// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.archaeopteryx;
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;
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
import org.forester.phylogeny.data.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 {
- public enum EXT_NODE_DATA_RETURN_ON {
- CONSOLE, WINODW;
- }
- 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<String, WebLink> _weblinks = null;
- 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 _graphics_export_x = -1;
- private int _graphics_export_y = -1;
- private short _ov_max_width = 80;
- private short _ov_max_height = 80;
- private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
- private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
- private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
- private boolean _show_scale = false;
- private boolean _show_branch_length_values = false;
- private boolean _show_overview = true;
- private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
- private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
- private boolean _editable = true;
- private boolean _nh_parsing_replace_underscores = false;
- private boolean _nh_parsing_extract_pfam_taxonomy_codes = false;
- private boolean _internal_number_are_confidence_for_nh_parsing = false;
- private boolean _display_sequence_relations = false;
- private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
- private boolean _background_color_gradient = false;
- private boolean _show_domain_labels = true;
- private boolean _abbreviate_scientific_names = false;
- private boolean _color_labels_same_as_parent_branch = false;
- private boolean _show_default_node_shapes = false;
- private NodeShape _default_node_shape = NodeShape.CIRCLE;
- private NodeFill _default_node_fill = NodeFill.GRADIENT;
- private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
- private boolean _taxonomy_colorize_node_shapes = false;
- 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;
- private File _path_to_local_clustalo = 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", "nodisplay", "no" }, { "Confidence Values", "display", "?" },
+ { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
+ { "Visual Styles/Branch Colors", "display", "no" }, { "Branch Widths", "display", "no" },
+ { "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 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 use_style = 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_gene_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 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_domain_architectures = 9;
+ final static int show_binary_characters = 10;
+ final static int show_binary_character_counts = 11;
+ final static int show_seq_names = 12;
+ final static int show_sequence_acc = 13;
+ final static int display_internal_data = 14;
+ final static int dynamically_hide_data = 15;
+ final static int show_taxonomy_scientific_names = 16;
+ final static int show_taxonomy_common_names = 17;
+ final static int color_according_to_annotation = 18;
+ final static int show_seq_symbols = 19;
+ final static int node_data_popup = 20;
+ final static int show_relation_confidence = 21;
+ final static int show_vector_data = 22;
+ final static int show_taxonomy_images = 23;
+ final static int show_properties = 24;
+ final static int show_gene_names = 25;
+ static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
+ // ----------------
+ // Function colors
+ // ----------------
+ private static Hashtable<String, Color> _annotation_colors;
+ // ----------------
+ // Domain colors
+ // ----------------
+ private static Hashtable<String, Color> _domain_colors;
+ // ----------------
+ // Species 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" },
- { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, { "Event", "display", "?" },
- { "Taxonomy Colorize", "display", "no" }, { "Colorize Branches", "display", "no" },
- { "Use Branch-Widths", "display", "no" }, { "Show Custom Nodes", "display", "yes" },
- { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" },
- { "Binary Char Counts", "nodisplay", "no" }, { "Prot/Gene Name", "display", "yes" },
- { "Prot/Gene Acc", "display", "no" }, { "Show Internal Data", "display", "yes" },
- { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" },
- { "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" },
- { "Prot/Gene Symbol", "display", "yes" }, { "Rollover", "display", "yes" },
- { "Relation Confidence", "display", "no" }, { "Vector Data", "display", "no" },
- { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" } };
- final static String clickto_options[][] = {
- { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
- { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
- { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "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 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 EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
+ private int _frame_x_size;
+ private int _frame_y_size;
