2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
7 // Copyright (C) 2000-2001 Washington University School of Medicine
8 // and Howard Hughes Medical Institute
9 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
10 // All rights reserved
12 // This library is free software; you can redistribute it and/or
13 // modify it under the terms of the GNU Lesser General Public
14 // License as published by the Free Software Foundation; either
15 // version 2.1 of the License, or (at your option) any later version.
17 // This library is distributed in the hope that it will be useful,
18 // but WITHOUT ANY WARRANTY; without even the implied warranty of
19 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20 // Lesser General Public License for more details.
22 // You should have received a copy of the GNU Lesser General Public
23 // License along with this library; if not, write to the Free Software
24 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
26 // Contact: phylosoft @ gmail . com
27 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
29 package org.forester.archaeopteryx;
31 import java.awt.Color;
32 import java.io.BufferedReader;
34 import java.io.FileReader;
35 import java.io.IOException;
36 import java.io.InputStreamReader;
38 import java.util.Arrays;
39 import java.util.Hashtable;
41 import java.util.SortedMap;
42 import java.util.StringTokenizer;
43 import java.util.TreeMap;
45 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
46 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
47 import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE;
48 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
49 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
50 import org.forester.phylogeny.data.NodeData.NODE_DATA;
51 import org.forester.phylogeny.data.NodeVisualData;
52 import org.forester.phylogeny.data.NodeVisualData.NodeFill;
53 import org.forester.phylogeny.data.NodeVisualData.NodeShape;
54 import org.forester.util.ForesterUtil;
56 public final class Configuration {
58 final static String clickto_options[][] = {
59 { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
60 { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree(s)", "display" },
61 { "Colorize Node", "display" }, { "Change Node Font", "display" }, { "Open Sequence DB", "display" }, { "Go to PDB", "display" },
62 { "Open Taxonomy DB", "display" }, { "Blast", "display" }, { "Cut Subtree", "display" },
63 { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" },
64 { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Sort Descendants", "display" },
65 { "Return", "display" }, { "Select Node(s)", "display" } };
66 final static int display_node_data = 0;
67 final static int collapse_uncollapse = 1;
68 final static int reroot = 2;
69 final static int subtree = 3;
70 final static int swap = 4;
71 final static int color_subtree = 5;
72 final static int color_node_font = 6;
73 final static int change_node_font = 7;
74 final static int open_seq_web = 8;
75 final static int open_pdb_web = 9;
76 final static int open_tax_web = 10;
77 final static int blast = 11;
78 final static int cut_subtree = 12;
79 final static int copy_subtree = 13;
80 final static int paste_subtree = 14;
81 final static int delete_subtree_or_node = 15;
82 final static int add_new_node = 16;
83 final static int edit_node_data = 17;
84 final static int sort_descendents = 18;
85 final static int get_ext_desc_data = 19;
86 final static int select_nodes = 20;
90 final static String display_options[][] = {
91 { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
92 { "Seq Annotations", "nodisplay", "no" }, { "Confidence Values", "display", "?" },
93 { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
94 { "Use Branch Colors", "display", "no" }, { "Use Branch Widths", "display", "no" },
95 { "Show Custom Nodes", "display", "yes" }, { "Protein Domains", "nodisplay", "no" },
96 { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
97 { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" },
98 { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
99 { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
100 { "Colorize by Annotation", "nodisplay", "no" }, { "Seq Symbol", "display", "yes" },
101 { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
102 { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
103 { "Properties", "nodisplay", "no" }, { "Gene Name", "display", "yes" } };
104 final static int display_as_phylogram = 0;
105 final static int show_node_names = 1;
106 final static int show_tax_code = 2;
107 final static int show_annotation = 3;
108 final static int write_confidence_values = 4;
109 final static int write_events = 5;
110 final static int color_according_to_species = 6;
111 final static int color_branches = 7;
112 final static int width_branches = 8;
113 final static int show_custom_node_shapes = 9;
114 final static int show_domain_architectures = 10;
115 final static int show_binary_characters = 11;
116 final static int show_binary_character_counts = 12;
117 final static int show_seq_names = 13;
118 final static int show_sequence_acc = 14;
119 final static int display_internal_data = 15;
120 final static int dynamically_hide_data = 16;
121 final static int show_taxonomy_scientific_names = 17;
122 final static int show_taxonomy_common_names = 18;
123 final static int color_according_to_annotation = 19;
124 final static int show_seq_symbols = 20;
125 final static int node_data_popup = 21;
126 final static int show_relation_confidence = 22;
127 final static int show_vector_data = 23;
128 final static int show_taxonomy_images = 24;
129 final static int show_properties = 25;
130 final static int show_gene_names = 26;
131 static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
135 private static Hashtable<String, Color> _annotation_colors;
139 private static Hashtable<String, Color> _domain_colors;
143 private static Hashtable<String, Color> _species_colors;
144 private static String DEFAULT_FONT_FAMILY = "";
145 private static final int DEPRECATED = -2;
146 private static final String DISPLAY_COLOR_KEY = "display_color";
147 // ---------------------------
148 // Display options for trees
149 // ---------------------------
150 // ---------------------------------
151 // Pertaining to the config itself
152 // ---------------------------------
153 // Full path to config (may be URL)
