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 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 { "Return", "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 NODE_DATA _ext_desc_data_to_return = NODE_DATA.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;
258 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
259 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
260 DEFAULT_FONT_FAMILY = font_name;
264 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
265 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
269 static String getDefaultFontFamilyName() {
270 return DEFAULT_FONT_FAMILY;
273 public Configuration() {
274 this( null, false, false, false );
277 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
278 if ( ForesterUtil.isEmpty( cf ) ) {
279 config_filename = default_config_filename;
282 config_filename = cf;
284 setDisplayColors( new TreeMap<String, Color>() );
285 config_filename = config_filename.trim();
288 // If URL, open accordingly
290 u = new URL( config_filename );
292 final InputStreamReader isr = new InputStreamReader( u.openStream() );
293 final BufferedReader bf = new BufferedReader( isr );
296 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
297 + config_filename + "]" );
299 catch ( final Exception e ) {
300 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
301 + config_filename + "]: " + e.getLocalizedMessage() );
304 catch ( final Exception e ) {
305 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
306 + config_filename + "]" );
310 // Otherwise, open as a file
311 File f = new File( config_filename );
313 f = new File( config_filename + ".txt" );
315 if ( f.exists() && f.canRead() ) {
317 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
321 catch ( final Exception e ) {
323 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
324 + config_filename + "]: " + e );
330 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
331 + config_filename + "]" );
337 boolean displaySequenceRelations() {
338 return _display_sequence_relations;
341 boolean doCheckOption( final int which ) {
342 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
343 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
346 boolean doDisplayClickToOption( final int which ) {
347 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
350 boolean doDisplayOption( final int which ) {
351 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
355 * Will attempt to use the phylogeny to determine whether to check
356 * this or not (e.g. phylogram)
359 boolean doGuessCheckOption( final int which ) {
360 return display_options[ which ][ 2 ].equals( "?" );
363 Map<String, Color> getAnnotationColors() {
364 if ( _annotation_colors == null ) {
365 _annotation_colors = new Hashtable<String, Color>();
367 return _annotation_colors;
370 public String getBaseFontFamilyName() {
371 return _base_font_family_name;
374 int getBaseFontSize() {
375 return _base_font_size;
378 CLADOGRAM_TYPE getCladogramType() {
379 return _cladogram_type;
382 private int getClickToIndex( final String name ) {
384 if ( name.equals( "edit_info" ) ) {
385 index = Configuration.display_node_data;
387 .printWarningMessage( Constants.PRG_NAME,
388 "configuration key [edit_info] is deprecated, use [display node data] instead" );
390 else if ( name.equals( "display_node_data" ) ) {
391 index = Configuration.display_node_data;
393 else if ( name.equals( "collapse_uncollapse" ) ) {
394 index = Configuration.collapse_uncollapse;
396 else if ( name.equals( "reroot" ) ) {
397 index = Configuration.reroot;
399 else if ( name.equals( "subtree" ) ) {
400 index = Configuration.subtree;
402 else if ( name.equals( "swap" ) ) {
403 index = Configuration.swap;
405 else if ( name.equals( "sort_descendants" ) ) {
406 index = Configuration.sort_descendents;
408 else if ( name.equals( "get_ext_descendents_data" ) ) {
409 index = Configuration.get_ext_desc_data;
411 else if ( name.equals( "display_sequences" ) ) {
413 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
416 else if ( name.equals( "open_seq_web" ) ) {
417 index = Configuration.open_seq_web;
419 else if ( name.equals( "open_pdb_web" ) ) {
420 index = Configuration.open_pdb_web;
422 else if ( name.equals( "open_tax_web" ) ) {
423 index = Configuration.open_tax_web;
425 else if ( name.equals( "blast" ) ) {
426 index = Configuration.blast;
428 else if ( name.equals( "cut_subtree" ) ) {
429 index = Configuration.cut_subtree;
431 else if ( name.equals( "copy_subtree" ) ) {
432 index = Configuration.copy_subtree;
434 else if ( name.equals( "paste_subtree" ) ) {
435 index = Configuration.paste_subtree;
437 else if ( name.equals( "delete" ) ) {
438 index = Configuration.delete_subtree_or_node;
440 else if ( name.equals( "add_new_node" ) ) {
441 index = Configuration.add_new_node;
443 else if ( name.equals( "edit_node_data" ) ) {
444 index = Configuration.edit_node_data;
446 else if ( name.equals( "select_nodes" ) ) {
447 index = Configuration.select_nodes;