+ private int _graphics_export_x = -1;
+ private int _graphics_export_y = -1;
private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
- private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
- private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
- private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
+ private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
+ private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
+ private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
+ private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
- private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
- private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
- private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
- private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
+ 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 EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
- private static String DEFAULT_FONT_FAMILY = "";
+ private int _max_base_font_size = 20;
+ private boolean _midpoint_root = false;
+ private int _min_base_font_size = 2;
+ private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
+ private boolean _nh_parsing_replace_underscores = false;
+ private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
+ private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
+ private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
+ private short _ov_max_height = 80;
+ private short _ov_max_width = 80;
+ private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
+ private File _path_to_local_fastme = null;
+ private File _path_to_local_mafft = null;
+ private File _path_to_local_raxml = null;
+ private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
+ private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
+ private boolean _show_annotation_ref_source = true;
+ private boolean _show_branch_length_values = false;
+ private boolean _show_default_node_shapes_external = false;
+ private boolean _show_default_node_shapes_internal = false;
+ private boolean _show_domain_labels = true;
+ private boolean _show_overview = true;
+ private boolean _show_scale = false;
+ private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
+ private UI _ui = UI.UNKNOWN;
+ private boolean _use_tabbed_display = false;
+ private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
static {
for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
else {
config_filename = cf;
}
- setWebLinks( new TreeMap<String, WebLink>() );
setDisplayColors( new TreeMap<String, Color>() );
config_filename = config_filename.trim();
URL u = null;
}
}
- private void createWebLink( final String url_str, final String desc, final String source_identifier ) {
- WebLink weblink = null;
- boolean ex = false;
- try {
- weblink = new WebLink( new URL( url_str.trim() ), desc.trim(), source_identifier.trim() );
- }
- catch ( final MalformedURLException e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not create URL from [" + url_str + "]" );
- ex = true;
- }
- if ( !ex && ( weblink != null ) ) {
- getWebLinks().put( weblink.getSourceIdentifier().toLowerCase(), weblink );
- }
+ public String getBaseFontFamilyName() {
+ return _base_font_family_name;
+ }
+
+ public int getDefaultBootstrapSamples() {
+ return _default_bootstrap_samples;
+ }
+
+ public NodeFill getDefaultNodeFill() {
+ return _default_node_fill;
+ }
+
+ public NodeShape getDefaultNodeShape() {
+ return _default_node_shape;
+ }
+
+ public short getDefaultNodeShapeSize() {
+ return _default_node_shape_size;
+ }
+
+ public Color getDomainStructureBaseColor() {
+ return _domain_structure_base_color;
+ }
+
+ public Color getDomainStructureFontColor() {
+ return _domain_structure_font_color;
+ }
+
+ public NODE_DATA getExtDescNodeDataToReturn() {
+ return _ext_desc_data_to_return;
+ }
+
+ public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
+ return _ext_node_data_return_on;
+ }
+
+ public int getFrameXSize() {
+ return _frame_x_size;
+ }
+
+ public int getFrameYSize() {
+ return _frame_y_size;
+ }
+
+ public String getLabelForGetExtDescendentsData() {
+ return _label_for_get_ext_descendents_data;
+ }
+
+ public File getPathToLocalFastme() {
+ return _path_to_local_fastme;
+ }
+
+ public File getpathToLocalMafft() {
+ return _path_to_local_mafft;
+ }
+
+ public File getPathToLocalRaxml() {
+ return _path_to_local_raxml;
+ }
+
+ public boolean isAbbreviateScientificTaxonNames() {
+ return _abbreviate_scientific_names;
+ }
+
+ public boolean isBackgroundColorGradient() {
+ return _background_color_gradient;
+ }
+
+ public boolean isColorByTaxonomicGroup() {
+ return false;
+ }
+
+ public boolean isColorLabelsSameAsParentBranch() {
+ return _color_labels_same_as_parent_branch;
+ }
+
+ public boolean isMidpointReroot() {
+ return _midpoint_root;
+ }
+
+ public boolean isShowAnnotationRefSource() {
+ return _show_annotation_ref_source;
+ }
+
+ public boolean isShowDefaultNodeShapesExternal() {
+ return _show_default_node_shapes_external;
+ }
+
