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.NodeDataField;
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 public enum EXT_NODE_DATA_RETURN_ON {
59 BUFFER_ONLY, CONSOLE, WINODW;
67 CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN
69 final static String clickto_options[][] = {
70 { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
71 { "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "display" },
72 { "Colorize Node(s)", "display" }, { "Change Node Font(s)", "display" },
73 { "Colorize Subtree(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "display" },
74 { "Open Taxonomy DB", "display" }, { "Launch BLAST", "display" }, { "Cut Subtree", "display" },
75 { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" },
76 { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Sort Descendants", "display" },
77 { "List Node Data", "display" }, { "Select Node(s)", "display" } };
78 private final static String DEFAULT_SPECIES_COLORS[][] = {
79 { "BRAFL", "0x00FFFF" }, { "SPHGR", "0x9620F0" }, { "STRPU", "0x9620F0" }, { "CIOIN", "0xFF1CAE" },
80 { "CIOSA", "0xFF2CAE" }, { "BOVIN", "0x5C3317" }, { "CANFA", "0x8B2323" }, { "HUMAN", "0xFF2400" },
81 { "PANTR", "0xCC2400" }, { "MOUSE", "0xFF7F00" }, { "RAT", "0xFFEF00" }, { "MONDO", "0xEE9A49" },
82 { "ORNAN", "0xCD853F" }, { "XENLA", "0x6BAA23" }, { "XENTR", "0x6BAA23" }, { "CHICK", "0xFFC125" },
83 { "FUGRU", "0x0000FF" }, { "BRARE", "0x0000DD" }, { "DANRE", "0x0000BB" }, { "TETNG", "0x0000AA" },
84 { "ORYLA", "0x000088" }, { "GASAC", "0x000066" }, { "CAEEL", "0x666699" }, { "CAEBR", "0xB0B0B0" },
85 { "DROME", "0x663366" }, { "DROPS", "0x996699" }, { "APIME", "0x7A7700" }, { "AEDAE", "0x8C5900" },
86 { "TRICA", "0x918E00" }, { "NEMVE", "0x0066CC" }, { "HYDVU", "0x3399FF" }, { "LUBBA", "0xF7B5CB" },
87 { "GEOCY", "0xF5A0BD" }, { "AMPQE", "0x009966" }, { "SUBDO", "0xC790B9" }, { "MONBE", "0xFC0FC0" },
88 { "DICPU", "0xFFCC33" }, { "DICDI", "0xFFCC00" }, { "ENTHI", "0x5959AB" }, { "ARATH", "0x00FF00" },
89 { "POPTR", "0x006400" }, { "VITVI", "0x00CD00" }, { "GLYMA", "0x00FF7F" }, { "ORYSA", "0x008B00" },
90 { "ORYSJ", "0x008C00" }, { "SORBI", "0x00EE76" }, { "SELMO", "0x238E23" }, { "PHYPA", "0x09F911" },
91 { "OSTLU", "0x7FFF00" }, { "OSTTA", "0x7FFF00" }, { "OSTRC", "0x7FFF00" }, { "MICPU", "0x66CD00" },
92 { "MIC99", "0x66CD00" }, { "CHLRE", "0xB3EE3A" }, { "VOLCA", "0xC0FF3E" }, { "CHLSP", "0x6B8E23" },
93 { "CYAME", "0xD02090" }, { "YEAST", "0xAAAAAA" }, { "BACFR", "0xFF0000" }, { "BACTN", "0xFFFF00" },
94 { "MYXXD", "0x0000FF" }, { "STIAU", "0x00FFFF" }, { "BACOV", "0x8C5900" }, { "BACUN", "0x66CD00" },
95 { "PORGI", "0x918E00" } };
96 final static int display_node_data = 0;
97 final static int collapse_uncollapse = 1;
98 final static int reroot = 2;
99 final static int subtree = 3;
100 final static int swap = 4;
101 final static int color_node_font = 5;
102 final static int change_node_font = 6;
103 final static int color_subtree = 7;
104 final static int open_seq_web = 8;
105 final static int open_pdb_web = 9;
106 final static int open_tax_web = 10;
107 final static int blast = 11;
108 final static int cut_subtree = 12;
109 final static int copy_subtree = 13;
110 final static int paste_subtree = 14;
111 final static int delete_subtree_or_node = 15;
112 final static int add_new_node = 16;
113 final static int edit_node_data = 17;
114 final static int sort_descendents = 18;
115 final static int get_ext_desc_data = 19;
116 final static int select_nodes = 20;
117 // ------------------
119 // ------------------
120 final static String display_options[][] = {
121 { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
122 { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" },
123 { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
124 { "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" },
125 { "Branch Widths", "display", "no" }, { "Domain Architectures", "display", "no" },
126 { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
127 { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" },
128 { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
129 { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
130 { "Colorize by Annotation", "display", "no" }, { "Seq Symbol", "display", "yes" },
131 { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
132 { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
133 { "Properties", "display", "no" }, { "Gene Name", "display", "yes" },
134 { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" } };
135 final static int display_as_phylogram = 0;
136 final static int show_node_names = 1;
137 final static int show_tax_code = 2;
138 final static int show_annotation = 3;
139 final static int write_confidence_values = 4;
140 final static int write_events = 5;
141 final static int color_according_to_species = 6;
142 final static int color_according_to_sequence = 7;
143 final static int use_style = 8;
144 final static int width_branches = 9;
145 final static int show_domain_architectures = 10;
146 final static int show_binary_characters = 11;
147 final static int show_binary_character_counts = 12;
148 final static int show_seq_names = 13;
149 final static int show_sequence_acc = 14;
150 final static int display_internal_data = 15;
151 final static int dynamically_hide_data = 16;
152 final static int show_taxonomy_scientific_names = 17;
153 final static int show_taxonomy_common_names = 18;
154 final static int color_according_to_annotation = 19;
155 final static int show_seq_symbols = 20;
156 final static int node_data_popup = 21;
157 final static int show_relation_confidence = 22;
158 final static int show_vector_data = 23;
159 final static int show_taxonomy_images = 24;
160 final static int show_properties = 25;
161 final static int show_gene_names = 26;
162 final static int show_mol_seqs = 27;
163 final static int write_branch_length_values = 28;
164 static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
165 private static Hashtable<String, Color> _sequence_colors;
166 private static Hashtable<String, Color> _annotation_colors;
167 private static Hashtable<String, Color> _domain_colors;
168 private static Hashtable<String, Color> _species_colors;
169 private static String DEFAULT_FONT_FAMILY = "";
170 private static final int DEPRECATED = -2;
171 private static final String DISPLAY_COLOR_KEY = "display_color";
172 // ---------------------------
173 // Display options for trees
174 // ---------------------------
175 // ---------------------------------
176 // Pertaining to the config itself
177 // ---------------------------------
178 // Full path to config (may be URL)
179 String config_filename;
180 // This option is selected in the dropdown
181 int default_clickto = Configuration.display_node_data;