154 String config_filename;
155 // This option is selected in the dropdown
156 int default_clickto = Configuration.display_node_data;
157 String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
161 TreeColorSet tree_color_set;
165 TreeFontSet tree_font_set;
166 boolean verbose = Constants.VERBOSE_DEFAULT;
167 private boolean _abbreviate_scientific_names = false;
168 private boolean _antialias_screen = true;
169 private boolean _background_color_gradient = false;
170 private String _base_font_family_name = "";
171 private int _base_font_size = -1;
172 private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
173 private boolean _color_labels_same_as_parent_branch = false;
174 private int _default_bootstrap_samples = -1;
175 private NodeFill _default_node_fill = NodeFill.SOLID;
176 private NodeShape _default_node_shape = NodeShape.RECTANGLE;
177 private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
178 private SortedMap<String, Color> _display_colors = null;
179 private boolean _display_sequence_relations = false;
180 private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
181 private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
182 private boolean _editable = true;
183 private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
184 private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
185 private int _frame_x_size;
186 private int _frame_y_size;
187 private int _graphics_export_x = -1;
188 private int _graphics_export_y = -1;
189 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
190 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
191 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
192 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
193 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
194 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
195 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
196 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
197 private boolean _hide_controls_and_menus = false;
198 private boolean _internal_number_are_confidence_for_nh_parsing = false;
199 private String _label_for_get_ext_descendents_data = "";
200 private int _max_base_font_size = 20;
201 private boolean _midpoint_root = false;
202 private int _min_base_font_size = 2;
203 private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
204 private boolean _nh_parsing_replace_underscores = false;
205 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
206 private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
207 private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
208 private short _ov_max_height = 80;
209 private short _ov_max_width = 80;
210 private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
211 private File _path_to_local_fastme = null;
212 private File _path_to_local_mafft = null;
213 private File _path_to_local_raxml = null;
214 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
215 private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
216 private boolean _show_annotation_ref_source = true;
217 private boolean _show_branch_length_values = false;
218 private boolean _show_default_node_shapes_external = false;
219 private boolean _show_default_node_shapes_internal = false;
220 private boolean _show_domain_labels = true;
221 private boolean _show_overview = true;
222 private boolean _show_scale = false;
223 private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
224 private UI _ui = UI.UNKNOWN;
225 private boolean _use_tabbed_display = false;
226 private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
228 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
229 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
230 DEFAULT_FONT_FAMILY = font_name;
234 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
235 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
239 public Configuration() {
240 this( null, false, false, false );
243 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
244 if ( ForesterUtil.isEmpty( cf ) ) {
245 config_filename = default_config_filename;
248 config_filename = cf;
250 setDisplayColors( new TreeMap<String, Color>() );
251 config_filename = config_filename.trim();
254 // If URL, open accordingly
256 u = new URL( config_filename );
258 final InputStreamReader isr = new InputStreamReader( u.openStream() );
259 final BufferedReader bf = new BufferedReader( isr );
262 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
263 + config_filename + "]" );
265 catch ( final Exception e ) {
266 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
267 + config_filename + "]: " + e.getLocalizedMessage() );
270 catch ( final Exception e ) {
271 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
272 + config_filename + "]" );
276 // Otherwise, open as a file
277 File f = new File( config_filename );
279 f = new File( config_filename + ".txt" );
281 if ( f.exists() && f.canRead() ) {
283 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
287 catch ( final Exception e ) {
289 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
290 + config_filename + "]: " + e );
296 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
297 + config_filename + "]" );
303 public String getBaseFontFamilyName() {
304 return _base_font_family_name;
307 public int getDefaultBootstrapSamples() {
308 return _default_bootstrap_samples;
311 public NodeFill getDefaultNodeFill() {
312 return _default_node_fill;
315 public NodeShape getDefaultNodeShape() {
316 return _default_node_shape;
319 public short getDefaultNodeShapeSize() {
320 return _default_node_shape_size;
323 public Color getDomainStructureBaseColor() {
324 return _domain_structure_base_color;
327 public Color getDomainStructureFontColor() {
328 return _domain_structure_font_color;
331 public NODE_DATA getExtDescNodeDataToReturn() {
332 return _ext_desc_data_to_return;
335 public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
336 return _ext_node_data_return_on;
339 public int getFrameXSize() {
340 return _frame_x_size;
343 public int getFrameYSize() {
344 return _frame_y_size;
347 public String getLabelForGetExtDescendentsData() {
348 return _label_for_get_ext_descendents_data;
351 public File getPathToLocalFastme() {
352 return _path_to_local_fastme;
355 public File getpathToLocalMafft() {
356 return _path_to_local_mafft;
359 public File getPathToLocalRaxml() {