449 else if ( name.equals( "display_node_popup" ) ) {
450 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
451 "configuration key [display_node_popup] is deprecated" );
454 else if ( name.equals( "custom_option" ) ) {
455 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
458 else if ( name.equals( "color_subtree" ) ) {
459 index = Configuration.color_subtree;
461 else if ( name.equals( "change_node_font" ) ) {
462 index = Configuration.change_node_font;
464 else if ( name.equals( "color_node_font" ) ) {
465 index = Configuration.color_node_font;
467 else if ( name.equals( "color_subtree" ) ) {
468 index = Configuration.color_subtree;
473 int getClickToOptionsCount() {
474 return clickto_options.length;
477 String getClickToTitle( final int which ) {
478 return clickto_options[ which ][ 0 ];
481 public int getDefaultBootstrapSamples() {
482 return _default_bootstrap_samples;
485 int getDefaultDisplayClicktoOption() {
486 return default_clickto;
489 public NodeFill getDefaultNodeFill() {
490 return _default_node_fill;
493 public NodeShape getDefaultNodeShape() {
494 return _default_node_shape;
497 public short getDefaultNodeShapeSize() {
498 return _default_node_shape_size;
501 SortedMap<String, Color> getDisplayColors() {
502 return _display_colors;
505 String getDisplayTitle( final int which ) {
506 return display_options[ which ][ 0 ];
509 Map<String, Color> getDomainColors() {
510 if ( _domain_colors == null ) {
511 _domain_colors = new Hashtable<String, Color>();
513 return _domain_colors;
516 public NODE_DATA getExtDescNodeDataToReturn() {
517 return _ext_desc_data_to_return;
520 public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
521 return _ext_node_data_return_on;
524 public int getFrameXSize() {
525 return _frame_x_size;
528 public int getFrameYSize() {
529 return _frame_y_size;
532 int getGraphicsExportX() {
533 return _graphics_export_x;
536 int getGraphicsExportY() {
537 return _graphics_export_y;
540 Color getGuiBackgroundColor() {
541 return _gui_background_color;
544 Color getGuiButtonBackgroundColor() {
545 return _gui_button_background_color;
548 Color getGuiButtonBorderColor() {
549 return _gui_button_border_color;
552 Color getGuiButtonTextColor() {
553 return _gui_button_text_color;
556 Color getGuiCheckboxAndButtonActiveColor() {
557 return _gui_checkbox_and_button_active_color;
560 Color getGuiCheckboxTextColor() {
561 return _gui_checkbox_text_color;
564 Color getGuiMenuBackgroundColor() {
565 return _gui_menu_background_color;
568 Color getGuiMenuTextColor() {
569 return _gui_menu_text_color;
572 public String getLabelForGetExtDescendentsData() {
573 return _label_for_get_ext_descendents_data;
576 int getMaxBaseFontSize() {
577 return _max_base_font_size;
580 int getMinBaseFontSize() {
581 return _min_base_font_size;
584 double getMinConfidenceValue() {
585 return _min_confidence_value;
588 NODE_LABEL_DIRECTION getNodeLabelDirection() {
589 return _node_label_direction;
592 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
593 return _number_of_digits_after_comma_for_branch_length_values;
596 short getNumberOfDigitsAfterCommaForConfidenceValues() {
597 return _number_of_digits_after_comma_for_confidence_values;
600 short getOvMaxHeight() {
601 return _ov_max_height;
604 short getOvMaxWidth() {
605 return _ov_max_width;
608 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
609 return _ov_placement;
612 public File getPathToLocalFastme() {
613 return _path_to_local_fastme;
616 public File getPathToLocalMafft() {
617 return _path_to_local_mafft;
620 public File getPathToLocalRaxml() {
621 return _path_to_local_raxml;
624 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
625 return _phylogeny_graphics_type;
628 float getPrintLineWidth() {
629 return _print_line_width;
632 Hashtable<String, Color> getSequenceColors() {
633 if ( _sequence_colors == null ) {
634 _sequence_colors = new Hashtable<String, Color>();
636 return _sequence_colors;
639 Hashtable<String, Color> getSpeciesColors() {
640 if ( _species_colors == null ) {
643 return _species_colors;
646 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
647 return _taxonomy_extraction;
650 public double getVectorDataHeight() {
651 return _vector_data_height;
654 public Color getVectorDataMaxColor() {
655 return _vector_data_max_color;
658 public Color getVectorDataMeanColor() {
659 return _vector_data_mean_color;
662 public Color getVectorDataMinColor() {
663 return _vector_data_min_color;
666 public int getVectorDataWidth() {
667 return _vector_data_width;
670 private final void initSpeciesColors() {
671 _species_colors = new Hashtable<String, Color>();
672 for( final String[] s : DEFAULT_SPECIES_COLORS ) {
673 _species_colors.put( s[ 0 ], Color.decode( s[ 1 ] ) );
677 public boolean isAbbreviateScientificTaxonNames() {
678 return _abbreviate_scientific_names;
681 boolean isAntialiasScreen() {
682 if ( ForesterUtil.isMac() ) {
683 //Apple Macintosh graphics are slow, turn off anti-alias.