182 String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
186 TreeColorSet tree_color_set;
190 TreeFontSet tree_font_set;
191 boolean verbose = Constants.VERBOSE_DEFAULT;
192 private boolean _abbreviate_scientific_names = false;
193 private boolean _antialias_screen = true;
194 private boolean _background_color_gradient = false;
195 private String _base_font_family_name = "";
196 private int _base_font_size = -1;
197 private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
198 private boolean _color_labels_same_as_parent_branch = false;
199 private int _default_bootstrap_samples = -1;
200 private NodeFill _default_node_fill = NodeFill.SOLID;
201 private NodeShape _default_node_shape = NodeShape.RECTANGLE;
202 private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
203 private SortedMap<String, Color> _display_colors = null;
204 private boolean _display_sequence_relations = false;
205 private boolean _editable = true;
206 private NodeDataField _ext_desc_data_to_return = NodeDataField.UNKNOWN;
207 private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
208 private int _frame_x_size;
209 private int _frame_y_size;
210 private int _graphics_export_x = -1;
211 private int _graphics_export_y = -1;
212 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
213 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
214 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
215 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
216 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
217 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
218 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
219 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
220 private boolean _hide_controls_and_menus = false;
221 private boolean _internal_number_are_confidence_for_nh_parsing = false;
222 private String _label_for_get_ext_descendents_data = "";
223 private int _max_base_font_size = 20;
224 private boolean _midpoint_root = false;
225 private int _min_base_font_size = 2;
226 private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
227 private boolean _nh_parsing_replace_underscores = false;
228 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
229 private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
230 private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
231 private short _ov_max_height = 80;
232 private short _ov_max_width = 80;
233 private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
234 private File _path_to_local_fastme = null;
235 private File _path_to_local_mafft = null;
236 private File _path_to_local_raxml = null;
237 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
238 private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
239 private boolean _show_annotation_ref_source = true;
240 private boolean _show_default_node_shapes_external = false;
241 private boolean _show_default_node_shapes_for_marked_nodes = false;
242 private boolean _show_default_node_shapes_internal = false;
243 private boolean _show_domain_labels = true;
244 private boolean _show_overview = true;
245 private boolean _show_scale = false;
246 private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
247 private UI _ui = UI.UNKNOWN;
248 private boolean _use_tabbed_display = false;
249 private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
250 private Color _vector_data_min_color = Color.BLUE;
251 private Color _vector_data_max_color = Color.YELLOW;
252 private Color _vector_data_mean_color = Color.WHITE;
253 private double _vector_data_height = 12;
254 private int _vector_data_width = 120;
255 private boolean _line_up_renderable_node_data = true;
256 private boolean _right_align_domains = false;
257 private boolean _allow_thick_strokes = false;
259 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
260 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
261 DEFAULT_FONT_FAMILY = font_name;
265 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
266 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
270 static String getDefaultFontFamilyName() {
271 return DEFAULT_FONT_FAMILY;
274 public Configuration() {
275 this( null, false, false, false );
278 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
279 if ( ForesterUtil.isEmpty( cf ) ) {
280 config_filename = default_config_filename;
283 config_filename = cf;
285 setDisplayColors( new TreeMap<String, Color>() );
286 config_filename = config_filename.trim();
289 // If URL, open accordingly
291 u = new URL( config_filename );
293 final InputStreamReader isr = new InputStreamReader( u.openStream() );
294 final BufferedReader bf = new BufferedReader( isr );
297 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
298 + config_filename + "]" );
300 catch ( final Exception e ) {
301 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
302 + config_filename + "]: " + e.getLocalizedMessage() );
305 catch ( final Exception e ) {
306 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
307 + config_filename + "]" );
311 // Otherwise, open as a file
312 File f = new File( config_filename );
314 f = new File( config_filename + ".txt" );
316 if ( f.exists() && f.canRead() ) {
318 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
322 catch ( final Exception e ) {
324 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
325 + config_filename + "]: " + e );
331 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
332 + config_filename + "]" );
338 boolean displaySequenceRelations() {
339 return _display_sequence_relations;
342 boolean doCheckOption( final int which ) {
343 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
344 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
347 boolean doDisplayClickToOption( final int which ) {
348 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
351 boolean doDisplayOption( final int which ) {
352 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
356 * Will attempt to use the phylogeny to determine whether to check
357 * this or not (e.g. phylogram)
360 boolean doGuessCheckOption( final int which ) {
361 return display_options[ which ][ 2 ].equals( "?" );
364 Map<String, Color> getAnnotationColors() {
365 if ( _annotation_colors == null ) {
366 _annotation_colors = new Hashtable<String, Color>();
368 return _annotation_colors;
371 public String getBaseFontFamilyName() {
372 return _base_font_family_name;
375 int getBaseFontSize() {
376 return _base_font_size;
379 CLADOGRAM_TYPE getCladogramType() {
380 return _cladogram_type;
383 private int getClickToIndex( final String name ) {
385 if ( name.equals( "edit_info" ) ) {
386 index = Configuration.display_node_data;
388 .printWarningMessage( Constants.PRG_NAME,
