// 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.phylogeny.data.NodeVisualization;
-import org.forester.phylogeny.data.NodeVisualization.NodeFill;
-import org.forester.phylogeny.data.NodeVisualization.NodeShape;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
+import org.forester.phylogeny.data.NodeDataField;
+import org.forester.phylogeny.data.NodeVisualData;
+import org.forester.phylogeny.data.NodeVisualData.NodeFill;
+import org.forester.phylogeny.data.NodeVisualData.NodeShape;
import org.forester.util.ForesterUtil;
public final class Configuration {
- static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
- private static final String WEB_LINK_KEY = "web_link";
- private static final String DISPLAY_COLOR_KEY = "display_color";
- private static final int DEPRECATED = -2;
- private UI _ui = UI.UNKNOWN;
- private boolean _use_tabbed_display = false;
- private boolean _hide_controls_and_menus = false;
- private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
- private SortedMap<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 int _default_bootstrap_samples = -1;
- private boolean _show_default_node_shapes = false;
- private NodeShape _default_node_shape = NodeShape.CIRCLE;
- private NodeFill _default_node_fill = NodeFill.GRADIENT;
- private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
- private boolean _taxonomy_colorize_node_shapes = false;
+ public enum EXT_NODE_DATA_RETURN_ON {
+ BUFFER_ONLY, CONSOLE, WINODW;
+ }
+
+ public enum UI {
+ CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN
+ }
+
+ static enum TRIPLET {
+ FALSE, TRUE, UNKNOWN
+ }
+ final static String clickto_options[][] = {
+ { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
+ { "Go to Sub/Supertree", "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" },
+ { "List Node Data", "display" }, { "Select Node(s)", "display" } , { "Uncollapse All", "display" }, { "Order Subtree", "display" }, };
+ private final static String DEFAULT_SPECIES_COLORS[][] = {
+ { "BRAFL", "0x00FFFF" }, { "SPHGR", "0x9620F0" }, { "STRPU", "0x9620F0" }, { "CIOIN", "0xFF1CAE" },
+ { "CIOSA", "0xFF2CAE" }, { "BOVIN", "0x5C3317" }, { "CANFA", "0x8B2323" }, { "HUMAN", "0xFF2400" },
+ { "PANTR", "0xCC2400" }, { "MOUSE", "0xFF7F00" }, { "RAT", "0xFFEF00" }, { "MONDO", "0xEE9A49" },
+ { "ORNAN", "0xCD853F" }, { "XENLA", "0x6BAA23" }, { "XENTR", "0x6BAA23" }, { "CHICK", "0xFFC125" },
+ { "FUGRU", "0x0000FF" }, { "BRARE", "0x0000DD" }, { "DANRE", "0x0000BB" }, { "TETNG", "0x0000AA" },
+ { "ORYLA", "0x000088" }, { "GASAC", "0x000066" }, { "CAEEL", "0x666699" }, { "CAEBR", "0xB0B0B0" },
+ { "DROME", "0x663366" }, { "DROPS", "0x996699" }, { "APIME", "0x7A7700" }, { "AEDAE", "0x8C5900" },
+ { "TRICA", "0x918E00" }, { "NEMVE", "0x0066CC" }, { "HYDVU", "0x3399FF" }, { "LUBBA", "0xF7B5CB" },
+ { "GEOCY", "0xF5A0BD" }, { "AMPQE", "0x009966" }, { "SUBDO", "0xC790B9" }, { "MONBE", "0xFC0FC0" },
+ { "DICPU", "0xFFCC33" }, { "DICDI", "0xFFCC00" }, { "ENTHI", "0x5959AB" }, { "ARATH", "0x00FF00" },
+ { "POPTR", "0x006400" }, { "VITVI", "0x00CD00" }, { "GLYMA", "0x00FF7F" }, { "ORYSA", "0x008B00" },
+ { "ORYSJ", "0x008C00" }, { "SORBI", "0x00EE76" }, { "SELMO", "0x238E23" }, { "PHYPA", "0x09F911" },
+ { "OSTLU", "0x7FFF00" }, { "OSTTA", "0x7FFF00" }, { "OSTRC", "0x7FFF00" }, { "MICPU", "0x66CD00" },
+ { "MIC99", "0x66CD00" }, { "CHLRE", "0xB3EE3A" }, { "VOLCA", "0xC0FF3E" }, { "CHLSP", "0x6B8E23" },
+ { "CYAME", "0xD02090" }, { "YEAST", "0xAAAAAA" }, { "BACFR", "0xFF0000" }, { "BACTN", "0xFFFF00" },
+ { "MYXXD", "0x0000FF" }, { "STIAU", "0x00FFFF" }, { "BACOV", "0x8C5900" }, { "BACUN", "0x66CD00" },
+ { "PORGI", "0x918E00" } };
+ 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;
+ final static int uncollapse_all = 21;
+ final static int order_subtree = 22;
+
+ // ------------------
+ // 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" }, { "Domain Architectures", "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" },
+ { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" }
+ , { "Taxonomy Rank", "display", "no" }, { "Show External Data", "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_gene_names = 13;
+ final static int show_seq_names = 13;
final static int show_sequence_acc = 14;
final static int display_internal_data = 15;
final static int dynamically_hide_data = 16;
final static int show_taxonomy_scientific_names = 17;
final static int show_taxonomy_common_names = 18;
final static int color_according_to_annotation = 19;
- final static int show_gene_symbols = 20;
+ final static int show_seq_symbols = 20;
final static int node_data_popup = 21;
final static int show_relation_confidence = 22;
final static int show_vector_data = 23;
final static int show_taxonomy_images = 24;
final static int show_properties = 25;
- // ------------------
- // Click-to options
- // ------------------
- final static int display_node_data = 0;
- final static int collapse_uncollapse = 1;
- final static int reroot = 2;
- final static int subtree = 3;
- final static int swap = 4;
- final static int color_subtree = 5;
- final static int open_seq_web = 6;
- final static int open_tax_web = 7;
- final static int blast = 8;
- final static int cut_subtree = 9;
- final static int copy_subtree = 10;
- final static int paste_subtree = 11;
- final static int delete_subtree_or_node = 12;
- final static int add_new_node = 13;
- final static int edit_node_data = 14;
- final static int sort_descendents = 15;
+ final static int show_gene_names = 26;
+ final static int show_mol_seqs = 27;
+ final static int write_branch_length_values = 28;
+ final static int show_tax_rank = 29;
+ final static int display_external_data = 30;
+
+ 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" },
- { "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" } };
// This option is selected in the dropdown
int default_clickto = Configuration.display_node_data;
+ String default_config_filename = AptxConstants.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;
