X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FOptions.java;h=cb067ab265a8b65660e3167a695e85714fc3300c;hb=10f90f7787d4b1287a910d4e6ae895da14866929;hp=083a6b1bd6eb532cfd566ef1974a5e0367d92d3c;hpb=bb78bbf463fdbb67cfa123c94ddaa1e8f1d3c356;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java index 083a6b1..cb067ab 100644 --- a/forester/java/src/org/forester/archaeopteryx/Options.java +++ b/forester/java/src/org/forester/archaeopteryx/Options.java @@ -27,6 +27,10 @@ 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.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 +41,47 @@ 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 TAXONOMY_EXTRACTION _taxonomy_extraction; + 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(); @@ -154,7 +161,7 @@ final public class Options { _editable = true; _background_color_gradient = false; _show_default_node_shapes = false; - if ( Util.isUsOrCanada() ) { + if ( AptxUtil.isUsOrCanada() ) { _print_size_x = Constants.US_LETTER_SIZE_X; _print_size_y = Constants.US_LETTER_SIZE_Y; } @@ -179,11 +186,30 @@ final public class Options { _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; - _nh_parsing_extract_pfam_taxonomy_codes = 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 boolean isAbbreviateScientificTaxonNames() { @@ -214,8 +240,8 @@ final public class Options { return _editable; } - final boolean isExtractPfamTaxonomyCodesInNhParsing() { - return _nh_parsing_extract_pfam_taxonomy_codes; + final TAXONOMY_EXTRACTION getTaxonomyExtraction() { + return _taxonomy_extraction; } final boolean isGraphicsExportUsingActualSize() { @@ -318,8 +344,8 @@ final public class Options { _editable = editable; } - 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 setTaxonomyExtractio( final TAXONOMY_EXTRACTION taxonomy_extraction ) { + _taxonomy_extraction = taxonomy_extraction; } final void setGraphicsExportUsingActualSize( final boolean graphics_export_using_actual_size ) { @@ -456,7 +482,7 @@ final public class Options { instance.setNumberOfDigitsAfterCommaForConfidenceValues( configuration .getNumberOfDigitsAfterCommaForConfidenceValues() ); } - instance.setExtractPfamTaxonomyCodesInNhParsing( configuration.isExtractPfamTaxonomyCodesInNhParsing() ); + instance.setTaxonomyExtractio( configuration.getTaxonomyExtraction() ); instance.setReplaceUnderscoresInNhParsing( configuration.isReplaceUnderscoresInNhParsing() ); instance.setInternalNumberAreConfidenceForNhParsing( configuration .isInternalNumberAreConfidenceForNhParsing() ); @@ -494,15 +520,18 @@ final public class Options { } instance.setTaxonomyColorizeNodeShapes( configuration.isTaxonomyColorizeNodeShapes() ); instance.setShowDefaultNodeShapes( configuration.isShowDefaultNodeShapes() ); + if ( configuration.getExtDescNodeDataToReturn() != null ) { + instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() ); + } } return instance; } - static enum CLADOGRAM_TYPE { + public static enum CLADOGRAM_TYPE { NON_LINED_UP, EXT_NODE_SUM_DEP, TOTAL_NODE_SUM_DEP; } - static enum NODE_LABEL_DIRECTION { + public static enum NODE_LABEL_DIRECTION { HORIZONTAL, RADIAL; } @@ -528,7 +557,15 @@ final public class Options { } } - static enum PHYLOGENY_GRAPHICS_TYPE { + 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; + } }