686 return _antialias_screen;
689 public boolean isBackgroundColorGradient() {
690 return _background_color_gradient;
693 public boolean isColorByTaxonomicGroup() {
697 public boolean isColorLabelsSameAsParentBranch() {
698 return _color_labels_same_as_parent_branch;
702 * Convenience method.
704 * @return true if value in configuration file was 'yes'
706 boolean isDrawAsPhylogram() {
707 return doCheckOption( display_as_phylogram );
710 boolean isEditable() {
715 * Only used by ArchaeoptryxE.
718 boolean isHideControlPanelAndMenubar() {
719 return _hide_controls_and_menus;
722 boolean isInternalNumberAreConfidenceForNhParsing() {
723 return _internal_number_are_confidence_for_nh_parsing;
726 final public boolean isLineUpRendarableNodeData() {
727 return _line_up_renderable_node_data;
730 public boolean isMidpointReroot() {
731 return _midpoint_root;
734 boolean isReplaceUnderscoresInNhParsing() {
735 return _nh_parsing_replace_underscores;
738 final public boolean isRightLineUpDomains() {
739 return _right_align_domains;
742 public boolean isShowAnnotationRefSource() {
743 return _show_annotation_ref_source;
746 public boolean isShowDefaultNodeShapesExternal() {
747 return _show_default_node_shapes_external;
750 public boolean isShowDefaultNodeShapesForMarkedNodes() {
751 return _show_default_node_shapes_for_marked_nodes;
754 public boolean isShowDefaultNodeShapesInternal() {
755 return _show_default_node_shapes_internal;
758 public boolean isShowDomainLabels() {
759 return _show_domain_labels;
762 boolean isShowOverview() {
763 return _show_overview;
766 boolean isShowScale() {
770 final boolean isUseNativeUI() {
771 if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
774 return _ui == UI.NATIVE;
778 * Only used by ArchaeoptryxE.
781 boolean isUseTabbedDisplay() {
782 return _use_tabbed_display;
785 boolean isValidatePhyloXmlAgainstSchema() {
786 return _validate_against_phyloxml_xsd_schema;
789 private boolean parseBoolean( final String str ) {
790 final String my_str = str.trim().toLowerCase();
791 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
794 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
798 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
803 private double parseDouble( final String str ) {
806 d = Double.parseDouble( str.trim() );
808 catch ( final Exception e ) {
809 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
815 private float parseFloat( final String str ) {
818 f = Float.parseFloat( str.trim() );
820 catch ( final Exception e ) {
821 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
827 private int parseInt( final String str ) {
830 i = Integer.parseInt( str.trim() );
832 catch ( final Exception e ) {
833 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
839 private short parseShort( final String str ) {
842 i = Short.parseShort( str.trim() );
844 catch ( final Exception e ) {
845 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
851 private void processFontFamily( final StringTokenizer st ) {
852 setBaseFontFamilyName( "" );
853 final String font_str = ( ( String ) st.nextElement() ).trim();
854 final String[] fonts = font_str.split( ",+" );
855 for( String font : fonts ) {
856 font = font.replace( '_', ' ' ).trim();
857 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
858 setBaseFontFamilyName( font );
864 public void putDisplayColors( final String key, final Color color ) {
865 getDisplayColors().put( key, color );
869 * read each line of config file, process non-comment lines
870 * @throws IOException
872 private void readConfig( final BufferedReader conf_in ) throws IOException {
875 line = conf_in.readLine();
876 if ( line != null ) {
878 // skip comments and blank lines
879 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
880 // convert runs of spaces to tabs
881 line = line.replaceAll( "\\s+", "\t" );
882 final StringTokenizer st = new StringTokenizer( line, "\t" );
886 } while ( line != null );
889 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
890 _abbreviate_scientific_names = abbreviate_scientific_names;
893 public void setAddTaxonomyImagesCB( final boolean b ) {
894 display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no";
897 private void setAntialiasScreen( final boolean antialias_screen ) {
898 _antialias_screen = antialias_screen;
901 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
902 _background_color_gradient = background_color_gradient;
905 public void setBaseFontFamilyName( final String base_font_family_name ) {
906 _base_font_family_name = base_font_family_name;
909 public void setBaseFontSize( final int base_font_size ) {
910 _base_font_size = base_font_size;
913 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
914 _cladogram_type = cladogram_type;
917 public void setColorizeBranches( final boolean b ) {
918 display_options[ use_style ][ 2 ] = b ? "yes" : "no";
921 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
922 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
925 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
926 _default_bootstrap_samples = default_bootstrap_samples;
929 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
930 _default_node_fill = default_node_fill;
933 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
934 _default_node_shape = default_node_shape;
937 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
938 _default_node_shape_size = default_node_shape_size;
941 public void setDisplayAsPhylogram( final boolean b ) {
942 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
945 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
