// $Id: // FORESTER -- software libraries and applications // for evolutionary biology research and applications. // // Copyright (C) 2008-2009 Christian M. Zmasek // Copyright (C) 2008-2009 Burnham Institute for Medical Research // Copyright (C) 2000-2001 Washington University School of Medicine // and Howard Hughes Medical Institute // Copyright (C) 2003-2007 Ethalinda K.S. Cannon // All rights reserved // // This library is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free Software Foundation; either // version 2.1 of the License, or (at your option) any later version. // // This library is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU // Lesser General Public License for more details. // // You should have received a copy of the GNU Lesser General Public // License along with this library; if not, write to the Free Software // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com // WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; import java.awt.Color; import java.io.BufferedReader; import java.io.File; import java.io.FileReader; import java.io.IOException; import java.io.InputStreamReader; import java.net.URL; import java.util.Arrays; import java.util.Hashtable; import java.util.Map; import java.util.SortedMap; import java.util.StringTokenizer; import java.util.TreeMap; import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE; import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION; import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE; import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE; import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; import org.forester.phylogeny.data.NodeDataField; import org.forester.phylogeny.data.NodeVisualData; import org.forester.phylogeny.data.NodeVisualData.NodeFill; import org.forester.phylogeny.data.NodeVisualData.NodeShape; 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/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; final static int subtree = 3; final static int swap = 4; final static int color_node_font = 5; final static int change_node_font = 6; final static int color_subtree = 7; final static int open_seq_web = 8; final static int open_pdb_web = 9; final static int open_tax_web = 10; final static int blast = 11; final static int cut_subtree = 12; final static int copy_subtree = 13; final static int paste_subtree = 14; final static int delete_subtree_or_node = 15; final static int add_new_node = 16; final static int edit_node_data = 17; 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" }, { "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; final static int show_annotation = 3; final static int write_confidence_values = 4; final static int write_events = 5; final static int color_according_to_species = 6; 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; 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; private static Hashtable _domain_colors; private static Hashtable _species_colors; private static String DEFAULT_FONT_FAMILY = ""; private static final int DEPRECATED = -2; private static final String DISPLAY_COLOR_KEY = "display_color"; // --------------------------- // Display options for trees // --------------------------- // --------------------------------- // Pertaining to the config itself // --------------------------------- // Full path to config (may be URL) String config_filename; // This option is selected in the dropdown int default_clickto = Configuration.display_node_data; String default_config_filename = AptxConstants.DEFAULT_CONFIGURATION_FILE_NAME; // -------------- // Color set // -------------- TreeColorSet tree_color_set; // ------- // Fonts // ------- TreeFontSet tree_font_set; 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 = 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 = AptxConstants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; private SortedMap _display_colors = null; private boolean _display_sequence_relations = false; private boolean _editable = true; 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 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 = ""; private int _max_base_font_size = 20; private boolean _midpoint_root = false; private int _min_base_font_size = 2; 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 = 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; private File _path_to_local_fastme = null; 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 = AptxConstants.PDF_LINE_WIDTH_DEFAULT; private boolean _show_annotation_ref_source = true; 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; private boolean _show_scale = false; 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 = 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 = 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 : 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 = AptxConstants.DEFAULT_FONT_CHOICES[ AptxConstants.DEFAULT_FONT_CHOICES.length - 1 ]; } } public Configuration() { this( null, false, false, false ); } public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) { if ( ForesterUtil.isEmpty( cf ) ) { config_filename = default_config_filename; } else { config_filename = cf; } _could_read_config_file = false; setDisplayColors( new