+ public boolean isShowDefaultNodeShapesInternal() {
+ return _show_default_node_shapes_internal;
+ }
+
+ public boolean isShowDomainLabels() {
+ return _show_domain_labels;
+ }
+
+ public void putDisplayColors( final String key, final Color color ) {
+ getDisplayColors().put( key, color );
+ }
+
+ public void setAddTaxonomyImagesCB( final boolean b ) {
+ display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no";
+ }
+
+ public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
+ _abbreviate_scientific_names = abbreviate_scientific_names;
+ }
+
+ public void setBackgroundColorGradient( final boolean background_color_gradient ) {
+ _background_color_gradient = background_color_gradient;
+ }
+
+ public void setBaseFontFamilyName( final String base_font_family_name ) {
+ _base_font_family_name = base_font_family_name;
+ }
+
+ public void setBaseFontSize( final int base_font_size ) {
+ _base_font_size = base_font_size;
+ }
+
+ public void setColorizeBranches( final boolean b ) {
+ display_options[ use_style ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
+ _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
+ }
+
+ public void setDefaultNodeFill( final NodeFill default_node_fill ) {
+ _default_node_fill = default_node_fill;
+ }
+
+ public void setDefaultNodeShape( final NodeShape default_node_shape ) {
+ _default_node_shape = default_node_shape;
+ }
+
+ public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
+ _default_node_shape_size = default_node_shape_size;
+ }
+
+ public void setDisplayAsPhylogram( final boolean b ) {
+ display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setUseStyle( final boolean b ) {
+ display_options[ use_style ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
+ _display_colors = display_colors;
+ }
+
+ public void setDisplayConfidenceValues( final boolean b ) {
+ display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayInternalData( final boolean b ) {
+ display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayNodeNames( final boolean b ) {
+ display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplaySequenceAcc( final boolean b ) {
+ display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplaySequenceNames( final boolean b ) {
+ display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayGeneNames( final boolean b ) {
+ display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
+ _display_sequence_relations = display_sequence_relations;
+ }
+
+ public void setDisplaySequenceSymbols( final boolean b ) {
+ display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayTaxonomyCode( final boolean b ) {
+ display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayTaxonomyCommonNames( final boolean b ) {
+ display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayTaxonomyImages( final boolean b ) {
+ display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayTaxonomyScientificNames( final boolean b ) {
+ display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDynamicallyHideData( final boolean b ) {
+ display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
+ _ext_desc_data_to_return = ext_desc_data_to_return;
+ }
+
+ public void setFrameXSize( final int frame_x_size ) {
+ _frame_x_size = frame_x_size;
+ }
+
+ public void setFrameYSize( final int frame_y_size ) {
+ _frame_y_size = frame_y_size;
+ }
+
+ public void setMidpointReroot( final boolean midpoint_root ) {
+ _midpoint_root = midpoint_root;
+ }
+
+ public void setMinConfidenceValue( final double min_confidence_value ) {
+ _min_confidence_value = min_confidence_value;
+ }
+
+ public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
+ _node_label_direction = node_label_direction;
+ }
+
+ public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
+ _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
+ }
+
+ public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
+ _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
+ }
+
+ public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
+ _phylogeny_graphics_type = phylogeny_graphics_type;
+ }
+
+ public void setPrintLineWidth( final float print_line_width ) {
+ _print_line_width = print_line_width;
+ }
+
+ public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
+ _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
+ }
+
+ public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
+ _show_branch_length_values = show_branch_length_values;
+ }
+
+ public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
+ _show_default_node_shapes_external = show_default_node_shapes_external;
+ }
+
+ public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
+ _show_default_node_shapes_internal = show_default_node_shapes_internal;
+ }
+
+ public void setShowDomainLabels( final boolean show_domain_labels ) {
+ _show_domain_labels = show_domain_labels;
+ }
+
+ public void setShowScale( final boolean show_scale ) {
+ _show_scale = show_scale;
+ }
+
+ public void setTaxonomyColorize( final boolean b ) {
+ display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setUseBranchesWidths( final boolean b ) {
