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.NodeVisualization;
-import org.forester.phylogeny.data.NodeVisualization.NodeFill;
-import org.forester.phylogeny.data.NodeVisualization.NodeShape;
+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 _color_by_taxonomic_group;
- 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 _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 int _print_size_x;
- private int _print_size_y;
+ 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 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 NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style;
+ private boolean _nh_parsing_replace_underscores;
private NODE_LABEL_DIRECTION _node_label_direction;
- private Font _base_font;
- private boolean _match_whole_terms_only;
- private boolean _search_case_sensitive;
+ 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 boolean _inverse_search_result;
+ private int _print_size_x;
+ private int _print_size_y;
+ private boolean _print_using_actual_size;
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 TAXONOMY_EXTRACTION _taxonomy_extraction;
- private boolean _editable;
- private boolean _background_color_gradient;
- private boolean _show_domain_labels;
+ private boolean _search_case_sensitive;
private boolean _show_annotation_ref_source;
- 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_internal;
- private boolean _show_default_node_shapes_external;
private boolean _show_confidence_stddev;
- private NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style;
- private NODE_DATA _ext_desc_data_to_return;
+ 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();
return _ext_desc_data_to_return;
}
- public final boolean isShowDomainLabels() {
- return _show_domain_labels;
+ 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 void setShowAnnotationRefSource( final boolean show_annotation_ref_source ) {
- _show_annotation_ref_source = 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 ) {
_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;
}
return _background_color_gradient;
}
+ final boolean isColorByTaxonomicGroup() {
+ return _color_by_taxonomic_group;
+ }
+
final boolean isColorLabelsSameAsParentBranch() {
return _color_labels_same_as_parent_branch;
}
return _search_case_sensitive;
}
- final boolean isShowBranchLengthValues() {
- return _show_branch_length_values;
- }
-
- final boolean isColorByTaxonomicGroup() {
- return _color_by_taxonomic_group;
- }
-
boolean isShowConfidenceStddev() {
return _show_confidence_stddev;
}
return _show_scale;
}
- boolean isTaxonomyColorizeNodeShapes() {
- return _taxonomy_colorize_node_shapes;
- }
-
final void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
_abbreviate_scientific_names = abbreviate_scientific_names;
}
_cladogram_type = cladogram_type;
}
+ 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 ) {
_default_node_fill = default_node_fill;
}
_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 setColorByTaxonomicGroup( final boolean color_by_taxonomic_group ) {
- _color_by_taxonomic_group = color_by_taxonomic_group;
- }
-
void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
_show_confidence_stddev = show_confidence_stddev;
}
_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;
}
_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;
}
_min_confidence_value = MIN_CONFIDENCE_DEFAULT;
_print_black_and_white = false;
- _print_using_actual_size = 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 );
_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;
+ _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() );
if ( configuration.getDefaultNodeShapeSize() >= 0 ) {
instance.setDefaultNodeShapeSize( configuration.getDefaultNodeShapeSize() );
}
- instance.setTaxonomyColorizeNodeShapes( configuration.isTaxonomyColorizeNodeShapes() );
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;
}
}
public static enum CLADOGRAM_TYPE {
- NON_LINED_UP, EXT_NODE_SUM_DEP, TOTAL_NODE_SUM_DEP;
+ EXT_NODE_SUM_DEP, NON_LINED_UP, TOTAL_NODE_SUM_DEP;
}
public static enum NODE_LABEL_DIRECTION {
}
public static enum PHYLOGENY_GRAPHICS_TYPE {
- RECTANGULAR, TRIANGULAR, EURO_STYLE, ROUNDED, CONVEX, CURVED, UNROOTED, CIRCULAR;
+ 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;
}
}
- public boolean isAllowFontSizeChange() {
- return true;
+ 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