389 "configuration key [edit_info] is deprecated, use [display node data] instead" );
391 else if ( name.equals( "display_node_data" ) ) {
392 index = Configuration.display_node_data;
394 else if ( name.equals( "collapse_uncollapse" ) ) {
395 index = Configuration.collapse_uncollapse;
397 else if ( name.equals( "reroot" ) ) {
398 index = Configuration.reroot;
400 else if ( name.equals( "subtree" ) ) {
401 index = Configuration.subtree;
403 else if ( name.equals( "swap" ) ) {
404 index = Configuration.swap;
406 else if ( name.equals( "sort_descendants" ) ) {
407 index = Configuration.sort_descendents;
409 else if ( name.equals( "get_ext_descendents_data" ) ) {
410 index = Configuration.get_ext_desc_data;
412 else if ( name.equals( "display_sequences" ) ) {
414 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
417 else if ( name.equals( "open_seq_web" ) ) {
418 index = Configuration.open_seq_web;
420 else if ( name.equals( "open_pdb_web" ) ) {
421 index = Configuration.open_pdb_web;
423 else if ( name.equals( "open_tax_web" ) ) {
424 index = Configuration.open_tax_web;
426 else if ( name.equals( "blast" ) ) {
427 index = Configuration.blast;
429 else if ( name.equals( "cut_subtree" ) ) {
430 index = Configuration.cut_subtree;
432 else if ( name.equals( "copy_subtree" ) ) {
433 index = Configuration.copy_subtree;
435 else if ( name.equals( "paste_subtree" ) ) {
436 index = Configuration.paste_subtree;
438 else if ( name.equals( "delete" ) ) {
439 index = Configuration.delete_subtree_or_node;
441 else if ( name.equals( "add_new_node" ) ) {
442 index = Configuration.add_new_node;
444 else if ( name.equals( "edit_node_data" ) ) {
445 index = Configuration.edit_node_data;
447 else if ( name.equals( "select_nodes" ) ) {
448 index = Configuration.select_nodes;
450 else if ( name.equals( "display_node_popup" ) ) {
451 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
452 "configuration key [display_node_popup] is deprecated" );
455 else if ( name.equals( "custom_option" ) ) {
456 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
459 else if ( name.equals( "color_subtree" ) ) {
460 index = Configuration.color_subtree;
462 else if ( name.equals( "change_node_font" ) ) {
463 index = Configuration.change_node_font;
465 else if ( name.equals( "color_node_font" ) ) {
466 index = Configuration.color_node_font;
468 else if ( name.equals( "color_subtree" ) ) {
469 index = Configuration.color_subtree;
474 int getClickToOptionsCount() {
475 return clickto_options.length;
478 String getClickToTitle( final int which ) {
479 return clickto_options[ which ][ 0 ];
482 public int getDefaultBootstrapSamples() {
483 return _default_bootstrap_samples;
486 int getDefaultDisplayClicktoOption() {
487 return default_clickto;
490 public NodeFill getDefaultNodeFill() {
491 return _default_node_fill;
494 public NodeShape getDefaultNodeShape() {
495 return _default_node_shape;
498 public short getDefaultNodeShapeSize() {
499 return _default_node_shape_size;
502 SortedMap<String, Color> getDisplayColors() {
503 return _display_colors;
506 String getDisplayTitle( final int which ) {
507 return display_options[ which ][ 0 ];
510 Map<String, Color> getDomainColors() {
511 if ( _domain_colors == null ) {
512 _domain_colors = new Hashtable<String, Color>();
514 return _domain_colors;
517 public NodeDataField getExtDescNodeDataToReturn() {
518 return _ext_desc_data_to_return;
521 public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
522 return _ext_node_data_return_on;
525 public int getFrameXSize() {
526 return _frame_x_size;
529 public int getFrameYSize() {
530 return _frame_y_size;
533 int getGraphicsExportX() {
534 return _graphics_export_x;
537 int getGraphicsExportY() {
538 return _graphics_export_y;
541 Color getGuiBackgroundColor() {
542 return _gui_background_color;
545 Color getGuiButtonBackgroundColor() {
546 return _gui_button_background_color;
549 Color getGuiButtonBorderColor() {
550 return _gui_button_border_color;
553 Color getGuiButtonTextColor() {
554 return _gui_button_text_color;
557 Color getGuiCheckboxAndButtonActiveColor() {
558 return _gui_checkbox_and_button_active_color;
561 Color getGuiCheckboxTextColor() {
562 return _gui_checkbox_text_color;
565 Color getGuiMenuBackgroundColor() {
566 return _gui_menu_background_color;
569 Color getGuiMenuTextColor() {
570 return _gui_menu_text_color;
573 public String getLabelForGetExtDescendentsData() {
574 return _label_for_get_ext_descendents_data;
577 int getMaxBaseFontSize() {
578 return _max_base_font_size;
581 int getMinBaseFontSize() {
582 return _min_base_font_size;
585 double getMinConfidenceValue() {
586 return _min_confidence_value;
589 NODE_LABEL_DIRECTION getNodeLabelDirection() {
590 return _node_label_direction;
593 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
594 return _number_of_digits_after_comma_for_branch_length_values;
597 short getNumberOfDigitsAfterCommaForConfidenceValues() {
598 return _number_of_digits_after_comma_for_confidence_values;
601 short getOvMaxHeight() {
602 return _ov_max_height;
605 short getOvMaxWidth() {
606 return _ov_max_width;
609 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
610 return _ov_placement;
613 public File getPathToLocalFastme() {
614 return _path_to_local_fastme;
617 public File getPathToLocalMafft() {
618 return _path_to_local_mafft;
621 public File getPathToLocalRaxml() {
622 return _path_to_local_raxml;
625 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
626 return _phylogeny_graphics_type;
629 float getPrintLineWidth() {
630 return _print_line_width;
633 Hashtable<String, Color> getSequenceColors() {
634 if ( _sequence_colors == null ) {
635 _sequence_colors = new Hashtable<String, Color>();
637 return _sequence_colors;
640 Hashtable<String, Color> getSpeciesColors() {
641 if ( _species_colors == null ) {
644 return _species_colors;
647 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
648 return _taxonomy_extraction;
651 public double getVectorDataHeight() {
652 return _vector_data_height;
655 public Color getVectorDataMaxColor() {
656 return _vector_data_max_color;
659 public Color getVectorDataMeanColor() {
660 return _vector_data_mean_color;
663 public Color getVectorDataMinColor() {
664 return _vector_data_min_color;
667 public int getVectorDataWidth() {
668 return _vector_data_width;
671 private final void initSpeciesColors() {
672 _species_colors = new Hashtable<String, Color>();
673 for( final String[] s : DEFAULT_SPECIES_COLORS ) {
674 _species_colors.put( s[ 0 ], Color.decode( s[ 1 ] ) );
678 public boolean isAbbreviateScientificTaxonNames() {
679 return _abbreviate_scientific_names;
682 boolean isAntialiasScreen() {
683 if ( ForesterUtil.isMac() ) {
684 //Apple Macintosh graphics are slow, turn off anti-alias.