TreeMap() ); config_filename = config_filename.trim(); URL u = null; if ( is_url ) { // If URL, open accordingly try { u = new URL( config_filename ); try { final InputStreamReader isr = new InputStreamReader( u.openStream() ); final BufferedReader bf = new BufferedReader( isr ); readConfig( bf ); bf.close(); ForesterUtil.programMessage( AptxConstants.PRG_NAME, "successfully read from configuration url [" + config_filename + "]" ); _could_read_config_file = true; } catch ( final Exception e ) { ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "failed to read configuration from [" + config_filename + "]: " + e.getLocalizedMessage() ); } } catch ( final Exception e ) { ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "cannot find or open configuration url [" + config_filename + "]" ); } } else { // Otherwise, open as a file File f = new File( config_filename ); if ( !f.exists() ) { f = new File( config_filename + ".txt" ); } if ( f.exists() && f.canRead() ) { try { 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( AptxConstants.PRG_NAME, "failed to read configuration from [" + config_filename + "]: " + e ); } } } else { if ( verbose ) { ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "cannot find or open configuration file [" + config_filename + "]" ); } } } } public String getBaseFontFamilyName() { return _base_font_family_name; } public int getDefaultBootstrapSamples() { return _default_bootstrap_samples; } public NodeFill getDefaultNodeFill() { return _default_node_fill; } public NodeShape getDefaultNodeShape() { return _default_node_shape; } public short getDefaultNodeShapeSize() { return _default_node_shape_size; } public NodeDataField getExtDescNodeDataToReturn() { return _ext_desc_data_to_return; } public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() { return _ext_node_data_return_on; } public int getFrameXSize() { return _frame_x_size; } public int getFrameYSize() { return _frame_y_size; } public String getLabelForGetExtDescendentsData() { return _label_for_get_ext_descendents_data; } public File getPathToLocalFastme() { return _path_to_local_fastme; } public File getPathToLocalMafft() { return _path_to_local_mafft; } public File getPathToLocalRaxml() { return _path_to_local_raxml; } public 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; } public boolean isColorByTaxonomicGroup() { return false; } public boolean isColorLabelsSameAsParentBranch() { 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; } public boolean isShowDefaultNodeShapesExternal() { 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; } public boolean isShowDomainLabels() { return _show_domain_labels; } public void putDisplayColors( final String key, final Color color ) { getDisplayColors().put( key, color ); } public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) { _abbreviate_scientific_names = abbreviate_scientific_names; } public void 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; } public void setBaseFontFamilyName( final String base_font_family_name ) { _base_font_family_name = base_font_family_name; } public void setBaseFontSize( final int base_font_size ) { _base_font_size = base_font_size; } public void setColorizeBranches( final boolean b ) { display_options[ use_style ][ 2 ] = b ? "yes" : "no"; } public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) { _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch; } public void setDefaultNodeFill( final NodeFill default_node_fill ) { _default_node_fill = default_node_fill; } public void setDefaultNodeShape( final NodeShape default_node_shape ) { _default_node_shape = default_node_shape; } public void setDefaultNodeShapeSize( final short default_node_shape_size ) { _default_node_shape_size = default_node_shape_size; } public void setDisplayAsPhylogram( final boolean b ) { display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no"; } public void setDisplayColors( final SortedMap display_colors ) { _display_colors = display_colors; } public void setDisplayConfidenceValues( final boolean b ) { display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no"; } public void 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"; } public void setDisplaySequenceAcc( final boolean b ) { display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no"; } public void setDisplaySequenceNames( final boolean b ) { display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no"; } public void setDisplaySequenceRelations( final boolean display_sequence_relations ) { _display_sequence_relations = display_sequence_relations; } public void setDisplaySequenceSymbols( final boolean b ) { display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no"; } 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"; } public void setDisplayTaxonomyImages( final boolean b ) { display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no"; } public void setDisplayTaxonomyScientificNames( final boolean b ) { display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no"; } public void setDynamicallyHideData( final boolean b ) { display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no"; } public void setExtDescNodeDataToReturn( final NodeDataField