X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FOptions.java;h=f388e14994dda9af56cf16362b6c583b55baf7e3;hb=8571ac663cce8aade42941742402a8fe37c27ff4;hp=594c9abc3b5cab1d6dbd5289fe8d4f02480f5578;hpb=5958d8c92c06f76da04a466ef7636e93a640b6a3;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java index 594c9ab..f388e14 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.PhylogenyNodeI.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; @@ -37,44 +40,47 @@ 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 _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 boolean _show_confidence_stddev; + private NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style; + private NODE_DATA _ext_desc_data_to_return; private Options() { init(); @@ -184,6 +190,25 @@ final public class Options { _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 boolean isAbbreviateScientificTaxonNames() { @@ -494,6 +519,9 @@ final public class Options { } instance.setTaxonomyColorizeNodeShapes( configuration.isTaxonomyColorizeNodeShapes() ); instance.setShowDefaultNodeShapes( configuration.isShowDefaultNodeShapes() ); + if ( configuration.getExtDescNodeDataToReturn() != null ) { + instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() ); + } } return instance; } @@ -531,4 +559,12 @@ final public class Options { 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; + } }