+ display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
}
boolean displaySequenceRelations() {
return _annotation_colors;
}
- public String getBaseFontFamilyName() {
- return _base_font_family_name;
- }
-
int getBaseFontSize() {
return _base_font_size;
}
return _cladogram_type;
}
- private int getClickToIndex( final String name ) {
- int index = -1;
- if ( name.equals( "edit_info" ) ) {
- index = Configuration.display_node_data;
- ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "configuration key [edit_info] is deprecated, use [display node data] instead" );
- }
- else if ( name.equals( "display_node_data" ) ) {
- index = Configuration.display_node_data;
- }
- else if ( name.equals( "collapse_uncollapse" ) ) {
- index = Configuration.collapse_uncollapse;
- }
- else if ( name.equals( "reroot" ) ) {
- index = Configuration.reroot;
- }
- else if ( name.equals( "subtree" ) ) {
- index = Configuration.subtree;
- }
- else if ( name.equals( "swap" ) ) {
- index = Configuration.swap;
- }
- else if ( name.equals( "sort_descendants" ) ) {
- index = Configuration.sort_descendents;
- }
- else if ( name.equals( "get_ext_descendents_data" ) ) {
- index = Configuration.get_ext_desc_data;
- }
- else if ( name.equals( "display_sequences" ) ) {
- ForesterUtil
- .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
- return DEPRECATED;
- }
- else if ( name.equals( "open_seq_web" ) ) {
- index = Configuration.open_seq_web;
- }
- else if ( name.equals( "open_tax_web" ) ) {
- index = Configuration.open_tax_web;
- }
- else if ( name.equals( "blast" ) ) {
- index = Configuration.blast;
- }
- else if ( name.equals( "cut_subtree" ) ) {
- index = Configuration.cut_subtree;
- }
- else if ( name.equals( "copy_subtree" ) ) {
- index = Configuration.copy_subtree;
- }
- else if ( name.equals( "paste_subtree" ) ) {
- index = Configuration.paste_subtree;
- }
- else if ( name.equals( "delete" ) ) {
- index = Configuration.delete_subtree_or_node;
- }
- else if ( name.equals( "add_new_node" ) ) {
- index = Configuration.add_new_node;
- }
- else if ( name.equals( "edit_node_data" ) ) {
- index = Configuration.edit_node_data;
- }
- else if ( name.equals( "select_nodes" ) ) {
- index = Configuration.select_nodes;
- }
- else if ( name.equals( "display_node_popup" ) ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "configuration key [display_node_popup] is deprecated" );
- return DEPRECATED;
- }
- else if ( name.equals( "custom_option" ) ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
- return DEPRECATED;
- }
- else if ( name.equals( "color_subtree" ) ) {
- index = Configuration.color_subtree;
- }
- else if ( name.equals( "go_to_swiss_prot" ) ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" );
- return DEPRECATED;
- }
- return index;
- }
-
int getClickToOptionsCount() {
return clickto_options.length;
}
return clickto_options[ which ][ 0 ];
}
- public int getDefaultBootstrapSamples() {
- return _default_bootstrap_samples;
- }
-
- public File getpathToLocalMafft() {
- return _path_to_local_mafft;
- }
-
- public File getPathToLocalFastme() {
- return _path_to_local_fastme;
- }
-
- public File getPathToLocalRaxml() {
- return _path_to_local_raxml;
- }
-
int getDefaultDisplayClicktoOption() {
return default_clickto;
}
- public NodeFill getDefaultNodeFill() {
- return _default_node_fill;
- }
-
- public NodeShape getDefaultNodeShape() {
- return _default_node_shape;
- }
-
- public short getDefaultNodeShapeSize() {
- return _default_node_shape_size;
- }
-
SortedMap<String, Color> getDisplayColors() {
return _display_colors;
}
return _domain_colors;
}
- public Color getDomainStructureBaseColor() {
- return _domain_structure_base_color;
- }
-
- public Color getDomainStructureFontColor() {
- return _domain_structure_font_color;
- }
-
int getGraphicsExportX() {
return _graphics_export_x;
}
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;
}
- TreeColorSet getTreeColorSet() {
- return null;
- }
-
- TreeFontSet getTreeFontSet() {
- return null;
- }
-
- WebLink getWebLink( final String source ) {
- return getWebLinks().get( source );
- }
-
- Map<String, WebLink> getWebLinks() {
- return _weblinks;
- }
-
- public boolean isAbbreviateScientificTaxonNames() {
- return _abbreviate_scientific_names;
+ final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+ return _taxonomy_extraction;
}
boolean isAntialiasScreen() {
+ if ( ForesterUtil.isMac() ) {
+ //Apple Macintosh graphics are slow, turn off anti-alias.
+ return false;
+ }
return _antialias_screen;
}
- public boolean isBackgroundColorGradient() {
- return _background_color_gradient;
- }
-
- public boolean isColorLabelsSameAsParentBranch() {
- return _color_labels_same_as_parent_branch;
- }
-
/**
* Convenience method.
*
return _editable;
}
- boolean isExtractPfamTaxonomyCodesInNhParsing() {
- return _nh_parsing_extract_pfam_taxonomy_codes;
- }
-
- boolean isHasWebLink( final String source ) {
- return getWebLinks().containsKey( source );
- }
-
/**
* Only used by ArchaeoptryxE.
