// 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;
private boolean _editable;
private boolean _background_color_gradient;
private boolean _show_domain_labels;
+ 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;
+ 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;
init();
}
+ public NodeData.NODE_DATA getExtDescNodeDataToReturn() {
+ return _ext_desc_data_to_return;
+ }
+
+ public final boolean isShowDomainLabels() {
+ return _show_domain_labels;
+ }
+
+ 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 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 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 ( 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 = 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;
- _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
- _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
- _show_domain_labels = 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;
- }
-
- boolean isShowConfidenceStddev() {
- return _show_confidence_stddev;
- }
-
- void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
- _show_confidence_stddev = show_confidence_stddev;
- }
-
- NH_CONVERSION_SUPPORT_VALUE_STYLE getNhConversionSupportValueStyle() {
- return _nh_conversion_support_value_style;
- }
-
- void setNhConversionSupportValueStyle( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_value_style ) {
- _nh_conversion_support_value_style = nh_conversion_support_value_style;
+ final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+ return _taxonomy_extraction;
}
final boolean isAbbreviateScientificTaxonNames() {
return _editable;
}
- final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
- return _taxonomy_extraction;
- }
-
final boolean isGraphicsExportUsingActualSize() {
return _graphics_export_using_actual_size;
}
return _show_branch_length_values;
}
- public final boolean isShowDomainLabels() {
- return _show_domain_labels;
+ boolean isShowConfidenceStddev() {
+ return _show_confidence_stddev;
+ }
+
+ boolean isShowDefaultNodeShapesExternal() {
+ return _show_default_node_shapes_external;
+ }
+
+ boolean isShowDefaultNodeShapesInternal() {
+ return _show_default_node_shapes_internal;
}
final boolean isShowOverview() {
_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 setDefaultNodeFill( final NodeFill default_node_fill ) {
_default_node_fill = default_node_fill;
}
_editable = editable;
}
- final void setTaxonomyExtractio( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
- _taxonomy_extraction = taxonomy_extraction;
- }
-
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;
- }
-
- 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 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 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 ) {
_show_branch_length_values = show_branch_length_values;
}
- public void setShowDomainLabels( final boolean show_domain_labels ) {
- _show_domain_labels = show_domain_labels;
+ void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
+ _show_confidence_stddev = show_confidence_stddev;
+ }
+
+ 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 ) {
_taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
}
- final static Options createDefaultInstance() {
- return new Options();
+ final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
+ _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;
+ _taxonomy_colorize_node_shapes = false;
+ _show_branch_length_values = false;
+ _internal_number_are_confidence_for_nh_parsing = false;
+ _show_scale = false;
+ _antialias_screen = false;
+ _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 = 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;
+ _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;
}
- 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;
}
public final static Options createInstance( final Configuration configuration ) {
instance.setNumberOfDigitsAfterCommaForConfidenceValues( configuration
.getNumberOfDigitsAfterCommaForConfidenceValues() );
}
- instance.setTaxonomyExtractio( configuration.getTaxonomyExtraction() );
+ 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() );
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() );
}
return instance;
}
+ final static Options createDefaultInstance() {
+ return new Options();
+ }
+
public static enum CLADOGRAM_TYPE {
NON_LINED_UP, EXT_NODE_SUM_DEP, TOTAL_NODE_SUM_DEP;
}
HORIZONTAL, RADIAL;
}
+ public static enum PHYLOGENY_GRAPHICS_TYPE {
+ RECTANGULAR, TRIANGULAR, EURO_STYLE, ROUNDED, CONVEX, CURVED, UNROOTED, CIRCULAR;
+ }
+
static enum OVERVIEW_PLACEMENT_TYPE {
UPPER_LEFT( "upper left" ),
UPPER_RIGHT( "upper right" ),
}
}
- public static enum PHYLOGENY_GRAPHICS_TYPE {
- RECTANGULAR, TRIANGULAR, EURO_STYLE, ROUNDED, CONVEX, CURVED, UNROOTED, CIRCULAR;
- }
-
- public NodeData.NODE_DATA getExtDescNodeDataToReturn() {
- return _ext_desc_data_to_return;
- }
-
- public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
- _ext_desc_data_to_return = ext_desc_data_to_return;
+ public boolean isAllowFontSizeChange() {
+ return true;
}
}
git://source.jalview.org / jalview.git / blobdiff