchLengthValues() {
- return _show_branch_length_values;
+ final boolean isSearchWithRegex() {
+ return _search_with_regex;
}
boolean isShowConfidenceStddev() {
return _show_default_node_shapes_external;
}
+ boolean isShowDefaultNodeShapesForMarkedNodes() {
+ return _show_default_node_shapes_for_marked_nodes;
+ }
+
boolean isShowDefaultNodeShapesInternal() {
return _show_default_node_shapes_internal;
}
_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;
}
_search_case_sensitive = search_case_sensitive;
}
- final void setShowBranchLengthValues( final boolean show_branch_length_values ) {
- _show_branch_length_values = show_branch_length_values;
+ final void setSearchWithRegex( final boolean search_with_regex ) {
+ _search_with_regex = search_with_regex;
}
void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
_show_default_node_shapes_external = show_default_node_shapes_external;
}
+ 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;
+ }
+
void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
_show_default_node_shapes_internal = show_default_node_shapes_internal;
}
_taxonomy_extraction = taxonomy_extraction;
}
- final private void init() {
- _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;
- _antialias_print = true;
- _graphics_export_visible_only = false;
- _editable = true;
- _background_color_gradient = false;
- _show_default_node_shapes_internal = false;
- _show_default_node_shapes_external = 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;
- }
- _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_case_sensitive = false;
- _print_line_width = Constants.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;
- _nh_parsing_replace_underscores = false;
- _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
- _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
- _show_domain_labels = true;
- _show_annotation_ref_source = true;
- setAbbreviateScientificTaxonNames( false );
- _color_labels_same_as_parent_branch = false;
- _show_confidence_stddev = true;
- _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
- _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
- _line_up_renderable_node_data = false;
- _right_align_domains = false;
- }
-
- final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) {
- _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
- }
-
- final private void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
- _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
- }
-
public final static Options createInstance( final Configuration configuration ) {
final Options instance = createDefaultInstance();
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() );
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() ) );
}
}
instance.setShowDefaultNodeShapesInternal( configuration.isShowDefaultNodeShapesInternal() );
instance.setShowDefaultNodeShapesExternal( configuration.isShowDefaultNodeShapesExternal() );
+ instance.setShowDefaultNodeShapesForMarkedNodes( configuration.isShowDefaultNodeShapesForMarkedNodes() );
if ( configuration.getExtDescNodeDataToReturn() != null ) {
instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() );
}
return new Options();
}
- public static enum CLADOGRAM_TYPE {
- EXT_NODE_SUM_DEP, NON_LINED_UP, TOTAL_NODE_SUM_DEP;
+ final boolean isColorAllFoundNodesWhenColoringSubtree() {
+ return _color_all_found_nodes_when_coloring_subtree;
}
-
- public static enum NODE_LABEL_DIRECTION {
- HORIZONTAL, RADIAL;
+
+ 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;
}
- public static enum PHYLOGENY_GRAPHICS_TYPE {
- CIRCULAR, CONVEX, CURVED, EURO_STYLE, RECTANGULAR, ROUNDED, TRIANGULAR, UNROOTED;
+ final boolean isParseBeastStyleExtendedNexusTags() {
+ return _parse_beast_style_extended_nexus_tags;
}
- static enum OVERVIEW_PLACEMENT_TYPE {
- LOWER_LEFT( "lower left" ),
- LOWER_RIGHT( "lower right" ),
- UPPER_LEFT( "upper left" ),
- UPPER_RIGHT( "upper right" );
-
- private final String _name;
-
- private OVERVIEW_PLACEMENT_TYPE( final String name ) {
- _name = name;
- }
-
- @Override
- public String toString() {
- return _name;
- }
-
- public String toTag() {
- return toString().replaceAll( " ", "_" );
- }
+ final void setParseBeastStyleExtendedNexusTags( final boolean parse_beast_style_extended_nexus_tags ) {
+ _parse_beast_style_extended_nexus_tags = parse_beast_style_extended_nexus_tags;
}
-
- final public boolean isLineUpRendarableNodeData() {
- return _line_up_renderable_node_data;
+
+ final boolean isCollapsedWithAverageHeigh() {
+ return _collapsed_with_average_height;
}
- final public boolean isRightLineUpDomains() {
- return _right_align_domains;
+ final void setCollapsedWithAverageHeigh( final boolean collapsed_with_average_height ) {
+ _collapsed_with_average_height = collapsed_with_average_height;
}
- final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) {
- _line_up_renderable_node_data = line_up_renderable_node_data;
+ final boolean isShowAbbreviatedLabelsForCollapsedNodes() {
+ return _show_abbreviated_labels_for_collapsed_nodes;
}
-
- final public void setRightLineUpDomains( final boolean right_align_domains ) {
- _right_align_domains = right_align_domains;
+
+ 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