*
return _show_branch_length_values;
}
- public boolean isShowDefaultNodeShapes() {
- return _show_default_node_shapes;
- }
-
- public boolean isShowDomainLabels() {
- return _show_domain_labels;
- }
-
boolean isShowOverview() {
return _show_overview;
}
return _show_scale;
}
- public boolean isTaxonomyColorizeNodeShapes() {
- return _taxonomy_colorize_node_shapes;
- }
-
final boolean isUseNativeUI() {
- if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) {
+ if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
_ui = UI.NATIVE;
}
return _ui == UI.NATIVE;
return _validate_against_phyloxml_xsd_schema;
}
+ final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
+ _taxonomy_extraction = taxonomy_extraction;
+ }
+
+ private int getClickToIndex( final String name ) {
+ int index = -1;
+ if ( name.equals( "edit_info" ) ) {
+ index = Configuration.display_node_data;
+ ForesterUtil
+ .printWarningMessage( Constants.PRG_NAME,
+ "configuration key [edit_info] is deprecated, use [display node data] instead" );
+ }
+ else if ( name.equals( "display_node_data" ) ) {
+ index = Configuration.display_node_data;
+ }
+ else if ( name.equals( "collapse_uncollapse" ) ) {
+ index = Configuration.collapse_uncollapse;
+ }
+ else if ( name.equals( "reroot" ) ) {
+ index = Configuration.reroot;
+ }
+ else if ( name.equals( "subtree" ) ) {
+ index = Configuration.subtree;
+ }
+ else if ( name.equals( "swap" ) ) {
+ index = Configuration.swap;
+ }
+ else if ( name.equals( "sort_descendants" ) ) {
+ index = Configuration.sort_descendents;
+ }
+ else if ( name.equals( "get_ext_descendents_data" ) ) {
+ index = Configuration.get_ext_desc_data;
+ }
+ else if ( name.equals( "display_sequences" ) ) {
+ ForesterUtil
+ .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
+ return DEPRECATED;
+ }
+ else if ( name.equals( "open_seq_web" ) ) {
+ index = Configuration.open_seq_web;
+ }
+ else if ( name.equals( "open_pdb_web" ) ) {
+ index = Configuration.open_pdb_web;
+ }
+ else if ( name.equals( "open_tax_web" ) ) {
+ index = Configuration.open_tax_web;
+ }
+ else if ( name.equals( "blast" ) ) {
+ index = Configuration.blast;
+ }
+ else if ( name.equals( "cut_subtree" ) ) {
+ index = Configuration.cut_subtree;
+ }
+ else if ( name.equals( "copy_subtree" ) ) {
+ index = Configuration.copy_subtree;
+ }
+ else if ( name.equals( "paste_subtree" ) ) {
+ index = Configuration.paste_subtree;
+ }
+ else if ( name.equals( "delete" ) ) {
+ index = Configuration.delete_subtree_or_node;
+ }
+ else if ( name.equals( "add_new_node" ) ) {
+ index = Configuration.add_new_node;
+ }
+ else if ( name.equals( "edit_node_data" ) ) {
+ index = Configuration.edit_node_data;
+ }
+ else if ( name.equals( "select_nodes" ) ) {
+ index = Configuration.select_nodes;
+ }
+ else if ( name.equals( "display_node_popup" ) ) {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME,
+ "configuration key [display_node_popup] is deprecated" );
+ return DEPRECATED;
+ }
+ else if ( name.equals( "custom_option" ) ) {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
+ return DEPRECATED;
+ }
+ else if ( name.equals( "color_subtree" ) ) {
+ index = Configuration.color_subtree;
+ }
+ else if ( name.equals( "change_node_font" ) ) {
+ index = Configuration.change_node_font;
+ }
+ else if ( name.equals( "color_node_font" ) ) {
+ index = Configuration.color_node_font;
+ }
+ else if ( name.equals( "color_subtree" ) ) {
+ index = Configuration.color_subtree;
+ }
+ return index;
+ }
+
private boolean parseBoolean( final String str ) {
final String my_str = str.trim().toLowerCase();
if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
}
}
- public void putDisplayColors( final String key, final Color color ) {
- getDisplayColors().put( key, color );
- }
-
/**
* read each line of config file, process non-comment lines
* @throws IOException
} while ( line != null );
}
- public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
- _abbreviate_scientific_names = abbreviate_scientific_names;
- }
-
private void setAntialiasScreen( final boolean antialias_screen ) {
_antialias_screen = antialias_screen;
}
- public void setBackgroundColorGradient( final boolean background_color_gradient ) {
- _background_color_gradient = background_color_gradient;
- }
-
- public void setBaseFontFamilyName( final String base_font_family_name ) {
- _base_font_family_name = base_font_family_name;
- }
-
- public void setBaseFontSize( final int base_font_size ) {
- _base_font_size = base_font_size;
- }
-
private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
_cladogram_type = cladogram_type;
}
- public void setColorizeBranches( final boolean b ) {
- display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
