X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FOptions.java;h=4b75521b185b79a30cedd209997257ec53f8eb70;hb=09d0269700d3108a10d8e349e37384a9cad551ea;hp=babf160521465383100771aac319b37e206df39f;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java index babf160..4b75521 100644 --- a/forester/java/src/org/forester/archaeopteryx/Options.java +++ b/forester/java/src/org/forester/archaeopteryx/Options.java @@ -27,6 +27,9 @@ 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.util.ForesterUtil; /* @@ -34,40 +37,44 @@ import org.forester.util.ForesterUtil; */ final public class Options { - static final double MIN_CONFIDENCE_DEFAULT = 0.0; - private boolean _show_node_boxes; - 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; + 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; private Options() { init(); @@ -81,6 +88,18 @@ final public class Options { 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; } @@ -122,7 +141,10 @@ final public class Options { } final private void init() { - _show_node_boxes = false; + _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; @@ -131,6 +153,7 @@ final public class Options { _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; @@ -163,6 +186,14 @@ final public class Options { _color_labels_same_as_parent_branch = false; } + final boolean isAbbreviateScientificTaxonNames() { + return _abbreviate_scientific_names; + } + + boolean isAllowMagnificationOfTaxonomyImages() { + return true; + } + final boolean isAntialiasPrint() { return _antialias_print; } @@ -175,10 +206,6 @@ final public class Options { return _background_color_gradient; } - public final boolean isShowDomainLabels() { - return _show_domain_labels; - } - final boolean isColorLabelsSameAsParentBranch() { return _color_labels_same_as_parent_branch; } @@ -231,8 +258,8 @@ final public class Options { return _show_branch_length_values; } - final boolean isShowNodeBoxes() { - return _show_node_boxes; + public final boolean isShowDomainLabels() { + return _show_domain_labels; } final boolean isShowOverview() { @@ -243,6 +270,14 @@ final public class Options { return _show_scale; } + boolean isTaxonomyColorizeNodeShapes() { + return _taxonomy_colorize_node_shapes; + } + + 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; } @@ -255,20 +290,28 @@ final public class Options { _background_color_gradient = background_color_gradient; } - public void setShowDomainLabels( final boolean show_domain_labels ) { - _show_domain_labels = show_domain_labels; + final void setBaseFont( final Font base_font ) { + _base_font = base_font; + } + + final void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) { + _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 setBaseFont( final Font base_font ) { - _base_font = base_font; + final void setDefaultNodeFill( final NodeFill default_node_fill ) { + _default_node_fill = default_node_fill; } - final void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) { - _cladogram_type = cladogram_type; + 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 ) { @@ -365,8 +408,8 @@ final public class Options { _show_branch_length_values = show_branch_length_values; } - final void setShowNodeBoxes( final boolean show_node_boxes ) { - _show_node_boxes = show_node_boxes; + public void setShowDomainLabels( final boolean show_domain_labels ) { + _show_domain_labels = show_domain_labels; } final void setShowOverview( final boolean show_overview ) { @@ -377,10 +420,22 @@ final public class Options { _show_scale = show_scale; } + void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) { + _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes; + } + final static Options createDefaultInstance() { return new Options(); } + boolean isShowDefaultNodeShapes() { + return _show_default_node_shapes; + } + + void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) { + _show_default_node_shapes = show_default_node_shapes; + } + final static Options createInstance( final Configuration configuration ) { final Options instance = createDefaultInstance(); if ( configuration != null ) { @@ -428,18 +483,21 @@ 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.setTaxonomyColorizeNodeShapes( configuration.isTaxonomyColorizeNodeShapes() ); + instance.setShowDefaultNodeShapes( configuration.isShowDefaultNodeShapes() ); } 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; } @@ -473,9 +531,4 @@ final public class Options { static enum PHYLOGENY_GRAPHICS_TYPE { RECTANGULAR, TRIANGULAR, EURO_STYLE, ROUNDED, CONVEX, CURVED, UNROOTED, CIRCULAR; } - - boolean isAllowMagnificationOfTaxonomyImages() { - // TODO Auto-generated method stub - return true; - } }