360 return _path_to_local_raxml;
363 public boolean isAbbreviateScientificTaxonNames() {
364 return _abbreviate_scientific_names;
367 public boolean isBackgroundColorGradient() {
368 return _background_color_gradient;
371 public boolean isColorByTaxonomicGroup() {
375 public boolean isColorLabelsSameAsParentBranch() {
376 return _color_labels_same_as_parent_branch;
379 public boolean isMidpointReroot() {
380 return _midpoint_root;
383 public boolean isShowAnnotationRefSource() {
384 return _show_annotation_ref_source;
387 public boolean isShowDefaultNodeShapesExternal() {
388 return _show_default_node_shapes_external;
391 public boolean isShowDefaultNodeShapesInternal() {
392 return _show_default_node_shapes_internal;
395 public boolean isShowDomainLabels() {
396 return _show_domain_labels;
399 public void putDisplayColors( final String key, final Color color ) {
400 getDisplayColors().put( key, color );
403 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
404 _abbreviate_scientific_names = abbreviate_scientific_names;
407 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
408 _background_color_gradient = background_color_gradient;
411 public void setBaseFontFamilyName( final String base_font_family_name ) {
412 _base_font_family_name = base_font_family_name;
415 public void setBaseFontSize( final int base_font_size ) {
416 _base_font_size = base_font_size;
419 public void setColorizeBranches( final boolean b ) {
420 display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
423 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
424 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
427 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
428 _default_node_fill = default_node_fill;
431 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
432 _default_node_shape = default_node_shape;
435 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
436 _default_node_shape_size = default_node_shape_size;
439 public void setDisplayAsPhylogram( final boolean b ) {
440 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
443 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
444 _display_colors = display_colors;
447 public void setDisplayConfidenceValues( final boolean b ) {
448 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
451 public void setDisplayInternalData( final boolean b ) {
452 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
455 public void setDisplayNodeNames( final boolean b ) {
456 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
459 public void setDisplaySequenceAcc( final boolean b ) {
460 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
463 public void setDisplaySequenceNames( final boolean b ) {
464 display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no";
467 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
468 _display_sequence_relations = display_sequence_relations;
471 public void setDisplaySequenceSymbols( final boolean b ) {
472 display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no";
475 public void setDisplayTaxonomyCode( final boolean b ) {
476 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
479 public void setDisplayTaxonomyCommonNames( final boolean b ) {
480 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
483 public void setDisplayTaxonomyImages( final boolean b ) {
484 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
487 public void setDisplayTaxonomyScientificNames( final boolean b ) {
488 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
491 public void setDynamicallyHideData( final boolean b ) {
492 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
495 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
496 _ext_desc_data_to_return = ext_desc_data_to_return;
499 public void setFrameXSize( final int frame_x_size ) {
500 _frame_x_size = frame_x_size;
503 public void setFrameYSize( final int frame_y_size ) {
504 _frame_y_size = frame_y_size;
507 public void setMidpointReroot( final boolean midpoint_root ) {
508 _midpoint_root = midpoint_root;
511 public void setMinConfidenceValue( final double min_confidence_value ) {
512 _min_confidence_value = min_confidence_value;
515 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
516 _node_label_direction = node_label_direction;
519 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
520 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
523 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
524 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
527 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
528 _phylogeny_graphics_type = phylogeny_graphics_type;
531 public void setPrintLineWidth( final float print_line_width ) {
532 _print_line_width = print_line_width;
535 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
536 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
539 public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
540 _show_branch_length_values = show_branch_length_values;
543 public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
544 _show_default_node_shapes_external = show_default_node_shapes_external;
547 public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
548 _show_default_node_shapes_internal = show_default_node_shapes_internal;
551 public void setShowDomainLabels( final boolean show_domain_labels ) {
552 _show_domain_labels = show_domain_labels;
555 public void setShowScale( final boolean show_scale ) {
556 _show_scale = show_scale;
559 public void setTaxonomyColorize( final boolean b ) {
560 display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
563 public void setUseBranchesWidths( final boolean b ) {
564 display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
567 boolean displaySequenceRelations() {
568 return _display_sequence_relations;
571 boolean doCheckOption( final int which ) {
572 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
573 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
576 boolean doDisplayClickToOption( final int which ) {
577 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
580 boolean doDisplayOption( final int which ) {
581 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
585 * Will attempt to use the phylogeny to determine whether to check
586 * this or not (e.g. phylogram)
589 boolean doGuessCheckOption( final int which ) {
590 return display_options[ which ][ 2 ].equals( "?" );