687 return _antialias_screen;
690 public boolean isBackgroundColorGradient() {
691 return _background_color_gradient;
694 public boolean isColorByTaxonomicGroup() {
698 public boolean isColorLabelsSameAsParentBranch() {
699 return _color_labels_same_as_parent_branch;
703 * Convenience method.
705 * @return true if value in configuration file was 'yes'
707 boolean isDrawAsPhylogram() {
708 return doCheckOption( display_as_phylogram );
711 boolean isEditable() {
716 * Only used by ArchaeoptryxE.
719 boolean isHideControlPanelAndMenubar() {
720 return _hide_controls_and_menus;
723 boolean isInternalNumberAreConfidenceForNhParsing() {
724 return _internal_number_are_confidence_for_nh_parsing;
727 final public boolean isLineUpRendarableNodeData() {
728 return _line_up_renderable_node_data;
731 public boolean isMidpointReroot() {
732 return _midpoint_root;
735 boolean isReplaceUnderscoresInNhParsing() {
736 return _nh_parsing_replace_underscores;
739 final public boolean isRightLineUpDomains() {
740 return _right_align_domains;
743 public boolean isShowAnnotationRefSource() {
744 return _show_annotation_ref_source;
747 public boolean isShowDefaultNodeShapesExternal() {
748 return _show_default_node_shapes_external;
751 public boolean isShowDefaultNodeShapesForMarkedNodes() {
752 return _show_default_node_shapes_for_marked_nodes;
755 public boolean isShowDefaultNodeShapesInternal() {
756 return _show_default_node_shapes_internal;
759 public boolean isShowDomainLabels() {
760 return _show_domain_labels;
763 boolean isShowOverview() {
764 return _show_overview;
767 boolean isShowScale() {
771 final boolean isUseNativeUI() {
772 if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
775 return _ui == UI.NATIVE;
779 * Only used by ArchaeoptryxE.
782 boolean isUseTabbedDisplay() {
783 return _use_tabbed_display;
786 boolean isValidatePhyloXmlAgainstSchema() {
787 return _validate_against_phyloxml_xsd_schema;
790 private boolean parseBoolean( final String str ) {
791 final String my_str = str.trim().toLowerCase();
792 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
795 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
799 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
804 private double parseDouble( final String str ) {
807 d = Double.parseDouble( str.trim() );
809 catch ( final Exception e ) {
810 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
816 private float parseFloat( final String str ) {
819 f = Float.parseFloat( str.trim() );
821 catch ( final Exception e ) {
822 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
828 private int parseInt( final String str ) {
831 i = Integer.parseInt( str.trim() );
833 catch ( final Exception e ) {
834 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
840 private short parseShort( final String str ) {
843 i = Short.parseShort( str.trim() );
845 catch ( final Exception e ) {
846 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
852 private void processFontFamily( final StringTokenizer st ) {
853 setBaseFontFamilyName( "" );
854 final String font_str = ( ( String ) st.nextElement() ).trim();
855 final String[] fonts = font_str.split( ",+" );
856 for( String font : fonts ) {
857 font = font.replace( '_', ' ' ).trim();
858 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
859 setBaseFontFamilyName( font );
865 public void putDisplayColors( final String key, final Color color ) {
866 getDisplayColors().put( key, color );
870 * read each line of config file, process non-comment lines
871 * @throws IOException
873 private void readConfig( final BufferedReader conf_in ) throws IOException {
876 line = conf_in.readLine();
877 if ( line != null ) {
879 // skip comments and blank lines
880 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
881 // convert runs of spaces to tabs
882 line = line.replaceAll( "\\s+", "\t" );
883 final StringTokenizer st = new StringTokenizer( line, "\t" );
887 } while ( line != null );
890 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
891 _abbreviate_scientific_names = abbreviate_scientific_names;
894 public void setAddTaxonomyImagesCB( final boolean b ) {
895 display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no";
898 private void setAntialiasScreen( final boolean antialias_screen ) {
899 _antialias_screen = antialias_screen;
902 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
903 _background_color_gradient = background_color_gradient;
906 public void setBaseFontFamilyName( final String base_font_family_name ) {
907 _base_font_family_name = base_font_family_name;
910 public void setBaseFontSize( final int base_font_size ) {
911 _base_font_size = base_font_size;
914 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
915 _cladogram_type = cladogram_type;
918 public void setColorizeBranches( final boolean b ) {
919 display_options[ use_style ][ 2 ] = b ? "yes" : "no";
922 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
923 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
926 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
927 _default_bootstrap_samples = default_bootstrap_samples;
930 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
931 _default_node_fill = default_node_fill;
934 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
935 _default_node_shape = default_node_shape;
938 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
939 _default_node_shape_size = default_node_shape_size;
942 public void setDisplayAsPhylogram( final boolean b ) {
943 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
946 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
947 _display_colors = display_colors;
950 public void setDisplayConfidenceValues( final boolean b ) {
951 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
954 public void setDisplayGeneNames( final boolean b ) {
955 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
958 public void setDisplayInternalData( final boolean b ) {
959 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
962 public void setDisplayNodeNames( final boolean b ) {
963 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
966 public void setDisplaySequenceAcc( final boolean b ) {
967 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
970 public void setDisplaySequenceNames( final boolean b ) {
971 display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no";
974 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
975 _display_sequence_relations = display_sequence_relations;
978 public void setDisplaySequenceSymbols( final boolean b ) {
979 display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no";
982 public void setDisplayTaxonomyCode( final boolean b ) {
983 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
986 public void setDisplayTaxonomyCommonNames( final boolean b ) {
