From: cmzmasek@gmail.com Date: Wed, 22 Jan 2014 02:48:45 +0000 (+0000) Subject: cleanup X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5ea47511ea9c077b4b4709bed68ac31d6eee0477;p=jalview.git cleanup --- diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 689fde7..ab9802c 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -55,115 +55,34 @@ 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 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 _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.NO; - 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 _show_annotation_ref_source = 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.RECTANGLE; - private NodeFill _default_node_fill = NodeFill.SOLID; - 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 int display_as_phylogram = 0; - final static int show_node_names = 1; - final static int show_tax_code = 2; - final static int show_annotation = 3; - final static int write_confidence_values = 4; - final static int write_events = 5; + final static int add_new_node = 14; + final static int blast = 9; + final static String clickto_options[][] = { + { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" }, + { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, + { "Colorize Subtree/Node(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "display" }, + { "Open Taxonomy DB", "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" } }; + final static int collapse_uncollapse = 1; + final static int color_according_to_annotation = 19; 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 show_domain_architectures = 10; - final static int show_binary_characters = 11; - final static int show_binary_character_counts = 12; - final static int show_seq_names = 13; - final static int show_sequence_acc = 14; + final static int color_subtree = 5; + final static int copy_subtree = 11; + final static int cut_subtree = 10; + final static int delete_subtree_or_node = 13; + final static int display_as_phylogram = 0; final static int display_internal_data = 15; - final static int dynamically_hide_data = 16; - final static int show_taxonomy_scientific_names = 17; - final static int show_taxonomy_common_names = 18; - final static int color_according_to_annotation = 19; - final static int show_seq_symbols = 20; - final static int node_data_popup = 21; - final static int show_relation_confidence = 22; - final static int show_vector_data = 23; - final static int show_taxonomy_images = 24; - final static int show_properties = 25; - final static int show_gene_names = 26; // ------------------ // 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_pdb_web = 7; - final static int open_tax_web = 8; - final static int blast = 9; - final static int cut_subtree = 10; - final static int copy_subtree = 11; - final static int paste_subtree = 12; - final static int delete_subtree_or_node = 13; - final static int add_new_node = 14; - final static int edit_node_data = 15; - final static int sort_descendents = 16; - final static int get_ext_desc_data = 17; - final static int select_nodes = 18; - // --------------------------- - // Display options for trees - // --------------------------- - // --------------------------------- - // Pertaining to the config itself - // --------------------------------- - // 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" }, { "Seq Annotations", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, - { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "yes" }, + { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" }, { "Use Branch Colors", "display", "no" }, { "Use Branch Widths", "display", "no" }, { "Show Custom Nodes", "display", "yes" }, { "Protein Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" }, @@ -174,16 +93,66 @@ public final class Configuration { { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" }, { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" }, { "Properties", "nodisplay", "no" }, { "Gene Name", "display", "yes" } }; - final static String clickto_options[][] = { - { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" }, - { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, - { "Colorize Subtree/Node(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "display" }, - { "Open Taxonomy DB", "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" } }; + final static int dynamically_hide_data = 16; + final static int edit_node_data = 15; + final static int get_ext_desc_data = 17; + final static int node_data_popup = 21; + final static int open_pdb_web = 7; + final static int open_seq_web = 6; + final static int open_tax_web = 8; + final static int paste_subtree = 12; + final static int reroot = 2; + final static int select_nodes = 18; + final static int show_annotation = 3; + final static int show_binary_character_counts = 12; + final static int show_binary_characters = 11; + final static int show_custom_node_shapes = 9; + final static int show_domain_architectures = 10; + final static int show_gene_names = 26; + final static int show_node_names = 1; + final static int show_properties = 25; + final static int show_relation_confidence = 22; + final static int show_seq_names = 13; + final static int show_seq_symbols = 20; + final static int show_sequence_acc = 14; + final static int show_tax_code = 2; + final static int show_taxonomy_common_names = 18; + final static int show_taxonomy_images = 24; + final static int show_taxonomy_scientific_names = 17; + final static int show_vector_data = 23; + final static int sort_descendents = 16; + final static int subtree = 3; + final static int swap = 