593 Map<String, Color> getAnnotationColors() {
594 if ( _annotation_colors == null ) {
595 _annotation_colors = new Hashtable<String, Color>();
597 return _annotation_colors;
600 int getBaseFontSize() {
601 return _base_font_size;
604 CLADOGRAM_TYPE getCladogramType() {
605 return _cladogram_type;
608 int getClickToOptionsCount() {
609 return clickto_options.length;
612 String getClickToTitle( final int which ) {
613 return clickto_options[ which ][ 0 ];
616 int getDefaultDisplayClicktoOption() {
617 return default_clickto;
620 SortedMap<String, Color> getDisplayColors() {
621 return _display_colors;
624 String getDisplayTitle( final int which ) {
625 return display_options[ which ][ 0 ];
628 Map<String, Color> getDomainColors() {
629 if ( _domain_colors == null ) {
630 _domain_colors = new Hashtable<String, Color>();
632 return _domain_colors;
635 int getGraphicsExportX() {
636 return _graphics_export_x;
639 int getGraphicsExportY() {
640 return _graphics_export_y;
643 Color getGuiBackgroundColor() {
644 return _gui_background_color;
647 Color getGuiButtonBackgroundColor() {
648 return _gui_button_background_color;
651 Color getGuiButtonBorderColor() {
652 return _gui_button_border_color;
655 Color getGuiButtonTextColor() {
656 return _gui_button_text_color;
659 Color getGuiCheckboxAndButtonActiveColor() {
660 return _gui_checkbox_and_button_active_color;
663 Color getGuiCheckboxTextColor() {
664 return _gui_checkbox_text_color;
667 Color getGuiMenuBackgroundColor() {
668 return _gui_menu_background_color;
671 Color getGuiMenuTextColor() {
672 return _gui_menu_text_color;
675 int getMaxBaseFontSize() {
676 return _max_base_font_size;
679 int getMinBaseFontSize() {
680 return _min_base_font_size;
683 double getMinConfidenceValue() {
684 return _min_confidence_value;
687 NODE_LABEL_DIRECTION getNodeLabelDirection() {
688 return _node_label_direction;
691 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
692 return _number_of_digits_after_comma_for_branch_length_values;
695 short getNumberOfDigitsAfterCommaForConfidenceValues() {
696 return _number_of_digits_after_comma_for_confidence_values;
699 short getOvMaxHeight() {
700 return _ov_max_height;
703 short getOvMaxWidth() {
704 return _ov_max_width;
707 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
708 return _ov_placement;
711 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
712 return _phylogeny_graphics_type;
715 float getPrintLineWidth() {
716 return _print_line_width;
719 Hashtable<String, Color> getSpeciesColors() {
720 if ( _species_colors == null ) {
721 _species_colors = new Hashtable<String, Color>();
723 return _species_colors;
726 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
727 return _taxonomy_extraction;
730 boolean isAntialiasScreen() {
731 if ( ForesterUtil.isMac() ) {
732 //Apple Macintosh graphics are slow, turn off anti-alias.
735 return _antialias_screen;
739 * Convenience method.
741 * @return true if value in configuration file was 'yes'
743 boolean isDrawAsPhylogram() {
744 return doCheckOption( display_as_phylogram );
747 boolean isEditable() {
752 * Only used by ArchaeoptryxE.
755 boolean isHideControlPanelAndMenubar() {
756 return _hide_controls_and_menus;
759 boolean isInternalNumberAreConfidenceForNhParsing() {
760 return _internal_number_are_confidence_for_nh_parsing;
763 boolean isReplaceUnderscoresInNhParsing() {
764 return _nh_parsing_replace_underscores;
767 boolean isShowBranchLengthValues() {
768 return _show_branch_length_values;
771 boolean isShowOverview() {
772 return _show_overview;
775 boolean isShowScale() {
779 final boolean isUseNativeUI() {
780 if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
783 return _ui == UI.NATIVE;
787 * Only used by ArchaeoptryxE.
790 boolean isUseTabbedDisplay() {
791 return _use_tabbed_display;
794 boolean isValidatePhyloXmlAgainstSchema() {
795 return _validate_against_phyloxml_xsd_schema;
798 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
799 _taxonomy_extraction = taxonomy_extraction;
802 private int getClickToIndex( final String name ) {
804 if ( name.equals( "edit_info" ) ) {
805 index = Configuration.display_node_data;
807 .printWarningMessage( Constants.PRG_NAME,
808 "configuration key [edit_info] is deprecated, use [display node data] instead" );
810 else if ( name.equals( "display_node_data" ) ) {
811 index = Configuration.display_node_data;
813 else if ( name.equals( "collapse_uncollapse" ) ) {
814 index = Configuration.collapse_uncollapse;
816 else if ( name.equals( "reroot" ) ) {
817 index = Configuration.reroot;
819 else if ( name.equals( "subtree" ) ) {
820 index = Configuration.subtree;
822 else if ( name.equals( "swap" ) ) {
823 index = Configuration.swap;
825 else if ( name.equals( "sort_descendants" ) ) {
826 index = Configuration.sort_descendents;
828 else if ( name.equals( "get_ext_descendents_data" ) ) {
829 index = Configuration.get_ext_desc_data;
831 else if ( name.equals( "display_sequences" ) ) {
833 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
836 else if ( name.equals( "open_seq_web" ) ) {
837 index = Configuration.open_seq_web;
839 else if ( name.equals( "open_pdb_web" ) ) {
840 index = Configuration.open_pdb_web;
842 else if ( name.equals( "open_tax_web" ) ) {
843 index = Configuration.open_tax_web;
845 else if ( name.equals( "blast" ) ) {
846 index = Configuration.blast;
848 else if ( name.equals( "cut_subtree" ) ) {
849 index = Configuration.cut_subtree;
851 else if ( name.equals( "copy_subtree" ) ) {
852 index = Configuration.copy_subtree;
854 else if ( name.equals( "paste_subtree" ) ) {
855 index = Configuration.paste_subtree;
857 else if ( name.equals( "delete" ) ) {
858 index = Configuration.delete_subtree_or_node;
860 else if ( name.equals( "add_new_node" ) ) {
861 index = Configuration.add_new_node;
863 else if ( name.equals( "edit_node_data" ) ) {
864 index = Configuration.edit_node_data;
866 else if ( name.equals( "select_nodes" ) ) {
867 index = Configuration.select_nodes;
869 else if ( name.equals( "display_node_popup" ) ) {
870 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
871 "configuration key [display_node_popup] is deprecated" );
874 else if ( name.equals( "custom_option" ) ) {
875 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
878 else if ( name.equals( "color_subtree" ) ) {
879 index = Configuration.color_subtree;
