X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=5ae230fa3fe020263da53e2c0bbd9741c44e82e0;hb=e6ea1a1dcb0a9b96cad1bc08c3b80a6f876344d2;hp=064fc7db46e3b013a64365cbca33b2d241915f1f;hpb=6be89aad9f2003c1b2bb4a9e6581ac3537d556c2;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 064fc7d..5ae230f 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -24,7 +24,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; @@ -34,7 +34,6 @@ import java.io.File; import java.io.FileReader; import java.io.IOException; import java.io.InputStreamReader; -import java.net.MalformedURLException; import java.net.URL; import java.util.Arrays; import java.util.Hashtable; @@ -47,55 +46,63 @@ 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.phylogeny.data.NodeVisualization; -import org.forester.phylogeny.data.NodeVisualization.NodeFill; -import org.forester.phylogeny.data.NodeVisualization.NodeShape; +import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; +import org.forester.phylogeny.data.NodeData.NODE_DATA; +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 { - static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema"; - private static final String WEB_LINK_KEY = "web_link"; - private static final String DISPLAY_COLOR_KEY = "display_color"; - private static final int DEPRECATED = -2; - private UI _ui = UI.UNKNOWN; - private boolean _use_tabbed_display = false; - private boolean _hide_controls_and_menus = false; - private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT; - private SortedMap _weblinks = null; - private SortedMap _display_colors = null; - private boolean _antialias_screen = true; - private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR; - private String _base_font_family_name = ""; - private int _base_font_size = -1; - private int _graphics_export_x = -1; - private int _graphics_export_y = -1; - private short _ov_max_width = 80; - private short _ov_max_height = 80; - private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT; - private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT; - private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT; - private boolean _show_scale = false; - private boolean _show_branch_length_values = false; - private boolean _show_overview = true; - 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 = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT; - private boolean _editable = true; - private boolean _nh_parsing_replace_underscores = false; - private boolean _nh_parsing_extract_pfam_taxonomy_codes = false; - private boolean _internal_number_are_confidence_for_nh_parsing = false; - private boolean _display_sequence_relations = false; - private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT; - private boolean _background_color_gradient = false; - private boolean _show_domain_labels = true; - private boolean _abbreviate_scientific_names = false; - private boolean _color_labels_same_as_parent_branch = false; - private int _default_bootstrap_samples = -1; - private boolean _show_default_node_shapes = false; - private NodeShape _default_node_shape = NodeShape.CIRCLE; - private NodeFill _default_node_fill = NodeFill.GRADIENT; - private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; - private boolean _taxonomy_colorize_node_shapes = false; + 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" } }; + 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; + // ------------------ + // 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" } }; final static int display_as_phylogram = 0; final static int show_node_names = 1; final static int show_tax_code = 2; @@ -103,46 +110,36 @@ public final class Configuration { final static int write_confidence_values = 4; final static int write_events = 5; final static int color_according_to_species = 6; - final static int color_branches = 7; - final static int width_branches = 8; - final static int show_custom_node_shapes = 9; + 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_gene_names = 13; + 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_gene_symbols = 20; + 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; - // ------------------ - // Click-to options - // ------------------ - 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_subtree = 5; - final static int open_seq_web = 6; - final static int open_tax_web = 7; - final static int cut_subtree = 8; - final static int copy_subtree = 9; - final static int paste_subtree = 10; - final static int delete_subtree_or_node = 11; - final static int add_new_node = 12; - final static int edit_node_data = 13; - final static int blast = 14; - final static int sort_descendents = 15; + final static int show_gene_names = 26; + 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 // --------------------------- @@ -151,28 +148,9 @@ public final class Configuration { // --------------------------------- // Full path to config (may be URL) String config_filename; - String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME; - final static String display_options[][] = { - { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" }, - { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, { "Event", "display", "?" }, - { "Taxonomy Colorize", "display", "no" }, { "Colorize Branches", "display", "no" }, - { "Use Branch-Widths", "display", "no" }, { "Show Custom Nodes", "display", "yes" }, - { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" }, - { "Binary Char Counts", "nodisplay", "no" }, { "Prot/Gene Name", "display", "yes" }, - { "Prot/Gene Acc", "display", "no" }, { "Show Internal Data", "display", "yes" }, - { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" }, - { "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" }, - { "Prot/Gene