987 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
990 public void setDisplayTaxonomyImages( final boolean b ) {
991 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
994 public void setDisplayTaxonomyScientificNames( final boolean b ) {
995 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
998 public void setDynamicallyHideData( final boolean b ) {
999 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
1002 private void setEditable( final boolean editable ) {
1003 _editable = editable;
1006 public void setExtDescNodeDataToReturn( final NodeDataField ext_desc_data_to_return ) {
1007 _ext_desc_data_to_return = ext_desc_data_to_return;
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 public void setFrameXSize( final int frame_x_size ) {
1015 _frame_x_size = frame_x_size;
1018 public void setFrameYSize( final int frame_y_size ) {
1019 _frame_y_size = frame_y_size;
1022 private void setGraphicsExportX( final int graphics_export_x ) {
1023 _graphics_export_x = graphics_export_x;
1026 private void setGraphicsExportY( final int graphics_export_y ) {
1027 _graphics_export_y = graphics_export_y;
1030 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
1031 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
1035 * Set a key-value(s) tuple
1037 private void setKeyValue( final StringTokenizer st ) {
1038 final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
1039 if ( !st.hasMoreElements() ) {
1042 // Handle single value settings first:
1043 if ( key.equals( "default_click_to" ) ) {
1044 final String clickto_name = ( String ) st.nextElement();
1045 default_clickto = getClickToIndex( clickto_name );
1046 if ( default_clickto == -1 ) {
1047 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
1048 + "] for [default_click_to]" );
1049 default_clickto = 0;
1051 else if ( default_clickto == DEPRECATED ) {
1055 else if ( key.equals( "native_ui" ) ) {
1056 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
1057 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
1060 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
1061 _ui = UI.CROSSPLATFORM;
1063 else if ( my_str.equals( "?" ) ) {
1067 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
1072 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
1073 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
1075 else if ( key.equals( "antialias_screen" ) ) {
1076 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
1078 else if ( key.equals( "phylogeny_graphics_type" ) ) {
1079 final String type_str = ( ( String ) st.nextElement() ).trim();
1080 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
1081 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1083 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
1084 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1086 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
1087 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1089 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
1090 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1092 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
1093 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1095 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
1096 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1098 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
1099 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1101 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
1102 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1105 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1106 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1107 + "] for [phylogeny_graphics_type]" );
1110 else if ( key.equals( "min_confidence_value" ) ) {
1111 final String mcv_str = ( ( String ) st.nextElement() ).trim();
1112 final double d = parseDouble( mcv_str );
1113 setMinConfidenceValue( d );
1115 else if ( key.equals( "font_family" ) ) {
1116 processFontFamily( st );
1118 else if ( key.equals( "font_size" ) ) {
1119 final String size_str = ( ( String ) st.nextElement() ).trim();
1120 final int i = parseInt( size_str );
1122 setBaseFontSize( i );
1125 else if ( key.equals( "font_size_min" ) ) {
1126 final String size_str = ( ( String ) st.nextElement() ).trim();
1127 final int i = parseInt( size_str );
1129 setMinBaseFontSize( i );
1132 else if ( key.equals( "font_size_max" ) ) {
1133 final String size_str = ( ( String ) st.nextElement() ).trim();
1134 final int i = parseInt( size_str );
1136 setMaxBaseFontSize( i );
1139 else if ( key.equals( "graphics_export_x" ) ) {
1140 final String str = ( ( String ) st.nextElement() ).trim();
1141 final int i = parseInt( str );
1143 setGraphicsExportX( i );
1146 else if ( key.equals( "graphics_export_y" ) ) {
1147 final String str = ( ( String ) st.nextElement() ).trim();
1148 final int i = parseInt( str );
1150 setGraphicsExportY( i );
1153 else if ( key.equals( "pdf_export_line_width" ) ) {
1154 final String str = ( ( String ) st.nextElement() ).trim();
1155 final float f = parseFloat( str );
1157 setPrintLineWidth( f );
1160 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1161 "value for [pdf_export_line_width] cannot be zero or negative" );
1164 else if ( key.equals( "window_initial_size_x" ) ) {
1165 final String str = ( ( String ) st.nextElement() ).trim();
1166 final int i = parseInt( str );
1171 else if ( key.equals( "window_initial_size_y" ) ) {
1172 final String str = ( ( String ) st.nextElement() ).trim();
1173 final int i = parseInt( str );
1178 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1179 final String str = ( ( String ) st.nextElement() ).trim();
1180 final int i = parseInt( str );
1182 setDefaultBootstrapSamples( i );
1186 .printWarningMessage( Constants.PRG_NAME,
1187 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1190 else if ( key.equals( "mafft_local" ) ) {
1191 final String str = ( ( String ) st.nextElement() ).trim();
1192 if ( !ForesterUtil.isEmpty( str ) ) {
1193 setPathToLocalMafft( new File( str ) );
1196 else if ( key.equals( "fastme_local" ) ) {
1197 final String str = ( ( String ) st.nextElement() ).trim();
1198 if ( !ForesterUtil.isEmpty( str ) ) {
1199 setPathToLocalFastme( new File( str ) );
1202 else if ( key.equals( "raxml_local" ) ) {
1203 final String str = ( ( String ) st.nextElement() ).trim();
1204 if ( !ForesterUtil.isEmpty( str ) ) {
1205 setPathToLocalRaxml( new File( str ) );
1208 else if ( key.equals( "show_scale" ) ) {
1209 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1211 else if ( key.equals( "show_overview" ) ) {
1212 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1214 else if ( key.equals( "background_gradient" ) ) {