882 else if ( name.equals( "change_node_font" ) ) {
883 index = Configuration.change_node_font;
886 else if ( name.equals( "color_node_font" ) ) {
887 index = Configuration.color_node_font;
890 else if ( name.equals( "color_subtree" ) ) {
891 index = Configuration.color_subtree;
898 private boolean parseBoolean( final String str ) {
899 final String my_str = str.trim().toLowerCase();
900 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
903 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
907 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
912 private double parseDouble( final String str ) {
915 d = Double.parseDouble( str.trim() );
917 catch ( final Exception e ) {
918 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
924 private float parseFloat( final String str ) {
927 f = Float.parseFloat( str.trim() );
929 catch ( final Exception e ) {
930 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
936 private int parseInt( final String str ) {
939 i = Integer.parseInt( str.trim() );
941 catch ( final Exception e ) {
942 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
948 private short parseShort( final String str ) {
951 i = Short.parseShort( str.trim() );
953 catch ( final Exception e ) {
954 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
960 private void processFontFamily( final StringTokenizer st ) {
961 setBaseFontFamilyName( "" );
962 final String font_str = ( ( String ) st.nextElement() ).trim();
963 final String[] fonts = font_str.split( ",+" );
964 for( String font : fonts ) {
965 font = font.replace( '_', ' ' ).trim();
966 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
967 setBaseFontFamilyName( font );
974 * read each line of config file, process non-comment lines
975 * @throws IOException
977 private void readConfig( final BufferedReader conf_in ) throws IOException {
980 line = conf_in.readLine();
981 if ( line != null ) {
983 // skip comments and blank lines
984 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
985 // convert runs of spaces to tabs
986 line = line.replaceAll( "\\s+", "\t" );
987 final StringTokenizer st = new StringTokenizer( line, "\t" );
991 } while ( line != null );
994 private void setAntialiasScreen( final boolean antialias_screen ) {
995 _antialias_screen = antialias_screen;
998 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
999 _cladogram_type = cladogram_type;
1002 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
1003 _default_bootstrap_samples = default_bootstrap_samples;
1006 private void setEditable( final boolean editable ) {
1007 _editable = editable;
1010 private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
1011 _ext_node_data_return_on = ext_node_data_return_on;
1014 private void setGraphicsExportX( final int graphics_export_x ) {
1015 _graphics_export_x = graphics_export_x;
1018 private void setGraphicsExportY( final int graphics_export_y ) {
1019 _graphics_export_y = graphics_export_y;
1022 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
1023 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
1027 * Set a key-value(s) tuple
1029 private void setKeyValue( final StringTokenizer st ) {
1030 final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
1031 if ( !st.hasMoreElements() ) {
1034 // Handle single value settings first:
1035 if ( key.equals( "default_click_to" ) ) {
1036 final String clickto_name = ( String ) st.nextElement();
1037 default_clickto = getClickToIndex( clickto_name );
1038 if ( default_clickto == -1 ) {
1039 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
1040 + "] for [default_click_to]" );
1041 default_clickto = 0;
1043 else if ( default_clickto == DEPRECATED ) {
1047 else if ( key.equals( "native_ui" ) ) {
1048 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
1049 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
1052 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
1053 _ui = UI.CROSSPLATFORM;
1055 else if ( my_str.equals( "?" ) ) {
1059 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
1064 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
1065 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
1067 else if ( key.equals( "antialias_screen" ) ) {
1068 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
1070 else if ( key.equals( "phylogeny_graphics_type" ) ) {
1071 final String type_str = ( ( String ) st.nextElement() ).trim();
1072 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
1073 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1075 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
1076 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1078 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
1079 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1081 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
1082 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1084 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
1085 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1087 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
1088 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1090 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
1091 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1093 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
1094 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1097 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1098 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1099 + "] for [phylogeny_graphics_type]" );
1102 else if ( key.equals( "min_confidence_value" ) ) {
1103 final String mcv_str = ( ( String ) st.nextElement() ).trim();
1104 final double d = parseDouble( mcv_str );
1105 setMinConfidenceValue( d );
1107 else if ( key.equals( "font_family" ) ) {
1108 processFontFamily( st );
1110 else if ( key.equals( "font_size" ) ) {
1111 final String size_str = ( ( String ) st.nextElement() ).trim();
1112 final int i = parseInt( size_str );
1114 setBaseFontSize( i );
1117 else if ( key.equals( "font_size_min" ) ) {
1118 final String size_str = ( ( String ) st.nextElement() ).trim();
1119 final int i = parseInt( size_str );
1121 setMinBaseFontSize( i );
1124 else if ( key.equals( "font_size_max" ) ) {
1125 final String size_str = ( ( String ) st.nextElement() ).trim();
1126 final int i = parseInt( size_str );
1128 setMaxBaseFontSize( i );
1131 else if ( key.equals( "graphics_export_x" ) ) {
