// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.archaeopteryx;
import java.awt.Font;
-import org.forester.phylogeny.data.NodeVisualization;
-import org.forester.phylogeny.data.NodeVisualization.NodeFill;
-import org.forester.phylogeny.data.NodeVisualization.NodeShape;
+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.NodeVisualData;
+import org.forester.phylogeny.data.NodeVisualData.NodeFill;
+import org.forester.phylogeny.data.NodeVisualData.NodeShape;
import org.forester.util.ForesterUtil;
/*
*/
final public class Options {
- static final double MIN_CONFIDENCE_DEFAULT = 0.0;
- private boolean _show_branch_length_values;
- private boolean _internal_number_are_confidence_for_nh_parsing;
- private boolean _show_scale;
- private boolean _show_overview;
- private boolean _antialias_screen;
- private boolean _antialias_print;
- private boolean _graphics_export_visible_only;
- private int _print_size_x;
- private int _print_size_y;
- private double _min_confidence_value;
- private boolean _print_black_and_white;
- private boolean _print_using_actual_size;
- private boolean _graphics_export_using_actual_size;
- private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type;
- private CLADOGRAM_TYPE _cladogram_type;
- private OVERVIEW_PLACEMENT_TYPE _ov_placement;
- private NODE_LABEL_DIRECTION _node_label_direction;
- private Font _base_font;
- private boolean _match_whole_terms_only;
- private boolean _search_case_sensitive;
- private float _print_line_width;
- private boolean _inverse_search_result;
- private double _scale_bar_length;
- private short _number_of_digits_after_comma_for_confidence_values;
- private short _number_of_digits_after_comma_for_branch_length_values;
- private boolean _nh_parsing_replace_underscores;
- private boolean _nh_parsing_extract_pfam_taxonomy_codes;
- private boolean _editable;
- private boolean _background_color_gradient;
- private boolean _show_domain_labels;
- private boolean _color_labels_same_as_parent_branch;
- private boolean _abbreviate_scientific_names;
- private NodeVisualization.NodeShape _default_node_shape;
- private NodeVisualization.NodeFill _default_node_fill;
- private short _default_node_shape_size;
- private boolean _taxonomy_colorize_node_shapes;
- private boolean _show_default_node_shapes;
+ static final double MIN_CONFIDENCE_DEFAULT = 0.0;
+ private boolean _abbreviate_scientific_names;
+ private boolean _allow_errors_in_distance_to_parent;
+ private boolean _antialias_print;
+ private boolean _antialias_screen;
+ private boolean _background_color_gradient;
+ private Font _base_font;
+ private CLADOGRAM_TYPE _cladogram_type;
+ private boolean _color_by_taxonomic_group;
+ private boolean _color_labels_same_as_parent_branch;
+ private NodeVisualData.NodeFill _default_node_fill;
+ 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 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 double _min_confidence_value;
+ private NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style;
+ private boolean _nh_parsing_replace_underscores;
+ private NODE_LABEL_DIRECTION _node_label_direction;
+ private short _number_of_digits_after_comma_for_branch_length_values;
+ private short _number_of_digits_after_comma_for_confidence_values;
+ private OVERVIEW_PLACEMENT_TYPE _ov_placement;
+ 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 double _scale_bar_length;
+ private boolean _search_case_sensitive;
+ private boolean _show_annotation_ref_source;
+ private boolean _show_confidence_stddev;
+ 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() {
+ return _ext_desc_data_to_return;
+ }
+
+ public boolean isAllowErrorsInDistanceToParent() {
+ return _allow_errors_in_distance_to_parent;
+ }
+
+ public boolean isAllowFontSizeChange() {
+ return true;
+ }
+
+ public final boolean isShowAnnotationRefSource() {
+ return _show_annotation_ref_source;
+ }
+
+ public final boolean isShowDomainLabels() {
+ return _show_domain_labels;
+ }
+
+ public final void setAllowErrorsInDistanceToParent( final boolean allow_errors_in_distance_to_parent ) {
+ _allow_errors_in_distance_to_parent = allow_errors_in_distance_to_parent;
+ }
+
+ public void setBackgroundColorGradient( final boolean background_color_gradient ) {