1215 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1217 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1218 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1220 else if ( key.equals( "show_domain_labels" ) ) {
1221 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1223 else if ( key.equals( "show_seq_annotation_ref_sources" ) ) {
1224 setShowAnnotationRefSource( parseBoolean( ( String ) st.nextElement() ) );
1226 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1227 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1229 else if ( key.equals( "cladogram_type" ) ) {
1230 final String type_str = ( ( String ) st.nextElement() ).trim();
1231 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1232 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1234 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1235 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1237 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1238 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1241 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1242 + "] for [cladogram_type]" );
1245 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1247 .printWarningMessage( Constants.PRG_NAME,
1248 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1250 else if ( key.equals( "hide_controls_and_menus" ) ) {
1251 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1253 else if ( key.equals( "use_tabbed_display" ) ) {
1254 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1256 else if ( key.equals( "overview_width" ) ) {
1257 final short i = parseShort( ( ( String ) st.nextElement() ) );
1260 else if ( key.equals( "overview_height" ) ) {
1261 final short i = parseShort( ( ( String ) st.nextElement() ) );
1262 setOvMaxHeight( i );
1264 else if ( key.equals( "overview_placement_type" ) ) {
1265 final String type_str = ( ( String ) st.nextElement() ).trim();
1266 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1267 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1269 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1270 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1272 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1273 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1275 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1276 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1279 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1280 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1281 + "] for [overview_placement_type]" );
1284 else if ( key.equals( "node_label_direction" ) ) {
1285 final String type_str = ( ( String ) st.nextElement() ).trim();
1286 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1287 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1289 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1290 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1293 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1294 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1295 + "] for [node_label_direction]" );
1298 else if ( key.equals( "branch_length_value_digits" ) ) {
1299 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1301 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1304 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1305 + "] for [branch_length_value_digits]" );
1308 else if ( key.equals( "confidence_value_digits" ) ) {
1309 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1311 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1314 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1315 + "] for [confidence_value_digits]" );
1318 else if ( key.equals( "allow_editing" ) ) {
1319 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1321 else if ( key.equals( "display_sequence_relations" ) ) {
1322 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1324 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1325 final boolean r = parseBoolean( ( String ) st.nextElement() );
1326 if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
1328 .printWarningMessage( Constants.PRG_NAME,
1329 "attempt to extract taxonomies and replace underscores at the same time" );
1332 setReplaceUnderscoresInNhParsing( r );
1335 else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
1336 final String s = ( String ) st.nextElement();
1337 if ( s.equalsIgnoreCase( "no" ) ) {
1338 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1340 else if ( s.equalsIgnoreCase( "pfam_relaxed" ) ) {
1341 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1343 else if ( s.equalsIgnoreCase( "pfam_strict" ) ) {
1344 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1346 else if ( s.equalsIgnoreCase( "aggressive" ) ) {
1347 setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
1351 .printWarningMessage( Constants.PRG_NAME,
1352 "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
1354 + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
1356 if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
1358 .printWarningMessage( Constants.PRG_NAME,
1359 "attempt to extract taxonomies and replace underscores at the same time" );
1362 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1363 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1365 else if ( key.equals( "gui_background_color" ) ) {
1366 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1368 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1369 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1371 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1372 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1374 else if ( key.equals( "gui_button_text_color" ) ) {
1375 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1377 else if ( key.equals( "gui_button_background_color" ) ) {
1378 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1380 else if ( key.equals( "gui_menu_background_color" ) ) {
1381 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1383 else if ( key.equals( "gui_menu_text_color" ) ) {
1384 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1386 else if ( key.equals( "gui_button_border_color" ) ) {
1387 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1389 else if ( key.equals( "show_default_node_shapes_internal" ) ) {
1390 setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1392 else if ( key.equals( "show_default_node_shapes_external" ) ) {
1393 setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1395 else if ( key.equals( "show_node_shapes_for_nodes_with_vis_data" ) ) {
1396 setShowDefaultNodeShapesForMarkedNodes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1398 else if ( key.equals( "default_node_size" ) ) {
1399 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1400 setDefaultNodeShapeSize( i );
1402 else if ( key.equals( "default_node_fill" ) ) {
1403 final String fill_str = ( ( String ) st.nextElement() ).trim();
1404 if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.NONE.toString() ) ) {
