X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FOptions.java;h=f8aa3769270978ec3191f36e715767cbfe905d28;hb=789f3450d14e1f922072f4288833afab71993667;hp=43b8fecaa651f2a1b9b65abd6b513f4068ceafe2;hpb=656be28debec520e0e35a8b311114398a40ea366;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java index 43b8fec..f8aa376 100644 --- a/forester/java/src/org/forester/archaeopteryx/Options.java +++ b/forester/java/src/org/forester/archaeopteryx/Options.java @@ -78,7 +78,8 @@ final public class Options { 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; @@ -87,6 +88,30 @@ final public class Options { init(); } + public NodeData.NODE_DATA getExtDescNodeDataToReturn() { + return _ext_desc_data_to_return; + } + + public final boolean isShowDomainLabels() { + return _show_domain_labels; + } + + 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; } @@ -111,6 +136,10 @@ final public class Options { 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; } @@ -147,69 +176,8 @@ final public class Options { 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() { @@ -240,10 +208,6 @@ final public class Options { return _editable; } - final TAXONOMY_EXTRACTION getTaxonomyExtraction() { - return _taxonomy_extraction; - } - final boolean isGraphicsExportUsingActualSize() { return _graphics_export_using_actual_size; } @@ -284,8 +248,16 @@ final public class Options { 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() { @@ -312,10 +284,6 @@ final public class Options { _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; } @@ -324,10 +292,6 @@ final public class Options { _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; } @@ -344,10 +308,6 @@ final public class Options { _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 ) { @@ -378,16 +338,12 @@ 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 ) { @@ -434,8 +390,16 @@ final public class Options { _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 ) { @@ -450,16 +414,66 @@ final public class Options { _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes; } - final static Options createDefaultInstance() { - return new Options(); + final void setTaxonomyExtractio( final TAXONOMY_EXTRACTION taxonomy_extraction ) { + _taxonomy_extraction = taxonomy_extraction; } - boolean isShowDefaultNodeShapes() { - return _show_default_node_shapes; + 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; + 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; } - void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) { - _show_default_node_shapes = 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; + } + + 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 ) { @@ -519,7 +533,8 @@ final public class Options { 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() ); } @@ -527,6 +542,10 @@ final public class Options { 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; } @@ -535,6 +554,10 @@ final public class Options { 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" ), @@ -557,15 +580,7 @@ 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; + public boolean isAllowFontSizeChange() { + return true; } }