+ _background_color_gradient = background_color_gradient;
+ }
+
+ public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
+ _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
+ }
+
+ public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
+ _ext_desc_data_to_return = ext_desc_data_to_return;
+ }
+
+ public final void setShowAnnotationRefSource( final boolean show_annotation_ref_source ) {
+ _show_annotation_ref_source = show_annotation_ref_source;
+ }
+
+ public void setShowDomainLabels( final boolean show_domain_labels ) {
+ _show_domain_labels = show_domain_labels;
+ }
+
final Font getBaseFont() {
return _base_font;
}
return _min_confidence_value;
}
+ NH_CONVERSION_SUPPORT_VALUE_STYLE getNhConversionSupportValueStyle() {
+ return _nh_conversion_support_value_style;
+ }
+
final NODE_LABEL_DIRECTION getNodeLabelDirection() {
return _node_label_direction;
}
return _scale_bar_length;
}
- final private void init() {
- _default_node_shape = NodeShape.CIRCLE;
- _default_node_fill = NodeFill.GRADIENT;
- _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
- _taxonomy_colorize_node_shapes = false;
- _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 = false;
- if ( Util.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 = false;
- _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;
- _nh_parsing_extract_pfam_taxonomy_codes = false;
- _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
- _show_domain_labels = true;
- setAbbreviateScientificTaxonNames( false );
- _color_labels_same_as_parent_branch = false;
+ final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+ return _taxonomy_extraction;
}
final boolean isAbbreviateScientificTaxonNames() {
return _background_color_gradient;
}
+ final boolean isColorByTaxonomicGroup() {
+ return _color_by_taxonomic_group;
+ }
+
final boolean isColorLabelsSameAsParentBranch() {
return _color_labels_same_as_parent_branch;
}
return _editable;
}
- final boolean isExtractPfamTaxonomyCodesInNhParsing() {
- return _nh_parsing_extract_pfam_taxonomy_codes;
- }
-
final boolean isGraphicsExportUsingActualSize() {
return _graphics_export_using_actual_size;
}
return _search_case_sensitive;
}
- final boolean isShowBranchLengthValues() {
- return _show_branch_length_values;
+ boolean isShowConfidenceStddev() {
+ return _show_confidence_stddev;
}
- public final boolean isShowDomainLabels() {
- return _show_domain_labels;
+ boolean isShowDefaultNodeShapesExternal() {
+ return _show_default_node_shapes_external;
+ }
+
+ boolean isShowDefaultNodeShapesInternal() {
+ return _show_default_node_shapes_internal;
}
final boolean isShowOverview() {
return _show_scale;
}
- boolean isTaxonomyColorizeNodeShapes() {
- return _taxonomy_colorize_node_shapes;
- }
-
final void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
_abbreviate_scientific_names = abbreviate_scientific_names;
}
_antialias_screen = antialias_screen;
}
- public void setBackgroundColorGradient( final boolean background_color_gradient ) {
- _background_color_gradient = background_color_gradient;
- }
-
final void setBaseFont( final Font base_font ) {
_base_font = base_font;
}
_cladogram_type = cladogram_type;
}
- public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
- _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
+ final void setColorByTaxonomicGroup( final boolean color_by_taxonomic_group ) {
+ _color_by_taxonomic_group = color_by_taxonomic_group;
}
final void setDefaultNodeFill( final NodeFill default_node_fill ) {
_editable = editable;
}
- final void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) {
- _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes;
- }
-
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 ) {
_min_confidence_value = min_confidence_value;
}
- final void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
- _node_label_direction = node_label_direction;
+ void setNhConversionSupportValueStyle( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_value_style ) {
+ _nh_conversion_support_value_style = nh_conversion_support_value_style;
}
- 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 void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