+ boolean verbose = AptxConstants.VERBOSE_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 = AptxConstants.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 = AptxConstants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
+ private SortedMap<String, Color> _display_colors = null;
+ private boolean _display_sequence_relations = false;
+ private boolean _editable = true;
+ private NodeDataField _ext_desc_data_to_return = NodeDataField.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 Color _gui_background_color = AptxConstants.GUI_BACKGROUND_DEFAULT;
+ private Color _gui_button_background_color = AptxConstants.BUTTON_BACKGROUND_COLOR_DEFAULT;
+ private Color _gui_button_border_color = AptxConstants.BUTTON_BORDER_COLOR_DEFAULT;
+ private Color _gui_button_text_color = AptxConstants.BUTTON_TEXT_COLOR_DEFAULT;
+ private Color _gui_checkbox_and_button_active_color = AptxConstants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
+ private Color _gui_checkbox_text_color = AptxConstants.CHECKBOX_TEXT_COLOR_DEFAULT;
+ private Color _gui_menu_background_color = AptxConstants.MENU_BACKGROUND_COLOR_DEFAULT;
+ private Color _gui_menu_text_color = AptxConstants.MENU_TEXT_COLOR_DEFAULT;
+ private boolean _hide_controls_and_menus = false;
+ private boolean _internal_number_are_confidence_for_nh_parsing = false;
+ private String _label_for_get_ext_descendents_data = "";
+ private int _max_base_font_size = 20;
+ private boolean _midpoint_root = false;
+ private int _min_base_font_size = 2;
+ private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
+ private boolean _nh_parsing_replace_underscores = false;
private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
- private 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 Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
- private static String DEFAULT_FONT_FAMILY = "";
+ private short _number_of_digits_after_comma_for_branch_length_values = AptxConstants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
+ private short _number_of_digits_after_comma_for_confidence_values = AptxConstants.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 = AptxConstants.PDF_LINE_WIDTH_DEFAULT;
+ private boolean _show_annotation_ref_source = true;
+ private boolean _show_default_node_shapes_external = false;
+ private boolean _show_default_node_shapes_for_marked_nodes = 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 = AptxConstants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
+ private Color _vector_data_min_color = Color.BLUE;
+ private Color _vector_data_max_color = Color.YELLOW;
+ private Color _vector_data_mean_color = Color.WHITE;
+ private double _vector_data_height = 12;
+ private int _vector_data_width = 120;
+ private boolean _line_up_renderable_node_data = true;
+ private boolean _right_align_domains = false;
+ private boolean _allow_thick_strokes = false;
+ private boolean _could_read_config_file = false;
static {
- for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
+ for( final String font_name : AptxConstants.DEFAULT_FONT_CHOICES ) {
if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
DEFAULT_FONT_FAMILY = font_name;
break;
}
}
if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
- DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
+ DEFAULT_FONT_FAMILY = AptxConstants.DEFAULT_FONT_CHOICES[ AptxConstants.DEFAULT_FONT_CHOICES.length - 1 ];
}
}
else {
config_filename = cf;
}
- setWebLinks( new TreeMap<String, WebLink>() );
+ _could_read_config_file = false;
setDisplayColors( new TreeMap<String, Color>() );
config_filename = config_filename.trim();
URL u = null;
final BufferedReader bf = new BufferedReader( isr );
readConfig( bf );
bf.close();
- ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
+ ForesterUtil.programMessage( AptxConstants.PRG_NAME, "successfully read from configuration url ["
+ config_filename + "]" );
+ _could_read_config_file = true;
}
catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "failed to read configuration from ["
+ config_filename + "]: " + e.getLocalizedMessage() );
}
}
catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "cannot find or open configuration url ["
+ config_filename + "]" );
}
}
final BufferedReader bf = new BufferedReader( new FileReader( f ) );
readConfig( bf );
bf.close();
+ _could_read_config_file = true;
}
catch ( final Exception e ) {
if ( verbose ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "failed to read configuration from ["
+ config_filename + "]: " + e );
}
}
}
else {
if ( verbose ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "cannot find or open configuration file ["
+ config_filename + "]" );
}
}
}
}
- 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;
}
- boolean displaySequenceRelations() {
- return _display_sequence_relations;
+ public int getDefaultBootstrapSamples() {
+ return _default_bootstrap_samples;
}
- boolean doCheckOption( final int which ) {
- return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
- || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
+ public NodeFill getDefaultNodeFill() {
+ return _default_node_fill;
}
- boolean doDisplayClickToOption( final int which ) {
- return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
+ public NodeShape getDefaultNodeShape() {
+ return _default_node_shape;
}
- boolean doDisplayOption( final int which ) {
- return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
+ public short getDefaultNodeShapeSize() {
+ return _default_node_shape_size;
}
- /**
- * Will attempt to use the phylogeny to determine whether to check
- * this or not (e.g. phylogram)
- *
- */
- boolean doGuessCheckOption( final int which ) {
- return display_options[ which ][ 2 ].equals( "?" );
+ public NodeDataField getExtDescNodeDataToReturn() {
+ return _ext_desc_data_to_return;
}
- Map<String, Color> getAnnotationColors() {
- if ( _annotation_colors == null ) {
- _annotation_colors = new Hashtable<String, Color>();
- }
- return _annotation_colors;
+ public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
+ return _ext_node_data_return_on;
}
- public String getBaseFontFamilyName() {
- return _base_font_family_name;