946 _display_colors = display_colors;
949 public void setDisplayConfidenceValues( final boolean b ) {
950 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
953 public void setDisplayGeneNames( final boolean b ) {
954 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
957 public void setDisplayInternalData( final boolean b ) {
958 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
961 public void setDisplayNodeNames( final boolean b ) {
962 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
965 public void setDisplaySequenceAcc( final boolean b ) {
966 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
969 public void setDisplaySequenceNames( final boolean b ) {
970 display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no";
973 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
974 _display_sequence_relations = display_sequence_relations;
977 public void setDisplaySequenceSymbols( final boolean b ) {
978 display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no";
981 public void setDisplayTaxonomyCode( final boolean b ) {
982 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
985 public void setDisplayTaxonomyCommonNames( final boolean b ) {
986 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
989 public void setDisplayTaxonomyImages( final boolean b ) {
990 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
993 public void setDisplayTaxonomyScientificNames( final boolean b ) {
994 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
997 public void setDynamicallyHideData( final boolean b ) {
998 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
1001 private void setEditable( final boolean editable ) {
1002 _editable = editable;
1005 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
1006 _ext_desc_data_to_return = ext_desc_data_to_return;
1009 private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
1010 _ext_node_data_return_on = ext_node_data_return_on;
1013 public void setFrameXSize( final int frame_x_size ) {
1014 _frame_x_size = frame_x_size;
1017 public void setFrameYSize( final int frame_y_size ) {
1018 _frame_y_size = frame_y_size;
1021 private void setGraphicsExportX( final int graphics_export_x ) {
1022 _graphics_export_x = graphics_export_x;
1025 private void setGraphicsExportY( final int graphics_export_y ) {
1026 _graphics_export_y = graphics_export_y;
1029 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
1030 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
1034 * Set a key-value(s) tuple
1036 private void setKeyValue( final StringTokenizer st ) {
1037 final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
1038 if ( !st.hasMoreElements() ) {
1041 // Handle single value settings first:
1042 if ( key.equals( "default_click_to" ) ) {
1043 final String clickto_name = ( String ) st.nextElement();
1044 default_clickto = getClickToIndex( clickto_name );
1045 if ( default_clickto == -1 ) {
1046 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
1047 + "] for [default_click_to]" );
1048 default_clickto = 0;
1050 else if ( default_clickto == DEPRECATED ) {
1054 else if ( key.equals( "native_ui" ) ) {
1055 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
1056 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
1059 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
1060 _ui = UI.CROSSPLATFORM;
1062 else if ( my_str.equals( "?" ) ) {
1066 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
1071 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
1072 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
1074 else if ( key.equals( "antialias_screen" ) ) {
1075 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
1077 else if ( key.equals( "phylogeny_graphics_type" ) ) {
1078 final String type_str = ( ( String ) st.nextElement() ).trim();
1079 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
1080 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1082 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
1083 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1085 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
1086 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1088 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
1089 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1091 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
1092 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1094 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
1095 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1097 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
1098 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1100 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
1101 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1104 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1105 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1106 + "] for [phylogeny_graphics_type]" );
1109 else if ( key.equals( "min_confidence_value" ) ) {
1110 final String mcv_str = ( ( String ) st.nextElement() ).trim();
1111 final double d = parseDouble( mcv_str );
1112 setMinConfidenceValue( d );
1114 else if ( key.equals( "font_family" ) ) {
1115 processFontFamily( st );
1117 else if ( key.equals( "font_size" ) ) {
1118 final String size_str = ( ( String ) st.nextElement() ).trim();
1119 final int i = parseInt( size_str );
1121 setBaseFontSize( i );
1124 else if ( key.equals( "font_size_min" ) ) {
1125 final String size_str = ( ( String ) st.nextElement() ).trim();
1126 final int i = parseInt( size_str );
1128 setMinBaseFontSize( i );
