X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FOptions.java;h=8494510d51ff12dc7ea3b7f80113d08e281f8b9c;hb=803a2b32992b5944b73c6dfcb80ceb58c09b81c1;hp=f025733b3aed0c05da1b867b45624bee5f239d02;hpb=cc09a4de53fe2c95d71a0c93d6f894db2c845491;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java index f025733..8494510 100644 --- a/forester/java/src/org/forester/archaeopteryx/Options.java +++ b/forester/java/src/org/forester/archaeopteryx/Options.java @@ -21,12 +21,18 @@ // 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.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; +import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE; +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; import org.forester.util.ForesterUtil; /* @@ -34,100 +40,151 @@ import org.forester.util.ForesterUtil; */ final public class Options { - static final double MIN_CONFIDENCE_DEFAULT = 0.0; - private NodeShape _default_node_shape; - 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; - - enum NodeShape { - NONE, CIRCLE_WITH_GRADIENT, CIRCLE_SOLID, RECTANGLE_WITH_GRADIENT, RECTANGLE_SOLID; + 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 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 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 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 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_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 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 boolean _color_all_found_nodes_when_coloring_subtree; + private boolean _parse_beast_style_extended_nexus_tags; + private Options() { init(); } - final Font getBaseFont() { - return _base_font; + public NodeDataField getExtDescNodeDataToReturn() { + return _ext_desc_data_to_return; } - final CLADOGRAM_TYPE getCladogramType() { - return _cladogram_type; + public boolean isAllowErrorsInDistanceToParent() { + return _allow_errors_in_distance_to_parent; } - final double getMinConfidenceValue() { - return _min_confidence_value; + final public boolean isLineUpRendarableNodeData() { + return _line_up_renderable_node_data; } - final NODE_LABEL_DIRECTION getNodeLabelDirection() { - return _node_label_direction; + final public boolean isRightLineUpDomains() { + return _right_align_domains; } - final short getNumberOfDigitsAfterCommaForBranchLengthValues() { - return _number_of_digits_after_comma_for_branch_length_values; + public final boolean isShowAnnotationRefSource() { + return _show_annotation_ref_source; } - final short getNumberOfDigitsAfterCommaForConfidenceValues() { - return _number_of_digits_after_comma_for_confidence_values; + public final boolean isShowDomainLabels() { + return _show_domain_labels; } - final OVERVIEW_PLACEMENT_TYPE getOvPlacement() { - return _ov_placement; + public final void setAllowErrorsInDistanceToParent( final boolean allow_errors_in_distance_to_parent ) { + _allow_errors_in_distance_to_parent = allow_errors_in_distance_to_parent; } - final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() { - return _phylogeny_graphics_type; + public void setBackgroundColorGradient( final boolean background_color_gradient ) { + _background_color_gradient = background_color_gradient; } - final float getPrintLineWidth() { - return _print_line_width; + public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) { + _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch; } - final int getPrintSizeX() { - return _print_size_x; + public void setExtDescNodeDataToReturn( final NodeDataField ext_desc_data_to_return ) { + _ext_desc_data_to_return = ext_desc_data_to_return; } - final int getPrintSizeY() { - return _print_size_y; + final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) { + _line_up_renderable_node_data = line_up_renderable_node_data; } - final double getScaleBarLength() { - return _scale_bar_length; + 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; + } + + public void setShowDomainLabels( final boolean show_domain_labels ) { + _show_domain_labels = show_domain_labels; } final private void init() { - _default_node_shape = NodeShape.RECTANGLE_WITH_GRADIENT; - _show_branch_length_values = false; + _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; @@ -135,36 +192,114 @@ final public class Options { _graphics_export_visible_only = false; _editable = true; _background_color_gradient = 