+ public int getFrameXSize() {
+ return _frame_x_size;
}
- int getBaseFontSize() {
- return _base_font_size;
+ public int getFrameYSize() {
+ return _frame_y_size;
}
- CLADOGRAM_TYPE getCladogramType() {
- return _cladogram_type;
+ public String getLabelForGetExtDescendentsData() {
+ return _label_for_get_ext_descendents_data;
}
- private int getClickToIndex( final String name ) {
- int index = -1;
- if ( name.equals( "edit_info" ) ) {
- index = Configuration.display_node_data;
- ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "configuration key [edit_info] is deprecated, use [display node data] instead" );
- }
- else if ( name.equals( "display_node_data" ) ) {
- index = Configuration.display_node_data;
- }
- else if ( name.equals( "collapse_uncollapse" ) ) {
- index = Configuration.collapse_uncollapse;
- }
- else if ( name.equals( "reroot" ) ) {
- index = Configuration.reroot;
- }
- else if ( name.equals( "subtree" ) ) {
- index = Configuration.subtree;
- }
- else if ( name.equals( "swap" ) ) {
- index = Configuration.swap;
- }
- else if ( name.equals( "sort_descendants" ) ) {
- index = Configuration.sort_descendents;
- }
- else if ( name.equals( "display_sequences" ) ) {
- ForesterUtil
- .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
- return DEPRECATED;
- }
- else if ( name.equals( "open_seq_web" ) ) {
- index = Configuration.open_seq_web;
- }
- else if ( name.equals( "open_tax_web" ) ) {
- index = Configuration.open_tax_web;
- }
- else if ( name.equals( "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( "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;
+ public File getPathToLocalFastme() {
+ return _path_to_local_fastme;
}
- int getClickToOptionsCount() {
- return clickto_options.length;
+ public File getPathToLocalMafft() {
+ return _path_to_local_mafft;
}
- String getClickToTitle( final int which ) {
- return clickto_options[ which ][ 0 ];
+ public File getPathToLocalRaxml() {
+ return _path_to_local_raxml;
}
- public int getDefaultBootstrapSamples() {
- return _default_bootstrap_samples;
+ public double getVectorDataHeight() {
+ return _vector_data_height;
}
- int getDefaultDisplayClicktoOption() {
- return default_clickto;
+ public Color getVectorDataMaxColor() {
+ return _vector_data_max_color;
}
- public NodeFill getDefaultNodeFill() {
- return _default_node_fill;
+ public Color getVectorDataMeanColor() {
+ return _vector_data_mean_color;
}
- public NodeShape getDefaultNodeShape() {
- return _default_node_shape;
+ public Color getVectorDataMinColor() {
+ return _vector_data_min_color;
}
- public short getDefaultNodeShapeSize() {
- return _default_node_shape_size;
+ public int getVectorDataWidth() {
+ return _vector_data_width;
}
- SortedMap<String, Color> getDisplayColors() {
- return _display_colors;
+ public boolean isAbbreviateScientificTaxonNames() {
+ return _abbreviate_scientific_names;
}
- String getDisplayTitle( final int which ) {
- return display_options[ which ][ 0 ];
+ public boolean isAllowThickStrokes() {
+ return _allow_thick_strokes;
}
- Map<String, Color> getDomainColors() {
- if ( _domain_colors == null ) {
- _domain_colors = new Hashtable<String, Color>();
- }
- return _domain_colors;
+ public boolean isBackgroundColorGradient() {
+ return _background_color_gradient;
}
- public Color getDomainStructureBaseColor() {
- return _domain_structure_base_color;
+ public boolean isColorByTaxonomicGroup() {
+ return false;
}
- public Color getDomainStructureFontColor() {
- return _domain_structure_font_color;
+ public boolean isColorLabelsSameAsParentBranch() {
+ return _color_labels_same_as_parent_branch;
}
- int getGraphicsExportX() {
- return _graphics_export_x;
+ final public boolean isLineUpRendarableNodeData() {
+ return _line_up_renderable_node_data;
}
- int getGraphicsExportY() {
- return _graphics_export_y;
+ public boolean isMidpointReroot() {
+ return _midpoint_root;
}
- Color getGuiBackgroundColor() {
- return _gui_background_color;
+ final public boolean isRightLineUpDomains() {
+ return _right_align_domains;
}
- Color getGuiButtonBackgroundColor() {
- return _gui_button_background_color;
+ public boolean isShowAnnotationRefSource() {
+ return _show_annotation_ref_source;
}
- Color getGuiButtonBorderColor() {
- return _gui_button_border_color;
+ public boolean isShowDefaultNodeShapesExternal() {
+ return _show_default_node_shapes_external;
}
- Color getGuiButtonTextColor() {
- return _gui_button_text_color;
+ public boolean isShowDefaultNodeShapesForMarkedNodes() {
+ return _show_default_node_shapes_for_marked_nodes;
}
- Color getGuiCheckboxAndButtonActiveColor() {
- return _gui_checkbox_and_button_active_color;
+ public boolean isShowDefaultNodeShapesInternal() {
+ return _show_default_node_shapes_internal;
}
- Color getGuiCheckboxTextColor() {
- return _gui_checkbox_text_color;
+ public boolean isShowDomainLabels() {
+ return _show_domain_labels;
}
- Color getGuiMenuBackgroundColor() {
- return _gui_menu_background_color;
+ public void putDisplayColors( final String key, final Color color ) {
+ getDisplayColors().put( key, color );
}
- Color getGuiMenuTextColor() {
- return _gui_menu_text_color;
+ public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
+ _abbreviate_scientific_names = abbreviate_scientific_names;
}
- double getMinConfidenceValue() {
- return _min_confidence_value;
+ public void setAddTaxonomyImagesCB( final boolean b ) {
+ display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no";
}
- NODE_LABEL_DIRECTION getNodeLabelDirection() {
- return _node_label_direction;
+ public void setBackgroundColorGradient( final boolean background_color_gradient ) {
+ _background_color_gradient = background_color_gradient;
}
- short getNumberOfDigitsAfterCommaForBranchLengthValues() {
- return _number_of_digits_after_comma_for_branch_length_values;
+ public void setBaseFontFamilyName( final String base_font_family_name ) {
+ _base_font_family_name = base_font_family_name;
}
- short getNumberOfDigitsAfterCommaForConfidenceValues() {
- return _number_of_digits_after_comma_for_confidence_values;