1131 else if ( key.equals( "font_size_max" ) ) {
1132 final String size_str = ( ( String ) st.nextElement() ).trim();
1133 final int i = parseInt( size_str );
1135 setMaxBaseFontSize( i );
1138 else if ( key.equals( "graphics_export_x" ) ) {
1139 final String str = ( ( String ) st.nextElement() ).trim();
1140 final int i = parseInt( str );
1142 setGraphicsExportX( i );
1145 else if ( key.equals( "graphics_export_y" ) ) {
1146 final String str = ( ( String ) st.nextElement() ).trim();
1147 final int i = parseInt( str );
1149 setGraphicsExportY( i );
1152 else if ( key.equals( "pdf_export_line_width" ) ) {
1153 final String str = ( ( String ) st.nextElement() ).trim();
1154 final float f = parseFloat( str );
1156 setPrintLineWidth( f );
1159 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1160 "value for [pdf_export_line_width] cannot be zero or negative" );
1163 else if ( key.equals( "window_initial_size_x" ) ) {
1164 final String str = ( ( String ) st.nextElement() ).trim();
1165 final int i = parseInt( str );
1170 else if ( key.equals( "window_initial_size_y" ) ) {
1171 final String str = ( ( String ) st.nextElement() ).trim();
1172 final int i = parseInt( str );
1177 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1178 final String str = ( ( String ) st.nextElement() ).trim();
1179 final int i = parseInt( str );
1181 setDefaultBootstrapSamples( i );
1185 .printWarningMessage( Constants.PRG_NAME,
1186 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1189 else if ( key.equals( "mafft_local" ) ) {
1190 final String str = ( ( String ) st.nextElement() ).trim();
1191 if ( !ForesterUtil.isEmpty( str ) ) {
1192 setPathToLocalMafft( new File( str ) );
1195 else if ( key.equals( "fastme_local" ) ) {
1196 final String str = ( ( String ) st.nextElement() ).trim();
1197 if ( !ForesterUtil.isEmpty( str ) ) {
1198 setPathToLocalFastme( new File( str ) );
1201 else if ( key.equals( "raxml_local" ) ) {
1202 final String str = ( ( String ) st.nextElement() ).trim();
1203 if ( !ForesterUtil.isEmpty( str ) ) {
1204 setPathToLocalRaxml( new File( str ) );
1207 else if ( key.equals( "show_scale" ) ) {
1208 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1210 else if ( key.equals( "show_overview" ) ) {
1211 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1213 else if ( key.equals( "background_gradient" ) ) {
1214 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1216 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1217 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1219 else if ( key.equals( "show_domain_labels" ) ) {
1220 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1222 else if ( key.equals( "show_seq_annotation_ref_sources" ) ) {
1223 setShowAnnotationRefSource( parseBoolean( ( String ) st.nextElement() ) );
1225 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1226 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1228 else if ( key.equals( "cladogram_type" ) ) {
1229 final String type_str = ( ( String ) st.nextElement() ).trim();
1230 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1231 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1233 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1234 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1236 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1237 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1240 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1241 + "] for [cladogram_type]" );
1244 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1246 .printWarningMessage( Constants.PRG_NAME,
1247 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1249 else if ( key.equals( "hide_controls_and_menus" ) ) {
1250 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1252 else if ( key.equals( "use_tabbed_display" ) ) {
1253 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1255 else if ( key.equals( "overview_width" ) ) {
1256 final short i = parseShort( ( ( String ) st.nextElement() ) );
1259 else if ( key.equals( "overview_height" ) ) {
1260 final short i = parseShort( ( ( String ) st.nextElement() ) );
1261 setOvMaxHeight( i );
1263 else if ( key.equals( "overview_placement_type" ) ) {
1264 final String type_str = ( ( String ) st.nextElement() ).trim();
1265 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1266 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1268 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1269 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1271 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1272 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1274 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1275 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1278 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1279 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1280 + "] for [overview_placement_type]" );
1283 else if ( key.equals( "node_label_direction" ) ) {
1284 final String type_str = ( ( String ) st.nextElement() ).trim();
1285 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1286 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1288 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1289 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1292 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1293 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1294 + "] for [node_label_direction]" );
1297 else if ( key.equals( "branch_length_value_digits" ) ) {
1298 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1300 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1303 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1304 + "] for [branch_length_value_digits]" );