ext_desc_data_to_return ) { _ext_desc_data_to_return = ext_desc_data_to_return; } public void setFrameXSize( final int frame_x_size ) { _frame_x_size = frame_x_size; } public void setFrameYSize( final int frame_y_size ) { _frame_y_size = frame_y_size; } 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; } public void setMinConfidenceValue( final double min_confidence_value ) { _min_confidence_value = min_confidence_value; } public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) { _node_label_direction = node_label_direction; } public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) { _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values; } public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) { _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values; } public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) { _phylogeny_graphics_type = phylogeny_graphics_type; } public void setPrintLineWidth( final float print_line_width ) { _print_line_width = print_line_width; } public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) { _nh_parsing_replace_underscores = nh_parsing_replace_underscores; } 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; } public void setShowDomainLabels( final boolean show_domain_labels ) { _show_domain_labels = show_domain_labels; } public void setShowScale( final boolean show_scale ) { _show_scale = show_scale; } public void setUseStyle( final boolean b ) { display_options[ use_style ][ 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( 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; } 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; } else if ( name.equals( "subtree" ) ) { index = Configuration.subtree; } 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; } else if ( name.equals( "get_ext_descendents_data" ) ) { index = Configuration.get_ext_desc_data; } else if ( name.equals( "display_sequences" ) ) { ForesterUtil .printWarningMessage( AptxConstants.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( AptxConstants.PRG_NAME, "configuration key [display_node_popup] is deprecated" ); return DEPRECATED; } else if ( name.equals( "custom_option" ) ) { ForesterUtil.printWarningMessage( AptxConstants.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 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" ) ) { return true; } else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) { return false; } else { ForesterUtil.printWarningMessage( AptxConstants.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( AptxConstants.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( AptxConstants.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( AptxConstants.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( AptxConstants.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 ); } private void setAntialiasScreen( final boolean antialias_screen ) { _antialias_screen = antialias_screen; } private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) { _cladogram_type = cladogram_type; } private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) { _default_bootstrap_samples = default_bootstrap_samples; } private void setEditable( final boolean editable ) { _editable = editable; } private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) { _ext_node_data_return_on = ext_node_data_return_on; } //private void setGraphicsExportX( final int graphics_export_x ) { // _graphics_export_x = graphics_export_x; //} //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; } /** * Set a key-value(s) tuple */ private void setKeyValue( final StringTokenizer st ) { final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase(); if ( !st.hasMoreElements() ) { return; } // Handle single value settings first: if ( key.equals( "default_click_to" ) ) { final String clickto_name = ( String ) st.nextElement(); default_clickto = getClickToIndex( clickto_name ); if ( default_clickto == -1 ) { ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "invalid value [" + clickto_name + "] for [default_click_to]" ); default_clickto = 0; } else if ( default_clickto == DEPRECATED ) { // Deprecated. } } else if ( key.equals( "native_ui" ) ) { final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase(); if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) { _ui = UI.NATIVE; } else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) { _ui = UI.CROSSPLATFORM; } else if ( my_str.equals( "?" ) ) { _ui = UI.UNKNOWN; } else { ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse yes/no/? value from [" + my_str + "]" ); _ui = UI.UNKNOWN; } } else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) { setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "antialias_screen" ) ) { setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "phylogeny_graphics_type" ) ) { final String type_str = ( ( String ) st.nextElement() ).trim(); if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX ); } else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED ); } else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ); } else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED ); } else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); } else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ); } else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); } else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ); } else { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str + "] for [phylogeny_graphics_type]" ); } } else if ( key.equals( "min_confidence_value" ) ) { final String mcv_str = ( ( String ) st.nextElement() ).trim(); final double d = parseDouble( mcv_str ); setMinConfidenceValue( d ); } else if ( key.equals( "font_family" ) ) { processFontFamily( st ); } else if ( key.equals( "font_size" ) ) { final String size_str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( size_str ); if ( i > 0 ) { setBaseFontSize( i ); } } else if ( key.equals( "font_size_min" ) ) { final String size_str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( size_str ); if ( i > 0 ) { setMinBaseFontSize( i ); } } else if ( key.equals( "font_size_max" ) ) { final String size_str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( size_str ); if ( i > 1 ) { setMaxBaseFontSize( i ); } } else if ( key.equals( "pdf_export_line_width" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final float f = parseFloat( str ); if ( f > 0 ) { setPrintLineWidth( f ); } else { ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "value for [pdf_export_line_width] cannot be zero or negative" ); } } else if ( key.equals( "window_initial_size_x" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( str ); if ( i > 0 ) { setFrameXSize( i ); } } else if ( key.equals( "window_initial_size_y" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( str ); if ( i > 0 ) { setFrameYSize( i ); } } else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( str ); if ( i >= 0 ) { setDefaultBootstrapSamples( i ); } else { ForesterUtil .printWarningMessage( AptxConstants.PRG_NAME, "value for [default_number_of_bootstrap_resamples] cannot be negative" ); } } else if ( key.equals( "mafft_local" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); if ( !ForesterUtil.isEmpty( str ) ) { setPathToLocalMafft( new File( str ) ); } } else if ( key.equals( "fastme_local" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); if ( !ForesterUtil.isEmpty( str ) ) { setPathToLocalFastme( new File( str ) ); } } else if ( key.equals( "raxml_local" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); if ( !ForesterUtil.isEmpty( str ) ) { setPathToLocalRaxml( new File( str ) ); } } else if ( key.equals( "show_scale" ) ) { setShowScale( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "show_overview" ) ) { setShowOverview( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "background_gradient" ) ) { setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) { setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "show_domain_labels" ) ) { setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "show_seq_annotation_ref_sources" ) ) { setShowAnnotationRefSource( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "abbreviate_scientific_names" ) ) { setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "cladogram_type" ) ) { final String type_str = ( ( String ) st.nextElement() ).trim(); 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.LINED_UP.toString() ) ) { setCladogramType( Options.CLADOGRAM_TYPE.LINED_UP ); } else { ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str + "] for [cladogram_type]" ); } } else if ( key.equals( "hide_controls_and_menus" ) ) { _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() ); } else if ( key.equals( "use_tabbed_display" ) ) { _use_tabbed_display = parseBoolean( ( String ) st.nextElement() ); } else if ( key.equals( "overview_width" ) ) { final short i = parseShort( ( ( String ) st.nextElement() ) ); setOvMaxWidth( i ); } else if ( key.equals( "overview_height" ) ) { final short i = parseShort( ( ( String ) st.nextElement() ) ); setOvMaxHeight( i ); } else if ( key.equals( "overview_placement_type" ) ) { final String type_str = ( ( String ) st.nextElement() ).trim(); if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) { setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT ); } else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) { setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT ); } else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) { setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT ); } else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) { setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT ); } else { setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT ); ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str + "] for [overview_placement_type]" ); } } else if ( key.equals( "node_label_direction" ) ) { final String type_str = ( ( String ) st.nextElement() ).trim(); if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) { setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL ); } else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) { setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL ); } else { setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL ); ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str + "] for [node_label_direction]" ); } } else if ( key.equals( "branch_length_value_digits" ) ) { final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); if ( i >= 0 ) { setNumberOfDigitsAfterCommaForBranchLengthValue( i ); } else { ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "illegal value [" + i + "] for [branch_length_value_digits]" ); } } else if ( key.equals( "confidence_value_digits" ) ) { final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); if ( i >= 0 ) { setNumberOfDigitsAfterCommaForConfidenceValues( i ); } else { ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "illegal value [" + i + "] for [confidence_value_digits]" ); } } else if ( key.equals( "allow_editing" ) ) { setEditable( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "display_sequence_relations" ) ) { setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) { final boolean r = parseBoolean( ( String ) st.nextElement() ); if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) { ForesterUtil .printWarningMessage( AptxConstants.PRG_NAME, "attempt to extract taxonomies and replace underscores at the same time" ); } else { setReplaceUnderscoresInNhParsing( r ); } } else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) { final String s = ( String ) st.nextElement(); if ( s.equalsIgnoreCase( "no" ) ) { setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO ); } else if ( s.equalsIgnoreCase( "pfam_relaxed" ) ) { setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); } else if ( s.equalsIgnoreCase( "pfam_strict" ) ) { setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); } else if ( s.equalsIgnoreCase( "aggressive" ) ) { setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE ); } else { ForesterUtil .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( AptxConstants.PRG_NAME, "attempt to extract taxonomies and replace underscores at the same time" ); } } else if ( key.equals( "internal_labels_are_confidence_values" ) ) { setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) ); } else if ( key.equals( "gui_background_color" ) ) { _gui_background_color = Color.decode( ( String ) st.nextElement() ); } else if ( key.equals( "gui_checkbox_text_color" ) ) { _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() ); } else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) { _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() ); } else if ( key.equals( "gui_button_text_color" ) ) { _gui_button_text_color = Color.decode( ( String ) st.nextElement() ); } else if ( key.equals( "gui_button_background_color" ) ) { _gui_button_background_color = Color.decode( ( String ) st.nextElement() ); } else if ( key.equals( "gui_menu_background_color" ) ) { _gui_menu_background_color = Color.decode( ( String ) st.nextElement() ); } else if ( key.equals( "gui_menu_text_color" ) ) { _gui_menu_text_color = Color.decode( ( String ) st.nextElement() ); } 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_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 ); } else if ( key.equals( "default_node_fill" ) ) { final String fill_str = ( ( String ) st.nextElement() ).trim(); if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.NONE.toString() ) ) { setDefaultNodeFill( NodeFill.NONE ); } else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.GRADIENT.toString() ) ) { setDefaultNodeFill( NodeFill.GRADIENT ); } else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.SOLID.toString() ) ) { setDefaultNodeFill( NodeFill.SOLID ); } else { ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + fill_str + "] for [default_node_fill]" ); } } else if ( key.equals( "default_node_shape" ) ) { final String shape_str = ( ( String ) st.nextElement() ).trim(); if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.CIRCLE.toString() ) ) { setDefaultNodeShape( NodeShape.CIRCLE ); } else if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.RECTANGLE.toString() ) ) { setDefaultNodeShape( NodeShape.RECTANGLE ); } else { 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( "list_node_data_field" ) || key.equals( "ext_descendents_data_to_return" ) ) { final String s = ( ( String ) st.nextElement() ).trim(); if ( s.equalsIgnoreCase( "node_name" ) ) { setExtDescNodeDataToReturn( NodeDataField.NODE_NAME ); } else if ( s.equalsIgnoreCase( "sequence_acc" ) ) { setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_ACC ); } else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) { setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA ); } else if ( s.equalsIgnoreCase( "sequence_name" ) ) { setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_NAME ); } else if ( s.equalsIgnoreCase( "gene_name" ) ) { setExtDescNodeDataToReturn( NodeDataField.GENE_NAME ); } else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) { setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_SYMBOL ); } else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) { setExtDescNodeDataToReturn( NodeDataField.TAXONOMY_SCIENTIFIC_NAME ); } else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) { setExtDescNodeDataToReturn( NodeDataField.TAXONOMY_CODE ); } else if ( s.equalsIgnoreCase( "user_selected" ) ) { 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( AptxConstants.PRG_NAME, "unknown value [" + s + "] for [ext_descendents_data_to_return]" ); } } 