1405 setDefaultNodeFill( NodeFill.NONE );
1407 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.GRADIENT.toString() ) ) {
1408 setDefaultNodeFill( NodeFill.GRADIENT );
1410 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.SOLID.toString() ) ) {
1411 setDefaultNodeFill( NodeFill.SOLID );
1414 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1415 + "] for [default_node_fill]" );
1418 else if ( key.equals( "default_node_shape" ) ) {
1419 final String shape_str = ( ( String ) st.nextElement() ).trim();
1420 if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.CIRCLE.toString() ) ) {
1421 setDefaultNodeShape( NodeShape.CIRCLE );
1423 else if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.RECTANGLE.toString() ) ) {
1424 setDefaultNodeShape( NodeShape.RECTANGLE );
1427 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1428 + "] for [default_node_shape]" );
1431 else if ( key.equals( "midpoint_reroot" ) ) {
1432 setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) );
1434 else if ( key.equals( "list_node_data_field" ) || key.equals( "ext_descendents_data_to_return" ) ) {
1435 final String s = ( ( String ) st.nextElement() ).trim();
1436 if ( s.equalsIgnoreCase( "node_name" ) ) {
1437 setExtDescNodeDataToReturn( NodeDataField.NODE_NAME );
1439 else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
1440 setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_ACC );
1442 else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) {
1443 setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );
1445 else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
1446 setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_NAME );
1448 else if ( s.equalsIgnoreCase( "gene_name" ) ) {
1449 setExtDescNodeDataToReturn( NodeDataField.GENE_NAME );
1451 else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
1452 setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_SYMBOL );
1454 else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
1455 setExtDescNodeDataToReturn( NodeDataField.TAXONOMY_SCIENTIFIC_NAME );
1457 else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
1458 setExtDescNodeDataToReturn( NodeDataField.TAXONOMY_CODE );
1460 else if ( s.equalsIgnoreCase( "user_selected" ) ) {
1461 setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
1463 else if ( s.equalsIgnoreCase( "domains" ) ) {
1464 setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );
1466 else if ( s.equalsIgnoreCase( "domains_collapsed" ) ) {
1467 setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );
1469 else if ( s.equalsIgnoreCase( "seq_annotations" ) ) {
1470 setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );
1472 else if ( s.equalsIgnoreCase( "go_term_ids" ) ) {
1473 setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );
1476 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1477 + "] for [ext_descendents_data_to_return]" );
1480 else if ( key.equals( "list_node_data_custom_label" ) || key.equals( "label_for_get_ext_descendents_data" ) ) {
1481 final String s = ( ( String ) st.nextElement() ).trim();
1482 if ( !ForesterUtil.isEmpty( s ) && ( s.length() > 1 ) ) {
1483 setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
1486 else if ( key.equals( "list_node_data_in" ) || key.equals( "ext_descendents_data_to_return_on" ) ) {
1487 final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
1488 if ( s.equals( "console" ) ) {
1489 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
1491 else if ( s.equals( "window" ) ) {
1492 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
1494 else if ( s.equals( "buffer_only" ) ) {
1495 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
1498 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1499 + "] for [ext_descendents_data_to_return_on]" );
1502 else if ( key.equals( "vector_data_min_color" ) ) {
1503 _vector_data_min_color = Color.decode( ( String ) st.nextElement() );
1505 else if ( key.equals( "vector_data_max_color" ) ) {
1506 _vector_data_max_color = Color.decode( ( String ) st.nextElement() );
1508 else if ( key.equals( "vector_data_mean_color" ) ) {
1509 _vector_data_mean_color = Color.decode( ( String ) st.nextElement() );
1511 else if ( key.equals( "vector_data_width" ) ) {
1512 _vector_data_width = parseShort( ( String ) st.nextElement() );
1513 if ( _vector_data_width < 1 ) {
1514 _vector_data_width = 120;
1517 else if ( key.equals( "vector_data_height" ) ) {
1518 _vector_data_height = parseShort( ( String ) st.nextElement() );
1519 if ( _vector_data_height < 1 ) {
1520 _vector_data_height = 12;
1523 else if ( key.equals( "line_up_renderable_data" ) ) {
1524 setLineUpRendarableNodeData( parseBoolean( ( String ) st.nextElement() ) );
1526 else if ( key.equals( "right_align_domain_architectures" ) ) {
1527 setRightLineUpDomains( parseBoolean( ( String ) st.nextElement() ) );
1529 else if ( key.equals( "allow_thick_strokes" ) ) {
1530 _allow_thick_strokes = parseBoolean( ( String ) st.nextElement() );
1532 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1535 if ( key.equals( "phylogram" ) ) {
1536 key_index = Configuration.display_as_phylogram;
1538 else if ( key.equals( "rollover" ) ) {
1539 key_index = Configuration.node_data_popup;
1541 else if ( key.equals( "color_according_to_species" ) ) {
1542 key_index = Configuration.color_according_to_species;
1544 else if ( key.equals( "color_according_to_sequence" ) ) {
1545 key_index = Configuration.color_according_to_sequence;
1547 else if ( key.equals( "show_node_names" ) ) {
1548 key_index = Configuration.show_node_names;
1550 else if ( key.equals( "show_taxonomy_code" ) ) {
1551 key_index = Configuration.show_tax_code;
1553 else if ( key.equals( "write_confidence_values" ) ) {
1554 key_index = Configuration.write_confidence_values;
1556 else if ( key.equals( "write_branch_length_values" ) ) {
1557 key_index = Configuration.write_branch_length_values;
1559 else if ( key.equals( "write_events" ) ) {
1560 key_index = Configuration.write_events;
1562 else if ( key.equals( "use_visual_styles" ) ) {
1563 key_index = Configuration.use_style;
1565 else if ( key.equals( "color_branches" ) ) {
1566 key_index = Configuration.use_style;
1568 .printWarningMessage( Constants.PRG_NAME,
1569 "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" );
1571 else if ( key.equals( "width_branches" ) ) {
1572 key_index = Configuration.width_branches;
1574 else if ( key.equals( "show_domain_architectures" ) ) {
1575 key_index = Configuration.show_domain_architectures;
1577 else if ( key.equals( "show_msa" ) ) {
1578 key_index = Configuration.show_mol_seqs;
1580 else if ( key.equals( "show_annotations" ) ) {
1581 key_index = Configuration.show_annotation;
1583 else if ( key.equals( "show_binary_characters" ) ) {
