X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=43bc6ad20d2cffdf75456c9af390597a6afe4f31;hb=eb22dac14771c467104f57362e3a624d0140f897;hp=c1a109674befcc44c220168bb754d895dbaa7e1b;hpb=bf4f34e0511813622f68e54ffb783e4e6d92bfa4;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index c1a1096..43bc6ad 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; @@ -55,15 +55,44 @@ 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" }, - { "Colorize Node(s)", "display" }, { "Change Node Font(s)", "display" }, - { "Colorize Subtree(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "display" }, - { "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" } }; + { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" }, + { "Go to Sub/Supertree", "display" }, { "Swap Descendants", "display" }, + { "Colorize Node(s)", "display" }, { "Change Node Font(s)", "display" }, + { "Colorize Subtree(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "display" }, + { "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" }, + { "List Node Data", "display" }, { "Select Node(s)", "display" } , { "Uncollapse All", "display" }, { "Order Subtree", "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; @@ -85,23 +114,28 @@ public final class Configuration { final static int sort_descendents = 18; final static int get_ext_desc_data = 19; final static int select_nodes = 20; + final static int uncollapse_all = 21; + final static int order_subtree = 22; + // ------------------ // Click-to options // ------------------ final static String display_options[][] = { - { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" }, - { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" }, - { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" }, - { "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" }, - { "Branch Widths", "display", "no" }, { "Protein Domains", "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" } }; + { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" }, + { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" }, + { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" }, + { "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" } + , { "Taxonomy Rank", "display", "no" }, { "Show External Data", "display", "yes" }}; final static int display_as_phylogram = 0; final static int show_node_names = 1; final static int show_tax_code = 2; @@ -129,6 +163,11 @@ public final class Configuration { 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; + final static int show_tax_rank = 29; + final static int display_external_data = 30; + static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema"; private static Hashtable _sequence_colors; private static Hashtable _annotation_colors; @@ -147,7 +186,7 @@ public final class Configuration { String config_filename; // This option is selected in the dropdown int default_clickto = Configuration.display_node_data; - String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME; + String default_config_filename = AptxConstants.DEFAULT_CONFIGURATION_FILE_NAME; // -------------- // Color set // -------------- @@ -156,35 +195,33 @@ public final class Configuration { // Fonts // ------- TreeFontSet tree_font_set; - boolean verbose = Constants.VERBOSE_DEFAULT; + boolean verbose = AptxConstants.VERBOSE_DEFAULT; private boolean _abbreviate_scientific_names = false; private boolean _antialias_screen = true; private boolean _background_color_gradient = false; private String _base_font_family_name = ""; private int _base_font_size = -1; - private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT; + private CLADOGRAM_TYPE _cladogram_type = AptxConstants.CLADOGRAM_TYPE_DEFAULT; private boolean _color_labels_same_as_parent_branch = false; private int _default_bootstrap_samples = -1; private NodeFill _default_node_fill = NodeFill.SOLID; private NodeShape _default_node_shape = NodeShape.RECTANGLE; - private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; + private short _default_node_shape_size = AptxConstants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; private SortedMap _display_colors = null; private boolean _display_sequence_relations = false; 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; - private int _graphics_export_x = -1; - private int _graphics_export_y = -1; - private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT; - private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT; - private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT; - private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT; - private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT; - private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT; - private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT; - private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT; + private Color _gui_background_color = AptxConstants.GUI_BACKGROUND_DEFAULT; + private Color _gui_button_background_color = AptxConstants.BUTTON_BACKGROUND_COLOR_DEFAULT; + private Color _gui_button_border_color = AptxConstants.BUTTON_BORDER_COLOR_DEFAULT; + private Color _gui_button_text_color = AptxConstants.BUTTON_TEXT_COLOR_DEFAULT; + private Color _gui_checkbox_and_button_active_color = AptxConstants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT; + private Color _gui_checkbox_text_color = AptxConstants.CHECKBOX_TEXT_COLOR_DEFAULT; + private Color _gui_menu_background_color = AptxConstants.MENU_BACKGROUND_COLOR_DEFAULT; + private Color _gui_menu_text_color = AptxConstants.MENU_TEXT_COLOR_DEFAULT; private boolean _hide_controls_and_menus = false; private boolean _internal_number_are_confidence_for_nh_parsing = false; private String _label_for_get_ext_descendents_data = ""; @@ -194,8 +231,8 @@ public final class Configuration { private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT; private boolean _nh_parsing_replace_underscores = false; private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL; - private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT; - private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT; + private short _number_of_digits_after_comma_for_branch_length_values = AptxConstants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT; + private short _number_of_digits_after_comma_for_confidence_values = AptxConstants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT; private short _ov_max_height = 80; private short _ov_max_width = 80; private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT; @@ -203,10 +240,10 @@ public final class Configuration { private File _path_to_local_mafft = null; private File _path_to_local_raxml = null; private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR; - private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT; + private float _print_line_width = AptxConstants.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; @@ -214,24 +251,25 @@ public final class Configuration { private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.NO; 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 boolean _validate_against_phyloxml_xsd_schema = AptxConstants.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; - private boolean _right_align_domains; - + private boolean _line_up_renderable_node_data = true; + private boolean _right_align_domains = false; + private boolean _allow_thick_strokes = false; + private boolean _could_read_config_file = false; static { - for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) { + for( final String font_name : AptxConstants.DEFAULT_FONT_CHOICES ) { if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) { DEFAULT_FONT_FAMILY = font_name; break; } } if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) { - DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ]; + DEFAULT_FONT_FAMILY = AptxConstants.DEFAULT_FONT_CHOICES[ AptxConstants.DEFAULT_FONT_CHOICES.length - 1 ]; } } @@ -246,6 +284,7 @@ public final class Configuration { else { config_filename = cf; } + _could_read_config_file = false; setDisplayColors( new TreeMap() ); config_filename = config_filename.trim(); URL u = null; @@ -258,16 +297,17 @@ public final class Configuration { final BufferedReader bf = new BufferedReader( isr ); readConfig( bf ); bf.close(); - ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url [" + ForesterUtil.programMessage( AptxConstants.PRG_NAME, "successfully read from configuration url [" + config_filename + "]" ); + _could_read_config_file = true; } catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from [" + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "failed to read configuration from [" + config_filename + "]: " + e.getLocalizedMessage() ); } } catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url [" + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "cannot find or open configuration url [" + config_filename + "]" ); } } @@ -282,17 +322,18 @@ public final class Configuration { final BufferedReader bf = new BufferedReader( new FileReader( f ) ); readConfig( bf ); bf.close(); + _could_read_config_file = true; } catch ( final Exception e ) { if ( verbose ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from [" + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "failed to read configuration from [" + config_filename + "]: " + e ); } } } else { if ( verbose ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file [" + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "cannot find or open configuration file [" + config_filename + "]" ); } } @@ -319,7 +360,7 @@ public final class Configuration { return _default_node_shape_size; } - public NODE_DATA getExtDescNodeDataToReturn() { + public NodeDataField getExtDescNodeDataToReturn() { return _ext_desc_data_to_return; } @@ -351,10 +392,34 @@ 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; } @@ -367,10 +432,18 @@ 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; } @@ -379,6 +452,10 @@ 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; } @@ -391,14 +468,14 @@ 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; } @@ -435,10 +512,6 @@ 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; } @@ -447,9 +520,21 @@ 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 setDisplayExternalData( final boolean b ) { + display_options[ display_external_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"; @@ -463,10 +548,6 @@ 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; } @@ -478,6 +559,10 @@ public final class Configuration { public void setDisplayTaxonomyCode( final boolean b ) { display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no"; } + + public void setDisplayTaxonomyRank( final boolean b ) { + display_options[ show_tax_rank ][ 2 ] = b ? "yes" : "no"; + } public void setDisplayTaxonomyCommonNames( final boolean b ) { display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no"; @@ -495,7 +580,7 @@ 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; } @@ -507,6 +592,10 @@ 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; } @@ -539,14 +628,18 @@ 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; } @@ -559,246 +652,8 @@ public final class Configuration { _show_scale = show_scale; } - boolean displaySequenceRelations() { - return _display_sequence_relations; - } - - boolean doCheckOption( final int which ) { - return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) ) - || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) ); - } - - boolean doDisplayClickToOption( final int which ) { - return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" ); - } - - 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 getSpeciesColors() { - if ( _species_colors == null ) { - _species_colors = new Hashtable(); - } - return _species_colors; - } - - Hashtable getSequenceColors() { - if ( _sequence_colors == null ) { - _sequence_colors = new Hashtable(); - } - return _sequence_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; + public void setUseStyle( final boolean b ) { + display_options[ use_style ][ 2 ] = b ? "yes" : "no"; } private int getClickToIndex( final String name ) { @@ -806,8 +661,8 @@ public final class Configuration { 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" ); + .printWarningMessage( AptxConstants.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; @@ -815,6 +670,9 @@ public final class Configuration { else if ( name.equals( "collapse_uncollapse" ) ) { index = Configuration.collapse_uncollapse; } + else if ( name.equals( "uncollapse_all" ) ) { + index = Configuration.uncollapse_all; + } else if ( name.equals( "reroot" ) ) { index = Configuration.reroot; } @@ -824,6 +682,9 @@ public final class Configuration { else if ( name.equals( "swap" ) ) { index = Configuration.swap; } + else if ( name.equals( "order_subtree" ) ) { + index = Configuration.order_subtree; + } else if ( name.equals( "sort_descendants" ) ) { index = Configuration.sort_descendents; } @@ -832,7 +693,7 @@ public final class Configuration { } else if ( name.equals( "display_sequences" ) ) { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" ); + .printWarningMessage( AptxConstants.PRG_NAME, "configuration key [display_sequences] is deprecated" ); return DEPRECATED; } else if ( name.equals( "open_seq_web" ) ) { @@ -869,12 +730,12 @@ public final class Configuration { index = Configuration.select_nodes; } else if ( name.equals( "display_node_popup" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "configuration key [display_node_popup] is deprecated" ); + ForesterUtil.printWarningMessage( AptxConstants.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" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "configuration key [custom_option] is deprecated" ); return DEPRECATED; } else if ( name.equals( "color_subtree" ) ) { @@ -892,6 +753,13 @@ public final class Configuration { return index; } + private final void initSpeciesColors() { + _species_colors = new Hashtable(); + for( final String[] s : DEFAULT_SPECIES_COLORS ) { + _species_colors.put( s[ 0 ], Color.decode( s[ 1 ] ) ); + } + } + private boolean parseBoolean( final String str ) { final String my_str = str.trim().toLowerCase(); if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) { @@ -901,7 +769,7 @@ public final class Configuration { return false; } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse boolean value from [" + str + "]" ); return false; } } @@ -912,7 +780,7 @@ public final class Configuration { d = Double.parseDouble( str.trim() ); } catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse double from [" + str + "]" ); d = 0.0; } return d; @@ -924,7 +792,7 @@ public final class Configuration { f = Float.parseFloat( str.trim() ); } catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse float from [" + str + "]" ); f = 0.0f; } return f; @@ -936,7 +804,7 @@ public final class Configuration { i = Integer.parseInt( str.trim() ); } catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse integer from [" + str + "]" ); i = -1; } return i; @@ -948,7 +816,7 @@ public final class Configuration { i = Short.parseShort( str.trim() ); } catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse short from [" + str + "]" ); i = -1; } return i; @@ -969,7 +837,7 @@ public final class Configuration { /** * read each line of config file, process non-comment lines - * @throws IOException + * @throws IOException */ private void readConfig( final BufferedReader conf_in ) throws IOException { String line; @@ -1008,13 +876,13 @@ public final class Configuration { _ext_node_data_return_on = ext_node_data_return_on; } - private void setGraphicsExportX( final int graphics_export_x ) { - _graphics_export_x = graphics_export_x; - } + //private void setGraphicsExportX( final int graphics_export_x ) { + // _graphics_export_x = graphics_export_x; + //} - private void setGraphicsExportY( final int graphics_export_y ) { - _graphics_export_y = graphics_export_y; - } + //private void setGraphicsExportY( final int graphics_export_y ) { + // _graphics_export_y = graphics_export_y; + //} 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; @@ -1033,8 +901,8 @@ public final class Configuration { final String clickto_name = ( String ) st.nextElement(); default_clickto = getClickToIndex( clickto_name ); if ( default_clickto == -1 ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name - + "] for [default_click_to]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "invalid value [" + clickto_name + + "] for [default_click_to]" ); default_clickto = 0; } else if ( default_clickto == DEPRECATED ) { @@ -1053,8 +921,8 @@ public final class Configuration { _ui = UI.UNKNOWN; } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str - + "]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse yes/no/? value from [" + my_str + + "]" ); _ui = UI.UNKNOWN; } } @@ -1092,8 +960,8 @@ public final class Configuration { } else { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str - + "] for [phylogeny_graphics_type]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str + + "] for [phylogeny_graphics_type]" ); } } else if ( key.equals( "min_confidence_value" ) ) { @@ -1122,21 +990,7 @@ public final class Configuration { 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 ); - if ( i > 0 ) { - setGraphicsExportX( i ); - } - } - else if ( key.equals( "graphics_export_y" ) ) { - final String str = ( ( String ) st.nextElement() ).trim(); - final int i = parseInt( str ); - if ( i > 0 ) { - setGraphicsExportY( i ); + setMaxBaseFontSize( i ); } } else if ( key.equals( "pdf_export_line_width" ) ) { @@ -1146,8 +1000,8 @@ public final class Configuration { setPrintLineWidth( f ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "value for [pdf_export_line_width] cannot be zero or negative" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, + "value for [pdf_export_line_width] cannot be zero or negative" ); } } else if ( key.equals( "window_initial_size_x" ) ) { @@ -1172,8 +1026,8 @@ public final class Configuration { } else { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "value for [default_number_of_bootstrap_resamples] cannot be negative" ); + .printWarningMessage( AptxConstants.PRG_NAME, + "value for [default_number_of_bootstrap_resamples] cannot be negative" ); } } else if ( key.equals( "mafft_local" ) ) { @@ -1200,9 +1054,6 @@ 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() ) ); } @@ -1223,22 +1074,14 @@ public final class Configuration { if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) { setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP ); } - else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) { - setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP ); - } - else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) { - setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP ); + else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.LINED_UP.toString() ) ) { + setCladogramType( Options.CLADOGRAM_TYPE.LINED_UP ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str - + "] for [cladogram_type]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str + + "] for [cladogram_type]" ); } } - else if ( key.equals( "non_lined_up_cladogram" ) ) { - ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" ); - } else if ( key.equals( "hide_controls_and_menus" ) ) { _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() ); } @@ -1269,8 +1112,8 @@ public final class Configuration { } else { setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT ); - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str - + "] for [overview_placement_type]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str + + "] for [overview_placement_type]" ); } } else if ( key.equals( "node_label_direction" ) ) { @@ -1283,8 +1126,8 @@ public final class Configuration { } else { setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL ); - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str - + "] for [node_label_direction]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str + + "] for [node_label_direction]" ); } } else if ( key.equals( "branch_length_value_digits" ) ) { @@ -1293,8 +1136,8 @@ public final class Configuration { setNumberOfDigitsAfterCommaForBranchLengthValue( i ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i - + "] for [branch_length_value_digits]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "illegal value [" + i + + "] for [branch_length_value_digits]" ); } } else if ( key.equals( "confidence_value_digits" ) ) { @@ -1303,8 +1146,8 @@ public final class Configuration { setNumberOfDigitsAfterCommaForConfidenceValues( i ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i - + "] for [confidence_value_digits]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "illegal value [" + i + + "] for [confidence_value_digits]" ); } } else if ( key.equals( "allow_editing" ) ) { @@ -1317,8 +1160,8 @@ public final class Configuration { final boolean r = parseBoolean( ( String ) st.nextElement() ); if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "attempt to extract taxonomies and replace underscores at the same time" ); + .printWarningMessage( AptxConstants.PRG_NAME, + "attempt to extract taxonomies and replace underscores at the same time" ); } else { setReplaceUnderscoresInNhParsing( r ); @@ -1340,15 +1183,15 @@ public final class Configuration { } else { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "unknown value for \"taxonomy_extraction_in_nh_parsing\": " - + s - + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" ); + .printWarningMessage( AptxConstants.PRG_NAME, + "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + + s + + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" ); } if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "attempt to extract taxonomies and replace underscores at the same time" ); + .printWarningMessage( AptxConstants.PRG_NAME, + "attempt to extract taxonomies and replace underscores at the same time" ); } } else if ( key.equals( "internal_labels_are_confidence_values" ) ) { @@ -1378,21 +1221,15 @@ 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( "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 ); @@ -1409,8 +1246,8 @@ public final class Configuration { setDefaultNodeFill( NodeFill.SOLID ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str - + "] for [default_node_fill]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + fill_str + + "] for [default_node_fill]" ); } } else if ( key.equals( "default_node_shape" ) ) { @@ -1422,64 +1259,66 @@ public final class Configuration { setDefaultNodeShape( NodeShape.RECTANGLE ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str - + "] for [default_node_shape]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + shape_str + + "] for [default_node_shape]" ); } } 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]" ); + ForesterUtil.printWarningMessage( AptxConstants.