+ public void setBaseFontSize( final int base_font_size ) {
+ _base_font_size = base_font_size;
}
- short getOvMaxHeight() {
- return _ov_max_height;
+ public void setColorizeBranches( final boolean b ) {
+ display_options[ use_style ][ 2 ] = b ? "yes" : "no";
}
- short getOvMaxWidth() {
- return _ov_max_width;
+ public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
+ _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
}
- OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
- return _ov_placement;
+ public void setDefaultNodeFill( final NodeFill default_node_fill ) {
+ _default_node_fill = default_node_fill;
}
- PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
- return _phylogeny_graphics_type;
+ public void setDefaultNodeShape( final NodeShape default_node_shape ) {
+ _default_node_shape = default_node_shape;
}
- float getPrintLineWidth() {
- return _print_line_width;
+ public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
+ _default_node_shape_size = default_node_shape_size;
}
- Hashtable<String, Color> getSpeciesColors() {
- if ( _species_colors == null ) {
- _species_colors = new Hashtable<String, Color>();
- }
- return _species_colors;
+ public void setDisplayAsPhylogram( final boolean b ) {
+ display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
}
- TreeColorSet getTreeColorSet() {
- return null;
+ public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
+ _display_colors = display_colors;
}
- TreeFontSet getTreeFontSet() {
- return null;
+ public void setDisplayConfidenceValues( final boolean b ) {
+ display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
}
- WebLink getWebLink( final String source ) {
- return getWebLinks().get( source );
+ public void setDisplayGeneNames( final boolean b ) {
+ display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
}
- Map<String, WebLink> getWebLinks() {
- return _weblinks;
+ public void setDisplayInternalData( final boolean b ) {
+ display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayExternalData( final boolean b ) {
+ display_options[ display_external_data ][ 2 ] = b ? "yes" : "no";
}
- public boolean isAbbreviateScientificTaxonNames() {
- return _abbreviate_scientific_names;
+ public void setDisplayMultipleSequenceAlignment( final boolean b ) {
+ display_options[ show_mol_seqs ][ 2 ] = b ? "yes" : "no";
}
- boolean isAntialiasScreen() {
- return _antialias_screen;
+ public void setDisplayNodeNames( final boolean b ) {
+ display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
}
- public boolean isBackgroundColorGradient() {
- return _background_color_gradient;
+ public void setDisplaySequenceAcc( final boolean b ) {
+ display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
}
- public boolean isColorLabelsSameAsParentBranch() {
- return _color_labels_same_as_parent_branch;
+ public void setDisplaySequenceNames( final boolean b ) {
+ display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no";
}
- /**
- * Convenience method.
- *
- * @return true if value in configuration file was 'yes'
- */
- boolean isDrawAsPhylogram() {
- return doCheckOption( display_as_phylogram );
+ public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
+ _display_sequence_relations = display_sequence_relations;
}
- boolean isEditable() {
- return _editable;
+ public void setDisplaySequenceSymbols( final boolean b ) {
+ display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no";
}
- boolean isExtractPfamTaxonomyCodesInNhParsing() {
- return _nh_parsing_extract_pfam_taxonomy_codes;
+ public void setDisplayTaxonomyCode( final boolean b ) {
+ display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayTaxonomyRank( final boolean b ) {
+ display_options[ show_tax_rank ][ 2 ] = b ? "yes" : "no";
}
- boolean isHasWebLink( final String source ) {
- return getWebLinks().containsKey( source );
+ public void setDisplayTaxonomyCommonNames( final boolean b ) {
+ display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
}
- /**
- * Only used by ArchaeoptryxE.
- *
- */
- boolean isHideControlPanelAndMenubar() {
- return _hide_controls_and_menus;
+ public void setDisplayTaxonomyImages( final boolean b ) {
+ display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
}
- boolean isInternalNumberAreConfidenceForNhParsing() {
- return _internal_number_are_confidence_for_nh_parsing;
+ public void setDisplayTaxonomyScientificNames( final boolean b ) {
+ display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
}
- boolean isReplaceUnderscoresInNhParsing() {
- return _nh_parsing_replace_underscores;
+ public void setDynamicallyHideData( final boolean b ) {
+ display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
}
- boolean isShowBranchLengthValues() {
- return _show_branch_length_values;
+ public void setExtDescNodeDataToReturn( final NodeDataField ext_desc_data_to_return ) {
+ _ext_desc_data_to_return = ext_desc_data_to_return;
}
- public boolean isShowDefaultNodeShapes() {
- return _show_default_node_shapes;
+ public void setFrameXSize( final int frame_x_size ) {
+ _frame_x_size = frame_x_size;
}
- public boolean isShowDomainLabels() {
- return _show_domain_labels;
+ public void setFrameYSize( final int frame_y_size ) {
+ _frame_y_size = frame_y_size;
}
- boolean isShowOverview() {
- return _show_overview;
+ final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) {
+ _line_up_renderable_node_data = line_up_renderable_node_data;
}
- boolean isShowScale() {
- return _show_scale;
+ public void setMidpointReroot( final boolean midpoint_root ) {
+ _midpoint_root = midpoint_root;
}
- public boolean isTaxonomyColorizeNodeShapes() {
- return _taxonomy_colorize_node_shapes;
+ public void setMinConfidenceValue( final double min_confidence_value ) {
+ _min_confidence_value = min_confidence_value;
}
- final boolean isUseNativeUI() {
- if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) {
- _ui = UI.NATIVE;
- }
- return _ui == UI.NATIVE;
+ public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
+ _node_label_direction = node_label_direction;
}
- /**
- * Only used by ArchaeoptryxE.
