X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=8ec94abeb10270f98b19f8ea6dfac6abbfd0b996;hb=54d8e3a926c3cf3477199c8b85aca478230e223c;hp=1914d76082e317b192ec1e49f25d213a7e04c93a;hpb=70da437f494b483dac92a488bd3500e5add2e34e;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 1914d76..8ec94ab 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -47,7 +47,7 @@ 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.NodeDataField; import org.forester.phylogeny.data.NodeVisualData; import org.forester.phylogeny.data.NodeVisualData.NodeFill; import org.forester.phylogeny.data.NodeVisualData.NodeShape; @@ -55,6 +55,17 @@ import org.forester.util.ForesterUtil; public final class Configuration { + public enum EXT_NODE_DATA_RETURN_ON { + BUFFER_ONLY, CONSOLE, WINODW; + } + + public enum UI { + CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN + } + + static enum TRIPLET { + FALSE, TRUE, UNKNOWN + } final static String clickto_options[][] = { { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" }, { "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "display" }, @@ -63,7 +74,25 @@ public final class Configuration { { "Open Taxonomy DB", "display" }, { "Launch 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" } }; + { "List Node Data", "display" }, { "Select Node(s)", "display" } }; + private final static String DEFAULT_SPECIES_COLORS[][] = { + { "BRAFL", "0x00FFFF" }, { "SPHGR", "0x9620F0" }, { "STRPU", "0x9620F0" }, { "CIOIN", "0xFF1CAE" }, + { "CIOSA", "0xFF2CAE" }, { "BOVIN", "0x5C3317" }, { "CANFA", "0x8B2323" }, { "HUMAN", "0xFF2400" }, + { "PANTR", "0xCC2400" }, { "MOUSE", "0xFF7F00" }, { "RAT", "0xFFEF00" }, { "MONDO", "0xEE9A49" }, + { "ORNAN", "0xCD853F" }, { "XENLA", "0x6BAA23" }, { "XENTR", "0x6BAA23" }, { "CHICK", "0xFFC125" }, + { "FUGRU", "0x0000FF" }, { "BRARE", "0x0000DD" }, { "DANRE", "0x0000BB" }, { "TETNG", "0x0000AA" }, + { "ORYLA", "0x000088" }, { "GASAC", "0x000066" }, { "CAEEL", "0x666699" }, { "CAEBR", "0xB0B0B0" }, + { "DROME", "0x663366" }, { "DROPS", "0x996699" }, { "APIME", "0x7A7700" }, { "AEDAE", "0x8C5900" }, + { "TRICA", "0x918E00" }, { "NEMVE", "0x0066CC" }, { "HYDVU", "0x3399FF" }, { "LUBBA", "0xF7B5CB" }, + { "GEOCY", "0xF5A0BD" }, { "AMPQE", "0x009966" }, { "SUBDO", "0xC790B9" }, { "MONBE", "0xFC0FC0" }, + { "DICPU", "0xFFCC33" }, { "DICDI", "0xFFCC00" }, { "ENTHI", "0x5959AB" }, { "ARATH", "0x00FF00" }, + { "POPTR", "0x006400" }, { "VITVI", "0x00CD00" }, { "GLYMA", "0x00FF7F" }, { "ORYSA", "0x008B00" }, + { "ORYSJ", "0x008C00" }, { "SORBI", "0x00EE76" }, { "SELMO", "0x238E23" }, { "PHYPA", "0x09F911" }, + { "OSTLU", "0x7FFF00" }, { "OSTTA", "0x7FFF00" }, { "OSTRC", "0x7FFF00" }, { "MICPU", "0x66CD00" }, + { "MIC99", "0x66CD00" }, { "CHLRE", "0xB3EE3A" }, { "VOLCA", "0xC0FF3E" }, { "CHLSP", "0x6B8E23" }, + { "CYAME", "0xD02090" }, { "YEAST", "0xAAAAAA" }, { "BACFR", "0xFF0000" }, { "BACTN", "0xFFFF00" }, + { "MYXXD", "0x0000FF" }, { "STIAU", "0x00FFFF" }, { "BACOV", "0x8C5900" }, { "BACUN", "0x66CD00" }, + { "PORGI", "0x918E00" } }; final static int display_node_data = 0; final static int collapse_uncollapse = 1; final static int reroot = 2; @@ -90,18 +119,19 @@ public final class Configuration { // ------------------ final static String display_options[][] = { { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" }, - { "Seq Annotations", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, + { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" }, { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" }, - { "Visual Styles/Branch Colors", "display", "no" }, { "Branch Widths", "display", "no" }, - { "Protein Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" }, - { "Binary Char Counts", "nodisplay", "no" }, { "Seq Name", "display", "yes" }, - { "Seq Accession", "display", "no" }, { "Show Internal Data", "display", "yes" }, - { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" }, - { "Taxonomy Common", "display", "no" }, { "Colorize by Annotation", "nodisplay", "no" }, - { "Seq Symbol", "display", "yes" }, { "Rollover", "display", "yes" }, - { "Relation Confidence", "nodisplay", "no" }, { "Vector Data", "nodisplay", "no" }, - { "Taxonomy Images", "display", "no" }, { "Properties", "nodisplay", "no" }, - { "Gene Name", "display", "yes" } }; + { "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" }, + { "Branch Widths", "display", "no" }, { "Domain