X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=8cb5414d08f032ab5869214b8d940639552605ad;hb=733f051a048f64b6850314a08880f1f77a633db8;hp=11183b07e558445b4f6cc6bd769a45ba77569fb6;hpb=bb78bbf463fdbb67cfa123c94ddaa1e8f1d3c356;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 11183b0..8cb5414 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -24,7 +24,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; @@ -34,7 +34,6 @@ import java.io.File; import java.io.FileReader; import java.io.IOException; import java.io.InputStreamReader; -import java.net.MalformedURLException; import java.net.URL; import java.util.Arrays; import java.util.Hashtable; @@ -47,6 +46,8 @@ import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE; import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION; import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE; import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE; +import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; +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; @@ -54,23 +55,20 @@ import org.forester.util.ForesterUtil; public final class Configuration { - public enum UI { - NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN - } static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema"; - private static final String WEB_LINK_KEY = "web_link"; private static final String DISPLAY_COLOR_KEY = "display_color"; private static final int DEPRECATED = -2; private UI _ui = UI.UNKNOWN; private boolean _use_tabbed_display = false; private boolean _hide_controls_and_menus = false; private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT; - private SortedMap _weblinks = null; private SortedMap _display_colors = null; private boolean _antialias_screen = true; private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR; private String _base_font_family_name = ""; private int _base_font_size = -1; + private int _min_base_font_size = 2; + private int _max_base_font_size = 20; private int _graphics_export_x = -1; private int _graphics_export_y = -1; private short _ov_max_width = 80; @@ -85,7 +83,7 @@ public final class Configuration { private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT; private boolean _editable = true; private boolean _nh_parsing_replace_underscores = false; - private boolean _nh_parsing_extract_pfam_taxonomy_codes = false; + private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT; private boolean _internal_number_are_confidence_for_nh_parsing = false; private boolean _display_sequence_relations = false; private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT; @@ -93,12 +91,16 @@ public final class Configuration { private boolean _show_domain_labels = true; private boolean _abbreviate_scientific_names = false; private boolean _color_labels_same_as_parent_branch = false; - private int _default_bootstrap_samples = -1; - private boolean _show_default_node_shapes = false; - private NodeShape _default_node_shape = NodeShape.CIRCLE; - private NodeFill _default_node_fill = NodeFill.GRADIENT; + private boolean _show_default_node_shapes_internal = false; + private boolean _show_default_node_shapes_external = false; + private NodeShape _default_node_shape = NodeShape.RECTANGLE; + private NodeFill _default_node_fill = NodeFill.SOLID; private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; private boolean _taxonomy_colorize_node_shapes = false; + private int _default_bootstrap_samples = -1; + private File _path_to_local_mafft = null; + private File _path_to_local_fastme = null; + private File _path_to_local_raxml = null; final static int display_as_phylogram = 0; final static int show_node_names = 1; final static int show_tax_code = 2; @@ -119,12 +121,12 @@ public final class Configuration { final static int show_taxonomy_scientific_names = 17; final static int show_taxonomy_common_names = 18; final static int color_according_to_annotation = 19; - final static int show_property = 20; - final static int show_gene_symbols = 21; - final static int node_data_popup = 22; - final static int show_relation_confidence = 23; - final static int show_vector_data = 24; - final static int show_taxonomy_images = 25; + final static int show_gene_symbols = 20; + final static int node_data_popup = 21; + final static int show_relation_confidence = 22; + final static int show_vector_data = 23; + final static int show_taxonomy_images = 24; + final static int show_properties = 25; // ------------------ // Click-to options // ------------------ @@ -136,13 +138,16 @@ public final class Configuration { final static int color_subtree = 5; final static int open_seq_web = 6; final static int open_tax_web = 7; - final static int cut_subtree = 8; - final static int copy_subtree = 9; - final static int paste_subtree = 10; - final static int delete_subtree_or_node = 11; - final static int add_new_node = 12; - final static int edit_node_data = 13; - final static int blast = 14; + final static int blast = 8; + final static int cut_subtree = 9; + final static int copy_subtree = 10; + final static int paste_subtree = 11; + final static int delete_subtree_or_node = 12; + final static int add_new_node = 13; + final static int edit_node_data = 14; + final static int sort_descendents = 15; + final static int get_ext_desc_data = 16; + final static int select_nodes = 17; // --------------------------- // Display options for trees // --------------------------- @@ -154,23 +159,25 @@ public final class Configuration { String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME; final static String display_options[][] = { { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" }, - { "Annotation", "nodisplay", "no" }, { "Confidence Value", "display", "?" }, { "Event", "display", "?" }, - { "Taxonomy Colorize", "display", "yes" }, { "Colorize Branches", "display", "no" }, - { "Use Branch-Widths", "display", "no" }, { "Show Custom Nodes", "display", "yes" }, - { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" }, - { "Binary Char Counts", "nodisplay", "no" }, { "Prot/Gene Name", "display", "yes" }, - { "Prot/Gene Acc", "display", "no" }, { "Show Internal Data", "display", "yes" }, - { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" }, - { "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" }, - { "Property", "nodisplay", "no" }, { "Prot/Gene Symbol", "display", "yes" }, - { "Rollover", "display", "yes" }, { "Relation Confidence", "display", "no" }, - { "Vector Data", "display", "no" }, { "Taxonomy Images", "display", "no" } }; + { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, + { "Node Events", "display", "?" }, { "Taxonomy Colorize", "display", "yes" }, + { "Colorize Branches", "display", "no" }, { "Use Branch-Widths", "display", "no" }, + { "Show Custom Nodes", "display", "yes" }, { "Domains", "nodisplay", "no" }, + { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" }, + { "Seq Name", "display", "yes" }, { "Seq Acc", "display", "no" }, + { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" }, + { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" }, + { "Annotation Colorize", "nodisplay", "no" }, { "Seq Symbol", "display", "yes" }, + { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" }, + { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" }, + { "Properties", "nodisplay", "no" } }; final static String clickto_options[][] = { { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" }, { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" }, - { "Open Sequence Web", "nodisplay" }, { "Open Taxonomy Web", "nodisplay" }, { "Cut Subtree", "display" }, - { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" }, - { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Blast", "display" } }; + { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Blast", "display" }, + { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, + { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" }, + { "Sort Descendants", "display" }, { "Return", "display" }, { "Select Node(s)", "display" } }; // This option is selected in the dropdown int default_clickto = Configuration.display_node_data; // -------------- @@ -205,10 +212,16 @@ public final class Configuration { private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT; private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT; private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT; + private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN; + private String _label_for_get_ext_descendents_data = ""; + private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW; + private int _frame_x_size; + private int _frame_y_size; + private boolean _midpoint_root = false; private static String DEFAULT_FONT_FAMILY = ""; static { for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) { - if ( Arrays.binarySearch( Util.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) { + if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) { DEFAULT_FONT_FAMILY = font_name; break; } @@ -218,14 +231,17 @@ public final class Configuration { } } - public Configuration( final String cf, final boolean is_url, final boolean is_applet ) { + public Configuration() { + this( null, false, false, false ); + } + + public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) { if ( ForesterUtil.isEmpty( cf ) ) { config_filename = default_config_filename; } else { config_filename = cf; } - setWebLinks( new TreeMap() ); setDisplayColors( new TreeMap() ); config_filename = config_filename.trim(); URL u = null; @@ -264,62 +280,283 @@ public final class Configuration { bf.close(); } catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from [" - + config_filename + "]: " + e ); + if ( verbose ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from [" + + config_filename + "]: " + e ); + } } } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file [" - + config_filename + "]" ); + if ( verbose ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file [" + + config_filename + "]" ); + } } } } - private void createWebLink( final String url_str, final String desc, final String source_identifier ) { - WebLink weblink = null; - boolean ex = false; - try { - weblink = new WebLink( new URL( url_str.trim() ), desc.trim(), source_identifier.trim() ); - } - catch ( final MalformedURLException e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not create URL from [" + url_str + "]" ); - ex = true; - } - if ( !ex && ( weblink != null ) ) { - getWebLinks().put( weblink.getSourceIdentifier().toLowerCase(), weblink ); - } + public String getBaseFontFamilyName() { + return _base_font_family_name; } - Color getGuiBackgroundColor() { - return _gui_background_color; + public int getDefaultBootstrapSamples() { + return _default_bootstrap_samples; } - Color getGuiCheckboxTextColor() { - return _gui_checkbox_text_color; + public