- _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
- }
-
private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
_default_bootstrap_samples = default_bootstrap_samples;
}
- private void setPathToLocalMafft( final File path_to_local_mafft ) {
- _path_to_local_mafft = path_to_local_mafft;
- }
-
- private void setPathToLocalFastme( final File path_to_local_fastme ) {
- _path_to_local_fastme = path_to_local_fastme;
- }
-
- private void setPathToLocalRaxml( final File path_to_local_raxml ) {
- _path_to_local_raxml = path_to_local_raxml;
- }
-
- public File getPathToLocalClustalOmega() {
- return _path_to_local_clustalo;
- }
-
- public void setPathToLocalClustalOmega( final File path_to_local_clustalo ) {
- _path_to_local_clustalo = path_to_local_clustalo;
- }
-
- public void setDefaultNodeFill( final NodeFill default_node_fill ) {
- _default_node_fill = default_node_fill;
- }
-
- public void setDefaultNodeShape( final NodeShape default_node_shape ) {
- _default_node_shape = default_node_shape;
- }
-
- public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
- _default_node_shape_size = default_node_shape_size;
- }
-
- public void setDisplayAsPhylogram( final boolean b ) {
- display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
- _display_colors = display_colors;
- }
-
- public void setDisplayConfidenceValues( final boolean b ) {
- display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplayInternalData( final boolean b ) {
- display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplayNodeNames( final boolean b ) {
- display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplaySequenceAcc( final boolean b ) {
- display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplaySequenceNames( final boolean b ) {
- display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
- _display_sequence_relations = display_sequence_relations;
- }
-
- public void setDisplaySequenceSymbols( final boolean b ) {
- display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplayTaxonomyCode( final boolean b ) {
- display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplayTaxonomyCommonNames( final boolean b ) {
- display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplayTaxonomyImages( final boolean b ) {
- display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplayTaxonomyScientificNames( final boolean b ) {
- display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDynamicallyHideData( final boolean b ) {
- display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
- }
-
private void setEditable( final boolean editable ) {
_editable = editable;
}
- public void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) {
- _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes;
+ private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
+ _ext_node_data_return_on = ext_node_data_return_on;
}
private void setGraphicsExportX( final int graphics_export_x ) {
else if ( key.equals( "font_size" ) ) {
final String size_str = ( ( String ) st.nextElement() ).trim();
final int i = parseInt( size_str );
- setBaseFontSize( i );
+ if ( i > 0 ) {
+ setBaseFontSize( i );
+ }
+ }
+ else if ( key.equals( "font_size_min" ) ) {
+ final String size_str = ( ( String ) st.nextElement() ).trim();
+ final int i = parseInt( size_str );
+ if ( i > 0 ) {
+ setMinBaseFontSize( i );
+ }
+ }
+ else if ( key.equals( "font_size_max" ) ) {
+ final String size_str = ( ( String ) st.nextElement() ).trim();
+ final int i = parseInt( size_str );
+ if ( i > 1 ) {
+ setMaxBaseFontSize( i );
+ }
}
else if ( key.equals( "graphics_export_x" ) ) {
final String str = ( ( String ) st.nextElement() ).trim();
final int i = parseInt( str );
- setGraphicsExportX( i );
+ if ( i > 0 ) {
+ setGraphicsExportX( i );
+ }
}
else if ( key.equals( "graphics_export_y" ) ) {
final String str = ( ( String ) st.nextElement() ).trim();
final int i = parseInt( str );
- setGraphicsExportY( i );
+ if ( i > 0 ) {
+ setGraphicsExportY( i );
+ }
}
else if ( key.equals( "pdf_export_line_width" ) ) {
final String str = ( ( String ) st.nextElement() ).trim();
"value for [pdf_export_line_width] cannot be zero or negative" );
}
}
+ else if ( key.equals( "window_initial_size_x" ) ) {
+ final String str = ( ( String ) st.nextElement() ).trim();
+ final int i = parseInt( str );
+ if ( i > 0 ) {
+ setFrameXSize( i );
+ }
+ }
+ else if ( key.equals( "window_initial_size_y" ) ) {
+ final String str = ( ( String ) st.nextElement() ).trim();
+ final int i = parseInt( str );
+ if ( i > 0 ) {
+ setFrameYSize( i );
+ }
+ }
else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
final String str = ( ( String ) st.nextElement() ).trim();