4; + static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema"; + final static int width_branches = 8; + final static int write_confidence_values = 4; + final static int write_events = 5; + // ---------------- + // Function colors + // ---------------- + private static Hashtable _annotation_colors; + // ---------------- + // Domain colors + // ---------------- + private static Hashtable _domain_colors; + // ---------------- + // Species colors + // ---------------- + private static Hashtable _species_colors; + private static String DEFAULT_FONT_FAMILY = ""; + private static final int DEPRECATED = -2; + private static final String DISPLAY_COLOR_KEY = "display_color"; + // --------------------------- + // Display options for trees + // --------------------------- + // --------------------------------- + // Pertaining to the config itself + // --------------------------------- + // Full path to config (may be URL) + String config_filename; // This option is selected in the dropdown int default_clickto = Configuration.display_node_data; + String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME; // -------------- // Color set // -------------- @@ -192,37 +161,68 @@ 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 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 static String DEFAULT_FONT_FAMILY = ""; + 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 boolean _taxonomy_colorize_node_shapes = 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 ) { @@ -367,10 +367,22 @@ 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; } @@ -407,14 +419,6 @@ 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"; } @@ -503,6 +507,10 @@ 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; } @@ -600,14 +608,6 @@ 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; } @@ -679,6 +679,14 @@ 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; } @@ -1629,14 +1637,18 @@ public final class Configuration { } } - private void setShowAnnotationRefSource( final boolean b ) { - _show_annotation_ref_source = b; - } - private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) { _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data; } + private void setMaxBaseFontSize( final int max_base_font_size ) { + _max_base_font_size = max_base_font_size; + } + + private void setMinBaseFontSize( final int min_base_font_size ) { + _min_base_font_size = min_base_font_size; + } + private void setOvMaxHeight( final short ov_max_height ) { _ov_max_height = ov_max_height; } @@ -1661,6 +1673,10 @@ 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; } @@ -1674,30 +1690,14 @@ 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 - } - - public boolean isMidpointReroot() { - return _midpoint_root; - } - - public void setMidpointReroot( final boolean midpoint_root ) { - _midpoint_root = midpoint_root; - } - - public boolean isShowAnnotationRefSource() { - return _show_annotation_ref_source; - } - - public boolean isColorByTaxonomicGroup() { - return false; + FALSE, TRUE, UNKNOWN } } diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java index b533aa6..4f92653 100644 --- a/forester/java/src/org/forester/archaeopteryx/Options.java +++ b/forester/java/src/org/forester/archaeopteryx/Options.java @@ -444,7 +444,7 @@ final public class Options { _show_branch_length_values = false; _internal_number_are_confidence_for_nh_parsing = false; _show_scale = false; - _antialias_screen = false; + _antialias_screen = true; _antialias_print = true; _graphics_export_visible_only = false; _editable = true; diff --git a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java index bcf2574..201b460 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java +++ b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java @@ -36,34 +36,39 @@ import org.forester.util.ForesterUtil; */ public final class TreeColorSet { - public static final String OVERVIEW = "Overview"; public static final String ANNOTATION = "Annotation"; + public static final String BACKGROUND = "Background"; + public static final String BACKGROUND_GRADIENT_BOTTOM = "Background Gradient Bottom"; public static final String BINARY_DOMAIN_COMBINATIONS = "Binary Domain Combinations"; - public static final String DOMAINS = "Domains"; - public static final String DUPLICATION_OR_SPECATION = "Duplication or Specation"; - public static final String SPECIATION = "Speciation"; - public static final String DUPLICATION = "Duplication"; - public static final String MATCHING_NODES = "Matching Nodes"; - public static final String COLLAPSED = "Collapsed"; - public static final String NODE_BOX = "Node Box"; public static final String BRANCH = "Branch"; public static final String BRANCH_LENGTH = "Branch Length"; + public static final String COLLAPSED = "Collapsed"; public static final String CONFIDENCE = "Confidence"; - public static final String TAXONOMY = "Taxonomy"; + public static final String DOMAINS = "Domains"; + public static final String DUPLICATION = "Duplication"; + public static final String DUPLICATION_OR_SPECATION = "Duplication or Specation"; + public static final String MATCHING_NODES_A = "Matching A"; + public static final String MATCHING_NODES_A_AND_B = "Matching A and B"; + public static final String MATCHING_NODES_B = "Matching B"; + public static final String NODE_BOX = "Node Box"; + public static final String OVERVIEW = "Overview"; public static final String SEQUENCE = "Sequence"; - public static final String BACKGROUND_GRADIENT_BOTTOM = "Background Gradient Bottom"; - public static final String BACKGROUND = "Background"; - static final String[] SCHEME_NAMES = { "Default", "Black", "Black & White", "Silver", - "The Matrix", "White & Blue", "Cyan", "Clockwork", "Blue", "Blue & White", "Neon" }; + public static final String SPECIATION = "Speciation"; + public static final String TAXONOMY = "Taxonomy"; static final String[] COLOR_FIELDS = { BACKGROUND, BACKGROUND_GRADIENT_BOTTOM, SEQUENCE, - TAXONOMY, CONFIDENCE, BRANCH_LENGTH, BRANCH, NODE_BOX, COLLAPSED, MATCHING_NODES, DUPLICATION, SPECIATION, - DUPLICATION_OR_SPECATION, DOMAINS, BINARY_DOMAIN_COMBINATIONS, ANNOTATION, OVERVIEW }; + TAXONOMY, CONFIDENCE, BRANCH_LENGTH, BRANCH, NODE_BOX, COLLAPSED, MATCHING_NODES_A, MATCHING_NODES_B, + MATCHING_NODES_A_AND_B, DUPLICATION, SPECIATION, DUPLICATION_OR_SPECATION, DOMAINS, + BINARY_DOMAIN_COMBINATIONS, ANNOTATION, OVERVIEW }; + static final String[] SCHEME_NAMES = { "Default", "Black", "Black & White", "Silver", "Green", + "White & Blue", "Cyan", "Orange", "Blue", "Blue & White", "Neon" }; + // Color schemes: + private int _color_scheme; // All the color sets; better be the same # of sets as there are names! private final Color[][] _color_schemes = { { new Color( 0, 0, 0 ), // background_color new Color( 0, 100, 100 ), // background_color_gradient_bottom - new Color( 220, 220, 220 ), // sequence __ Default (same as Black) - new Color( 180, 180, 180 ), // taxonomy - new Color( 56, 176, 222 ), // support + new Color( 230, 230, 230 ), // sequence __ Default (same as Black) + new Color( 255, 220, 220 ), // taxonomy + new Color( 56, 176, 255 ), // support new Color( 140, 140, 140 ), // branch_length_color new Color( 255, 255, 255 ), // branch_color new Color( 255, 255, 255 ), // box_color @@ -80,9 +85,9 @@ public final class TreeColorSet { , new Color( 130, 130, 130 ) // overview }, { new Color( 0, 0, 0 ), // background_color new Color( 0, 255, 255 ), // background_color_gradient_bottom - new Color( 220, 220, 220 ), // sequence __ Black - new Color( 180, 180, 180 ), // taxonomy - new Color( 56, 176, 222 ), // support + new Color( 230, 230, 230 ), // sequence __ Black + new Color( 255, 220, 220 ), // taxonomy + new Color( 56, 176, 255 ), // support new Color( 140, 140, 140 ), // branch_length_color new Color( 255, 255, 255 ), // branch_color new Color( 255, 255, 255 ), // box_color @@ -269,28 +274,26 @@ public final class TreeColorSet { new Color( 27, 255, 0 ) // annotation , new Color( 77, 77, 255 ) // ov } }; - // Color schemes: - private int _color_scheme; - // The drawing colors - private Color seq_color; - private Color taxonomy_color; - private Color bootstrap_color; - private Color branch_length_color; - private Color branch_color; - private Color box_color; + private Color annotation_color; private Color background_color; private Color background_color_gradient_bottom; - private Color dup_box_color; - private Color spec_box_color; + private Color binary_domain_combinations_color; + private Color bootstrap_color; + private Color box_color; + private Color branch_color; + private Color branch_length_color; private Color collapse_fill_color; + private Color domains_color; + private Color dup_box_color; + private Color duplication_or_specation_color; private Color found_color_0; - private Color found_color_1; private Color found_color_0_and_1; - private Color duplication_or_specation_color; - private Color domains_color; - private Color binary_domain_combinations_color; - private Color annotation_color; + private Color found_color_1; private Color ov_color; + // The drawing colors + private Color seq_color; + private Color spec_box_color; + private Color taxonomy_color; private TreeColorSet() { // Hidden constructor. @@ -376,14 +379,14 @@ public final class TreeColorSet { return found_color_0; } - Color getFoundColor1() { - return found_color_1; - } - Color getFoundColor0and1() { return found_color_0_and_1; } + Color getFoundColor1() { + return found_color_1; + } + Color getGainedCharactersColor() { return Color.GREEN; } @@ -425,10 +428,6 @@ public final class TreeColorSet { } } - private void setColorForDefault( final int i, final Color color ) { - _color_schemes[ 0 ][ i ] = color; - } - /** * Switches colors between different schemes. */ @@ -459,6 +458,10 @@ public final class TreeColorSet { _color_scheme = color_scheme; } + private void setColorForDefault( final int i, final Color color ) { + _color_schemes[ 0 ][ i ] = color; + } + static TreeColorSet createInstance() { final TreeColorSet tcs = new TreeColorSet(); tcs.setColorSchema( 0 ); diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 407633e..7301784 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -704,19 +704,21 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } final Color calculateTaxonomyBasedColor( final Taxonomy tax ) { - if ( getOptions().isColorByTaxonomicGroup() && !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) { - boolean ex = false; - String group = null; - try { - group = TaxonomyUtil.getTaxGroupByTaxCode( tax.getTaxonomyCode() ); - } - catch ( final Exception e ) { - ex = true; - } - if ( !ex && !ForesterUtil.isEmpty( group ) ) { - final Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group ); - if ( c != null ) { - return c; + if ( getOptions().isColorByTaxonomicGroup() ) { + if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) { + boolean ex = false; + String group = null; + try { + group = TaxonomyUtil.getTaxGroupByTaxCode( tax.getTaxonomyCode() ); + } + catch ( final Exception e ) { + ex = true; + } + if ( !ex && !ForesterUtil.isEmpty( group ) ) { + final Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group ); + if ( c != null ) { + return c; + } } } return getTreeColorSet().getTaxonomyColor();