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 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<String, Color> _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 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;
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_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;
+ static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
+ private static Hashtable<String, Color> _sequence_colors;
+
+
+ private static Hashtable<String, Color> _annotation_colors;
+ private static Hashtable<String, Color> _domain_colors;
+ private static Hashtable<String, Color> _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
// ---------------------------
// ---------------------------------
// 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" },
- { "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" },
- { "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", "nodisplay", "no" }, { "Seq Symbol", "display", "yes" },
- { "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" } };
// 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
// --------------
// Fonts
// -------
TreeFontSet tree_font_set;
- // ----------------
- // Species colors
- // ----------------
- private static Hashtable<String, Color> _species_colors;
- // ----------------
- // Domain colors
- // ----------------
- private static Hashtable<String, Color> _domain_colors;
- // ----------------
- // Function colors
- // ----------------
- private static Hashtable<String, Color> _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<String, Color> _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 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 ) {
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;
}
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;
}
_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 ) {
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<String, Color> display_colors ) {
_display_colors = display_colors;
}
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;
}
_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 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";
- }
-
+
boolean displaySequenceRelations() {
return _display_sequence_relations;
}
return _base_font_size;
}
- int getMinBaseFontSize() {
- return _min_base_font_size;
- }
-
- int getMaxBaseFontSize() {
- return _max_base_font_size;
- }
-
CLADOGRAM_TYPE getCladogramType() {
return _cladogram_type;
}
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;
}
}
return _species_colors;
}
+
+ Hashtable<String, Color> getSequenceColors() {
+ if ( _sequence_colors == null ) {
+ _sequence_colors = new Hashtable<String, Color>();
+ }
+ return _sequence_colors;
+ }
final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
return _taxonomy_extraction;
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;
}
}
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 {
}
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 {
+ "] 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( "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( "write_events" ) ) {
key_index = Configuration.write_events;
}
+ else if ( key.equals( "use_visual_styles" ) ) {
+ key_index = Configuration.use_style;
+ }
else if ( key.equals( "color_branches" ) ) {
- key_index = Configuration.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( "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();
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() ) );
}
}
}
- 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;
}
_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;
}
}
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
}
}
git://source.jalview.org / jalview.git / blobdiff