- *
- */
- boolean isUseTabbedDisplay() {
- return _use_tabbed_display;
+ 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;
}
- boolean isValidatePhyloXmlAgainstSchema() {
- return _validate_against_phyloxml_xsd_schema;
+ 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;
+ }
+
+ final public void setRightLineUpDomains( final boolean right_align_domains ) {
+ _right_align_domains = right_align_domains;
+ }
+
+ public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
+ _show_default_node_shapes_external = show_default_node_shapes_external;
+ }
+
+ public void setShowDefaultNodeShapesForMarkedNodes( final boolean show_default_node_shapes_for_marked_nodes ) {
+ _show_default_node_shapes_for_marked_nodes = show_default_node_shapes_for_marked_nodes;
+ }
+
+ 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 setUseStyle( final boolean b ) {
+ display_options[ use_style ][ 2 ] = b ? "yes" : "no";
+ }
+
+ private int getClickToIndex( final String name ) {
+ int index = -1;
+ if ( name.equals( "edit_info" ) ) {
+ index = Configuration.display_node_data;
+ ForesterUtil
+ .printWarningMessage( AptxConstants.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( "uncollapse_all" ) ) {
+ index = Configuration.uncollapse_all;
+ }
+ 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( "order_subtree" ) ) {
+ index = Configuration.order_subtree;
+ }
+ 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( AptxConstants.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( AptxConstants.PRG_NAME,
+ "configuration key [display_node_popup] is deprecated" );
+ return DEPRECATED;
+ }
+ else if ( name.equals( "custom_option" ) ) {
+ ForesterUtil.printWarningMessage( AptxConstants.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 final void initSpeciesColors() {
+ _species_colors = new Hashtable<String, Color>();
+ for( final String[] s : DEFAULT_SPECIES_COLORS ) {
+ _species_colors.put( s[ 0 ], Color.decode( s[ 1 ] ) );
+ }
}
private boolean parseBoolean( final String str ) {
return false;
}
else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
return false;
}
}
private double parseDouble( final String str ) {
double d = 0.0;
try {
- d = Double.parseDouble( str );
+ d = Double.parseDouble( str.trim() );
}
catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse double from [" + str + "]" );
d = 0.0;
}
return d;
private float parseFloat( final String str ) {
float f = 0.0f;
try {
- f = Float.parseFloat( str );
+ f = Float.parseFloat( str.trim() );
}
catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse float from [" + str + "]" );
f = 0.0f;
}
return f;
private int parseInt( final String str ) {
int i = -1;
try {
- i = Integer.parseInt( str );
+ i = Integer.parseInt( str.trim() );
}
catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse integer from [" + str + "]" );
i = -1;
}
return i;
private short parseShort( final String str ) {
short i = -1;
try {
- i = Short.parseShort( str );
+ i = Short.parseShort( str.trim() );
}
catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse short from [" + str + "]" );
i = -1;
}
return i;
}
}
- 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
+ * @throws IOException
*/
private void readConfig( final BufferedReader conf_in ) throws IOException {
String line;
} while ( line != null );
}
- public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
- _abbreviate_scientific_names = abbreviate_scientific_names;
- }
-
private void setAntialiasScreen( final boolean antialias_screen ) {
_antialias_screen = antialias_screen;
}
- public void setBackgroundColorGradient( final boolean background_color_gradient ) {
- _background_color_gradient = background_color_gradient;
- }
-
- public void setBaseFontFamilyName( final String base_font_family_name ) {
- _base_font_family_name = base_font_family_name;
- }
-
- public void setBaseFontSize( final int base_font_size ) {
- _base_font_size = base_font_size;
- }
-
private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
_cladogram_type = cladogram_type;
}
- public void setColorizeBranches( final boolean b ) {
- display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
- _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
- }
-
private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
_default_bootstrap_samples = default_bootstrap_samples;
}
- public void setDefaultNodeFill( final NodeFill default_node_fill ) {
- _default_node_fill = default_node_fill;
- }
-
- public void setDefaultNodeShape( final NodeShape default_node_shape ) {
- _default_node_shape = default_node_shape;
- }
-
- public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
- _default_node_shape_size = default_node_shape_size;
- }
-
- public void setDisplayAsPhylogram( final boolean b ) {
- display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplayColors( final SortedMap<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 ) {
- _graphics_export_x = graphics_export_x;
- }
+ //private void setGraphicsExportX( final int graphics_export_x ) {
+ // _graphics_export_x = graphics_export_x;
+ //}
- private void setGraphicsExportY( final int graphics_export_y ) {
- _graphics_export_y = graphics_export_y;
- }
+ //private void setGraphicsExportY( final int graphics_export_y ) {
+ // _graphics_export_y = graphics_export_y;
+ //}
private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
_internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
* Set a key-value(s) tuple
*/
private void setKeyValue( final StringTokenizer st ) {
- String key = ( String ) st.nextElement();
- key = key.replace( ':', ' ' );
- key = key.trim();
- key = key.toLowerCase();
+ final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
+ if ( !st.hasMoreElements() ) {
+ return;
+ }
// Handle single value settings first:
if ( key.equals( "default_click_to" ) ) {
final String clickto_name = ( String ) st.nextElement();
default_clickto = getClickToIndex( clickto_name );
if ( default_clickto == -1 ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
- + "] for [default_click_to]" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "invalid value [" + clickto_name
+ + "] for [default_click_to]" );
default_clickto = 0;
}
else if ( default_clickto == DEPRECATED ) {
_ui = UI.UNKNOWN;
}
else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
- + "]" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
+ + "]" );
_ui = UI.UNKNOWN;
}
}
}
else {
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
- + "] for [phylogeny_graphics_type]" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str
+ + "] for [phylogeny_graphics_type]" );
}
}
else if ( key.equals( "min_confidence_value" ) ) {
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( "graphics_export_x" ) ) {
- final String str = ( ( String ) st.nextElement() ).trim();
- final int i = parseInt( str );
- setGraphicsExportX( 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( "graphics_export_y" ) ) {
- final String str = ( ( String ) st.nextElement() ).trim();
- final int i = parseInt( str );
- setGraphicsExportY( 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( "pdf_export_line_width" ) ) {
final String str = ( ( String ) st.nextElement() ).trim();
setPrintLineWidth( f );
}
else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "value for [pdf_export_line_width] cannot be zero or negative" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME,