Architectures", "display", "no" }, + { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" }, + { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" }, + { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" }, + { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" }, + { "Colorize by Annotation", "display", "no" }, { "Seq Symbol", "display", "yes" }, + { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" }, + { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" }, + { "Properties", "display", "no" }, { "Gene Name", "display", "yes" }, + { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" } }; final static int display_as_phylogram = 0; final static int show_node_names = 1; final static int show_tax_code = 2; @@ -109,37 +139,32 @@ public final class Configuration { final static int write_confidence_values = 4; final static int write_events = 5; final static int color_according_to_species = 6; - final static int use_style = 7; - final static int width_branches = 8; - final static int show_domain_architectures = 9; - final static int show_binary_characters = 10; - final static int show_binary_character_counts = 11; - final static int show_seq_names = 12; - final static int show_sequence_acc = 13; - final static int display_internal_data = 14; - final static int dynamically_hide_data = 15; - final static int show_taxonomy_scientific_names = 16; - final static int show_taxonomy_common_names = 17; - final static int color_according_to_annotation = 18; - final static int show_seq_symbols = 19; - final static int node_data_popup = 20; - final static int show_relation_confidence = 21; - final static int show_vector_data = 22; - final static int show_taxonomy_images = 23; - final static int show_properties = 24; - final static int show_gene_names = 25; + final static int color_according_to_sequence = 7; + final static int use_style = 8; + final static int width_branches = 9; + final static int show_domain_architectures = 10; + final static int show_binary_characters = 11; + final static int show_binary_character_counts = 12; + final static int show_seq_names = 13; + final static int show_sequence_acc = 14; + final static int display_internal_data = 15; + final static int dynamically_hide_data = 16; + 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_seq_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; + final static int show_gene_names = 26; + final static int show_mol_seqs = 27; + final static int write_branch_length_values = 28; static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema"; - // ---------------- - // Function colors - // ---------------- + private static Hashtable _sequence_colors; private static Hashtable _annotation_colors; - // ---------------- - // Domain colors - // ---------------- private static Hashtable _domain_colors; - // ---------------- - // Species colors - // ---------------- private static Hashtable _species_colors; private static String DEFAULT_FONT_FAMILY = ""; private static final int DEPRECATED = -2; @@ -177,10 +202,8 @@ public final class Configuration { private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; private SortedMap _display_colors = null; private boolean _display_sequence_relations = false; - private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT; - private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT; private boolean _editable = true; - private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN; + private NodeDataField _ext_desc_data_to_return = NodeDataField.UNKNOWN; 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; @@ -214,8 +237,8 @@ public final class Configuration { private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR; private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT; private boolean _show_annotation_ref_source = true; - private boolean _show_branch_length_values = false; private boolean _show_default_node_shapes_external = false; + private boolean _show_default_node_shapes_for_marked_nodes = false; private boolean _show_default_node_shapes_internal = false; private boolean _show_domain_labels = true; private boolean _show_overview = true; @@ -224,6 +247,14 @@ public final class Configuration { private UI _ui = UI.UNKNOWN; private boolean _use_tabbed_display = false; private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT; + private Color _vector_data_min_color = Color.BLUE; + private Color _vector_data_max_color = Color.YELLOW; + private Color _vector_data_mean_color = Color.WHITE; + private double _vector_data_height = 12; + private int _vector_data_width = 120; + private boolean _line_up_renderable_node_data = true; + private boolean _right_align_domains = false; + private boolean _allow_thick_strokes = false; static { for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) { if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) { @@ -320,15 +351,7 @@ public final class Configuration { return _default_node_shape_size; } - public Color getDomainStructureBaseColor() { - return _domain_structure_base_color; - } - - public Color getDomainStructureFontColor() { - return _domain_structure_font_color; - } - - public NODE_DATA getExtDescNodeDataToReturn() { + public NodeDataField getExtDescNodeDataToReturn() { return _ext_desc_data_to_return; } @@ -352,7 +375,7 @@ public final class Configuration { return _path_to_local_fastme; } - public File getpathToLocalMafft() { + public File getPathToLocalMafft() { return _path_to_local_mafft; } @@ -360,10 +383,34 @@ public final class Configuration { return _path_to_local_raxml; } + public double getVectorDataHeight() { + return _vector_data_height; + } + + public Color getVectorDataMaxColor() { + return _vector_data_max_color; + } + + public Color getVectorDataMeanColor() { + return _vector_data_mean_color; + } + + public Color getVectorDataMinColor() { + return _vector_data_min_color; + } + + public int getVectorDataWidth() { + return _vector_data_width; + } + public boolean isAbbreviateScientificTaxonNames() { return _abbreviate_scientific_names; } + public boolean isAllowThickStrokes() { + return _allow_thick_strokes; + } + public boolean isBackgroundColorGradient() { return _background_color_gradient; } @@ -376,10 +423,18 @@ public final class Configuration { return _color_labels_same_as_parent_branch; } + final public boolean isLineUpRendarableNodeData() { + return _line_up_renderable_node_data; + } + public boolean isMidpointReroot() { return _midpoint_root; } + final public boolean isRightLineUpDomains() { + return _right_align_domains; + } + public boolean isShowAnnotationRefSource() { return _show_annotation_ref_source; } @@ -388,6 +443,10 @@ public final class Configuration { return _show_default_node_shapes_external; } + public boolean isShowDefaultNodeShapesForMarkedNodes() { + return _show_default_node_shapes_for_marked_nodes; + } + public boolean isShowDefaultNodeShapesInternal() { return _show_default_node_shapes_internal; } @@ -400,14 +459,14 @@ public final class Configuration { getDisplayColors().put( key, color ); } - public void setAddTaxonomyImagesCB( final boolean b ) { - display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no"; - } - public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) { _abbreviate_scientific_names = abbreviate_scientific_names; } + public void setAddTaxonomyImagesCB( final boolean b ) { + display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no"; + } + public void setBackgroundColorGradient( final boolean background_color_gradient ) { _background_color_gradient = background_color_gradient; } @@ -444,10 +503,6 @@ public final class Configuration { display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no"; } - public void setUseStyle( final boolean b ) { - display_options[ use_style ][ 2 ] = b ? "yes" : "no"; - } - public void setDisplayColors( final SortedMap display_colors ) { _display_colors = display_colors; } @@ -456,10 +511,18 @@ public final class Configuration { display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no"; } + public void setDisplayGeneNames( final boolean b ) { + display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no"; + } + public void setDisplayInternalData( final boolean b ) { display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no"; } + public void setDisplayMultipleSequenceAlignment( final boolean b ) { + display_options[ show_mol_seqs ][ 2 ] = b ? "yes" : "no"; + } + public void setDisplayNodeNames( final boolean b ) { display_options[ show_node_names ][ 2 ] = b ? "yes" : "no"; } @@ -472,10 +535,6 @@ public final class Configuration { display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no"; } - public void setDisplayGeneNames( 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; } @@ -504,7 +563,7 @@ public final class Configuration { display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no"; } - public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) { + public void setExtDescNodeDataToReturn( final NodeDataField ext_desc_data_to_return ) { _ext_desc_data_to_return = ext_desc_data_to_return; } @@ -516,6 +575,10 @@ public final class Configuration { _frame_y_size = frame_y_size; } + final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) { + _line_up_renderable_node_data = line_up_renderable_node_data; + } + public void setMidpointReroot( final boolean midpoint_root ) { _midpoint_root = midpoint_root; } @@ -548,14 +611,18 @@ public final class Configuration { _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; + final public void setRightLineUpDomains( final boolean right_align_domains ) { + _right_align_domains = right_align_domains; } public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) { _show_default_node_shapes_external = show_default_node_shapes_external; } + public void setShowDefaultNodeShapesForMarkedNodes( final boolean show_default_node_shapes_for_marked_nodes ) { + _show_default_node_shapes_for_marked_nodes = show_default_node_shapes_for_marked_nodes; + } + public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) { _show_default_node_shapes_internal = show_default_node_shapes_internal; } @@ -568,434 +635,202 @@ public final class Configuration { _show_scale = show_scale; } - public void setTaxonomyColorize( final boolean b ) { - display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no"; + public void setUseStyle( final boolean b ) { + display_options[ use_style ][ 2 ] = b ? "yes" : "no"; } - public void setUseBranchesWidths( final boolean b ) { - display_options[ width_branches ][ 2 ] = b ? "yes" : "no"; + 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_pdb_web" ) ) { + index = Configuration.open_pdb_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; + } + else if ( name.equals( "change_node_font" ) ) { + index = Configuration.change_node_font; + } + else if ( name.equals( "color_node_font" ) ) { + index = Configuration.color_node_font; + } + else if ( name.equals( "color_subtree" ) ) { + index = Configuration.color_subtree; + } + return index; } - boolean displaySequenceRelations() { - return _display_sequence_relations; + private final void initSpeciesColors() { + _species_colors = new Hashtable(); + for( final String[] s : DEFAULT_SPECIES_COLORS ) { + _species_colors.put( s[ 0 ], Color.decode( s[ 1 ] ) ); + } } - boolean doCheckOption( final int which ) { - return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) ) - || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) ); + private boolean parseBoolean( final String str ) { + final String my_str = str.trim().toLowerCase(); + if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) { + return true; + } + else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) { + return false; + } + else { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" ); + return false; + } } - boolean doDisplayClickToOption( final int which ) { - return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" ); + private double parseDouble( final String str ) { + double d = 0.0; + try { + d = Double.parseDouble( str.trim() ); + } + catch ( final Exception e ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" ); + d = 0.0; + } + return d; } - boolean doDisplayOption( final int which ) { - return display_options[ which ][ 1 ].equalsIgnoreCase( "display" ); + private float parseFloat( final String str ) { + float f = 0.0f; + try { + f = Float.parseFloat( str.trim() ); + } + catch ( final Exception e ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" ); + f = 0.0f; + } + return f; } - /** - * Will attempt to use the phylogeny to determine whether to check - * this or not (e.g. phylogram) - * - */ - boolean doGuessCheckOption( final int which ) { - return display_options[ which ][ 2 ].equals( "?" ); + private int parseInt( final String str ) { + int i = -1; + try { + i = Integer.parseInt( str.trim() ); + } + catch ( final Exception e ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" ); + i = -1; + } + return i; } - Map getAnnotationColors() { - if ( _annotation_colors == null ) { - _annotation_colors = new Hashtable(); + private short parseShort( final String str ) { + short i = -1; + try { + i = Short.parseShort( str.trim() ); } - return _annotation_colors; + catch ( final Exception e ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" ); + i = -1; + } + return i; } - int getBaseFontSize() { - return _base_font_size; + private void processFontFamily( final StringTokenizer st ) { + setBaseFontFamilyName( "" ); + final String font_str = ( ( String ) st.nextElement() ).trim(); + final String[] fonts = font_str.split( ",+" ); + for( String font : fonts ) { + font = font.replace( '_', ' ' ).trim(); + if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) { + setBaseFontFamilyName( font ); + break; + } + } } - CLADOGRAM_TYPE getCladogramType() { - return _cladogram_type; - } - - int getClickToOptionsCount() { - return clickto_options.length; - } - - String getClickToTitle( final int which ) { - return clickto_options[ which ][ 0 ]; - } - - int getDefaultDisplayClicktoOption() { - return default_clickto; - } - - SortedMap getDisplayColors() { - return _display_colors; - } - - String getDisplayTitle( final int which ) { - return display_options[ which ][ 0 ]; - } - - Map getDomainColors() { - if ( _domain_colors == null ) { - _domain_colors = new Hashtable(); - } - return _domain_colors; - } - - int getGraphicsExportX() { - return _graphics_export_x; - } - - int getGraphicsExportY() { - return _graphics_export_y; - } - - 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; - } - - int getMaxBaseFontSize() { - return _max_base_font_size; - } - - int getMinBaseFontSize() { - return _min_base_font_size; - } - - double getMinConfidenceValue() { - return _min_confidence_value; - } - - NODE_LABEL_DIRECTION getNodeLabelDirection() { - return _node_label_direction; - } - - short getNumberOfDigitsAfterCommaForBranchLengthValues() { - return _number_of_digits_after_comma_for_branch_length_values; - } - - short getNumberOfDigitsAfterCommaForConfidenceValues() { - return _number_of_digits_after_comma_for_confidence_values; - } - - short getOvMaxHeight() { - return _ov_max_height; - } - - short getOvMaxWidth() { - return _ov_max_width; - } - - OVERVIEW_PLACEMENT_TYPE getOvPlacement() { - return _ov_placement; - } - - PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() { - return _phylogeny_graphics_type; - } - - float getPrintLineWidth() { - return _print_line_width; - } - - Hashtable getSpeciesColors() { - if ( _species_colors == null ) { - _species_colors = new Hashtable(); - } - return _species_colors; - } - - final TAXONOMY_EXTRACTION getTaxonomyExtraction() { - return _taxonomy_extraction; - } - - boolean isAntialiasScreen() { - if ( ForesterUtil.isMac() ) { - //Apple Macintosh graphics are slow, turn off anti-alias. - return false; - } - return _antialias_screen; - } - - /** - * Convenience method. - * - * @return true if value in configuration file was 'yes' - */ - boolean isDrawAsPhylogram() { - return doCheckOption( display_as_phylogram ); - } - - boolean isEditable() { - return _editable; - } - - /** - * Only used by ArchaeoptryxE. - * - */ - boolean isHideControlPanelAndMenubar() { - return _hide_controls_and_menus; - } - - boolean isInternalNumberAreConfidenceForNhParsing() { - return _internal_number_are_confidence_for_nh_parsing; - } - - boolean isReplaceUnderscoresInNhParsing() { - return _nh_parsing_replace_underscores; - } - - boolean isShowBranchLengthValues() { - return _show_branch_length_values; - } - - boolean isShowOverview() { - return _show_overview; - } - - boolean isShowScale() { - return _show_scale; - } - - final boolean isUseNativeUI() { - if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) { - _ui = UI.NATIVE; - } - return _ui == UI.NATIVE; - } - - /** - * Only used by ArchaeoptryxE. - * - */ - boolean isUseTabbedDisplay() { - return _use_tabbed_display; - } - - boolean isValidatePhyloXmlAgainstSchema() { - 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_pdb_web" ) ) { - index = Configuration.open_pdb_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; - } - else if ( name.equals( "change_node_font" ) ) { - index = Configuration.change_node_font; - } - else if ( name.equals( "color_node_font" ) ) { - index = Configuration.color_node_font; - } - 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" ) ) { - return true; - } - else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) { - return false; - } - else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" ); - return false; - } - } - - private double parseDouble( final String str ) { - double d = 0.0; - try { - d = Double.parseDouble( str.trim() ); - } - catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" ); - d = 0.0; - } - return d; - } - - private float parseFloat( final String str ) { - float f = 0.0f; - try { - f = Float.parseFloat( str.trim() ); - } - catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" ); - f = 0.0f; - } - return f; - } - - private int parseInt( final String str ) { - int i = -1; - try { - i = Integer.parseInt( str.trim() ); - } - catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" ); - i = -1; - } - return i; - } - - private short parseShort( final String str ) { - short i = -1; - try { - i = Short.parseShort( str.trim() ); - } - catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" ); - i = -1; - } - return i; - } - - private void processFontFamily( final StringTokenizer st ) { - setBaseFontFamilyName( "" ); - final String font_str = ( ( String ) st.nextElement() ).trim(); - final String[] fonts = font_str.split( ",+" ); - for( String font : fonts ) { - font = font.replace( '_', ' ' ).trim(); - if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) { - setBaseFontFamilyName( font ); - break; - } - } - } - - /** - * read each line of config file, process non-comment lines - * @throws IOException - */ - private void readConfig( final BufferedReader conf_in ) throws IOException { - String line; - do { - line = conf_in.readLine(); - if ( line != null ) { - line = line.trim(); - // skip comments and blank lines - if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) { - // convert runs of spaces to tabs - line = line.replaceAll( "\\s+", "\t" ); - final StringTokenizer st = new StringTokenizer( line, "\t" ); - setKeyValue( st ); - } - } - } while ( line != null ); + /** + * read each line of config file, process non-comment lines + * @throws IOException + */ + private void readConfig( final BufferedReader conf_in ) throws IOException { + String line; + do { + line = conf_in.readLine(); + if ( line != null ) { + line = line.trim(); + // skip comments and blank lines + if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) { + // convert runs of spaces to tabs + line = line.replaceAll( "\\s+", "\t" ); + final StringTokenizer st = new StringTokenizer( line, "\t" ); + setKeyValue( st ); + } + } + } while ( line != null ); } private void setAntialiasScreen( final boolean antialias_screen ) { @@ -1210,9 +1045,6 @@ public final class Configuration { else if ( key.equals( "show_overview" ) ) { setShowOverview( parseBoolean( ( String ) st.nextElement() ) ); } - else if ( key.equals( "show_branch_length_values" ) ) { - setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) ); - } else if ( key.equals( "background_gradient" ) ) { setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) ); } @@ -1388,26 +1220,15 @@ public final class Configuration { else if ( key.equals( "gui_button_border_color" ) ) { _gui_button_border_color = Color.decode( ( String ) st.nextElement() ); } - else if ( key.equals( "domain_structure_font_color" ) ) { - _domain_structure_font_color = Color.decode( ( String ) st.nextElement() ); - } - else if ( key.equals( "domain_structure_base_color" ) ) { - _domain_structure_base_color = Color.decode( ( String ) st.nextElement() ); - } - else if ( key.equals( "show_default_node_shapes" ) ) { - 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( "show_node_shapes_for_nodes_with_vis_data" ) ) { + setShowDefaultNodeShapesForMarkedNodes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) ); + } else if ( key.equals( "default_node_size" ) ) { final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); setDefaultNodeShapeSize( i ); @@ -1444,57 +1265,59 @@ public final class Configuration { else if ( key.equals( "midpoint_reroot" ) ) { setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) ); } - else if ( key.equals( "ext_descendents_data_to_return" ) ) { + else if ( key.equals( "list_node_data_field" ) || key.equals( "ext_descendents_data_to_return" ) ) { final String s = ( ( String ) st.nextElement() ).trim(); if ( s.equalsIgnoreCase( "node_name" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME ); + setExtDescNodeDataToReturn( NodeDataField.NODE_NAME ); } else if ( s.equalsIgnoreCase( "sequence_acc" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC ); + setExtDescNodeDataToReturn( NodeDataField.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 ); + setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA ); } else if ( s.equalsIgnoreCase( "sequence_name" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME ); + setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_NAME ); } else if ( s.equalsIgnoreCase( "gene_name" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.GENE_NAME ); + setExtDescNodeDataToReturn( NodeDataField.GENE_NAME ); } else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL ); + setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_SYMBOL ); } else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME ); + setExtDescNodeDataToReturn( NodeDataField.TAXONOMY_SCIENTIFIC_NAME ); } else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE ); - } - else if ( s.equalsIgnoreCase( "taxonomy_common_name" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_COMM0N_NAME ); + setExtDescNodeDataToReturn( NodeDataField.TAXONOMY_CODE ); } else if ( s.equalsIgnoreCase( "user_selected" ) ) { - setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN ); + setExtDescNodeDataToReturn( NodeDataField.UNKNOWN ); + } + else if ( s.equalsIgnoreCase( "domains" ) ) { + setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL ); + } + else if ( s.equalsIgnoreCase( "domains_collapsed" ) ) { + setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ); + } + else if ( s.equalsIgnoreCase( "seq_annotations" ) ) { + setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS ); + } + else if ( s.equalsIgnoreCase( "go_term_ids" ) ) { + setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS ); } 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" ) ) { + else if ( key.equals( "list_node_data_custom_label" ) || 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 { + if ( !ForesterUtil.isEmpty( s ) && ( s.length() > 1 ) ) { setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) ); } } - else if ( key.equals( "ext_descendents_data_to_return_on" ) ) { + else if ( key.equals( "list_node_data_in" ) || 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 ); @@ -1510,6 +1333,36 @@ public final class Configuration { + "] for [ext_descendents_data_to_return_on]" ); } } + else if ( key.equals( "vector_data_min_color" ) ) { + _vector_data_min_color = Color.decode( ( String ) st.nextElement() ); + } + else if ( key.equals( "vector_data_max_color" ) ) { + _vector_data_max_color = Color.decode( ( String ) st.nextElement() ); + } + else if ( key.equals( "vector_data_mean_color" ) ) { + _vector_data_mean_color = Color.decode( ( String ) st.nextElement() ); + } + else if ( key.equals( "vector_data_width" ) ) { + _vector_data_width = parseShort( ( String ) st.nextElement() ); + if ( _vector_data_width < 1 ) { + _vector_data_width = 120; + } + } + else if ( key.equals( "vector_data_height" ) ) { + _vector_data_height = parseShort( ( String ) st.nextElement() ); + if ( _vector_data_height < 1 ) { + _vector_data_height = 12; + } + } + else if ( key.equals( "line_up_renderable_data" ) ) { + setLineUpRendarableNodeData( parseBoolean( ( String ) st.nextElement() ) ); + } + else if ( key.equals( "right_align_domain_architectures" ) ) { + setRightLineUpDomains( parseBoolean( ( String ) st.nextElement() ) ); + } + else if ( key.equals( "allow_thick_strokes" ) ) { + _allow_thick_strokes = parseBoolean( ( String ) st.nextElement() ); + } else if ( st.countTokens() >= 2 ) { // counts the tokens that are not // yet retrieved! int key_index = -1; @@ -1522,6 +1375,9 @@ public final class Configuration { else if ( key.equals( "color_according_to_species" ) ) { key_index = Configuration.color_according_to_species; } + else if ( key.equals( "color_according_to_sequence" ) ) { + key_index = Configuration.color_according_to_sequence; + } else if ( key.equals( "show_node_names" ) ) { key_index = Configuration.show_node_names; } @@ -1531,6 +1387,9 @@ public final class Configuration { else if ( key.equals( "write_confidence_values" ) ) { key_index = Configuration.write_confidence_values; } + else if ( key.equals( "write_branch_length_values" ) ) { + key_index = Configuration.write_branch_length_values; + } else if ( key.equals( "write_events" ) ) { key_index = Configuration.write_events; } @@ -1549,6 +1408,9 @@ public final class Configuration { else if ( key.equals( "show_domain_architectures" ) ) { key_index = Configuration.show_domain_architectures; } + else if ( key.equals( "show_msa" ) ) { + key_index = Configuration.show_mol_seqs; + } else if ( key.equals( "show_annotations" ) ) { key_index = Configuration.show_annotation; } @@ -1625,6 +1487,10 @@ public final class Configuration { getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ), Color.decode( ( String ) st.nextElement() ) ); } + else if ( key.equals( "sequence_color" ) ) { + getSequenceColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ), + Color.decode( ( String ) st.nextElement() ) ); + } else if ( key.equals( "domain_color" ) ) { getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); } @@ -1699,19 +1565,241 @@ public final class Configuration { _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema; } - static String getDefaultFontFamilyName() { - return