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 ); @@ -1491,11 +1330,10 @@ public final class Configuration { setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s - + "] for [ext_descendents_data_to_return_on]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + s + + "] for [ext_descendents_data_to_return_on]" ); } } - else if ( key.equals( "vector_data_min_color" ) ) { _vector_data_min_color = Color.decode( ( String ) st.nextElement() ); } @@ -1505,7 +1343,6 @@ public final class Configuration { 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 ) { @@ -1518,16 +1355,15 @@ public final class Configuration { _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; @@ -1549,9 +1385,15 @@ public final class Configuration { else if ( key.equals( "show_taxonomy_code" ) ) { key_index = Configuration.show_tax_code; } + else if ( key.equals( "show_taxonomy_rank" ) ) { + key_index = Configuration.show_tax_rank; + } 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; } @@ -1561,8 +1403,8 @@ public final class Configuration { else if ( key.equals( "color_branches" ) ) { key_index = Configuration.use_style; ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" ); + .printWarningMessage( AptxConstants.PRG_NAME, + "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" ); } else if ( key.equals( "width_branches" ) ) { key_index = Configuration.width_branches; @@ -1570,6 +1412,9 @@ 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; } @@ -1594,6 +1439,9 @@ public final class Configuration { else if ( key.equals( "display_internal_data" ) ) { key_index = Configuration.display_internal_data; } + else if ( key.equals( "display_external_data" ) ) { + key_index = Configuration.display_external_data; + } else if ( key.equals( "dynamically_hide_data" ) ) { key_index = Configuration.dynamically_hide_data; } @@ -1638,7 +1486,7 @@ public final class Configuration { // Deprecated. } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: " + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown click-to option: " + click_to_name ); } } @@ -1655,23 +1503,23 @@ public final class Configuration { } else if ( key.equals( "annotation_color" ) ) { getAnnotationColors() - .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); + .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); } else if ( key.equals( "function_color" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "configuration key [function_color] is deprecated" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, + "configuration key [function_color] is deprecated" ); } else if ( key.equals( DISPLAY_COLOR_KEY ) ) { putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key - + "] in: " + config_filename ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown configuration key [" + key + + "] in: " + config_filename ); } } } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: " + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown configuration key [" + key + "] in: " + config_filename ); } } @@ -1724,61 +1572,244 @@ 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" ); } - public Color getVectorDataMinColor() { - return _vector_data_min_color; + /** + * 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( "?" ); } - public Color getVectorDataMaxColor() { - return _vector_data_max_color; + Map getAnnotationColors() { + if ( _annotation_colors == null ) { + _annotation_colors = new Hashtable(); + } + return _annotation_colors; } - public Color getVectorDataMeanColor() { - return _vector_data_mean_color; + int getBaseFontSize() { + return _base_font_size; } - public double getVectorDataHeight() { - return _vector_data_height; + CLADOGRAM_TYPE getCladogramType() { + return _cladogram_type; } - public int getVectorDataWidth() { - return _vector_data_width; + int getClickToOptionsCount() { + return clickto_options.length; } - - final public boolean isLineUpRendarableNodeData() { - - return _line_up_renderable_node_data; + + String getClickToTitle( final int which ) { + return clickto_options[ which ][ 0 ]; } - - final public boolean isRightLineUpDomains() { - - return _right_align_domains; + + int getDefaultDisplayClicktoOption() { + return default_clickto; } - - final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data) { - - _line_up_renderable_node_data = line_up_renderable_node_data; + + SortedMap getDisplayColors() { + return _display_colors; } - - final public void setRightLineUpDomains( final boolean right_align_domains ) { - - _right_align_domains = right_align_domains; + + String getDisplayTitle( final int which ) { + return display_options[ which ][ 0 ]; + } + + Map getDomainColors() { + if ( _domain_colors == null ) { + _domain_colors = new Hashtable(); + } + return _domain_colors; + } + + + 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; + } + + static int getGuiFontSize() { + return 11; } + 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; + } + + public 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; + } + + public boolean isInternalNumberAreConfidenceForNhParsing() { + return _internal_number_are_confidence_for_nh_parsing; + } + + public 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; + } + + public 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; + } + + public boolean isCouldReadConfigFile() { + return _could_read_config_file; + } + }