1132 final String str = ( ( String ) st.nextElement() ).trim();
1133 final int i = parseInt( str );
1135 setGraphicsExportX( i );
1138 else if ( key.equals( "graphics_export_y" ) ) {
1139 final String str = ( ( String ) st.nextElement() ).trim();
1140 final int i = parseInt( str );
1142 setGraphicsExportY( i );
1145 else if ( key.equals( "pdf_export_line_width" ) ) {
1146 final String str = ( ( String ) st.nextElement() ).trim();
1147 final float f = parseFloat( str );
1149 setPrintLineWidth( f );
1152 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1153 "value for [pdf_export_line_width] cannot be zero or negative" );
1156 else if ( key.equals( "window_initial_size_x" ) ) {
1157 final String str = ( ( String ) st.nextElement() ).trim();
1158 final int i = parseInt( str );
1163 else if ( key.equals( "window_initial_size_y" ) ) {
1164 final String str = ( ( String ) st.nextElement() ).trim();
1165 final int i = parseInt( str );
1170 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1171 final String str = ( ( String ) st.nextElement() ).trim();
1172 final int i = parseInt( str );
1174 setDefaultBootstrapSamples( i );
1178 .printWarningMessage( Constants.PRG_NAME,
1179 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1182 else if ( key.equals( "mafft_local" ) ) {
1183 final String str = ( ( String ) st.nextElement() ).trim();
1184 if ( !ForesterUtil.isEmpty( str ) ) {
1185 setPathToLocalMafft( new File( str ) );
1188 else if ( key.equals( "fastme_local" ) ) {
1189 final String str = ( ( String ) st.nextElement() ).trim();
1190 if ( !ForesterUtil.isEmpty( str ) ) {
1191 setPathToLocalFastme( new File( str ) );
1194 else if ( key.equals( "raxml_local" ) ) {
1195 final String str = ( ( String ) st.nextElement() ).trim();
1196 if ( !ForesterUtil.isEmpty( str ) ) {
1197 setPathToLocalRaxml( new File( str ) );
1200 else if ( key.equals( "show_scale" ) ) {
1201 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1203 else if ( key.equals( "show_overview" ) ) {
1204 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1206 else if ( key.equals( "show_branch_length_values" ) ) {
1207 setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
1209 else if ( key.equals( "background_gradient" ) ) {
1210 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1212 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1213 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1215 else if ( key.equals( "show_domain_labels" ) ) {
1216 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1218 else if ( key.equals( "show_seq_annotation_ref_sources" ) ) {
1219 setShowAnnotationRefSource( parseBoolean( ( String ) st.nextElement() ) );
1221 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1222 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1224 else if ( key.equals( "cladogram_type" ) ) {
1225 final String type_str = ( ( String ) st.nextElement() ).trim();
1226 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1227 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1229 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1230 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1232 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1233 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1236 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1237 + "] for [cladogram_type]" );
1240 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1242 .printWarningMessage( Constants.PRG_NAME,
1243 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1245 else if ( key.equals( "hide_controls_and_menus" ) ) {
1246 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1248 else if ( key.equals( "use_tabbed_display" ) ) {
1249 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1251 else if ( key.equals( "overview_width" ) ) {
1252 final short i = parseShort( ( ( String ) st.nextElement() ) );
1255 else if ( key.equals( "overview_height" ) ) {
1256 final short i = parseShort( ( ( String ) st.nextElement() ) );
1257 setOvMaxHeight( i );
1259 else if ( key.equals( "overview_placement_type" ) ) {
1260 final String type_str = ( ( String ) st.nextElement() ).trim();
1261 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1262 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1264 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1265 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1267 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1268 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1270 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1271 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1274 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1275 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1276 + "] for [overview_placement_type]" );
1279 else if ( key.equals( "node_label_direction" ) ) {
1280 final String type_str = ( ( String ) st.nextElement() ).trim();
1281 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1282 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1284 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1285 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1288 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1289 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1290 + "] for [node_label_direction]" );
1293 else if ( key.equals( "branch_length_value_digits" ) ) {
1294 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1296 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1299 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1300 + "] for [branch_length_value_digits]" );
1303 else if ( key.equals( "confidence_value_digits" ) ) {
1304 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1306 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1309 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1310 + "] for [confidence_value_digits]" );
1313 else if ( key.equals( "allow_editing" ) ) {
1314 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1316 else if ( key.equals( "display_sequence_relations" ) ) {
1317 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1319 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1320 final boolean r = parseBoolean( ( String ) st.nextElement() );
1321 if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
1323 .printWarningMessage( Constants.PRG_NAME,
1324 "attempt to extract taxonomies and replace underscores at the same time" );