DEFAULT_FONT_FAMILY; + boolean displaySequenceRelations() { + return _display_sequence_relations; } - public enum EXT_NODE_DATA_RETURN_ON { - BUFFER_ONLY, CONSOLE, WINODW; + boolean doCheckOption( final int which ) { + return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) ) + || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) ); } - public enum UI { - CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN + boolean doDisplayClickToOption( final int which ) { + return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" ); } - static enum TRIPLET { - FALSE, TRUE, UNKNOWN + boolean doDisplayOption( final int which ) { + return display_options[ which ][ 1 ].equalsIgnoreCase( "display" ); + } + + /** + * Will attempt to use the phylogeny to determine whether to check + * this or not (e.g. phylogram) + * + */ + boolean doGuessCheckOption( final int which ) { + return display_options[ which ][ 2 ].equals( "?" ); + } + + Map getAnnotationColors() { + if ( _annotation_colors == null ) { + _annotation_colors = new Hashtable(); + } + return _annotation_colors; + } + + int getBaseFontSize() { + return _base_font_size; + } + + CLADOGRAM_TYPE getCladogramType() { + return _cladogram_type; + } + + int getClickToOptionsCount() { + return clickto_options.length; + } + + String getClickToTitle( final int which ) { + return clickto_options[ which ][ 0 ]; + } + + int getDefaultDisplayClicktoOption() { + return default_clickto; + } + + SortedMap getDisplayColors() { + return _display_colors; + } + + String getDisplayTitle( final int which ) { + return display_options[ which ][ 0 ]; + } + + Map getDomainColors() { + if ( _domain_colors == null ) { + _domain_colors = new Hashtable(); + } + return _domain_colors; + } + + int getGraphicsExportX() { + return _graphics_export_x; + } + + int getGraphicsExportY() { + return _graphics_export_y; + } + + 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; + } + + int getMaxBaseFontSize() { + return _max_base_font_size; + } + + int getMinBaseFontSize() { + return _min_base_font_size; + } + + double getMinConfidenceValue() { + return _min_confidence_value; + } + + NODE_LABEL_DIRECTION getNodeLabelDirection() { + return _node_label_direction; + } + + short getNumberOfDigitsAfterCommaForBranchLengthValues() { + return _number_of_digits_after_comma_for_branch_length_values; + } + + short getNumberOfDigitsAfterCommaForConfidenceValues() { + return _number_of_digits_after_comma_for_confidence_values; + } + + short getOvMaxHeight() { + return _ov_max_height; + } + + short getOvMaxWidth() { + return _ov_max_width; + } + + OVERVIEW_PLACEMENT_TYPE getOvPlacement() { + return _ov_placement; + } + + PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() { + return _phylogeny_graphics_type; + } + + float getPrintLineWidth() { + return _print_line_width; + } + + Hashtable getSequenceColors() { + if ( _sequence_colors == null ) { + _sequence_colors = new Hashtable(); + } + return _sequence_colors; + } + + Hashtable getSpeciesColors() { + if ( _species_colors == null ) { + initSpeciesColors(); + } + return _species_colors; + } + + final TAXONOMY_EXTRACTION getTaxonomyExtraction() { + return _taxonomy_extraction; + } + + boolean isAntialiasScreen() { + return _antialias_screen; + } + + /** + * Convenience method. + * + * @return true if value in configuration file was 'yes' + */ + boolean isDrawAsPhylogram() { + return doCheckOption( display_as_phylogram ); + } + + boolean isEditable() { + return _editable; + } + + /** + * Only used by ArchaeoptryxE. + * + */ + boolean isHideControlPanelAndMenubar() { + return _hide_controls_and_menus; + } + + boolean isInternalNumberAreConfidenceForNhParsing() { + return _internal_number_are_confidence_for_nh_parsing; + } + + boolean isReplaceUnderscoresInNhParsing() { + return _nh_parsing_replace_underscores; + } + + boolean isShowOverview() { + return _show_overview; + } + + boolean isShowScale() { + return _show_scale; + } + + final boolean isUseNativeUI() { + if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) { + _ui = UI.NATIVE; + } + return _ui == UI.NATIVE; + } + + /** + * Only used by ArchaeoptryxE. + * + */ + boolean isUseTabbedDisplay() { + return _use_tabbed_display; + } + + boolean isValidatePhyloXmlAgainstSchema() { + return _validate_against_phyloxml_xsd_schema; + } + + final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) { + _taxonomy_extraction = taxonomy_extraction; + } + + static String getDefaultFontFamilyName() { + return DEFAULT_FONT_FAMILY; } }