1307 else if ( key.equals( "confidence_value_digits" ) ) {
1308 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1310 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1313 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1314 + "] for [confidence_value_digits]" );
1317 else if ( key.equals( "allow_editing" ) ) {
1318 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1320 else if ( key.equals( "display_sequence_relations" ) ) {
1321 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1323 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1324 final boolean r = parseBoolean( ( String ) st.nextElement() );
1325 if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
1327 .printWarningMessage( Constants.PRG_NAME,
1328 "attempt to extract taxonomies and replace underscores at the same time" );
1331 setReplaceUnderscoresInNhParsing( r );
1334 else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
1335 final String s = ( String ) st.nextElement();
1336 if ( s.equalsIgnoreCase( "no" ) ) {
1337 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1339 else if ( s.equalsIgnoreCase( "pfam_relaxed" ) ) {
1340 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1342 else if ( s.equalsIgnoreCase( "pfam_strict" ) ) {
1343 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1345 else if ( s.equalsIgnoreCase( "aggressive" ) ) {
1346 setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
1350 .printWarningMessage( Constants.PRG_NAME,
1351 "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
1353 + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
1355 if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
1357 .printWarningMessage( Constants.PRG_NAME,
1358 "attempt to extract taxonomies and replace underscores at the same time" );
1361 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1362 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1364 else if ( key.equals( "gui_background_color" ) ) {
1365 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1367 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1368 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1370 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1371 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1373 else if ( key.equals( "gui_button_text_color" ) ) {
1374 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1376 else if ( key.equals( "gui_button_background_color" ) ) {
1377 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1379 else if ( key.equals( "gui_menu_background_color" ) ) {
1380 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1382 else if ( key.equals( "gui_menu_text_color" ) ) {
1383 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1385 else if ( key.equals( "gui_button_border_color" ) ) {
1386 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1388 else if ( key.equals( "show_default_node_shapes_internal" ) ) {
1389 setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1391 else if ( key.equals( "show_default_node_shapes_external" ) ) {
1392 setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1394 else if ( key.equals( "show_node_shapes_for_nodes_with_vis_data" ) ) {
1395 setShowDefaultNodeShapesForMarkedNodes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1397 else if ( key.equals( "default_node_size" ) ) {
1398 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1399 setDefaultNodeShapeSize( i );
1401 else if ( key.equals( "default_node_fill" ) ) {
1402 final String fill_str = ( ( String ) st.nextElement() ).trim();
1403 if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.NONE.toString() ) ) {
1404 setDefaultNodeFill( NodeFill.NONE );
1406 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.GRADIENT.toString() ) ) {
1407 setDefaultNodeFill( NodeFill.GRADIENT );
1409 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.SOLID.toString() ) ) {
1410 setDefaultNodeFill( NodeFill.SOLID );
1413 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1414 + "] for [default_node_fill]" );
1417 else if ( key.equals( "default_node_shape" ) ) {
1418 final String shape_str = ( ( String ) st.nextElement() ).trim();
1419 if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.CIRCLE.toString() ) ) {
1420 setDefaultNodeShape( NodeShape.CIRCLE );
1422 else if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.RECTANGLE.toString() ) ) {
1423 setDefaultNodeShape( NodeShape.RECTANGLE );
1426 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1427 + "] for [default_node_shape]" );
1430 else if ( key.equals( "midpoint_reroot" ) ) {
1431 setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) );
1433 else if ( key.equals( "ext_descendents_data_to_return" ) ) {
1434 final String s = ( ( String ) st.nextElement() ).trim();
1435 if ( s.equalsIgnoreCase( "node_name" ) ) {
1436 setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
1438 else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
1439 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
1441 else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) {
1442 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ_FASTA );
1444 else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
1445 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
1447 else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
1448 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
1450 else if ( s.equalsIgnoreCase( "gene_name" ) ) {
1451 setExtDescNodeDataToReturn( NODE_DATA.GENE_NAME );
1453 else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
