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 {
+ EXT_NODE_SUM_DEP, NON_LINED_UP, TOTAL_NODE_SUM_DEP;
+ }
+
+ 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 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 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;
init();
}
- public NodeData.NODE_DATA getExtDescNodeDataToReturn() {
- return NodeData.NODE_DATA.DOMAINS_ALL;
- // TODO fix me
- // FIXME remove me
- // ~~~~~~
- //return _ext_desc_data_to_return;
+ public NodeDataField getExtDescNodeDataToReturn() {
+ return _ext_desc_data_to_return;
}
public boolean isAllowErrorsInDistanceToParent() {
return _allow_errors_in_distance_to_parent;
}
+ final public boolean isLineUpRendarableNodeData() {
+ return _line_up_renderable_node_data;
+ }
+
+ final public boolean isRightLineUpDomains() {
+ return _right_align_domains;
+ }
+
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;
}
+ 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;
+ if ( AptxUtil.isUsOrCanada() ) {
+ _print_size_x = AptxConstants.US_LETTER_SIZE_X;
+ _print_size_y = AptxConstants.US_LETTER_SIZE_Y;
+ }
+ else {
+ _print_size_x = AptxConstants.A4_SIZE_X;
+ _print_size_y = AptxConstants.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_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;
+ }
+
+ 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 _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 isSearchWithRegex() {
+ return _search_with_regex;
+ }
+
boolean isShowConfidenceStddev() {
return _show_confidence_stddev;
}
_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 setSearchWithRegex( final boolean search_with_regex ) {
+ _search_with_regex = search_with_regex;
+ }
+
void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
_show_confidence_stddev = show_confidence_stddev;
}
_show_default_node_shapes_external = show_default_node_shapes_external;
}
- void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
- _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;
}
+ void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
+ _show_default_node_shapes_internal = show_default_node_shapes_internal;
+ }
+
final void setShowOverview( final boolean show_overview ) {
_show_overview = show_overview;
}
_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;
- _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;
- 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_with_regex = false;
- _search_case_sensitive = true;
- _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 = false;
- _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
- _ext_desc_data_to_return = NODE_DATA.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 ) {
- _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 ) {
final static Options createDefaultInstance() {
return new Options();
}
-
- public static enum CLADOGRAM_TYPE {
- EXT_NODE_SUM_DEP, NON_LINED_UP, TOTAL_NODE_SUM_DEP;
- }
-
- 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 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 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;
- }
}
git://source.jalview.org / jalview.git / blobdiff