X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=2a4b7dd3f6f3827e02703004a565c65de675fed7;hb=4e20c9132065232b26afd38e8ce371b353a2686d;hp=5d354cc082a7b4be5c45a4bbc659973b6bd0730c;hpb=56fcc7953ce4896eed89a3129d862e0aaf2d65e1;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 5d354cc..2a4b7dd 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -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; @@ -49,61 +48,60 @@ import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE; import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE; import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; import org.forester.phylogeny.data.NodeData.NODE_DATA; -import org.forester.phylogeny.data.NodeVisualization; -import org.forester.phylogeny.data.NodeVisualization.NodeFill; -import org.forester.phylogeny.data.NodeVisualization.NodeShape; +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 _min_base_font_size = 2; - private int _max_base_font_size = 20; - private int _graphics_export_x = -1; - private int _graphics_export_y = -1; - private short _ov_max_width = 80; - 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 TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY; - 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 boolean _show_default_node_shapes_internal = false; - private boolean _show_default_node_shapes_external = 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; - private int _default_bootstrap_samples = -1; - private File _path_to_local_mafft = null; - private File _path_to_local_fastme = null; - private File _path_to_local_raxml = null; + final static 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; @@ -111,46 +109,34 @@ 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 blast = 8; - final static int cut_subtree = 9; - final static int copy_subtree = 10; - final static int paste_subtree = 11; - final static int delete_subtree_or_node = 12; - final static int add_new_node = 13; - final static int edit_node_data = 14; - final static int sort_descendents = 15; - final static int get_ext_desc_data = 16; - final static int select_nodes = 17; + 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 // --------------------------- @@ -159,30 +145,9 @@ 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", "?" }, - { "Node Events", "display", "?" }, { "Taxonomy Colorize", "display", "yes" }, - { "Colorize Branches", "display", "no" }, { "Use Branch-Widths", "display", "no" }, - { "Show Custom Nodes", "display", "yes" }, { "Domains", "nodisplay", "no" }, - { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" }, - { "Seq Name", "display", "yes" }, { "Seq Acc", "display", "no" }, - { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" }, - { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" }, - { "Annotation Colorize", "nodisplay", "no" }, { "Seq Symbol", "display", "yes" }, - { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" }, - { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" }, - { "Properties", "nodisplay", "no" } }; - final static String clickto_options[][] = { - { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" }, - { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" }, - { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Blast", "display" }, - { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, - { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" }, - { "Sort Descendants", "display" }, { "Return", "display" }, { "Select Node(s)", "display" } }; // This option is selected in the dropdown int default_clickto = Configuration.display_node_data; + String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME; // -------------- // Color set // -------------- @@ -191,36 +156,72 @@ 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 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_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 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 String _label_for_get_ext_descendents_data = ""; private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW; private int _frame_x_size; private int _frame_y_size; - private static String DEFAULT_FONT_FAMILY = ""; + private int _graphics_export_x = -1; + private int _graphics_export_y = -1; + private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT; + private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT; + private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT; + private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT; + private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT; + private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT; + private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT; + private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT; + private 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; + 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; static { for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) { if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) { @@ -244,7 +245,6 @@ public final class Configuration { else { config_filename = cf; } - setWebLinks( new TreeMap() ); setDisplayColors( new TreeMap() ); config_filename = config_filename.trim(); URL u = null; @@ -350,7 +350,7 @@ public final class Configuration { return _path_to_local_fastme; } - public File getpathToLocalMafft() { + public File getPathToLocalMafft() { return _path_to_local_mafft; } @@ -366,10 +366,22 @@ public final class Configuration { 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; } @@ -382,14 +394,14 @@ public final class Configuration { return _show_domain_labels; } - public boolean isTaxonomyColorizeNodeShapes() { - return _taxonomy_colorize_node_shapes; - } - public void putDisplayColors( final String key, final Color color ) { getDisplayColors().put( key, color ); } + public void 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; } @@ -406,16 +418,8 @@ public final class Configuration { _base_font_size = base_font_size; } - private void setMaxBaseFontSize( final int max_base_font_size ) { - _max_base_font_size = max_base_font_size; - } - - private void setMinBaseFontSize( final int min_base_font_size ) { - _min_base_font_size = min_base_font_size; - } - public void setColorizeBranches( final boolean b ) { - display_options[ color_branches ][ 2 ] = b ? "yes" : "no"; + display_options[ use_style ][ 2 ] = b ? "yes" : "no"; } public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) { @@ -438,6 +442,10 @@ public final class Configuration { display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no"; } + public void setUseStyle( final boolean b ) { + display_options[ use_style ][ 2 ] = b ? "yes" : "no"; + } + public void setDisplayColors( final SortedMap display_colors ) { _display_colors = display_colors; } @@ -459,6 +467,10 @@ public final class Configuration { } 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"; } @@ -467,7 +479,7 @@ public final class Configuration { } public void setDisplaySequenceSymbols( final boolean b ) { - display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no"; + display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no"; } public void setDisplayTaxonomyCode( final boolean b ) { @@ -502,6 +514,10 @@ public final class Configuration { _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; } @@ -550,18 +566,6 @@ public final class Configuration { _show_scale = show_scale; } - public void setTaxonomyColorize( final boolean b ) { - display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no"; - } - - public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) { - _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes; - } - - public void setUseBranchesWidths( final boolean b ) { - display_options[ width_branches ][ 2 ] = b ? "yes" : "no"; - } - boolean displaySequenceRelations() { return _display_sequence_relations; } @@ -599,14 +603,6 @@ public final class Configuration { return _base_font_size; } - int getMinBaseFontSize() { - return _min_base_font_size; - } - - int getMaxBaseFontSize() { - return _max_base_font_size; - } - CLADOGRAM_TYPE getCladogramType() { return _cladogram_type; } @@ -678,6 +674,14 @@ 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; } @@ -721,19 +725,22 @@ public final class Configuration { return _species_colors; } - final TAXONOMY_EXTRACTION getTaxonomyExtraction() { - return _taxonomy_extraction; - } - - WebLink getWebLink( final String source ) { - return getWebLinks().get( source ); + Hashtable getSequenceColors() { + if ( _sequence_colors == null ) { + _sequence_colors = new Hashtable(); + } + return _sequence_colors; } - Map getWebLinks() { - return _weblinks; + 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; } @@ -750,10 +757,6 @@ public final class Configuration { return _editable; } - boolean isHasWebLink( final String source ) { - return getWebLinks().containsKey( source ); - } - /** * Only used by ArchaeoptryxE. * @@ -783,7 +786,7 @@ public final class Configuration { } final boolean isUseNativeUI() { - if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) { + if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) { _ui = UI.NATIVE; } return _ui == UI.NATIVE; @@ -805,25 +808,6 @@ public final class Configuration { _taxonomy_extraction = taxonomy_extraction; } - void setWebLinks( final SortedMap weblinks ) { - _weblinks = weblinks; - } - - 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 ); - } - } - private int getClickToIndex( final String name ) { int index = -1; if ( name.equals( "edit_info" ) ) { @@ -861,6 +845,9 @@ public final class Configuration { 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; } @@ -900,9 +887,14 @@ public final class Configuration { 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; + 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; } @@ -1227,6 +1219,9 @@ 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() ) ); } @@ -1341,15 +1336,21 @@ public final class Configuration { if ( s.equalsIgnoreCase( "no" ) ) { setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO ); } - else if ( s.equalsIgnoreCase( "yes" ) ) { - setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES ); + 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( "pfam" ) ) { - setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + else if ( s.equalsIgnoreCase( "aggressive" ) ) { + setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + s ); + ForesterUtil + .printWarningMessage( Constants.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 @@ -1410,13 +1411,13 @@ 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 { @@ -1426,10 +1427,10 @@ 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 { @@ -1437,8 +1438,8 @@ 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(); @@ -1448,12 +1449,18 @@ public final class Configuration { 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 ); } @@ -1463,6 +1470,9 @@ public final class Configuration { 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 ); } @@ -1497,16 +1507,35 @@ public final class Configuration { + "] for [ext_descendents_data_to_return_on]" ); } } + // + else if ( key.equals( "vector_data_min_color" ) ) { + _vector_data_min_color = Color.decode( ( String ) st.nextElement() ); + } + else if ( key.equals( "vector_data_max_color" ) ) { + _vector_data_max_color = Color.decode( ( String ) st.nextElement() ); + } + else if ( key.equals( "vector_data_mean_color" ) ) { + _vector_data_mean_color = Color.decode( ( String ) st.nextElement() ); + } + // + else if ( key.equals( "vector_data_width" ) ) { + _vector_data_width = parseShort( ( String ) st.nextElement() ); + if ( _vector_data_width < 1 ) { + _vector_data_width = 120; + } + } + else if ( key.equals( "vector_data_height" ) ) { + _vector_data_height = parseShort( ( String ) st.nextElement() ); + if ( _vector_data_height < 1 ) { + _vector_data_height = 12; + } + } + // else if ( 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; @@ -1514,61 +1543,33 @@ 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; } @@ -1581,31 +1582,24 @@ 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; } @@ -1627,9 +1621,6 @@ 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(); @@ -1655,7 +1646,12 @@ 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() ) ); @@ -1671,17 +1667,6 @@ 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 ); @@ -1698,6 +1683,14 @@ public final class Configuration { _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; } @@ -1722,6 +1715,10 @@ public final class Configuration { _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; } @@ -1735,14 +1732,34 @@ public final class Configuration { } public enum EXT_NODE_DATA_RETURN_ON { - CONSOLE, WINODW, BUFFER_ONLY; + BUFFER_ONLY, CONSOLE, WINODW; } public enum UI { - NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN + CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN } static enum TRIPLET { - TRUE, FALSE, UNKNOWN + FALSE, TRUE, UNKNOWN + } + + public Color getVectorDataMinColor() { + return _vector_data_min_color; + } + + public Color getVectorDataMaxColor() { + return _vector_data_max_color; + } + + public Color getVectorDataMeanColor() { + return _vector_data_mean_color; + } + + public double getVectorDataHeight() { + return _vector_data_height; + } + + public int getVectorDataWidth() { + return _vector_data_width; } }