Symbol", "display", "yes" }, { "Rollover", "display", "yes" }, - { "Relation Confidence", "display", "no" }, { "Vector Data", "display", "no" }, - { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" } }; - final static String clickto_options[][] = { - { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" }, - { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" }, - { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Cut Subtree", "display" }, - { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" }, - { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Blast", "nodisplay" }, { "Sort Descendants", "display" } }; // This option is selected in the dropdown int default_clickto = Configuration.display_node_data; + String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME; // -------------- // Color set // -------------- @@ -181,31 +159,67 @@ public final class Configuration { // Fonts // ------- TreeFontSet tree_font_set; - // ---------------- - // Species colors - // ---------------- - private static Hashtable _species_colors; - // ---------------- - // Domain colors - // ---------------- - private static Hashtable _domain_colors; - // ---------------- - // Function colors - // ---------------- - private static Hashtable _annotation_colors; boolean verbose = Constants.VERBOSE_DEFAULT; - private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL; + 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 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 SortedMap _display_colors = null; + private boolean _display_sequence_relations = false; + private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT; + private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT; + private boolean _editable = true; + private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN; + private 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_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT; - private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT; - private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_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_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT; - private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT; - private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT; - private static String DEFAULT_FONT_FAMILY = ""; + 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 = 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 _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 = Constants.PDF_LINE_WIDTH_DEFAULT; + private boolean _show_annotation_ref_source = true; + private boolean _show_branch_length_values = false; + private boolean _show_default_node_shapes_external = false; + private boolean _show_default_node_shapes_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 = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT; static { for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) { if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) { @@ -229,7 +243,6 @@ public final class Configuration { else { config_filename = cf; } - setWebLinks( new TreeMap() ); setDisplayColors( new TreeMap() ); config_filename = config_filename.trim(); URL u = null; @@ -283,21 +296,274 @@ public final class Configuration { } } - private void createWebLink( final String url_str, final String desc, final String source_identifier ) { - WebLink weblink = null; - boolean ex = false; - try { - weblink = new WebLink( new URL( url_str.trim() ), desc.trim(), source_identifier.trim() ); - } - catch ( final MalformedURLException e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not create URL from [" + url_str + "]" ); - ex = true; - } - if ( !ex && ( weblink != null ) ) { - getWebLinks().put( weblink.getSourceIdentifier().toLowerCase(), weblink ); - } + public String getBaseFontFamilyName() { + return _base_font_family_name; + } + + 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 Color getDomainStructureBaseColor() { + return _domain_structure_base_color; + } + + public Color getDomainStructureFontColor() { + return _domain_structure_font_color; + } + + public NODE_DATA 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 boolean isAbbreviateScientificTaxonNames() { + return _abbreviate_scientific_names; + } + + public boolean isBackgroundColorGradient() { + return _background_color_gradient; + } + + public boolean isColorByTaxonomicGroup() { + return false; + } + + public boolean isColorLabelsSameAsParentBranch() { + return _color_labels_same_as_parent_branch; + } + + public boolean isMidpointReroot() { + return _midpoint_root; + } + + public boolean isShowAnnotationRefSource() { + return _show_annotation_ref_source; + } + + public boolean isShowDefaultNodeShapesExternal() { + return _show_default_node_shapes_external; + } + + public boolean isShowDefaultNodeShapesInternal() { + return _show_default_node_shapes_internal; + } + + public boolean isShowDomainLabels() { + return _show_domain_labels; + } + + public void putDisplayColors( final String key, final Color color ) { + 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 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 setUseStyle( final boolean b ) { + display_options[ use_style ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayColors( final SortedMap display_colors ) { + _display_colors = display_colors; + } + + public void setDisplayConfidenceValues( final boolean b ) { + display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayInternalData( final boolean b ) { + display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayNodeNames( final boolean b ) { + display_options[ show_node_names ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplaySequenceAcc( final boolean b ) { + display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplaySequenceNames( final boolean b ) { + display_options[ show_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; + } + + 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 setDisplayTaxonomyCommonNames( final boolean b ) { + display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayTaxonomyImages( final boolean b ) { + display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayTaxonomyScientificNames( final boolean b ) { + display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no"; + } + + public void setDynamicallyHideData( final boolean b ) { + display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no"; + } + + public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) { + _ext_desc_data_to_return = ext_desc_data_to_return; + } + + public void setFrameXSize( final int frame_x_size ) { + _frame_x_size = frame_x_size; + } + + public void setFrameYSize( final int frame_y_size ) { + _frame_y_size = frame_y_size; + } + + public void 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; + } + + public void setShowBranchLengthValues( final boolean show_branch_length_values ) { + _show_branch_length_values = show_branch_length_values; + } + + public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) { + _show_default_node_shapes_external = show_default_node_shapes_external; + } + + public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) { + _show_default_node_shapes_internal = show_default_node_shapes_internal; } + public void setShowDomainLabels( final boolean show_domain_labels ) { + _show_domain_labels = show_domain_labels; + } + + public void setShowScale( final boolean show_scale ) { + _show_scale = show_scale; + } + boolean displaySequenceRelations() { return _display_sequence_relations; } @@ -331,10 +597,6 @@ public final class Configuration { return _annotation_colors; } - public String getBaseFontFamilyName() { - return _base_font_family_name; - } - int getBaseFontSize() { return _base_font_size; } @@ -343,80 +605,6 @@ public final class Configuration { return _cladogram_type; } - private int getClickToIndex( final String name ) { - int index = -1; - if ( name.equals( "edit_info" ) ) { - index = Configuration.display_node_data; - ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "configuration key [edit_info] is deprecated, use [display node data] instead" ); - } - else if ( name.equals( "display_node_data" ) ) { - index = Configuration.display_node_data; - } - else if ( name.equals( "collapse_uncollapse" ) ) { - index = Configuration.collapse_uncollapse; - } - else if ( name.equals( "reroot" ) ) { - index = Configuration.reroot; - } - else if ( name.equals( "subtree" ) ) { - index = Configuration.subtree; - } - else if ( name.equals( "swap" ) ) { - index = Configuration.swap; - } - else if ( name.equals( "sort_descendants" ) ) { - index = Configuration.sort_descendents; - } - else if ( name.equals( "display_sequences" ) ) { - ForesterUtil - .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" ); - return DEPRECATED; - } - else if ( name.equals( "open_seq_web" ) ) { - index = Configuration.open_seq_web; - } - else if ( name.equals( "open_tax_web" ) ) { - index = Configuration.open_tax_web; - } - else if ( name.equals( "cut_subtree" ) ) { - index = Configuration.cut_subtree; - } - else if ( name.equals( "copy_subtree" ) ) { - index = Configuration.copy_subtree; - } - else if ( name.equals( "paste_subtree" ) ) { - index = Configuration.paste_subtree; - } - else if ( name.equals( "delete" ) ) { - index = Configuration.delete_subtree_or_node; - } - else if ( name.equals( "add_new_node" ) ) { - index = Configuration.add_new_node; - } - else if ( name.equals( "edit_node_data" ) ) { - index = Configuration.edit_node_data; - } - else if ( name.equals( "display_node_popup" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "configuration key [display_node_popup] is deprecated" ); - return DEPRECATED; - } - else if ( name.equals( "custom_option" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" ); - return DEPRECATED; - } - else if ( name.equals( "color_subtree" ) ) { - index = Configuration.color_subtree; - } - else if ( name.equals( "go_to_swiss_prot" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" ); - return DEPRECATED; - } - return index; - } - int getClickToOptionsCount() { return clickto_options.length; } @@ -425,26 +613,10 @@ public final class Configuration { return clickto_options[ which ][ 0 ]; } - public int getDefaultBootstrapSamples() { - return _default_bootstrap_samples; - } - int getDefaultDisplayClicktoOption() { return default_clickto; } - public NodeFill getDefaultNodeFill() { - return _default_node_fill; - } - - public NodeShape getDefaultNodeShape() { - return _default_node_shape; - } - - public short getDefaultNodeShapeSize() { - return _default_node_shape_size; - } - SortedMap getDisplayColors() { return _display_colors; } @@ -460,14 +632,6 @@ public final class Configuration { return _domain_colors; } - public Color getDomainStructureBaseColor() { - return _domain_structure_base_color; - } - - public Color getDomainStructureFontColor() { - return _domain_structure_font_color; - } - int getGraphicsExportX() { return _graphics_export_x; } @@ -508,6 +672,14 @@ public final class Configuration { 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; } @@ -550,39 +722,26 @@ public final class Configuration { } return _species_colors; } - - TreeColorSet getTreeColorSet() { - return null; - } - - TreeFontSet getTreeFontSet() { - return null; - } - - WebLink getWebLink( final String