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; - } + _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; - _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_with_regex = false; _search_case_sensitive = false; - _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT; + _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 = 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; + _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; - _nh_parsing_extract_pfam_taxonomy_codes = false; - _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT; + _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; + } + + final CLADOGRAM_TYPE getCladogramType() { + return _cladogram_type; + } + + final NodeFill getDefaultNodeFill() { + return _default_node_fill; + } + + final NodeShape getDefaultNodeShape() { + return _default_node_shape; + } + + final short getDefaultNodeShapeSize() { + return _default_node_shape_size; + } + + final double getMinConfidenceValue() { + 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; + } + + final short getNumberOfDigitsAfterCommaForBranchLengthValues() { + return _number_of_digits_after_comma_for_branch_length_values; + } + + final short getNumberOfDigitsAfterCommaForConfidenceValues() { + return _number_of_digits_after_comma_for_confidence_values; + } + + final OVERVIEW_PLACEMENT_TYPE getOvPlacement() { + return _ov_placement; + } + + final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() { + return _phylogeny_graphics_type; + } + + final float getPrintLineWidth() { + return _print_line_width; + } + + final double getScaleBarLength() { + return _scale_bar_length; + } + + final TAXONOMY_EXTRACTION getTaxonomyExtraction() { + return _taxonomy_extraction; + } + + final boolean isAbbreviateScientificTaxonNames() { + return _abbreviate_scientific_names; + } + + boolean isAllowMagnificationOfTaxonomyImages() { + return true; } final boolean isAntialiasPrint() { @@ -179,8 +314,8 @@ final public class Options { return _background_color_gradient; } - public final boolean isShowDomainLabels() { - return _show_domain_labels; + final boolean isColorByTaxonomicGroup() { + return _color_by_taxonomic_group; } final boolean isColorLabelsSameAsParentBranch() { @@ -191,10 +326,6 @@ final public class Options { return _editable; } - final boolean isExtractPfamTaxonomyCodesInNhParsing() { - return _nh_parsing_extract_pfam_taxonomy_codes; - } - final boolean isGraphicsExportUsingActualSize() { return _graphics_export_using_actual_size; } @@ -231,12 +362,24 @@ final public class Options { return _search_case_sensitive; } - final boolean isShowBranchLengthValues() { - return _show_branch_length_values; + final boolean isSearchWithRegex() { + return _search_with_regex; } - final NodeShape getDefaultNodeShape() { - return _default_node_shape; + boolean isShowConfidenceStddev() { + return _show_confidence_stddev; + } + + boolean isShowDefaultNodeShapesExternal() { + return _show_default_node_shapes_external; + } + + boolean isShowDefaultNodeShapesForMarkedNodes() { + return _show_default_node_shapes_for_marked_nodes; + } + + boolean isShowDefaultNodeShapesInternal() { + return _show_default_node_shapes_internal; } final boolean isShowOverview() { @@ -247,6 +390,10 @@ final public class Options { return _show_scale; } + final void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) { + _abbreviate_scientific_names = abbreviate_scientific_names; + } + final void setAntialiasPrint( final boolean antialias_print ) { _antialias_print = antialias_print; } @@ -255,18 +402,6 @@ final public class Options { _antialias_screen = antialias_screen; } - public void setBackgroundColorGradient( final boolean background_color_gradient ) { - _background_color_gradient = background_color_gradient; - } - - public void setShowDomainLabels( final boolean show_domain_labels ) { - _show_domain_labels = show_domain_labels; - } - - 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 setBaseFont( final Font base_font ) { _base_font = base_font; } @@ -275,26 +410,28 @@ final public class Options { _cladogram_type = cladogram_type; } - final void setEditable( final boolean editable ) { - _editable = editable; + final void setColorByTaxonomicGroup( final boolean color_by_taxonomic_group ) { + _color_by_taxonomic_group = color_by_taxonomic_group; } - 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 