1327 setReplaceUnderscoresInNhParsing( r );
1330 else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
1331 final String s = ( String ) st.nextElement();
1332 if ( s.equalsIgnoreCase( "no" ) ) {
1333 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1335 else if ( s.equalsIgnoreCase( "pfam_relaxed" ) ) {
1336 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1338 else if ( s.equalsIgnoreCase( "pfam_strict" ) ) {
1339 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1341 else if ( s.equalsIgnoreCase( "aggressive" ) ) {
1342 setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
1346 .printWarningMessage( Constants.PRG_NAME,
1347 "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
1349 + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
1351 if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
1353 .printWarningMessage( Constants.PRG_NAME,
1354 "attempt to extract taxonomies and replace underscores at the same time" );
1357 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1358 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1360 else if ( key.equals( "gui_background_color" ) ) {
1361 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1363 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1364 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1366 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1367 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1369 else if ( key.equals( "gui_button_text_color" ) ) {
1370 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1372 else if ( key.equals( "gui_button_background_color" ) ) {
1373 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1375 else if ( key.equals( "gui_menu_background_color" ) ) {
1376 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1378 else if ( key.equals( "gui_menu_text_color" ) ) {
1379 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1381 else if ( key.equals( "gui_button_border_color" ) ) {
1382 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1384 else if ( key.equals( "domain_structure_font_color" ) ) {
1385 _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
1387 else if ( key.equals( "domain_structure_base_color" ) ) {
1388 _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
1390 else if ( key.equals( "show_default_node_shapes" ) ) {
1392 .printWarningMessage( Constants.PRG_NAME,
1393 "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" );
1394 final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() );
1395 setShowDefaultNodeShapesInternal( b );
1396 setShowDefaultNodeShapesExternal( b );
1398 else if ( key.equals( "show_default_node_shapes_internal" ) ) {
1399 setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1401 else if ( key.equals( "show_default_node_shapes_external" ) ) {
1402 setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1404 else if ( key.equals( "default_node_size" ) ) {
1405 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1406 setDefaultNodeShapeSize( i );
1408 else if ( key.equals( "default_node_fill" ) ) {
1409 final String fill_str = ( ( String ) st.nextElement() ).trim();
1410 if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.NONE.toString() ) ) {
1411 setDefaultNodeFill( NodeFill.NONE );
1413 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.GRADIENT.toString() ) ) {
1414 setDefaultNodeFill( NodeFill.GRADIENT );
1416 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.SOLID.toString() ) ) {
1417 setDefaultNodeFill( NodeFill.SOLID );
1420 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1421 + "] for [default_node_fill]" );
1424 else if ( key.equals( "default_node_shape" ) ) {
1425 final String shape_str = ( ( String ) st.nextElement() ).trim();
1426 if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.CIRCLE.toString() ) ) {
1427 setDefaultNodeShape( NodeShape.CIRCLE );
1429 else if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.RECTANGLE.toString() ) ) {
1430 setDefaultNodeShape( NodeShape.RECTANGLE );
1433 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1434 + "] for [default_node_shape]" );
1437 else if ( key.equals( "midpoint_reroot" ) ) {
1438 setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) );
1440 else if ( key.equals( "ext_descendents_data_to_return" ) ) {
1441 final String s = ( ( String ) st.nextElement() ).trim();
1442 if ( s.equalsIgnoreCase( "node_name" ) ) {
1443 setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
1445 else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
1446 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
1448 else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) {
1449 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ_FASTA );
1451 else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
1452 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
1454 else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
1455 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
1457 else if ( s.equalsIgnoreCase( "gene_name" ) ) {
1458 setExtDescNodeDataToReturn( NODE_DATA.GENE_NAME );
1460 else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
1461 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
1463 else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
1464 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME );
1466 else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
1467 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
1469 else if ( s.equalsIgnoreCase( "taxonomy_common_name" ) ) {
1470 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_COMM0N_NAME );
1472 else if ( s.equalsIgnoreCase( "user_selected" ) ) {
1473 setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
1476 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1477 + "] for [ext_descendents_data_to_return]" );
1480 else if ( key.equals( "label_for_get_ext_descendents_data" ) ) {
1481 final String s = ( ( String ) st.nextElement() ).trim();
1482 if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) {
1483 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s
1484 + "] for [label_for_get_ext_descendents_data]" );
1487 setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
1490 else if ( key.equals( "ext_descendents_data_to_return_on" ) ) {
1491 final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
1492 if ( s.equals( "console" ) ) {
1493 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