source ) { - return getWebLinks().get( source ); - } - - Map getWebLinks() { - return _weblinks; + + Hashtable getSequenceColors() { + if ( _sequence_colors == null ) { + _sequence_colors = new Hashtable(); + } + return _sequence_colors; } - public boolean isAbbreviateScientificTaxonNames() { - return _abbreviate_scientific_names; + 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; } - public boolean isBackgroundColorGradient() { - return _background_color_gradient; - } - - public boolean isColorLabelsSameAsParentBranch() { - return _color_labels_same_as_parent_branch; - } - /** * Convenience method. * @@ -596,14 +755,6 @@ public final class Configuration { return _editable; } - boolean isExtractPfamTaxonomyCodesInNhParsing() { - return _nh_parsing_extract_pfam_taxonomy_codes; - } - - boolean isHasWebLink( final String source ) { - return getWebLinks().containsKey( source ); - } - /** * Only used by ArchaeoptryxE. * @@ -624,14 +775,6 @@ public final class Configuration { return _show_branch_length_values; } - public boolean isShowDefaultNodeShapes() { - return _show_default_node_shapes; - } - - public boolean isShowDomainLabels() { - return _show_domain_labels; - } - boolean isShowOverview() { return _show_overview; } @@ -640,27 +783,118 @@ public final class Configuration { return _show_scale; } - public boolean isTaxonomyColorizeNodeShapes() { - return _taxonomy_colorize_node_shapes; - } - final boolean isUseNativeUI() { - if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) { + 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; + return _ui == UI.NATIVE; + } + + /** + * Only used by ArchaeoptryxE. + * + */ + boolean isUseTabbedDisplay() { + return _use_tabbed_display; + } + + boolean isValidatePhyloXmlAgainstSchema() { + return _validate_against_phyloxml_xsd_schema; + } + + final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) { + _taxonomy_extraction = taxonomy_extraction; + } + + private int getClickToIndex( final String name ) { + int index = -1; + if ( name.equals( "edit_info" ) ) { + index = Configuration.display_node_data; + ForesterUtil + .printWarningMessage( Constants.PRG_NAME, + "configuration key [edit_info] is deprecated, use [display node data] instead" ); + } + else if ( name.equals( "display_node_data" ) ) { + index = Configuration.display_node_data; + } + else if ( name.equals( "collapse_uncollapse" ) ) { + index = Configuration.collapse_uncollapse; + } + else if ( name.equals( "reroot" ) ) { + index = Configuration.reroot; + } + else if ( name.equals( "subtree" ) ) { + index = Configuration.subtree; + } + else if ( name.equals( "swap" ) ) { + index = Configuration.swap; + } + else if ( name.equals( "sort_descendants" ) ) { + index = Configuration.sort_descendents; + } + else if ( name.equals( "get_ext_descendents_data" ) ) { + index = Configuration.get_ext_desc_data; + } + else if ( name.equals( "display_sequences" ) ) { + ForesterUtil + .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" ); + return DEPRECATED; + } + else if ( name.equals( "open_seq_web" ) ) { + index = Configuration.open_seq_web; + } + else if ( name.equals( "open_pdb_web" ) ) { + index = Configuration.open_pdb_web; + } + else if ( name.equals( "open_tax_web" ) ) { + index = Configuration.open_tax_web; + } + else if ( name.equals( "blast" ) ) { + index = Configuration.blast; + } + else if ( name.equals( "cut_subtree" ) ) { + index = Configuration.cut_subtree; + } + else if ( name.equals( "copy_subtree" ) ) { + index = Configuration.copy_subtree; + } + else if ( name.equals( "paste_subtree" ) ) { + index = Configuration.paste_subtree; + } + else if ( name.equals( "delete" ) ) { + index = Configuration.delete_subtree_or_node; + } + else if ( name.equals( "add_new_node" ) ) { + index = Configuration.add_new_node; + } + else if ( name.equals( "edit_node_data" ) ) { + index = Configuration.edit_node_data; + } + else if ( name.equals( "select_nodes" ) ) { + index = Configuration.select_nodes; + } + else if ( name.equals( "display_node_popup" ) ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, + "configuration key [display_node_popup] is deprecated" ); + return DEPRECATED; + } + else if ( name.equals( "custom_option" ) ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" ); + return DEPRECATED; + } + else if ( name.equals( "color_subtree" ) ) { + index = Configuration.color_subtree; + } + else if ( name.equals( "change_node_font" ) ) { + index = Configuration.change_node_font; + } + else if ( name.equals( "color_node_font" ) ) { + index = Configuration.color_node_font; + } + else if ( name.equals( "color_subtree" ) ) { + index = Configuration.color_subtree; + } + return index; } private boolean parseBoolean( final String str ) { @@ -680,7 +914,7 @@ public final class Configuration { private double parseDouble( final String str ) { double d = 0.0; try { - d = Double.parseDouble( str ); + d = Double.parseDouble( str.trim() ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" ); @@ -692,7 +926,7 @@ public final class Configuration { private float parseFloat( final String str ) { float f = 0.0f; try { - f = Float.parseFloat( str ); + f = Float.parseFloat( str.trim() ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" ); @@ -704,7 +938,7 @@ public final class Configuration { private int parseInt( final String str ) { int i = -1; try { - i = Integer.parseInt( str ); + i = Integer.parseInt( str.trim() ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" ); @@ -716,7 +950,7 @@ public final class Configuration { private short parseShort( final String str ) { short i = -1; try { - i = Short.parseShort( str ); + i = Short.parseShort( str.trim() ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" ); @@ -738,10 +972,6 @@ public final class Configuration { } } - public void putDisplayColors( final String key, final Color color ) { - getDisplayColors().put( key, color ); - } - /** * read each line of config file, process non-comment lines * @throws IOException @@ -763,116 +993,24 @@ public final class Configuration { } while ( line != null ); } - public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) { - _abbreviate_scientific_names = abbreviate_scientific_names; - } - private void setAntialiasScreen( final boolean antialias_screen ) { _antialias_screen = antialias_screen; } - public void setBackgroundColorGradient( final boolean background_color_gradient ) { - _background_color_gradient = background_color_gradient; - } - - public void setBaseFontFamilyName( final String base_font_family_name ) { - _base_font_family_name = base_font_family_name; - } - - public void setBaseFontSize( final int base_font_size ) { - _base_font_size = base_font_size; - } - private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) { _cladogram_type = cladogram_type; } - public void setColorizeBranches( final boolean b ) { - display_options[ color_branches ][ 2 ] = b ? "yes" : "no"; - } - - public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) { - _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch; - } - private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) { _default_bootstrap_samples = default_bootstrap_samples; } - public void setDefaultNodeFill( final NodeFill default_node_fill ) { - _default_node_fill = default_node_fill; - } - - public void setDefaultNodeShape( final NodeShape default_node_shape ) { - _default_node_shape = default_node_shape; - } - - public void setDefaultNodeShapeSize( final short default_node_shape_size ) { - _default_node_shape_size = default_node_shape_size; - } - - public void setDisplayAsPhylogram( final boolean b ) { - display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplayColors( final SortedMap display_colors ) { - _display_colors = display_colors; - } - - public void setDisplayConfidenceValues( final boolean b ) { - display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplayInternalData( final boolean b ) { - display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplayNodeNames( final boolean b ) { - display_options[ show_node_names ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplaySequenceAcc( final boolean b ) { - display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplaySequenceNames( final boolean b ) { - display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplaySequenceRelations( final boolean display_sequence_relations ) { - _display_sequence_relations = display_sequence_relations; - } - - public void setDisplaySequenceSymbols( final boolean b ) { - display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplayTaxonomyCode( final boolean b ) { - display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplayTaxonomyCommonNames( final boolean b ) { - display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplayTaxonomyImages( final boolean b ) { - display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplayTaxonomyScientificNames( final boolean b ) { - display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no"; - } - - public void setDynamicallyHideData( final boolean b ) { - display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no"; - } - private void setEditable( final boolean editable ) { _editable = editable; } - public void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) { - _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes; + private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) { + _ext_node_data_return_on = ext_node_data_return_on; } private void setGraphicsExportX( final int graphics_export_x ) { @@ -891,10 +1029,10 @@ public final class Configuration { * Set a key-value(s) tuple */ private void setKeyValue( final StringTokenizer st ) { - String key = ( String ) st.nextElement(); - key = key.replace( ':', ' ' ); - key = key.trim(); - key = key.toLowerCase(); + final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase(); + if ( !st.hasMoreElements() ) { + return; + } // Handle single value settings first: if ( key.equals( "default_click_to" ) ) { final String clickto_name = ( String ) st.nextElement(); @@ -974,17 +1112,37 @@ public final class Configuration { else if ( key.equals( "font_size" ) ) { final String size_str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( size_str ); - setBaseFontSize( i ); + if ( i > 0 ) { + setBaseFontSize( i ); + } + } + else if ( key.equals( "font_size_min" ) ) { + final String size_str = ( ( String ) st.nextElement() ).trim(); + final int i = parseInt( size_str ); + if ( i > 0 ) { + setMinBaseFontSize( i ); + } + } + else if ( key.equals( "font_size_max" ) ) { + final String size_str = ( ( String ) st.nextElement() ).trim(); + final int i = parseInt( size_str ); + if ( i > 1 ) { + setMaxBaseFontSize( i ); + } } else if ( key.equals( "graphics_export_x" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( str ); - setGraphicsExportX( i ); + if ( i > 0 ) { + setGraphicsExportX( i ); + } } else if ( key.equals( "graphics_export_y" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( str ); - setGraphicsExportY( i ); + if ( i > 0 ) { + setGraphicsExportY( i ); + } } else if ( key.equals( "pdf_export_line_width" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); @@ -997,6 +1155,20 @@ public final class Configuration { "value for [pdf_export_line_width] cannot be zero or negative" ); } } + else if ( key.equals( "window_initial_size_x" ) ) { + final String str = ( ( String ) st.nextElement() ).trim(); + final