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() > 1 ) ) { setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) ); } } 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 ); } else if ( s.equals( "window" ) ) { setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW ); } else if ( s.equals( "buffer_only" ) ) { setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ); } else { ForesterUtil.printWarningMessage( 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() ); } 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; if ( key.equals( "phylogram" ) ) { key_index = Configuration.display_as_phylogram; } else if ( key.equals( "rollover" ) ) { key_index = Configuration.node_data_popup; } 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; } 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; } else if ( key.equals( "use_visual_styles" ) ) { key_index = Configuration.use_style; } else if ( key.equals( "color_branches" ) ) { key_index = Configuration.use_style; ForesterUtil .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; } 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; } else if ( key.equals( "show_binary_characters" ) ) { key_index = Configuration.show_binary_characters; } else if ( key.equals( "show_binary_character_counts" ) ) { key_index = Configuration.show_binary_character_counts; } else if ( key.equals( "show_seq_names" ) ) { key_index = Configuration.show_seq_names; } else if ( key.equals( "show_gene_names" ) ) { key_index = Configuration.show_gene_names; } else if ( key.equals( "show_seq_symbols" ) ) { key_index = Configuration.show_seq_symbols; } else if ( key.equals( "show_seq_acc" ) ) { key_index = Configuration.show_sequence_acc; } 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; } else if ( key.equals( "show_taxonomy_scientific_names" ) ) { key_index = Configuration.show_taxonomy_scientific_names; } else if ( key.equals( "show_taxonomy_common_names" ) ) { key_index = Configuration.show_taxonomy_common_names; } else if ( key.equals( "show_taxonomy_images" ) ) { key_index = Configuration.show_taxonomy_images; } else if ( key.equals( "color_according_to_annotation" ) ) { key_index = Configuration.color_according_to_annotation; } else if ( key.equals( "show_vector_data" ) ) { key_index = Configuration.show_vector_data; } else if ( key.equals( "show_properties" ) ) { key_index = Configuration.show_properties; } else if ( key.equals( "show_relation_confidence" ) ) { key_index = Configuration.show_relation_confidence; } // If we've found the key, set the values if ( key_index >= 0 ) { display_options[ key_index ][ 1 ] = ( String ) st.nextElement(); display_options[ key_index ][ 2 ] = ( String ) st.nextElement(); // otherwise, keep looking } else { if ( key_index == DEPRECATED ) { // Deprecated. } else if ( key.equals( "click_to" ) ) { final String click_to_name = ( String ) st.nextElement(); key_index = getClickToIndex( click_to_name ); if ( key_index >= 0 ) { clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement(); } else if ( key_index == DEPRECATED ) { // Deprecated. } else { ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown click-to option: " + click_to_name ); } } else if ( key.equals( "species_color" ) ) { 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() ) ); } else if ( key.equals( "annotation_color" ) ) { getAnnotationColors() .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); } else if ( key.equals( "function_color" ) ) { 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( AptxConstants.PRG_NAME, "unknown configuration key [" + key + "] in: " + config_filename ); } } } else { ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown configuration key [" + key + "] in: " + config_filename ); } } private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) { _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data; } private void setMaxBaseFontSize( final int max_base_font_size ) { _max_base_font_size = max_base_font_size; } private void setMinBaseFontSize( final int min_base_font_size ) { _min_base_font_size = min_base_font_size; } private void setOvMaxHeight( final short ov_max_height ) { _ov_max_height = ov_max_height; } private void setOvMaxWidth( final short ov_max_width ) { _ov_max_width = ov_max_width; } private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) { _ov_placement = ov_placement; } private void setPathToLocalFastme( final File path_to_local_fastme ) { _path_to_local_fastme = path_to_local_fastme; } private void setPathToLocalMafft( final File path_to_local_mafft ) { _path_to_local_mafft = path_to_local_mafft; } private void setPathToLocalRaxml( final File path_to_local_raxml ) { _path_to_local_raxml = path_to_local_raxml; } private void setShowAnnotationRefSource( final boolean b ) { _show_annotation_ref_source = b; } private void setShowOverview( final boolean show_overview ) { _show_overview = show_overview; } private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) { _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema; } 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; } 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; } public String getConfigFilename() { return config_filename; } }