1454 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
1456 else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
1457 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME );
1459 else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
1460 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
1462 else if ( s.equalsIgnoreCase( "taxonomy_common_name" ) ) {
1463 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_COMM0N_NAME );
1465 else if ( s.equalsIgnoreCase( "user_selected" ) ) {
1466 setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
1469 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1470 + "] for [ext_descendents_data_to_return]" );
1473 else if ( key.equals( "label_for_get_ext_descendents_data" ) ) {
1474 final String s = ( ( String ) st.nextElement() ).trim();
1475 if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) {
1476 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s
1477 + "] for [label_for_get_ext_descendents_data]" );
1480 setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
1483 else if ( key.equals( "ext_descendents_data_to_return_on" ) ) {
1484 final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
1485 if ( s.equals( "console" ) ) {
1486 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
1488 else if ( s.equals( "window" ) ) {
1489 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
1491 else if ( s.equals( "buffer_only" ) ) {
1492 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
1495 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1496 + "] for [ext_descendents_data_to_return_on]" );
1499 else if ( key.equals( "vector_data_min_color" ) ) {
1500 _vector_data_min_color = Color.decode( ( String ) st.nextElement() );
1502 else if ( key.equals( "vector_data_max_color" ) ) {
1503 _vector_data_max_color = Color.decode( ( String ) st.nextElement() );
1505 else if ( key.equals( "vector_data_mean_color" ) ) {
1506 _vector_data_mean_color = Color.decode( ( String ) st.nextElement() );
1508 else if ( key.equals( "vector_data_width" ) ) {
1509 _vector_data_width = parseShort( ( String ) st.nextElement() );
1510 if ( _vector_data_width < 1 ) {
1511 _vector_data_width = 120;
1514 else if ( key.equals( "vector_data_height" ) ) {
1515 _vector_data_height = parseShort( ( String ) st.nextElement() );
1516 if ( _vector_data_height < 1 ) {
1517 _vector_data_height = 12;
1520 else if ( key.equals( "line_up_renderable_data" ) ) {
1521 setLineUpRendarableNodeData( parseBoolean( ( String ) st.nextElement() ) );
1523 else if ( key.equals( "right_align_domain_architectures" ) ) {
1524 setRightLineUpDomains( parseBoolean( ( String ) st.nextElement() ) );
1526 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1529 if ( key.equals( "phylogram" ) ) {
1530 key_index = Configuration.display_as_phylogram;
1532 else if ( key.equals( "rollover" ) ) {
1533 key_index = Configuration.node_data_popup;
1535 else if ( key.equals( "color_according_to_species" ) ) {
1536 key_index = Configuration.color_according_to_species;
1538 else if ( key.equals( "color_according_to_sequence" ) ) {
1539 key_index = Configuration.color_according_to_sequence;
1541 else if ( key.equals( "show_node_names" ) ) {
1542 key_index = Configuration.show_node_names;
1544 else if ( key.equals( "show_taxonomy_code" ) ) {
1545 key_index = Configuration.show_tax_code;
1547 else if ( key.equals( "write_confidence_values" ) ) {
1548 key_index = Configuration.write_confidence_values;
1550 else if ( key.equals( "write_branch_length_values" ) ) {
1551 key_index = Configuration.write_branch_length_values;
1553 else if ( key.equals( "write_events" ) ) {
1554 key_index = Configuration.write_events;
1556 else if ( key.equals( "use_visual_styles" ) ) {
1557 key_index = Configuration.use_style;
1559 else if ( key.equals( "color_branches" ) ) {
1560 key_index = Configuration.use_style;
1562 .printWarningMessage( Constants.PRG_NAME,
1563 "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" );
1565 else if ( key.equals( "width_branches" ) ) {
1566 key_index = Configuration.width_branches;
1568 else if ( key.equals( "show_domain_architectures" ) ) {
1569 key_index = Configuration.show_domain_architectures;
1571 else if ( key.equals( "show_msa" ) ) {
1572 key_index = Configuration.show_mol_seqs;
1574 else if ( key.equals( "show_annotations" ) ) {
1575 key_index = Configuration.show_annotation;
1577 else if ( key.equals( "show_binary_characters" ) ) {
1578 key_index = Configuration.show_binary_characters;
1580 else if ( key.equals( "show_binary_character_counts" ) ) {
1581 key_index = Configuration.show_binary_character_counts;
1583 else if ( key.equals( "show_seq_names" ) ) {
1584 key_index = Configuration.show_seq_names;
1586 else if ( key.equals( "show_gene_names" ) ) {
1587 key_index = Configuration.show_gene_names;
1589 else if ( key.equals( "show_seq_symbols" ) ) {
1590 key_index = Configuration.show_seq_symbols;
1592 else if ( key.equals( "show_seq_acc" ) ) {
1593 key_index = Configuration.show_sequence_acc;
1595 else if ( key.equals( "display_internal_data" ) ) {
1596 key_index = Configuration.display_internal_data;
1598 else if ( key.equals( "dynamically_hide_data" ) ) {
1599 key_index = Configuration.dynamically_hide_data;
1601 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1602 key_index = Configuration.show_taxonomy_scientific_names;
1604 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1605 key_index = Configuration.show_taxonomy_common_names;
1607 else if ( key.equals( "show_taxonomy_images" ) ) {