int i = parseInt( str ); + if ( i > 0 ) { + setFrameXSize( i ); + } + } + else if ( key.equals( "window_initial_size_y" ) ) { + final String str = ( ( String ) st.nextElement() ).trim(); + final int i = parseInt( str ); + if ( i > 0 ) { + setFrameYSize( i ); + } + } else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( str ); @@ -1009,6 +1181,24 @@ public final class Configuration { "value for [default_number_of_bootstrap_resamples] cannot be negative" ); } } + else if ( key.equals( "mafft_local" ) ) { + final String str = ( ( String ) st.nextElement() ).trim(); + if ( !ForesterUtil.isEmpty( str ) ) { + setPathToLocalMafft( new File( str ) ); + } + } + else if ( key.equals( "fastme_local" ) ) { + final String str = ( ( String ) st.nextElement() ).trim(); + if ( !ForesterUtil.isEmpty( str ) ) { + setPathToLocalFastme( new File( str ) ); + } + } + else if ( key.equals( "raxml_local" ) ) { + final String str = ( ( String ) st.nextElement() ).trim(); + if ( !ForesterUtil.isEmpty( str ) ) { + setPathToLocalRaxml( new File( str ) ); + } + } else if ( key.equals( "show_scale" ) ) { setShowScale( parseBoolean( ( String ) st.nextElement() ) ); } @@ -1027,6 +1217,9 @@ public final class Configuration { 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() ) ); } @@ -1058,11 +1251,11 @@ public final class Configuration { _use_tabbed_display = parseBoolean( ( String ) st.nextElement() ); } else if ( key.equals( "overview_width" ) ) { - final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); + final short i = parseShort( ( ( String ) st.nextElement() ) ); setOvMaxWidth( i ); } else if ( key.equals( "overview_height" ) ) { - final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); + final short i = parseShort( ( ( String ) st.nextElement() ) ); setOvMaxHeight( i ); } else if ( key.equals( "overview_placement_type" ) ) { @@ -1127,7 +1320,7 @@ public final class Configuration { } else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) { final boolean r = parseBoolean( ( String ) st.nextElement() ); - if ( r && isExtractPfamTaxonomyCodesInNhParsing() ) { + if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) { ForesterUtil .printWarningMessage( Constants.PRG_NAME, "attempt to extract taxonomies and replace underscores at the same time" ); @@ -1136,15 +1329,31 @@ public final class Configuration { setReplaceUnderscoresInNhParsing( r ); } } - else if ( key.equals( "extract_taxonomy_codes_in_nh_parsing" ) ) { - final boolean e = parseBoolean( ( String ) st.nextElement() ); - if ( e && isReplaceUnderscoresInNhParsing() ) { + else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) { + final String s = ( String ) st.nextElement(); + if ( s.equalsIgnoreCase( "no" ) ) { + setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO ); + } + else if ( s.equalsIgnoreCase( "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( Constants.PRG_NAME, - "attempt to extract taxonomies and replace underscores at the same time" ); + "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + + s + + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" ); } - else { - setExtractPfamTaxonomyCodesInNhParsing( e ); + if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) { + ForesterUtil + .printWarningMessage( Constants.PRG_NAME, + "attempt to extract taxonomies and replace underscores at the same time" ); } } else if ( key.equals( "internal_labels_are_confidence_values" ) ) { @@ -1181,7 +1390,18 @@ public final class Configuration { _domain_structure_base_color = Color.decode( ( String ) st.nextElement() ); } else if ( key.equals( "show_default_node_shapes" ) ) { - setShowDefaultNodeShapes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) ); + ForesterUtil + .printWarningMessage( Constants.PRG_NAME, + "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" ); + final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() ); + setShowDefaultNodeShapesInternal( b ); + setShowDefaultNodeShapesExternal( b ); + } + else if ( key.equals( "show_default_node_shapes_internal" ) ) { + setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) ); + } + else if ( key.equals( "show_default_node_shapes_external" ) ) { + setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) ); } else if ( key.equals( "default_node_size" ) ) { final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); @@ -1189,13 +1409,13 @@ public final class Configuration { } else if ( key.equals( "default_node_fill" ) ) { final String fill_str = ( ( String ) st.nextElement() ).trim(); - if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.NONE.toString() ) ) { + if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.NONE.toString() ) ) { setDefaultNodeFill( NodeFill.NONE ); } - else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.GRADIENT.toString() ) ) { + else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.GRADIENT.toString() ) ) { setDefaultNodeFill( NodeFill.GRADIENT ); } - else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.SOLID.toString() ) ) { + else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.SOLID.toString() ) ) { setDefaultNodeFill( NodeFill.SOLID ); } else { @@ -1205,10 +1425,10 @@ public final class Configuration { } else if ( key.equals( "default_node_shape" ) ) { final String shape_str = ( ( String ) st.nextElement() ).trim(); - if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.CIRCLE.toString() ) ) { + if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.CIRCLE.toString() ) ) { setDefaultNodeShape( NodeShape.CIRCLE ); } - else if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.RECTANGLE.toString() ) ) { + else if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.RECTANGLE.toString() ) ) { setDefaultNodeShape( NodeShape.RECTANGLE ); } else { @@ -1216,19 +1436,80 @@ public final class Configuration { + "] for [default_node_shape]" ); } } - else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) { - setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) ); + else if ( key.equals( "midpoint_reroot" ) ) { + setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) ); + } + else if ( key.equals( "ext_descendents_data_to_return" ) ) { + final String s = ( ( String ) st.nextElement() ).trim(); + if ( s.equalsIgnoreCase( "node_name" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME ); + } + else if ( s.equalsIgnoreCase( "sequence_acc" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC ); + } + else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ); + } + else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ ); + } + else if ( s.equalsIgnoreCase( "sequence_name" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME ); + } + else if ( s.equalsIgnoreCase( "gene_name" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.GENE_NAME ); + } + else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL ); + } + else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME ); + } + else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE ); + } + else if ( s.equalsIgnoreCase( "taxonomy_common_name" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_COMM0N_NAME ); + } + else if ( s.equalsIgnoreCase( "user_selected" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN ); + } + else { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s + + "] for [ext_descendents_data_to_return]" ); + } + } + else if ( key.equals( "label_for_get_ext_descendents_data" ) ) { + final String s = ( ( String ) st.nextElement() ).trim(); + if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s + + "] for [label_for_get_ext_descendents_data]" ); + } + else { + setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) ); + } + } + else if ( key.equals( "ext_descendents_data_to_return_on" ) ) { + final String s = ( ( String ) st.nextElement() ).trim().toLowerCase(); + if ( s.equals( "console" ) ) { + setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE ); + } + else if ( s.equals( "window" ) ) { + setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW ); + } + else if ( s.equals( "buffer_only" ) ) { + setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ); + } + else { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s + + "] for [ext_descendents_data_to_return_on]" ); + } } else if ( st.countTokens() >= 2 ) { // counts the tokens that are not // yet retrieved! int key_index = -1; - if ( key.equals( "use_real_br_lengths" ) || key.equals( "phylogram" ) ) { + if ( key.equals( "phylogram" ) ) { key_index = Configuration.display_as_phylogram; - if ( key.equals( "use_real_br_lengths" ) ) { - ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "configuration key [use_real_br_lengths] is deprecated, use [phylogram] instead" ); - } } else if ( key.equals( "rollover" ) ) { key_index = Configuration.node_data_popup; @@ -1236,61 +1517,33 @@ public final class Configuration { else if ( key.equals( "color_according_to_species" ) ) { key_index = Configuration.color_according_to_species; } + else if ( key.equals( "color_according_to_sequence" ) ) { + key_index = Configuration.color_according_to_sequence; + } else if ( key.equals( "show_node_names" ) ) { key_index = Configuration.show_node_names; } - else if ( key.equals( "show_taxonomy" ) || key.equals( "show_taxonomy_code" ) ) { + else if ( key.equals( "show_taxonomy_code" ) ) { key_index = Configuration.show_tax_code; - if ( key.equals( "show_taxonomy" ) ) { - ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "configuration key [show_taxonomy] is deprecated, use [show_taxonomy_code] instead" ); - } - } - else if ( key.equals( "write_br_length_values" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "configuration key [write_br_length_values] is deprecated" ); - key_index = DEPRECATED; } - else if ( key.equals( "write_bootstrap_values" ) || key.equals( "write_confidence_values" ) ) { + else if ( key.equals( "write_confidence_values" ) ) { key_index = Configuration.write_confidence_values; - if ( key.equals( "write_bootstrap_values" ) ) { - ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "configuration key [write_bootstrap_values] is deprecated, use [write_confidence_values] instead" ); - } } - else if ( key.equals( "write_events" ) || key.equals( "write_dup_spec" ) ) { + else if ( key.equals( "write_events" ) ) { key_index = Configuration.write_events; - if ( key.equals( "write_dup_spec" ) ) { - ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "configuration key [write_dup_spec] is deprecated, use [write_events] instead" ); - } + } + else if ( key.equals( "use_visual_styles" ) ) { + key_index = Configuration.use_style; } else if ( key.equals( "color_branches" ) ) { - key_index = Configuration.color_branches; + key_index = Configuration.use_style; + ForesterUtil + .printWarningMessage( Constants.