final int i = parseInt( str );
"value for [default_number_of_bootstrap_resamples] cannot be negative" );
}
}
- else if ( key.equals( "clustalo_local" ) ) {
- final String str = ( ( String ) st.nextElement() ).trim();
- if ( !ForesterUtil.isEmpty( str ) ) {
- setPathToLocalClustalOmega( new File( str ) );
- }
- }
else if ( key.equals( "mafft_local" ) ) {
final String str = ( ( String ) st.nextElement() ).trim();
if ( !ForesterUtil.isEmpty( str ) ) {
else if ( key.equals( "show_domain_labels" ) ) {
setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
}
+ else if ( key.equals( "show_seq_annotation_ref_sources" ) ) {
+ setShowAnnotationRefSource( parseBoolean( ( String ) st.nextElement() ) );
+ }
else if ( key.equals( "abbreviate_scientific_names" ) ) {
setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
}
}
else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
final boolean r = parseBoolean( ( String ) st.nextElement() );
- if ( r && isExtractPfamTaxonomyCodesInNhParsing() ) {
+ if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
ForesterUtil
.printWarningMessage( Constants.PRG_NAME,
"attempt to extract taxonomies and replace underscores at the same time" );
setReplaceUnderscoresInNhParsing( r );
}
}
- else if ( key.equals( "extract_taxonomy_codes_in_nh_parsing" ) ) {
- final boolean e = parseBoolean( ( String ) st.nextElement() );
- if ( e && isReplaceUnderscoresInNhParsing() ) {
+ else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
+ final String s = ( String ) st.nextElement();
+ if ( s.equalsIgnoreCase( "no" ) ) {
+ setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
+ }
+ else if ( s.equalsIgnoreCase( "pfam_relaxed" ) ) {
+ setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ }
+ else if ( s.equalsIgnoreCase( "pfam_strict" ) ) {
+ setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ }
+ else if ( s.equalsIgnoreCase( "aggressive" ) ) {
+ setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
+ }
+ else {
ForesterUtil
.printWarningMessage( Constants.PRG_NAME,
- "attempt to extract taxonomies and replace underscores at the same time" );
+ "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
+ + s
+ + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
}
- else {
- setExtractPfamTaxonomyCodesInNhParsing( e );
+ if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
+ ForesterUtil
+ .printWarningMessage( Constants.PRG_NAME,
+ "attempt to extract taxonomies and replace underscores at the same time" );
}
}
else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
_domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
}
else if ( key.equals( "show_default_node_shapes" ) ) {
- setShowDefaultNodeShapes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
+ ForesterUtil
+ .printWarningMessage( Constants.PRG_NAME,
+ "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" );
+ final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() );
+ setShowDefaultNodeShapesInternal( b );
+ setShowDefaultNodeShapesExternal( b );
+ }
+ else if ( key.equals( "show_default_node_shapes_internal" ) ) {
+ setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
+ }
+ else if ( key.equals( "show_default_node_shapes_external" ) ) {
+ setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
}
else if ( key.equals( "default_node_size" ) ) {
final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
}
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( "ext_descendents_data_to_return" ) ) {
final String s = ( ( String ) st.nextElement() ).trim();
else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
}
+ else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) {
+ setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ_FASTA );
+ }
else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
}
else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
}
+ else if ( s.equalsIgnoreCase( "gene_name" ) ) {
+ setExtDescNodeDataToReturn( NODE_DATA.GENE_NAME );
+ }
else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
}
else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
}
+ else if ( s.equalsIgnoreCase( "taxonomy_common_name" ) ) {
+ setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_COMM0N_NAME );
+ }
else if ( s.equalsIgnoreCase( "user_selected" ) ) {
setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
}
else if ( s.equals( "window" ) ) {
setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
}
+ else if ( s.equals( "buffer_only" ) ) {
+ setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
+ }
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
+ "] for [ext_descendents_data_to_return_on]" );
else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
// yet retrieved!