+ _node_label_direction = node_label_direction;
}
final void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
_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;
}
- public void setShowDomainLabels( final boolean show_domain_labels ) {
- _show_domain_labels = show_domain_labels;
+ void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
+ _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;
}
final void setShowOverview( final boolean show_overview ) {
_show_scale = show_scale;
}
- void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
- _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
+ final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
+ _taxonomy_extraction = taxonomy_extraction;
}
- final static Options createDefaultInstance() {
- return new Options();
+ 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;
+ 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 = 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;
}
- boolean isShowDefaultNodeShapes() {
- return _show_default_node_shapes;
+ 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;
}
- void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
- _show_default_node_shapes = show_default_node_shapes;
+ 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 static Options createInstance( final Configuration configuration ) {
+ 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() );
instance.setOvPlacement( configuration.getOvPlacement() );
instance.setPrintLineWidth( configuration.getPrintLineWidth() );
instance.setNumberOfDigitsAfterCommaForConfidenceValues( configuration
.getNumberOfDigitsAfterCommaForConfidenceValues() );
}
- instance.setExtractPfamTaxonomyCodesInNhParsing( configuration.isExtractPfamTaxonomyCodesInNhParsing() );
+ instance.setTaxonomyExtraction( configuration.getTaxonomyExtraction() );
instance.setReplaceUnderscoresInNhParsing( configuration.isReplaceUnderscoresInNhParsing() );
instance.setInternalNumberAreConfidenceForNhParsing( configuration
.isInternalNumberAreConfidenceForNhParsing() );
instance.setEditable( configuration.isEditable() );
instance.setColorLabelsSameAsParentBranch( configuration.isColorLabelsSameAsParentBranch() );
instance.setShowDomainLabels( configuration.isShowDomainLabels() );
+ instance.setShowAnnotationRefSource( configuration.isShowAnnotationRefSource() );
instance.setAbbreviateScientificTaxonNames( configuration.isAbbreviateScientificTaxonNames() );
if ( configuration.getMinConfidenceValue() != MIN_CONFIDENCE_DEFAULT ) {
instance.setMinConfidenceValue( configuration.getMinConfidenceValue() );
if ( configuration.getDefaultNodeShapeSize() >= 0 ) {
instance.setDefaultNodeShapeSize( configuration.getDefaultNodeShapeSize() );
}
- instance.setTaxonomyColorizeNodeShapes( configuration.isTaxonomyColorizeNodeShapes() );
- instance.setShowDefaultNodeShapes( configuration.isShowDefaultNodeShapes() );
+ instance.setShowDefaultNodeShapesInternal( configuration.isShowDefaultNodeShapesInternal() );
+ instance.setShowDefaultNodeShapesExternal( configuration.isShowDefaultNodeShapesExternal() );
+ if ( configuration.getExtDescNodeDataToReturn() != null ) {
+ instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() );
+ }
+ instance.setRightLineUpDomains( configuration.isRightLineUpDomains() );
+ instance.setLineUpRendarableNodeData( configuration.isLineUpRendarableNodeData() );
+ instance.setAllowErrorsInDistanceToParent( false );
}
return instance;
}
- static enum CLADOGRAM_TYPE {
- NON_LINED_UP, EXT_NODE_SUM_DEP, TOTAL_NODE_SUM_DEP;
+ final static Options createDefaultInstance() {
+ return new Options();
+ }
+
+ public static enum CLADOGRAM_TYPE {
+ EXT_NODE_SUM_DEP, NON_LINED_UP, TOTAL_NODE_SUM_DEP;
}
- static enum NODE_LABEL_DIRECTION {
+ 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 {
- UPPER_LEFT( "upper left" ),
- UPPER_RIGHT( "upper right" ),
LOWER_LEFT( "lower left" ),
- LOWER_RIGHT( "lower right" );
+ LOWER_RIGHT( "lower right" ),
+ UPPER_LEFT( "upper left" ),
+ UPPER_RIGHT( "upper right" );
private final String _name;
}
}
- static enum PHYLOGENY_GRAPHICS_TYPE {
- RECTANGULAR, TRIANGULAR, EURO_STYLE, ROUNDED, CONVEX, CURVED, UNROOTED, CIRCULAR;
+ 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