+ "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" ) ) {
}
else {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "value for [default_number_of_bootstrap_resamples] cannot be negative" );
+ .printWarningMessage( AptxConstants.PRG_NAME,
+ "value for [default_number_of_bootstrap_resamples] cannot be negative" );
+ }
+ }
+ else if ( key.equals( "mafft_local" ) ) {
+ final String str = ( ( String ) st.nextElement() ).trim();
+ if ( !ForesterUtil.isEmpty( str ) ) {
+ setPathToLocalMafft( new File( str ) );
+ }
+ }
+ else if ( key.equals( "fastme_local" ) ) {
+ final String str = ( ( String ) st.nextElement() ).trim();
+ if ( !ForesterUtil.isEmpty( str ) ) {
+ setPathToLocalFastme( new File( str ) );
+ }
+ }
+ else if ( key.equals( "raxml_local" ) ) {
+ final String str = ( ( String ) st.nextElement() ).trim();
+ if ( !ForesterUtil.isEmpty( str ) ) {
+ setPathToLocalRaxml( new File( str ) );
}
}
else if ( key.equals( "show_scale" ) ) {
else if ( key.equals( "show_overview" ) ) {
setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
}
- else if ( key.equals( "show_branch_length_values" ) ) {
- setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
- }
else if ( key.equals( "background_gradient" ) ) {
setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
}
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() ) );
}
if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
}
- else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
- setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
- }
- else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
- setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
+ else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.LINED_UP.toString() ) ) {
+ setCladogramType( Options.CLADOGRAM_TYPE.LINED_UP );
}
else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
- + "] for [cladogram_type]" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str
+ + "] for [cladogram_type]" );
}
}
- else if ( key.equals( "non_lined_up_cladogram" ) ) {
- ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
- }
else if ( key.equals( "hide_controls_and_menus" ) ) {
_hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
}
_use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
}
else if ( key.equals( "overview_width" ) ) {
- final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
+ final short i = parseShort( ( ( String ) st.nextElement() ) );
setOvMaxWidth( i );
}
else if ( key.equals( "overview_height" ) ) {
- final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
+ final short i = parseShort( ( ( String ) st.nextElement() ) );
setOvMaxHeight( i );
}
else if ( key.equals( "overview_placement_type" ) ) {
}
else {
setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
- + "] for [overview_placement_type]" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str
+ + "] for [overview_placement_type]" );
}
}
else if ( key.equals( "node_label_direction" ) ) {
}
else {
setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
- + "] for [node_label_direction]" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str
+ + "] for [node_label_direction]" );
}
}
else if ( key.equals( "branch_length_value_digits" ) ) {
setNumberOfDigitsAfterCommaForBranchLengthValue( i );
}
else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
- + "] for [branch_length_value_digits]" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "illegal value [" + i
+ + "] for [branch_length_value_digits]" );
}
}
else if ( key.equals( "confidence_value_digits" ) ) {
setNumberOfDigitsAfterCommaForConfidenceValues( i );
}
else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
- + "] for [confidence_value_digits]" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "illegal value [" + i
+ + "] for [confidence_value_digits]" );
}
}
else if ( key.equals( "allow_editing" ) ) {
}
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" );
+ .printWarningMessage( AptxConstants.PRG_NAME,
+ "attempt to extract taxonomies and replace underscores at the same time" );
}
else {
setReplaceUnderscoresInNhParsing( r );
}
}
- else if ( key.equals( "extract_taxonomy_codes_in_nh_parsing" ) ) {
- final boolean e = parseBoolean( ( String ) st.nextElement() );
- if ( e && isReplaceUnderscoresInNhParsing() ) {
- ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "attempt to extract taxonomies and replace underscores at the same time" );
+ 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 {
- setExtractPfamTaxonomyCodesInNhParsing( e );
+ ForesterUtil
+ .printWarningMessage( AptxConstants.PRG_NAME,
+ "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
+ + s
+ + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
+ }
+ if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
+ ForesterUtil
+ .printWarningMessage( AptxConstants.PRG_NAME,
+ "attempt to extract taxonomies and replace underscores at the same time" );
}
}
else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
else if ( key.equals( "gui_button_border_color" ) ) {
_gui_button_border_color = Color.decode( ( String ) st.nextElement() );
}
- else if ( key.equals( "domain_structure_font_color" ) ) {
- _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
+ else if ( key.equals( "show_default_node_shapes_internal" ) ) {
+ setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
}
- else if ( key.equals( "domain_structure_base_color" ) ) {
- _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
+ else if ( key.equals( "show_default_node_shapes_external" ) ) {
+ setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
}
- else if ( key.equals( "show_default_node_shapes" ) ) {
- setShowDefaultNodeShapes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
+ else if ( key.equals( "show_node_shapes_for_nodes_with_vis_data" ) ) {
+ setShowDefaultNodeShapesForMarkedNodes( 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 {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
- + "] for [default_node_fill]" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + fill_str
+ + "] for [default_node_fill]" );
}
}
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 {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
- + "] for [default_node_shape]" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + shape_str
+ + "] for [default_node_shape]" );
+ }
+ }
+ else if ( key.equals( "midpoint_reroot" ) ) {
+ setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) );
+ }
+ else if ( key.equals( "list_node_data_field" ) || key.equals( "ext_descendents_data_to_return" ) ) {
+ final String s = ( ( String ) st.nextElement() ).trim();
+ if ( s.equalsIgnoreCase( "node_name" ) ) {
+ setExtDescNodeDataToReturn( NodeDataField.NODE_NAME );
+ }
+ else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
+ setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_ACC );
+ }
+ else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) {
+ setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );
+ }
+ else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
+ setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_NAME );
+ }
+ else if ( s.equalsIgnoreCase( "gene_name" ) ) {
+ setExtDescNodeDataToReturn( NodeDataField.GENE_NAME );
+ }
+ else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
+ setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_SYMBOL );
+ }
+ else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
+ setExtDescNodeDataToReturn( NodeDataField.TAXONOMY_SCIENTIFIC_NAME );
+ }
+ else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
+ setExtDescNodeDataToReturn( NodeDataField.TAXONOMY_CODE );
+ }
+ else if ( s.equalsIgnoreCase( "user_selected" ) ) {
+ setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
+ }
+ else if ( s.equalsIgnoreCase( "domains" ) ) {
+ setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );
+ }
+ else if ( s.equalsIgnoreCase( "domains_collapsed" ) ) {
+ setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );
+ }
+ else if ( s.equalsIgnoreCase( "seq_annotations" ) ) {
+ setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );
+ }
+ else if ( s.equalsIgnoreCase( "go_term_ids" ) ) {
+ setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );
+ }
+ else {
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + s
+ + "] for [ext_descendents_data_to_return]" );
+ }
+ }
+ else if ( key.equals( "list_node_data_custom_label" ) || key.equals( "label_for_get_ext_descendents_data" ) ) {
+ final String s = ( ( String ) st.nextElement() ).trim();
+ if ( !ForesterUtil.isEmpty( s ) && ( s.length() > 1 ) ) {
+ setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
+ }
+ }
+ else if ( key.equals( "list_node_data_in" ) || key.equals( "ext_descendents_data_to_return_on" ) ) {
+ final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
+ if ( s.equals( "console" ) ) {
+ setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
+ }
+ else if ( s.equals( "window" ) ) {
+ setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
+ }
+ else if ( s.equals( "buffer_only" ) ) {
+ setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
+ }
+ else {
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + s
+ + "] for [ext_descendents_data_to_return_on]" );
}
}
- else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
- setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
+ else if ( key.equals( "vector_data_min_color" ) ) {
+ _vector_data_min_color = Color.decode( ( String ) st.nextElement() );
+ }
+ else if ( key.equals( "vector_data_max_color" ) ) {
+ _vector_data_max_color = Color.decode( ( String ) st.nextElement() );
+ }
+ else if ( key.equals( "vector_data_mean_color" ) ) {
+ _vector_data_mean_color = Color.decode( ( String ) st.nextElement() );
+ }
+ else if ( key.equals( "vector_data_width" ) ) {
+ _vector_data_width = parseShort( ( String ) st.nextElement() );
+ if ( _vector_data_width < 1 ) {
+ _vector_data_width = 120;
+ }
+ }
+ else if ( key.equals( "vector_data_height" ) ) {
+ _vector_data_height = parseShort( ( String ) st.nextElement() );
+ if ( _vector_data_height < 1 ) {
+ _vector_data_height = 12;
+ }
+ }
+ else if ( key.equals( "line_up_renderable_data" ) ) {
+ setLineUpRendarableNodeData( parseBoolean( ( String ) st.nextElement() ) );
+ }
+ else if ( key.equals( "right_align_domain_architectures" ) ) {
+ setRightLineUpDomains( parseBoolean( ( String ) st.nextElement() ) );
+ }
+ else if ( key.equals( "allow_thick_strokes" ) ) {
+ _allow_thick_strokes = parseBoolean( ( String ) st.nextElement() );
}
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( "color_according_to_species" ) ) {
key_index = Configuration.color_according_to_species;
}
+ else if ( key.equals( "color_according_to_sequence" ) ) {
+ key_index = Configuration.color_according_to_sequence;
+ }
else if ( key.equals( "show_node_names" ) ) {
key_index = Configuration.show_node_names;
}
- else if ( key.equals( "show_taxonomy" ) || key.equals( "show_taxonomy_code" ) ) {
+ else if ( key.equals( "show_taxonomy_code" ) ) {
key_index = Configuration.show_tax_code;
- if ( key.equals( "show_taxonomy" ) ) {
- ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "configuration key [show_taxonomy] is deprecated, use [show_taxonomy_code] instead" );
- }
}
- else if ( key.equals( "write_br_length_values" ) ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "configuration key [write_br_length_values] is deprecated" );
- key_index = DEPRECATED;
+ else if ( key.equals( "show_taxonomy_rank" ) ) {
+ key_index = Configuration.show_tax_rank;
}
- 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_branch_length_values" ) ) {
+ key_index = Configuration.write_branch_length_values;
+ }
+ 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( AptxConstants.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_msa" ) ) {
+ key_index = Configuration.show_mol_seqs;
+ }
else if ( key.equals( "show_annotations" ) ) {
key_index = Configuration.show_annotation;
}
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( "display_external_data" ) ) {
+ key_index = Configuration.display_external_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();
// Deprecated.
}
else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown click-to option: "
+ click_to_name );
}
}
else if ( key.equals( "species_color" ) ) {
- getSpeciesColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
+ getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
+ Color.decode( ( String ) st.nextElement() ) );
+ }
+ else if ( key.equals( "sequence_color" ) ) {
+ getSequenceColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
+ Color.decode( ( String ) st.nextElement() ) );
}
else if ( key.equals( "domain_color" ) ) {
getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
}
else if ( key.equals( "annotation_color" ) ) {
getAnnotationColors()
- .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
+ .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
}
else if ( key.equals( "function_color" ) ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "configuration key [function_color] is deprecated" );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME,
+ "configuration key [function_color] is deprecated" );
}
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 );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown configuration key [" + key
+ + "] in: " + config_filename );
}
}
}
else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown configuration key [" + key + "] in: "
+ config_filename );
}
}
- public void setMinConfidenceValue( final double min_confidence_value ) {
- _min_confidence_value = min_confidence_value;
- }
-
- public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
- _node_label_direction = node_label_direction;
+ private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
+ _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
}
- public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short _number_of_digits_after_comma_for_branch_length_values ) {
- this._number_of_digits_after_comma_for_branch_length_values = _number_of_digits_after_comma_for_branch_length_values;
+ private void setMaxBaseFontSize( final int max_base_font_size ) {
+ _max_base_font_size = max_base_font_size;
}
- public void setNumberOfDigitsAfterCommaForConfidenceValues( final short _number_of_digits_after_comma_for_confidence_values ) {
- this._number_of_digits_after_comma_for_confidence_values = _number_of_digits_after_comma_for_confidence_values;
+ private void setMinBaseFontSize( final int min_base_font_size ) {
+ _min_base_font_size = min_base_font_size;
}
private void setOvMaxHeight( final short ov_max_height ) {