int key_index = -1;
- if ( key.equals( "use_real_br_lengths" ) || key.equals( "phylogram" ) ) {
+ if ( key.equals( "phylogram" ) ) {
key_index = Configuration.display_as_phylogram;
- if ( key.equals( "use_real_br_lengths" ) ) {
- ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "configuration key [use_real_br_lengths] is deprecated, use [phylogram] instead" );
- }
}
else if ( key.equals( "rollover" ) ) {
key_index = Configuration.node_data_popup;
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;
}
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;
}
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();
}
}
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( "domain_color" ) ) {
getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
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 );
_label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
}
- public String getLabelForGetExtDescendentsData() {
- return _label_for_get_ext_descendents_data;
- }
-
- public void setMinConfidenceValue( final double min_confidence_value ) {
- _min_confidence_value = min_confidence_value;
- }
-
- public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
- _node_label_direction = node_label_direction;
- }
-
- public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
- _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
+ private void setMaxBaseFontSize( final int max_base_font_size ) {
+ _max_base_font_size = max_base_font_size;
}
- public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
- _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
+ private void setMinBaseFontSize( final int min_base_font_size ) {
+ _min_base_font_size = min_base_font_size;
}
private void setOvMaxHeight( final short ov_max_height ) {
_ov_placement = ov_placement;
}
- public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
- _phylogeny_graphics_type = phylogeny_graphics_type;
- }
-
- public void setPrintLineWidth( final float print_line_width ) {
- _print_line_width = print_line_width;
- }
-
- public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
- _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
+ private void setPathToLocalFastme( final File path_to_local_fastme ) {
+ _path_to_local_fastme = path_to_local_fastme;
}
- public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
- _show_branch_length_values = show_branch_length_values;
+ private void setPathToLocalMafft( final File path_to_local_mafft ) {
+ _path_to_local_mafft = path_to_local_mafft;
}
- public void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
- _show_default_node_shapes = show_default_node_shapes;
+ private void setPathToLocalRaxml( final File path_to_local_raxml ) {
+ _path_to_local_raxml = path_to_local_raxml;
}
- public void setShowDomainLabels( final boolean show_domain_labels ) {
- _show_domain_labels = show_domain_labels;
+ private void setShowAnnotationRefSource( final boolean b ) {
+ _show_annotation_ref_source = b;
}
private void setShowOverview( final boolean show_overview ) {
_show_overview = show_overview;
}
- public void setShowScale( final boolean show_scale ) {
- _show_scale = show_scale;
- }
-
- public void setTaxonomyColorize( final boolean b ) {
- display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
- _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
- }
-
- public void setUseBranchesWidths( final boolean b ) {
- display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
- }
-
private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
_validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
}
- void setWebLinks( final SortedMap<String, WebLink> weblinks ) {
- _weblinks = weblinks;
- }
-
static String getDefaultFontFamilyName() {
return DEFAULT_FONT_FAMILY;
}
- static enum TRIPLET {
- TRUE, FALSE, UNKNOWN
+ public enum EXT_NODE_DATA_RETURN_ON {
+ BUFFER_ONLY, CONSOLE, WINODW;
}
public enum UI {
- NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN
- }
-
- public NODE_DATA getExtDescNodeDataToReturn() {
- return _ext_desc_data_to_return;
- }
-
- public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
- _ext_desc_data_to_return = ext_desc_data_to_return;
- }
-
- public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
- return _ext_node_data_return_on;
+ CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN
}
- private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
- _ext_node_data_return_on = ext_node_data_return_on;
+ static enum TRIPLET {
+ FALSE, TRUE, UNKNOWN
}
}