X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FOptions.java;h=a228d299268bf0a931b3281ec59b91bb26e65542;hb=c0439ed8b088887ffea2faf11bc7897333287cb3;hp=dede12ebad344bac17dbdb58baaf914e527270b1;hpb=236967e4df09b7a3fd6659a8131aa97ef9906a28;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java index dede12e..a228d29 100644 --- a/forester/java/src/org/forester/archaeopteryx/Options.java +++ b/forester/java/src/org/forester/archaeopteryx/Options.java @@ -41,7 +41,7 @@ import org.forester.util.ForesterUtil; final public class Options { public static enum CLADOGRAM_TYPE { - EXT_NODE_SUM_DEP, NON_LINED_UP, TOTAL_NODE_SUM_DEP; + LINED_UP, NON_LINED_UP; } public static enum NODE_LABEL_DIRECTION { @@ -51,6 +51,12 @@ final public class Options { public static enum PHYLOGENY_GRAPHICS_TYPE { CIRCULAR, CONVEX, CURVED, EURO_STYLE, RECTANGULAR, ROUNDED, TRIANGULAR, UNROOTED; } + + static enum PHYLOGENY_DISPLAY_TYPE { + CLADOGRAM, + ALIGNED_PHYLOGRAM, + UNALIGNED_PHYLOGRAM + } static enum OVERVIEW_PLACEMENT_TYPE { LOWER_LEFT( "lower left" ), @@ -73,6 +79,7 @@ final public class Options { return toString().replaceAll( " ", "_" ); } } + static final double MIN_CONFIDENCE_DEFAULT = 0.0; private boolean _abbreviate_scientific_names; private boolean _allow_errors_in_distance_to_parent; @@ -88,7 +95,7 @@ final public class Options { private short _default_node_shape_size; private boolean _editable; private NodeDataField _ext_desc_data_to_return; - private boolean _graphics_export_using_actual_size; + 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; @@ -104,9 +111,7 @@ final public class Options { private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type; private boolean _print_black_and_white; private float _print_line_width; - private int _print_size_x; - private int _print_size_y; - private boolean _print_using_actual_size; + private final boolean _print_using_actual_size = true; private double _scale_bar_length; private boolean _search_case_sensitive; private boolean _show_annotation_ref_source; @@ -120,7 +125,11 @@ final public class Options { 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 boolean _collapsed_with_average_height; + private boolean _show_abbreviated_labels_for_collapsed_nodes; + private Options() { init(); } @@ -184,7 +193,7 @@ final public class Options { final private void init() { _default_node_shape = NodeShape.CIRCLE; _default_node_fill = NodeFill.GRADIENT; - _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; + _default_node_shape_size = AptxConstants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; _internal_number_are_confidence_for_nh_parsing = false; _show_scale = false; _antialias_screen = true; @@ -195,34 +204,26 @@ final public class Options { _show_default_node_shapes_internal = false; _show_default_node_shapes_external = false; _show_default_node_shapes_for_marked_nodes = 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; - } + _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 = true; - _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; _taxonomy_extraction = TAXONOMY_EXTRACTION.NO; - _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT; + _cladogram_type = AptxConstants.CLADOGRAM_TYPE_DEFAULT; _show_domain_labels = true; _show_annotation_ref_source = true; setAbbreviateScientificTaxonNames( false ); @@ -232,6 +233,8 @@ final public class Options { _ext_desc_data_to_return = NodeDataField.UNKNOWN; _line_up_renderable_node_data = true; _right_align_domains = false; + _collapsed_with_average_height = true; + _show_abbreviated_labels_for_collapsed_nodes = true; } final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) { @@ -294,14 +297,6 @@ final public class Options { return _print_line_width; } - final int getPrintSizeX() { - return _print_size_x; - } - - final int getPrintSizeY() { - return _print_size_y; - } - final double getScaleBarLength() { return _scale_bar_length; } @@ -446,18 +441,8 @@ final public class Options { _editable = editable; } - 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 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 ) { @@ -499,19 +484,7 @@ 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; } @@ -588,12 +561,6 @@ final public class Options { 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() ) ); } @@ -629,4 +596,39 @@ final public class Options { final static Options createDefaultInstance() { return new Options(); } + + final boolean isColorAllFoundNodesWhenColoringSubtree() { + return _color_all_found_nodes_when_coloring_subtree; + } + + 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; + } + + final boolean isParseBeastStyleExtendedNexusTags() { + return _parse_beast_style_extended_nexus_tags; + } + + final void setParseBeastStyleExtendedNexusTags( final boolean parse_beast_style_extended_nexus_tags ) { + _parse_beast_style_extended_nexus_tags = parse_beast_style_extended_nexus_tags; + } + + final boolean isCollapsedWithAverageHeigh() { + return _collapsed_with_average_height; + } + + final void setCollapsedWithAverageHeigh( final boolean collapsed_with_average_height ) { + _collapsed_with_average_height = collapsed_with_average_height; + } + + final boolean isShowAbbreviatedLabelsForCollapsedNodes() { + return _show_abbreviated_labels_for_collapsed_nodes; + } + + final void setShowAbbreviatedLabelsForCollapsedNodes(final boolean show_abbreviated_labels_for_collapsed_nodes) { + _show_abbreviated_labels_for_collapsed_nodes = show_abbreviated_labels_for_collapsed_nodes; + } + + + }