NodeFill getDefaultNodeFill() { + return _default_node_fill; } - Color getGuiCheckboxAndButtonActiveColor() { - return _gui_checkbox_and_button_active_color; + public NodeShape getDefaultNodeShape() { + return _default_node_shape; } - Color getGuiButtonTextColor() { - return _gui_button_text_color; + public short getDefaultNodeShapeSize() { + return _default_node_shape_size; } - Color getGuiButtonBackgroundColor() { - return _gui_button_background_color; + public Color getDomainStructureBaseColor() { + return _domain_structure_base_color; } - Color getGuiMenuBackgroundColor() { - return _gui_menu_background_color; + public Color getDomainStructureFontColor() { + return _domain_structure_font_color; } - Color getGuiMenuTextColor() { - return _gui_menu_text_color; + public NODE_DATA getExtDescNodeDataToReturn() { + return _ext_desc_data_to_return; } - Color getGuiButtonBorderColor() { - return _gui_button_border_color; + public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() { + return _ext_node_data_return_on; + } + + public int getFrameXSize() { + return _frame_x_size; + } + + public int getFrameYSize() { + return _frame_y_size; + } + + public String getLabelForGetExtDescendentsData() { + return _label_for_get_ext_descendents_data; + } + + public File getPathToLocalFastme() { + return _path_to_local_fastme; + } + + public File getpathToLocalMafft() { + return _path_to_local_mafft; + } + + public File getPathToLocalRaxml() { + return _path_to_local_raxml; + } + + public boolean isAbbreviateScientificTaxonNames() { + return _abbreviate_scientific_names; + } + + public boolean isBackgroundColorGradient() { + return _background_color_gradient; + } + + public boolean isColorLabelsSameAsParentBranch() { + return _color_labels_same_as_parent_branch; + } + + public boolean isShowDefaultNodeShapesExternal() { + return _show_default_node_shapes_external; + } + + public boolean isShowDefaultNodeShapesInternal() { + return _show_default_node_shapes_internal; + } + + public boolean isShowDomainLabels() { + return _show_domain_labels; + } + + public boolean isTaxonomyColorizeNodeShapes() { + return _taxonomy_colorize_node_shapes; + } + + public void putDisplayColors( final String key, final Color color ) { + getDisplayColors().put( key, color ); + } + + public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) { + _abbreviate_scientific_names = abbreviate_scientific_names; + } + + public void setBackgroundColorGradient( final boolean background_color_gradient ) { + _background_color_gradient = background_color_gradient; + } + + public void setBaseFontFamilyName( final String base_font_family_name ) { + _base_font_family_name = base_font_family_name; + } + + public void setBaseFontSize( final int base_font_size ) { + _base_font_size = base_font_size; + } + + private void setMaxBaseFontSize( final int max_base_font_size ) { + _max_base_font_size = max_base_font_size; + } + + private void setMinBaseFontSize( final int min_base_font_size ) { + _min_base_font_size = min_base_font_size; + } + + public void setColorizeBranches( final boolean b ) { + display_options[ color_branches ][ 2 ] = b ? "yes" : "no"; + } + + 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 setDefaultNodeFill( final NodeFill default_node_fill ) { + _default_node_fill = default_node_fill; + } + + public void setDefaultNodeShape( final NodeShape default_node_shape ) { + _default_node_shape = default_node_shape; + } + + public void setDefaultNodeShapeSize( final short default_node_shape_size ) { + _default_node_shape_size = default_node_shape_size; + } + + public void setDisplayAsPhylogram( final boolean b ) { + display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayColors( final SortedMap display_colors ) { + _display_colors = display_colors; + } + + public void setDisplayConfidenceValues( final boolean b ) { + display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayInternalData( final boolean b ) { + display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayNodeNames( final boolean b ) { + display_options[ show_node_names ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplaySequenceAcc( final boolean b ) { + display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplaySequenceNames( final boolean b ) { + display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplaySequenceRelations( final boolean display_sequence_relations ) { + _display_sequence_relations = display_sequence_relations; + } + + public void setDisplaySequenceSymbols( final boolean b ) { + display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayTaxonomyCode( final boolean b ) { + display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayTaxonomyCommonNames( final boolean b ) { + display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayTaxonomyImages( final boolean b ) { + display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayTaxonomyScientificNames( final boolean b ) { + display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no"; + } + + public void setDynamicallyHideData( final boolean b ) { + display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no"; + } + + public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) { + _ext_desc_data_to_return = ext_desc_data_to_return; + } + + public void setFrameXSize( final int frame_x_size ) { + _frame_x_size = frame_x_size; + } + + public void setFrameYSize( final int frame_y_size ) { + _frame_y_size = frame_y_size; + } + + public void setMinConfidenceValue( final double min_confidence_value ) { + _min_confidence_value = min_confidence_value; + } + + public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) { + _node_label_direction = node_label_direction; + } + + public void setNumberOfDigitsAfterCommaForBranchLengthValue( 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; + } + + public 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 void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) { + _phylogeny_graphics_type = phylogeny_graphics_type; + } + + public void setPrintLineWidth( final float print_line_width ) { + _print_line_width = print_line_width; + } + + public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) { + _nh_parsing_replace_underscores = nh_parsing_replace_underscores; + } + + public void setShowBranchLengthValues( final boolean show_branch_length_values ) { + _show_branch_length_values = show_branch_length_values; + } + + public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) { + _show_default_node_shapes_external = show_default_node_shapes_external; + } + + public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) { + _show_default_node_shapes_internal = show_default_node_shapes_internal; + } + + public void setShowDomainLabels( final boolean show_domain_labels ) { + _show_domain_labels = show_domain_labels; + } + + public void setShowScale( final boolean show_scale ) { + _show_scale = show_scale; + } + + public void setTaxonomyColorize( final boolean b ) { + display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no"; + } + + public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) { + _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes; + } + + public void setUseBranchesWidths( final boolean b ) { + display_options[ width_branches ][ 2 ] = b ? "yes" : "no"; } boolean displaySequenceRelations() { @@ -355,87 +592,20 @@ public final class Configuration { return _annotation_colors; } - public String getBaseFontFamilyName() { - return _base_font_family_name; - } - int getBaseFontSize() { return _base_font_size; } - CLADOGRAM_TYPE getCladogramType() { - return _cladogram_type; + int getMinBaseFontSize() { + return _min_base_font_size; } - private int getClickToIndex( final String name ) { - int index = -1; - if ( name.equals( "edit_info" ) ) { - index = Configuration.display_node_data; - ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "configuration key [edit_info] is deprecated, use [display node data] instead" ); - } - else if ( name.equals( "display_node_data" ) ) { - index = Configuration.display_node_data; - } - else if ( name.equals( "collapse_uncollapse" ) ) { - index = Configuration.collapse_uncollapse; - } - else if ( name.equals( "reroot" ) ) { - index = Configuration.reroot; - } - else if ( name.equals( "subtree" ) ) { - index = Configuration.subtree; - } - else if ( name.equals( "swap" ) ) { - index = Configuration.swap; - } - else if ( name.equals( "display_sequences" ) ) { - ForesterUtil - .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" ); - return DEPRECATED; - } - else if ( name.equals( "open_seq_web" ) ) { - index = Configuration.open_seq_web; - } - else if ( name.equals( "open_tax_web" ) ) { - index = Configuration.open_tax_web; - } - else if ( name.equals( "cut_subtree" ) ) { - index = Configuration.cut_subtree; - } - else if ( name.equals( "copy_subtree" ) ) { - index = Configuration.copy_subtree; - } - else if ( name.equals( "paste_subtree" ) ) { - index = Configuration.paste_subtree; - } - else if ( name.equals( "delete" ) ) { - index = Configuration.delete_subtree_or_node; - } - else if ( name.equals( "add_new_node" ) ) { - index = Configuration.add_new_node; - } - else if ( name.equals( "edit_node_data" ) ) { - index = Configuration.edit_node_data; - } - else if ( name.equals( "display_node_popup" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "configuration key [display_node_popup] is deprecated" ); - return DEPRECATED; - } - else if ( name.equals( "custom_option" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" ); - return DEPRECATED; - } - else if ( name.equals( "color_subtree" ) ) { - index = Configuration.color_subtree; - } - else if ( name.equals( "go_to_swiss_prot" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" ); - return DEPRECATED; - } - return index; + int getMaxBaseFontSize() { + return _max_base_font_size; + } + + CLADOGRAM_TYPE getCladogramType() { + return _cladogram_type; } int getClickToOptionsCount() { @@ -473,8 +643,36 @@ public final class Configuration { return _graphics_export_y; } - public int getDefaultBootstrapSamples() { - return _default_bootstrap_samples; + Color getGuiBackgroundColor() { + return _gui_background_color; + } + + Color getGuiButtonBackgroundColor() { + return _gui_button_background_color; + } + + Color getGuiButtonBorderColor() { + return _gui_button_border_color; + } + + Color getGuiButtonTextColor() { + return _gui_button_text_color; + } + + Color getGuiCheckboxAndButtonActiveColor() { + return _gui_checkbox_and_button_active_color; + } + + Color getGuiCheckboxTextColor() { + return _gui_checkbox_text_color; + } + + Color getGuiMenuBackgroundColor() { + return _gui_menu_background_color; + } + + Color getGuiMenuTextColor() { + return _gui_menu_text_color; } double getMinConfidenceValue() { @@ -515,35 +713,23 @@ public final class Configuration { Hashtable getSpeciesColors() { if ( _species_colors == null ) { - _species_colors = new Hashtable(); - } - return _species_colors; - } - - TreeColorSet getTreeColorSet() { - return null; - } - - TreeFontSet getTreeFontSet() { - return null; - } - - WebLink getWebLink( final String source ) { - return getWebLinks().get( source ); + _species_colors = new Hashtable(); + } + return _species_colors; } - Map getWebLinks() { - return _weblinks; + final TAXONOMY_EXTRACTION getTaxonomyExtraction() { + return _taxonomy_extraction; } boolean isAntialiasScreen() { + if ( AptxUtil.isMac() ) { + // Apple Macintosh graphics are slow, turn off anti-alias. + return false; + } return _antialias_screen; } - public boolean isBackgroundColorGradient() { - return _background_color_gradient; - } - /** * Convenience method. * @@ -557,14 +743,6 @@ public final class Configuration { return _editable; } - boolean isExtractPfamTaxonomyCodesInNhParsing() { - return _nh_parsing_extract_pfam_taxonomy_codes; - } - - boolean isHasWebLink( final String source ) { - return getWebLinks().containsKey( source ); - } - /** * Only used by ArchaeoptryxE. * @@ -594,7 +772,7 @@ public final class Configuration { } final boolean isUseNativeUI() { - if ( ( _ui == UI.UNKNOWN ) && Util.isMac() && Util.isJava15() ) { + if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() ) { _ui = UI.NATIVE; } return _ui == UI.NATIVE; @@ -612,6 +790,89 @@ public final class Configuration { return _validate_against_phyloxml_xsd_schema; } + final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) { + _taxonomy_extraction = taxonomy_extraction; + } + + private int getClickToIndex( final String name ) { + int index = -1; + if ( name.equals( "edit_info" ) ) { + index = Configuration.display_node_data; + ForesterUtil + .printWarningMessage( Constants.PRG_NAME, + "configuration key [edit_info] is deprecated, use [display node data] instead" ); + } + else if ( name.equals( "display_node_data" ) ) { + index = Configuration.display_node_data; + } + else if ( name.equals( "collapse_uncollapse" ) ) { + index = Configuration.collapse_uncollapse; + } + else if ( name.equals( "reroot" ) ) { + index = Configuration.reroot; + } + else if ( name.equals( "subtree" ) ) { + index = Configuration.subtree; + } + else if ( name.equals( "swap" ) ) { + index = Configuration.swap; + } + else if ( name.equals( "sort_descendants" ) ) { + index = Configuration.sort_descendents; + } + else if ( name.equals( "get_ext_descendents_data" ) ) { + index = Configuration.get_ext_desc_data; + } + else if ( name.equals( "display_sequences" ) ) { + ForesterUtil + .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" ); + return DEPRECATED; + } + else if ( name.equals( "open_seq_web" ) ) { + index = Configuration.open_seq_web; + } + else if ( name.equals( "open_tax_web" ) ) { + index = Configuration.open_tax_web; + } + else if ( name.equals( "blast" ) ) { + index = Configuration.blast; + } + else if ( name.equals( "cut_subtree" ) ) { + index = Configuration.cut_subtree; + } + else if ( name.equals( "copy_subtree" ) ) { + index = Configuration.copy_subtree; + } + else if ( name.equals( "paste_subtree" ) ) { + index = Configuration.paste_subtree; + } + else if ( name.equals( "delete" ) ) { + index = Configuration.delete_subtree_or_node; + } + else if ( name.equals( "add_new_node" ) ) { + index = Configuration.add_new_node; + } + else if ( name.equals( "edit_node_data" ) ) { + index = Configuration.edit_node_data; + } + else if ( name.equals( "select_nodes" ) ) { + index = Configuration.select_nodes; + } + else if ( name.equals( "display_node_popup" ) ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, + "configuration key [display_node_popup] is deprecated" ); + return DEPRECATED; + } + else if ( name.equals( "custom_option" ) ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" ); + return DEPRECATED; + } + else if ( name.equals( "color_subtree" ) ) { + index = Configuration.color_subtree; + } + return index; + } + private boolean parseBoolean( final String str ) { final String my_str = str.trim().toLowerCase(); if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) { @@ -629,7 +890,7 @@ public final class Configuration { private double parseDouble( final String str ) { double d = 0.0; try { - d = Double.parseDouble( str ); + d = Double.parseDouble( str.trim() ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" ); @@ -641,7 +902,7 @@ public final class Configuration { private float parseFloat( final String str ) { float f = 0.0f; try { - f = Float.parseFloat( str ); + f = Float.parseFloat( str.trim() ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" ); @@ -653,7 +914,7 @@ public final class Configuration { private int parseInt( final String str ) { int i = -1; try { - i = Integer.parseInt( str ); + i = Integer.parseInt( str.trim() ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" ); @@ -665,7 +926,7 @@ public final class Configuration { private short parseShort( final String str ) { short i = -1; try { - i = Short.parseShort( str ); + i = Short.parseShort( str.trim() ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" ); @@ -680,7 +941,7 @@ public final class Configuration { final String[] fonts = font_str.split( ",+" ); for( String font : fonts ) { font = font.replace( '_', ' ' ).trim(); - if ( Arrays.binarySearch( Util.getAvailableFontFamiliesSorted(), font ) >= 0 ) { + if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) { setBaseFontFamilyName( font ); break; } @@ -712,48 +973,20 @@ public final class Configuration { _antialias_screen = antialias_screen; } - public void setBackgroundColorGradient( final boolean background_color_gradient ) { - _background_color_gradient = background_color_gradient; - } - - private void setBaseFontFamilyName( final String base_font_family_name ) { - _base_font_family_name = base_font_family_name; - } - - private void setBaseFontSize( final int base_font_size ) { - _base_font_size = base_font_size; - } - - private void setShowDomainLabels( final boolean show_domain_labels ) { - _show_domain_labels = show_domain_labels; - } - - private void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) { - _abbreviate_scientific_names = abbreviate_scientific_names; - } - - private void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) { - _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch; - } - private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) { _cladogram_type = cladogram_type; } - void setDisplayColors( final SortedMap display_colors ) { - _display_colors = display_colors; - } - - private void setDisplaySequenceRelations( final boolean display_sequence_relations ) { - _display_sequence_relations = display_sequence_relations; + private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) { + _default_bootstrap_samples = default_bootstrap_samples; } private void setEditable( final boolean editable ) { _editable = editable; } - private void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) { - _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes; + private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) { + _ext_node_data_return_on = ext_node_data_return_on; } private void setGraphicsExportX( final int graphics_export_x ) { @@ -764,10 +997,6 @@ public final class Configuration { _graphics_export_y = graphics_export_y; } - private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) { - _default_bootstrap_samples = default_bootstrap_samples; - } - private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) { _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing; } @@ -776,10 +1005,10 @@ public final class Configuration { * Set a key-value(s) tuple */ private void setKeyValue( final StringTokenizer st ) { - String key = ( String ) st.nextElement(); - key = key.replace( ':', ' ' ); - key = key.trim(); - key = key.toLowerCase(); + final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase(); + if ( !st.hasMoreElements() ) { + return; + } // Handle single value settings first: if ( key.equals( "default_click_to" ) ) { final String clickto_name = ( String ) st.nextElement(); @@ -859,17 +1088,37 @@ public final class Configuration { else if ( key.equals( "font_size" ) ) { final String size_str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( size_str ); - setBaseFontSize( i ); + if ( i > 0 ) { + setBaseFontSize( i ); + } + } + else if ( key.equals( "font_size_min" ) ) { + final String size_str = ( ( String ) st.nextElement() ).trim(); + final int i = parseInt( size_str ); + if ( i > 0 ) { + setMinBaseFontSize( i ); + } + } + else if ( key.equals( "font_size_max" ) ) { + final String size_str = ( ( String ) st.nextElement() ).trim(); + final int i = parseInt( size_str ); + if ( i > 1 ) { + setMaxBaseFontSize( i ); + } } else if ( key.equals( "graphics_export_x" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( str ); - setGraphicsExportX( i ); + if ( i > 0 ) { + setGraphicsExportX( i ); + } } else if ( key.equals( "graphics_export_y" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( str ); - setGraphicsExportY( i ); + if ( i > 0 ) { + setGraphicsExportY( i ); + } } else if ( key.equals( "pdf_export_line_width" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); @@ -882,6 +1131,20 @@ public final class Configuration { "value for [pdf_export_line_width] cannot be zero or negative" ); } } + else if ( key.equals( "window_initial_size_x" ) ) { + final String str = ( ( String ) st.nextElement() ).trim(); + final int i = parseInt( str ); + if ( i > 0 ) { + setFrameXSize( i ); + } + } + else if ( key.equals( "window_initial_size_y" ) ) { + final String str = ( ( String ) st.nextElement() ).trim(); + final int i = parseInt( str ); + if ( i > 0 ) { + setFrameYSize( i ); + } + } else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( str ); @@ -894,6 +1157,24 @@ public final class Configuration { "value for [default_number_of_bootstrap_resamples] cannot be negative" ); } } + else if ( key.equals( "mafft_local" ) ) { + final String str = ( ( String ) st.nextElement() ).trim(); + if ( !ForesterUtil.isEmpty( str ) ) { + setPathToLocalMafft( new File( str ) ); + } + } + else if ( key.equals( "fastme_local" ) ) { + final String str = ( ( String ) st.nextElement() ).trim(); + if ( !ForesterUtil.isEmpty( str ) ) { + setPathToLocalFastme( new File( str ) ); + } + } + else if ( key.equals( "raxml_local" ) ) { + final String str = ( ( String ) st.nextElement() ).trim(); + if ( !ForesterUtil.isEmpty( str ) ) { + setPathToLocalRaxml( new File( str ) ); + } + } else if ( key.equals( "show_scale" ) ) { setShowScale( parseBoolean( ( String ) st.nextElement() ) ); } @@ -943,11 +1224,11 @@ public final class Configuration { _use_tabbed_display = parseBoolean( ( String ) st.nextElement() ); } else if ( key.equals( "overview_width" ) ) { - final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); + final short i = parseShort( ( ( String ) st.nextElement() ) ); setOvMaxWidth( i ); } else if ( key.equals( "overview_height" ) ) { - final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); + final short i = parseShort( ( ( String ) st.nextElement() ) ); setOvMaxHeight( i ); } else if ( key.equals( "overview_placement_type" ) ) { @@ -1012,7 +1293,7 @@ public final class Configuration { } else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) { final boolean r = parseBoolean( ( String ) st.nextElement() ); - if ( r && isExtractPfamTaxonomyCodesInNhParsing() ) { + if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) { ForesterUtil .printWarningMessage( Constants.PRG_NAME, "attempt to extract taxonomies and replace underscores at the same time" ); @@ -1021,16 +1302,26 @@ public final class Configuration { setReplaceUnderscoresInNhParsing( r ); } } - else if ( key.equals( "extract_taxonomy_codes_in_nh_parsing" ) ) { - final boolean e = parseBoolean( ( String ) st.nextElement() ); - if ( e && isReplaceUnderscoresInNhParsing() ) { + else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) { + final String s = ( String ) st.nextElement(); + if ( s.equalsIgnoreCase( "no" ) ) { + setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO ); + } + else if ( s.equalsIgnoreCase( "yes" ) ) { + setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + } + else if ( s.equalsIgnoreCase( "pfam" ) ) { + setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + } + else { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, + "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + s ); + } + if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) { ForesterUtil .printWarningMessage( Constants.PRG_NAME, "attempt to extract taxonomies and replace underscores at the same time" ); } - else { - setExtractPfamTaxonomyCodesInNhParsing( e ); - } } else if ( key.equals( "internal_labels_are_confidence_values" ) ) { setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) ); @@ -1066,7 +1357,18 @@ public final class Configuration { _domain_structure_base_color = Color.decode( ( String ) st.nextElement() ); } else if ( key.equals( "show_default_node_shapes" ) ) { - setShowDefaultNodeShapes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) ); + ForesterUtil + .printWarningMessage( Constants.PRG_NAME, + "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" ); + final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() ); + setShowDefaultNodeShapesInternal( b ); + setShowDefaultNodeShapesExternal( b ); + } + else if ( key.equals( "show_default_node_shapes_internal" ) ) { + setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) ); + } + else if ( key.equals( "show_default_node_shapes_external" ) ) { + setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) ); } else if ( key.equals( "default_node_size" ) ) { final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); @@ -1104,6 +1406,69 @@ public final class Configuration { else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) { setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) ); } + else if ( key.equals( "midpoint_reroot" ) ) { + setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) ); + } + else if ( key.equals( "ext_descendents_data_to_return" ) ) { + final String s = ( ( String ) st.nextElement() ).trim(); + if ( s.equalsIgnoreCase( "node_name" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME ); + } + else if ( s.equalsIgnoreCase( "sequence_acc" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC ); + } + else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ); + } + else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ ); + } + else if ( s.equalsIgnoreCase( "sequence_name" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME ); + } + else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL ); + } + else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME ); + } + else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE ); + } + else if ( s.equalsIgnoreCase( "user_selected" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN ); + } + else { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s + + "] for [ext_descendents_data_to_return]" ); + } + } + else if ( key.equals( "label_for_get_ext_descendents_data" ) ) { + final String s = ( ( String ) st.nextElement() ).trim(); + if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s + + "] for [label_for_get_ext_descendents_data]" ); + } + else { + setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) ); + } + } + else if ( key.equals( "ext_descendents_data_to_return_on" ) ) { + final String s = ( ( String ) st.nextElement() ).trim().toLowerCase(); + if ( s.equals( "console" ) ) { + setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE ); + } + else if ( s.equals( "window" ) ) { + setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW ); + } + else if ( s.equals( "buffer_only" ) ) { + setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ); + } + else { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s + + "] for [ext_descendents_data_to_return_on]" ); + } + } else if ( st.countTokens() >= 2 ) { // counts the tokens that are not // yet retrieved! int key_index = -1; @@ -1225,12 +1590,12 @@ public final class Configuration { else if ( key.equals( "color_according_to_annotation" ) ) { key_index = Configuration.color_according_to_annotation; } - else if ( key.equals( "show_property" ) ) { - key_index = Configuration.show_property; - } else if ( key.equals( "show_vector_data" ) ) { key_index = Configuration.show_vector_data; } + else if ( key.equals( "show_properties" ) ) { + key_index = Configuration.show_properties; + } else if ( key.equals( "show_relation_confidence" ) ) { key_index = Configuration.show_relation_confidence; } @@ -1276,18 +1641,7 @@ public final class Configuration { "configuration key [function_color] is deprecated" ); } else if ( key.equals( DISPLAY_COLOR_KEY ) ) { - getDisplayColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); - } - else if ( key.equals( WEB_LINK_KEY ) ) { - if ( st.countTokens() == 3 ) { - createWebLink( ( String ) st.nextElement(), - ( String ) st.nextElement(), - ( String ) st.nextElement() ); - } - else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "illegal format in configuration file for key [" + key + "]" ); - } + putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key @@ -1301,20 +1655,8 @@ public final class Configuration { } } - private void setMinConfidenceValue( final double min_confidence_value ) { - _min_confidence_value = min_confidence_value; - } - - void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) { - _node_label_direction = node_label_direction; - } - - private void setNumberOfDigitsAfterCommaForBranchLengthValue( final short _number_of_digits_after_comma_for_branch_length_values ) { - this._number_of_digits_after_comma_for_branch_length_values = _number_of_digits_after_comma_for_branch_length_values; - } - - private void setNumberOfDigitsAfterCommaForConfidenceValues( final short _number_of_digits_after_comma_for_confidence_values ) { - this._number_of_digits_after_comma_for_confidence_values = _number_of_digits_after_comma_for_confidence_values; + private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) { + _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data; } private void setOvMaxHeight( final short ov_max_height ) { @@ -1329,103 +1671,47 @@ public final class Configuration { _ov_placement = ov_placement; } - void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) { - _phylogeny_graphics_type = phylogeny_graphics_type; - } - - private void setPrintLineWidth( final float print_line_width ) { - _print_line_width = print_line_width; + private void setPathToLocalFastme( final File path_to_local_fastme ) { + _path_to_local_fastme = path_to_local_fastme; } - private void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) { - _nh_parsing_replace_underscores = nh_parsing_replace_underscores; + private void setPathToLocalMafft( final File path_to_local_mafft ) { + _path_to_local_mafft = path_to_local_mafft; } - private void setShowBranchLengthValues( final boolean show_branch_length_values ) { - _show_branch_length_values = show_branch_length_values; + private void setPathToLocalRaxml( final File path_to_local_raxml ) { + _path_to_local_raxml = path_to_local_raxml; } private void setShowOverview( final boolean show_overview ) { _show_overview = show_overview; } - private void setShowScale( final boolean show_scale ) { - _show_scale = show_scale; - } - private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) { _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema; } - void setWebLinks( final SortedMap weblinks ) { - _weblinks = weblinks; - } - static String getDefaultFontFamilyName() { return DEFAULT_FONT_FAMILY; } - static enum TRIPLET { - TRUE, FALSE, UNKNOWN - } - - public Color getDomainStructureFontColor() { - return _domain_structure_font_color; - } - - public Color getDomainStructureBaseColor() { - return _domain_structure_base_color; - } - - public boolean isColorLabelsSameAsParentBranch() { - return _color_labels_same_as_parent_branch; - } - - public boolean isShowDomainLabels() { - return _show_domain_labels; - } - - public boolean isAbbreviateScientificTaxonNames() { - return _abbreviate_scientific_names; - } - - public NodeShape getDefaultNodeShape() { - return _default_node_shape; - } - - private void setDefaultNodeShape( final NodeShape default_node_shape ) { - _default_node_shape = default_node_shape; - } - - private void setDefaultNodeFill( final NodeFill default_node_fill ) { - _default_node_fill = default_node_fill; - } - - public NodeFill getDefaultNodeFill() { - return _default_node_fill; - } - - private void setDefaultNodeShapeSize( final short default_node_shape_size ) { - _default_node_shape_size = default_node_shape_size; - } - - public short getDefaultNodeShapeSize() { - return _default_node_shape_size; + public enum EXT_NODE_DATA_RETURN_ON { + CONSOLE, WINODW, BUFFER_ONLY; } - private void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) { - _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes; + public enum UI { + NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN } - public boolean isTaxonomyColorizeNodeShapes() { - return _taxonomy_colorize_node_shapes; + static enum TRIPLET { + TRUE, FALSE, UNKNOWN } - public boolean isShowDefaultNodeShapes() { - return _show_default_node_shapes; + public boolean isMidpointReroot() { + return _midpoint_root; } - private void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) { - _show_default_node_shapes = show_default_node_shapes; + public void setMidpointReroot( final boolean midpoint_root ) { + _midpoint_root = midpoint_root; } }