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( "color_orthologous" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "configuration key [color_orthologous] is deprecated" ); - } - else if ( key.equals( "color_subtree_neighbors" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "configuration key [color_subtree_neighbors] is deprecated" ); - } - else if ( key.equals( "color_super_orthologous" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "configuration key [color_super_orthologous] is deprecated" ); - } - else if ( key.equals( "mark_nodes_with_box" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "configuration key [mark_nodes_with_box] is deprecated" ); - key_index = DEPRECATED; - } else if ( key.equals( "show_domain_architectures" ) ) { key_index = Configuration.show_domain_architectures; } @@ -1303,31 +1556,24 @@ public final class Configuration { 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_gene_symbols" ) ) { - key_index = Configuration.show_gene_symbols; + else if ( key.equals( "show_seq_symbols" ) ) { + key_index = Configuration.show_seq_symbols; } - else if ( key.equals( "show_sequence_acc" ) ) { + else if ( key.equals( "show_seq_acc" ) ) { key_index = Configuration.show_sequence_acc; } - else if ( key.equals( "show_node_ids" ) ) { - ForesterUtil - .printWarningMessage( Constants.PRG_NAME, "configuration key [show_node_ids] is deprecated" ); - key_index = DEPRECATED; - } else if ( key.equals( "display_internal_data" ) ) { key_index = Configuration.display_internal_data; } else if ( key.equals( "dynamically_hide_data" ) ) { key_index = Configuration.dynamically_hide_data; } - else if ( key.equals( "show_taxonomy_names" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "configuration key [show_taxonomy_names] is deprecated" ); - key_index = DEPRECATED; - } else if ( key.equals( "show_taxonomy_scientific_names" ) ) { key_index = Configuration.show_taxonomy_scientific_names; } @@ -1349,9 +1595,6 @@ public final class Configuration { else if ( key.equals( "show_relation_confidence" ) ) { key_index = Configuration.show_relation_confidence; } - else if ( key.equals( "show_custom_node_shapes" ) ) { - key_index = Configuration.show_custom_node_shapes; - } // If we've found the key, set the values if ( key_index >= 0 ) { display_options[ key_index ][ 1 ] = ( String ) st.nextElement(); @@ -1377,7 +1620,12 @@ public final class Configuration { } } else if ( key.equals( "species_color" ) ) { - getSpeciesColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); + 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() ) ); @@ -1393,17 +1641,6 @@ public final class Configuration { else if ( key.equals( DISPLAY_COLOR_KEY ) ) { putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); } - else if ( key.equals( WEB_LINK_KEY ) ) { - if ( st.countTokens() == 3 ) { - createWebLink( ( String ) st.nextElement(), - ( String ) st.nextElement(), - ( String ) st.nextElement() ); - } - else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "illegal format in configuration file for key [" + key + "]" ); - } - } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: " + config_filename ); @@ -1416,20 +1653,16 @@ public final class Configuration { } } - 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; + private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) { + _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data; } - public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short _number_of_digits_after_comma_for_branch_length_values ) { - this._number_of_digits_after_comma_for_branch_length_values = _number_of_digits_after_comma_for_branch_length_values; + private void setMaxBaseFontSize( final int max_base_font_size ) { + _max_base_font_size = max_base_font_size; } - public void setNumberOfDigitsAfterCommaForConfidenceValues( final short _number_of_digits_after_comma_for_confidence_values ) { - this._number_of_digits_after_comma_for_confidence_values = _number_of_digits_after_comma_for_confidence_values; + private void setMinBaseFontSize( final int min_base_font_size ) { + _min_base_font_size = min_base_font_size; } private void setOvMaxHeight( final short ov_max_height ) { @@ -1444,67 +1677,43 @@ public final class Configuration { _ov_placement = ov_placement; } - 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; + private void setPathToLocalFastme( final File path_to_local_fastme ) { + _path_to_local_fastme = path_to_local_fastme; } - public void setShowBranchLengthValues( final boolean show_branch_length_values ) { - _show_branch_length_values = show_branch_length_values; + private void setPathToLocalMafft( final File path_to_local_mafft ) { + _path_to_local_mafft = path_to_local_mafft; } - public void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) { - _show_default_node_shapes = show_default_node_shapes; + private void setPathToLocalRaxml( final File path_to_local_raxml ) { + _path_to_local_raxml = path_to_local_raxml; } - public void setShowDomainLabels( final boolean show_domain_labels ) { - _show_domain_labels = show_domain_labels; + private void setShowAnnotationRefSource( final boolean b ) { + _show_annotation_ref_source = b; } private void setShowOverview( final boolean show_overview ) { _show_overview = show_overview; } - public void setShowScale( final boolean show_scale ) { - _show_scale = show_scale; - } - - public void setTaxonomyColorize( final boolean b ) { - display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no"; - } - - public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) { - _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes; - } - - public void setUseBranchesWidths( final boolean b ) { - display_options[ width_branches ][ 2 ] = b ? "yes" : "no"; - } - private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) { _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema; } - void setWebLinks( final SortedMap weblinks ) { - _weblinks = weblinks; - } - static String getDefaultFontFamilyName() { return DEFAULT_FONT_FAMILY; } - static enum TRIPLET { - TRUE, FALSE, UNKNOWN + public enum EXT_NODE_DATA_RETURN_ON { + BUFFER_ONLY, CONSOLE, WINODW; } public enum UI { - NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN + CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN + } + + static enum TRIPLET { + FALSE, TRUE, UNKNOWN } }