1495 else if ( s.equals( "window" ) ) {
1496 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
1498 else if ( s.equals( "buffer_only" ) ) {
1499 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
1502 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1503 + "] for [ext_descendents_data_to_return_on]" );
1506 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1509 if ( key.equals( "phylogram" ) ) {
1510 key_index = Configuration.display_as_phylogram;
1512 else if ( key.equals( "rollover" ) ) {
1513 key_index = Configuration.node_data_popup;
1515 else if ( key.equals( "color_according_to_species" ) ) {
1516 key_index = Configuration.color_according_to_species;
1518 else if ( key.equals( "show_node_names" ) ) {
1519 key_index = Configuration.show_node_names;
1521 else if ( key.equals( "show_taxonomy_code" ) ) {
1522 key_index = Configuration.show_tax_code;
1524 else if ( key.equals( "write_confidence_values" ) ) {
1525 key_index = Configuration.write_confidence_values;
1527 else if ( key.equals( "write_events" ) ) {
1528 key_index = Configuration.write_events;
1530 else if ( key.equals( "color_branches" ) ) {
1531 key_index = Configuration.color_branches;
1533 else if ( key.equals( "width_branches" ) ) {
1534 key_index = Configuration.width_branches;
1536 else if ( key.equals( "show_domain_architectures" ) ) {
1537 key_index = Configuration.show_domain_architectures;
1539 else if ( key.equals( "show_annotations" ) ) {
1540 key_index = Configuration.show_annotation;
1542 else if ( key.equals( "show_binary_characters" ) ) {
1543 key_index = Configuration.show_binary_characters;
1545 else if ( key.equals( "show_binary_character_counts" ) ) {
1546 key_index = Configuration.show_binary_character_counts;
1548 else if ( key.equals( "show_seq_names" ) ) {
1549 key_index = Configuration.show_seq_names;
1551 else if ( key.equals( "show_gene_names" ) ) {
1552 key_index = Configuration.show_gene_names;
1554 else if ( key.equals( "show_seq_symbols" ) ) {
1555 key_index = Configuration.show_seq_symbols;
1557 else if ( key.equals( "show_seq_acc" ) ) {
1558 key_index = Configuration.show_sequence_acc;
1560 else if ( key.equals( "display_internal_data" ) ) {
1561 key_index = Configuration.display_internal_data;
1563 else if ( key.equals( "dynamically_hide_data" ) ) {
1564 key_index = Configuration.dynamically_hide_data;
1566 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1567 key_index = Configuration.show_taxonomy_scientific_names;
1569 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1570 key_index = Configuration.show_taxonomy_common_names;
1572 else if ( key.equals( "show_taxonomy_images" ) ) {
1573 key_index = Configuration.show_taxonomy_images;
1575 else if ( key.equals( "color_according_to_annotation" ) ) {
1576 key_index = Configuration.color_according_to_annotation;
1578 else if ( key.equals( "show_vector_data" ) ) {
1579 key_index = Configuration.show_vector_data;
1581 else if ( key.equals( "show_properties" ) ) {
1582 key_index = Configuration.show_properties;
1584 else if ( key.equals( "show_relation_confidence" ) ) {
1585 key_index = Configuration.show_relation_confidence;
1587 else if ( key.equals( "show_custom_node_shapes" ) ) {
1588 key_index = Configuration.show_custom_node_shapes;
1590 // If we've found the key, set the values
1591 if ( key_index >= 0 ) {
1592 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1593 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1594 // otherwise, keep looking
1597 if ( key_index == DEPRECATED ) {
1600 else if ( key.equals( "click_to" ) ) {
1601 final String click_to_name = ( String ) st.nextElement();
1602 key_index = getClickToIndex( click_to_name );
1603 if ( key_index >= 0 ) {
1604 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1606 else if ( key_index == DEPRECATED ) {
1610 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1614 else if ( key.equals( "species_color" ) ) {
1615 getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
1616 Color.decode( ( String ) st.nextElement() ) );
1618 else if ( key.equals( "domain_color" ) ) {
1619 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1621 else if ( key.equals( "annotation_color" ) ) {
1622 getAnnotationColors()
1623 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1625 else if ( key.equals( "function_color" ) ) {
1626 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1627 "configuration key [function_color] is deprecated" );
1629 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1630 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1633 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1634 + "] in: " + config_filename );
1639 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1640 + config_filename );
1644 private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
1645 _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
1648 private void setMaxBaseFontSize( final int max_base_font_size ) {
1649 _max_base_font_size = max_base_font_size;
1652 private void setMinBaseFontSize( final int min_base_font_size ) {
1653 _min_base_font_size = min_base_font_size;
1656 private void setOvMaxHeight( final short ov_max_height ) {
1657 _ov_max_height = ov_max_height;
1660 private void setOvMaxWidth( final short ov_max_width ) {
1661 _ov_max_width = ov_max_width;
1664 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1665 _ov_placement = ov_placement;
1668 private void setPathToLocalFastme( final File path_to_local_fastme ) {
1669 _path_to_local_fastme = path_to_local_fastme;
1672 private void setPathToLocalMafft( final File path_to_local_mafft ) {
1673 _path_to_local_mafft = path_to_local_mafft;
1676 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
1677 _path_to_local_raxml = path_to_local_raxml;
1680 private void setShowAnnotationRefSource( final boolean b ) {
1681 _show_annotation_ref_source = b;
1684 private void setShowOverview( final boolean show_overview ) {
1685 _show_overview = show_overview;
1688 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1689 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1692 static String getDefaultFontFamilyName() {
1693 return DEFAULT_FONT_FAMILY;
1696 public enum EXT_NODE_DATA_RETURN_ON {
1697 BUFFER_ONLY, CONSOLE, WINODW;
1701 CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN
1704 static enum TRIPLET {
1705 FALSE, TRUE, UNKNOWN