1584 key_index = Configuration.show_binary_characters;
1586 else if ( key.equals( "show_binary_character_counts" ) ) {
1587 key_index = Configuration.show_binary_character_counts;
1589 else if ( key.equals( "show_seq_names" ) ) {
1590 key_index = Configuration.show_seq_names;
1592 else if ( key.equals( "show_gene_names" ) ) {
1593 key_index = Configuration.show_gene_names;
1595 else if ( key.equals( "show_seq_symbols" ) ) {
1596 key_index = Configuration.show_seq_symbols;
1598 else if ( key.equals( "show_seq_acc" ) ) {
1599 key_index = Configuration.show_sequence_acc;
1601 else if ( key.equals( "display_internal_data" ) ) {
1602 key_index = Configuration.display_internal_data;
1604 else if ( key.equals( "dynamically_hide_data" ) ) {
1605 key_index = Configuration.dynamically_hide_data;
1607 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1608 key_index = Configuration.show_taxonomy_scientific_names;
1610 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1611 key_index = Configuration.show_taxonomy_common_names;
1613 else if ( key.equals( "show_taxonomy_images" ) ) {
1614 key_index = Configuration.show_taxonomy_images;
1616 else if ( key.equals( "color_according_to_annotation" ) ) {
1617 key_index = Configuration.color_according_to_annotation;
1619 else if ( key.equals( "show_vector_data" ) ) {
1620 key_index = Configuration.show_vector_data;
1622 else if ( key.equals( "show_properties" ) ) {
1623 key_index = Configuration.show_properties;
1625 else if ( key.equals( "show_relation_confidence" ) ) {
1626 key_index = Configuration.show_relation_confidence;
1628 // If we've found the key, set the values
1629 if ( key_index >= 0 ) {
1630 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1631 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1632 // otherwise, keep looking
1635 if ( key_index == DEPRECATED ) {
1638 else if ( key.equals( "click_to" ) ) {
1639 final String click_to_name = ( String ) st.nextElement();
1640 key_index = getClickToIndex( click_to_name );
1641 if ( key_index >= 0 ) {
1642 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1644 else if ( key_index == DEPRECATED ) {
1648 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1652 else if ( key.equals( "species_color" ) ) {
1653 getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
1654 Color.decode( ( String ) st.nextElement() ) );
1656 else if ( key.equals( "sequence_color" ) ) {
1657 getSequenceColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
1658 Color.decode( ( String ) st.nextElement() ) );
1660 else if ( key.equals( "domain_color" ) ) {
1661 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1663 else if ( key.equals( "annotation_color" ) ) {
1664 getAnnotationColors()
1665 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1667 else if ( key.equals( "function_color" ) ) {
1668 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1669 "configuration key [function_color] is deprecated" );
1671 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1672 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1675 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1676 + "] in: " + config_filename );
1681 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1682 + config_filename );
1686 private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
1687 _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
1690 final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) {
1691 _line_up_renderable_node_data = line_up_renderable_node_data;
1694 private void setMaxBaseFontSize( final int max_base_font_size ) {
1695 _max_base_font_size = max_base_font_size;
1698 public void setMidpointReroot( final boolean midpoint_root ) {
1699 _midpoint_root = midpoint_root;
1702 private void setMinBaseFontSize( final int min_base_font_size ) {
1703 _min_base_font_size = min_base_font_size;
1706 public void setMinConfidenceValue( final double min_confidence_value ) {
1707 _min_confidence_value = min_confidence_value;
1710 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
1711 _node_label_direction = node_label_direction;
1714 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
1715 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
1718 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
1719 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
1722 private void setOvMaxHeight( final short ov_max_height ) {
1723 _ov_max_height = ov_max_height;
1726 private void setOvMaxWidth( final short ov_max_width ) {
1727 _ov_max_width = ov_max_width;
1730 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1731 _ov_placement = ov_placement;
1734 private void setPathToLocalFastme( final File path_to_local_fastme ) {
1735 _path_to_local_fastme = path_to_local_fastme;
1738 private void setPathToLocalMafft( final File path_to_local_mafft ) {
1739 _path_to_local_mafft = path_to_local_mafft;
1742 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
1743 _path_to_local_raxml = path_to_local_raxml;
1746 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
1747 _phylogeny_graphics_type = phylogeny_graphics_type;
1750 public void setPrintLineWidth( final float print_line_width ) {
1751 _print_line_width = print_line_width;
1754 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
1755 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
1758 final public void setRightLineUpDomains( final boolean right_align_domains ) {
1759 _right_align_domains = right_align_domains;
1762 private void setShowAnnotationRefSource( final boolean b ) {
1763 _show_annotation_ref_source = b;
1766 public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
1767 _show_default_node_shapes_external = show_default_node_shapes_external;
1770 public void setShowDefaultNodeShapesForMarkedNodes( final boolean show_default_node_shapes_for_marked_nodes ) {
1771 _show_default_node_shapes_for_marked_nodes = show_default_node_shapes_for_marked_nodes;
1774 public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
1775 _show_default_node_shapes_internal = show_default_node_shapes_internal;
1778 public void setShowDomainLabels( final boolean show_domain_labels ) {
1779 _show_domain_labels = show_domain_labels;
1782 private void setShowOverview( final boolean show_overview ) {
1783 _show_overview = show_overview;
1786 public void setShowScale( final boolean show_scale ) {
1787 _show_scale = show_scale;
1790 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
1791 _taxonomy_extraction = taxonomy_extraction;
1794 public void setUseStyle( final boolean b ) {
1795 display_options[ use_style ][ 2 ] = b ? "yes" : "no";
1798 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1799 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1802 public boolean isAllowThickStrokes() {
1803 return _allow_thick_strokes;