_ov_placement = ov_placement;
}
- public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
- _phylogeny_graphics_type = phylogeny_graphics_type;
+ private void setPathToLocalFastme( final File path_to_local_fastme ) {
+ _path_to_local_fastme = path_to_local_fastme;
}
- public void setPrintLineWidth( final float print_line_width ) {
- _print_line_width = print_line_width;
+ private void setPathToLocalMafft( final File path_to_local_mafft ) {
+ _path_to_local_mafft = path_to_local_mafft;
}
- public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
- _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
+ private void setPathToLocalRaxml( final File path_to_local_raxml ) {
+ _path_to_local_raxml = path_to_local_raxml;
}
- public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
- _show_branch_length_values = show_branch_length_values;
+ private void setShowAnnotationRefSource( final boolean b ) {
+ _show_annotation_ref_source = b;
}
- public void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
- _show_default_node_shapes = show_default_node_shapes;
+ private void setShowOverview( final boolean show_overview ) {
+ _show_overview = show_overview;
}
- public void setShowDomainLabels( final boolean show_domain_labels ) {
- _show_domain_labels = show_domain_labels;
+ private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
+ _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
}
- private void setShowOverview( final boolean show_overview ) {
- _show_overview = show_overview;
+ boolean displaySequenceRelations() {
+ return _display_sequence_relations;
}
- public void setShowScale( final boolean show_scale ) {
- _show_scale = show_scale;
+ boolean doCheckOption( final int which ) {
+ return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
+ || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
+ }
+
+ boolean doDisplayClickToOption( final int which ) {
+ return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
}
- public void setTaxonomyColorize( final boolean b ) {
- display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
+ boolean doDisplayOption( final int which ) {
+ return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
}
- public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
- _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
+ /**
+ * Will attempt to use the phylogeny to determine whether to check
+ * this or not (e.g. phylogram)
+ *
+ */
+ boolean doGuessCheckOption( final int which ) {
+ return display_options[ which ][ 2 ].equals( "?" );
}
- public void setUseBranchesWidths( final boolean b ) {
- display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
+ Map<String, Color> getAnnotationColors() {
+ if ( _annotation_colors == null ) {
+ _annotation_colors = new Hashtable<String, Color>();
+ }
+ return _annotation_colors;
}
- private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
- _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
+ int getBaseFontSize() {
+ return _base_font_size;
+ }
+
+ CLADOGRAM_TYPE getCladogramType() {
+ return _cladogram_type;
+ }
+
+ int getClickToOptionsCount() {
+ return clickto_options.length;
+ }
+
+ String getClickToTitle( final int which ) {
+ return clickto_options[ which ][ 0 ];
+ }
+
+ int getDefaultDisplayClicktoOption() {
+ return default_clickto;
+ }
+
+ SortedMap<String, Color> getDisplayColors() {
+ return _display_colors;
+ }
+
+ String getDisplayTitle( final int which ) {
+ return display_options[ which ][ 0 ];
+ }
+
+ Map<String, Color> getDomainColors() {
+ if ( _domain_colors == null ) {
+ _domain_colors = new Hashtable<String, Color>();
+ }
+ return _domain_colors;
+ }
+
+
+ Color getGuiBackgroundColor() {
+ return _gui_background_color;
+ }
+
+ Color getGuiButtonBackgroundColor() {
+ return _gui_button_background_color;
+ }
+
+ Color getGuiButtonBorderColor() {
+ return _gui_button_border_color;
+ }
+
+ Color getGuiButtonTextColor() {
+ return _gui_button_text_color;
+ }
+
+ Color getGuiCheckboxAndButtonActiveColor() {
+ return _gui_checkbox_and_button_active_color;
+ }
+
+ Color getGuiCheckboxTextColor() {
+ return _gui_checkbox_text_color;
+ }
+
+ Color getGuiMenuBackgroundColor() {
+ return _gui_menu_background_color;
+ }
+
+ Color getGuiMenuTextColor() {
+ return _gui_menu_text_color;
+ }
+
+ static int getGuiFontSize() {
+ return 11;
+ }
+
+ int getMaxBaseFontSize() {
+ return _max_base_font_size;
+ }
+
+ int getMinBaseFontSize() {
+ return _min_base_font_size;
+ }
+
+ double getMinConfidenceValue() {
+ return _min_confidence_value;
+ }
+
+ NODE_LABEL_DIRECTION getNodeLabelDirection() {
+ return _node_label_direction;
+ }
+
+ short getNumberOfDigitsAfterCommaForBranchLengthValues() {
+ return _number_of_digits_after_comma_for_branch_length_values;
+ }
+
+ short getNumberOfDigitsAfterCommaForConfidenceValues() {
+ return _number_of_digits_after_comma_for_confidence_values;
+ }
+
+ short getOvMaxHeight() {
+ return _ov_max_height;
+ }
+
+ short getOvMaxWidth() {
+ return _ov_max_width;
+ }
+
+ OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
+ return _ov_placement;
+ }
+
+ PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
+ return _phylogeny_graphics_type;
+ }
+
+ float getPrintLineWidth() {
+ return _print_line_width;
+ }
+
+ Hashtable<String, Color> getSequenceColors() {
+ if ( _sequence_colors == null ) {
+ _sequence_colors = new Hashtable<String, Color>();
+ }
+ return _sequence_colors;
+ }
+
+ Hashtable<String, Color> getSpeciesColors() {
+ if ( _species_colors == null ) {
+ initSpeciesColors();
+ }
+ return _species_colors;
+ }
+
+ public final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+ return _taxonomy_extraction;
+ }
+
+ boolean isAntialiasScreen() {
+ return _antialias_screen;
+ }
+
+ /**
+ * Convenience method.
+ *
+ * @return true if value in configuration file was 'yes'
+ */
+ boolean isDrawAsPhylogram() {
+ return doCheckOption( display_as_phylogram );
+ }
+
+ boolean isEditable() {
+ return _editable;
+ }
+
+ /**
+ * Only used by ArchaeoptryxE.
+ *
+ */
+ boolean isHideControlPanelAndMenubar() {
+ return _hide_controls_and_menus;
+ }
+
+ public boolean isInternalNumberAreConfidenceForNhParsing() {
+ return _internal_number_are_confidence_for_nh_parsing;
+ }
+
+ public boolean isReplaceUnderscoresInNhParsing() {
+ return _nh_parsing_replace_underscores;
+ }
+
+ boolean isShowOverview() {
+ return _show_overview;
+ }
+
+ boolean isShowScale() {
+ return _show_scale;
+ }
+
+ final boolean isUseNativeUI() {
+ if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
+ _ui = UI.NATIVE;
+ }
+ return _ui == UI.NATIVE;
+ }
+
+ /**
+ * Only used by ArchaeoptryxE.
+ *
+ */
+ boolean isUseTabbedDisplay() {
+ return _use_tabbed_display;
+ }
+
+ public boolean isValidatePhyloXmlAgainstSchema() {
+ return _validate_against_phyloxml_xsd_schema;
}
- void setWebLinks( final SortedMap<String, WebLink> weblinks ) {
- _weblinks = weblinks;
+ final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
+ _taxonomy_extraction = taxonomy_extraction;
}
static String getDefaultFontFamilyName() {
return DEFAULT_FONT_FAMILY;
}
- static enum TRIPLET {
- TRUE, FALSE, UNKNOWN
+ public boolean isCouldReadConfigFile() {
+ return _could_read_config_file;
}
- public enum UI {
- NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN
- }
+
}
git://source.jalview.org / jalview.git / blobdiff