1608 key_index = Configuration.show_taxonomy_images;
1610 else if ( key.equals( "color_according_to_annotation" ) ) {
1611 key_index = Configuration.color_according_to_annotation;
1613 else if ( key.equals( "show_vector_data" ) ) {
1614 key_index = Configuration.show_vector_data;
1616 else if ( key.equals( "show_properties" ) ) {
1617 key_index = Configuration.show_properties;
1619 else if ( key.equals( "show_relation_confidence" ) ) {
1620 key_index = Configuration.show_relation_confidence;
1622 // If we've found the key, set the values
1623 if ( key_index >= 0 ) {
1624 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1625 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1626 // otherwise, keep looking
1629 if ( key_index == DEPRECATED ) {
1632 else if ( key.equals( "click_to" ) ) {
1633 final String click_to_name = ( String ) st.nextElement();
1634 key_index = getClickToIndex( click_to_name );
1635 if ( key_index >= 0 ) {
1636 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1638 else if ( key_index == DEPRECATED ) {
1642 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1646 else if ( key.equals( "species_color" ) ) {
1647 getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
1648 Color.decode( ( String ) st.nextElement() ) );
1650 else if ( key.equals( "sequence_color" ) ) {
1651 getSequenceColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
1652 Color.decode( ( String ) st.nextElement() ) );
1654 else if ( key.equals( "domain_color" ) ) {
1655 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1657 else if ( key.equals( "annotation_color" ) ) {
1658 getAnnotationColors()
1659 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1661 else if ( key.equals( "function_color" ) ) {
1662 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1663 "configuration key [function_color] is deprecated" );
1665 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1666 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1669 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1670 + "] in: " + config_filename );
1675 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1676 + config_filename );
1680 private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
1681 _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
1684 final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) {
1685 _line_up_renderable_node_data = line_up_renderable_node_data;
1688 private void setMaxBaseFontSize( final int max_base_font_size ) {
1689 _max_base_font_size = max_base_font_size;
1692 public void setMidpointReroot( final boolean midpoint_root ) {
1693 _midpoint_root = midpoint_root;
1696 private void setMinBaseFontSize( final int min_base_font_size ) {
1697 _min_base_font_size = min_base_font_size;
1700 public void setMinConfidenceValue( final double min_confidence_value ) {
1701 _min_confidence_value = min_confidence_value;
1704 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
1705 _node_label_direction = node_label_direction;
1708 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
1709 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
1712 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
1713 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
1716 private void setOvMaxHeight( final short ov_max_height ) {
1717 _ov_max_height = ov_max_height;
1720 private void setOvMaxWidth( final short ov_max_width ) {
1721 _ov_max_width = ov_max_width;
1724 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1725 _ov_placement = ov_placement;
1728 private void setPathToLocalFastme( final File path_to_local_fastme ) {
1729 _path_to_local_fastme = path_to_local_fastme;
1732 private void setPathToLocalMafft( final File path_to_local_mafft ) {
1733 _path_to_local_mafft = path_to_local_mafft;
1736 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
1737 _path_to_local_raxml = path_to_local_raxml;
1740 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
1741 _phylogeny_graphics_type = phylogeny_graphics_type;
1744 public void setPrintLineWidth( final float print_line_width ) {
1745 _print_line_width = print_line_width;
1748 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
1749 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
1752 final public void setRightLineUpDomains( final boolean right_align_domains ) {
1753 _right_align_domains = right_align_domains;
1756 private void setShowAnnotationRefSource( final boolean b ) {
1757 _show_annotation_ref_source = b;
1760 public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
1761 _show_default_node_shapes_external = show_default_node_shapes_external;
1764 public void setShowDefaultNodeShapesForMarkedNodes( final boolean show_default_node_shapes_for_marked_nodes ) {
1765 _show_default_node_shapes_for_marked_nodes = show_default_node_shapes_for_marked_nodes;
1768 public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
1769 _show_default_node_shapes_internal = show_default_node_shapes_internal;
1772 public void setShowDomainLabels( final boolean show_domain_labels ) {
1773 _show_domain_labels = show_domain_labels;
1776 private void setShowOverview( final boolean show_overview ) {
1777 _show_overview = show_overview;
1780 public void setShowScale( final boolean show_scale ) {
1781 _show_scale = show_scale;
1784 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
1785 _taxonomy_extraction = taxonomy_extraction;
1788 public void setUseStyle( final boolean b ) {
1789 display_options[ use_style ][ 2 ] = b ? "yes" : "no";
1792 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1793 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;