setDefaultNodeFill( final NodeFill default_node_fill ) { + _default_node_fill = default_node_fill; } - 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 setDefaultNodeShape( final NodeShape default_node_shape ) { + _default_node_shape = default_node_shape; + } + + final void setDefaultNodeShapeSize( final short default_node_shape_size ) { + _default_node_shape_size = default_node_shape_size; + } + + final void setEditable( final boolean editable ) { + _editable = editable; } 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 ) { @@ -313,16 +450,12 @@ final public class Options { _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 ) { @@ -340,19 +473,7 @@ final public class Options { 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; } @@ -365,12 +486,24 @@ final public class Options { _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; } - final void setDefaultNodeShape( final NodeShape default_node_shape ) { - _default_node_shape = default_node_shape; + 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 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 ) { @@ -381,17 +514,17 @@ final public class Options { _show_scale = show_scale; } - final static Options createDefaultInstance() { - return new Options(); + final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) { + _taxonomy_extraction = taxonomy_extraction; } - 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() ); @@ -405,23 +538,18 @@ final public class Options { 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.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() ) ); } @@ -432,58 +560,45 @@ final public class Options { if ( configuration.getPhylogenyGraphicsType() != null ) { instance.setPhylogenyGraphicsType( configuration.getPhylogenyGraphicsType() ); } + if ( configuration.getDefaultNodeFill() != null ) { + instance.setDefaultNodeFill( configuration.getDefaultNodeFill() ); + } + if ( configuration.getDefaultNodeShape() != null ) { + instance.setDefaultNodeShape( configuration.getDefaultNodeShape() ); + } + if ( configuration.getDefaultNodeShapeSize() >= 0 ) { + instance.setDefaultNodeShapeSize( configuration.getDefaultNodeShapeSize() ); + } + instance.setShowDefaultNodeShapesInternal( configuration.isShowDefaultNodeShapesInternal() ); + instance.setShowDefaultNodeShapesExternal( configuration.isShowDefaultNodeShapesExternal() ); + instance.setShowDefaultNodeShapesForMarkedNodes( configuration.isShowDefaultNodeShapesForMarkedNodes() ); + if ( configuration.getExtDescNodeDataToReturn() != null ) { + instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() ); + } + instance.setRightLineUpDomains( configuration.isRightLineUpDomains() ); + instance.setLineUpRendarableNodeData( configuration.isLineUpRendarableNodeData() ); + instance.setAllowErrorsInDistanceToParent( false ); } return instance; } - final void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) { - _abbreviate_scientific_names = abbreviate_scientific_names; - } - - final boolean isAbbreviateScientificTaxonNames() { - return _abbreviate_scientific_names; - } - - static enum CLADOGRAM_TYPE { - NON_LINED_UP, EXT_NODE_SUM_DEP, TOTAL_NODE_SUM_DEP; + final static Options createDefaultInstance() { + return new Options(); } - static enum NODE_LABEL_DIRECTION { - HORIZONTAL, RADIAL; + final boolean isColorAllFoundNodesWhenColoringSubtree() { + return _color_all_found_nodes_when_coloring_subtree; } - - static enum OVERVIEW_PLACEMENT_TYPE { - UPPER_LEFT( "upper left" ), - UPPER_RIGHT( "upper right" ), - LOWER_LEFT( "lower left" ), - LOWER_RIGHT( "lower 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 setColorAllFoundNodesWhenColoringSubtree( final boolean color_all_found_nodes_when_coloring_subtree ) { + _color_all_found_nodes_when_coloring_subtree = color_all_found_nodes_when_coloring_subtree; } - static enum PHYLOGENY_GRAPHICS_TYPE { - RECTANGULAR, TRIANGULAR, EURO_STYLE, ROUNDED, CONVEX, CURVED, UNROOTED, CIRCULAR; - } - - boolean isAllowMagnificationOfTaxonomyImages() { - return true; + final boolean isParseBeastStyleExtendedNexusTags() { + return _parse_beast_style_extended_nexus_tags; } - int getDefaultNodeBoxSize() { - // TODO make variable ~~ - return 8; + final void setParseBeastStyleExtendedNexusTags( boolean parse_beast_style_extended_nexus_tags ) { + _parse_beast_style_extended_nexus_tags = parse_beast_style_extended_nexus_tags; } }