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_internal = false;
242 private boolean _show_domain_labels = true;
243 private boolean _show_overview = true;
244 private boolean _show_scale = false;
245 private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
246 private UI _ui = UI.UNKNOWN;
247 private boolean _use_tabbed_display = false;
248 private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
249 private Color _vector_data_min_color = Color.BLUE;
250 private Color _vector_data_max_color = Color.YELLOW;
251 private Color _vector_data_mean_color = Color.WHITE;
252 private double _vector_data_height = 12;
253 private int _vector_data_width = 120;
254 private boolean _line_up_renderable_node_data;
255 private boolean _right_align_domains;
257 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
258 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
259 DEFAULT_FONT_FAMILY = font_name;
263 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
264 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
268 static String getDefaultFontFamilyName() {
269 return DEFAULT_FONT_FAMILY;
272 public Configuration() {
273 this( null, false, false, false );
276 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
277 if ( ForesterUtil.isEmpty( cf ) ) {
278 config_filename = default_config_filename;
281 config_filename = cf;
283 setDisplayColors( new TreeMap<String, Color>() );
284 config_filename = config_filename.trim();
287 // If URL, open accordingly
289 u = new URL( config_filename );
291 final InputStreamReader isr = new InputStreamReader( u.openStream() );
292 final BufferedReader bf = new BufferedReader( isr );
295 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
296 + config_filename + "]" );
298 catch ( final Exception e ) {
299 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
300 + config_filename + "]: " + e.getLocalizedMessage() );
303 catch ( final Exception e ) {
304 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
305 + config_filename + "]" );
309 // Otherwise, open as a file
310 File f = new File( config_filename );
312 f = new File( config_filename + ".txt" );
314 if ( f.exists() && f.canRead() ) {
316 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
320 catch ( final Exception e ) {
322 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
323 + config_filename + "]: " + e );
329 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
330 + config_filename + "]" );
336 boolean displaySequenceRelations() {
337 return _display_sequence_relations;
340 boolean doCheckOption( final int which ) {
341 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
342 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
345 boolean doDisplayClickToOption( final int which ) {
346 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
349 boolean doDisplayOption( final int which ) {
350 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
354 * Will attempt to use the phylogeny to determine whether to check
355 * this or not (e.g. phylogram)
358 boolean doGuessCheckOption( final int which ) {
359 return display_options[ which ][ 2 ].equals( "?" );
362 Map<String, Color> getAnnotationColors() {
363 if ( _annotation_colors == null ) {
364 _annotation_colors = new Hashtable<String, Color>();
366 return _annotation_colors;
369 public String getBaseFontFamilyName() {
370 return _base_font_family_name;
373 int getBaseFontSize() {
374 return _base_font_size;
377 CLADOGRAM_TYPE getCladogramType() {
378 return _cladogram_type;
381 private int getClickToIndex( final String name ) {
383 if ( name.equals( "edit_info" ) ) {
384 index = Configuration.display_node_data;
386 .printWarningMessage( Constants.PRG_NAME,
387 "configuration key [edit_info] is deprecated, use [display node data] instead" );
389 else if ( name.equals( "display_node_data" ) ) {
390 index = Configuration.display_node_data;
392 else if ( name.equals( "collapse_uncollapse" ) ) {
393 index = Configuration.collapse_uncollapse;
395 else if ( name.equals( "reroot" ) ) {
396 index = Configuration.reroot;
398 else if ( name.equals( "subtree" ) ) {
399 index = Configuration.subtree;
401 else if ( name.equals( "swap" ) ) {
402 index = Configuration.swap;
404 else if ( name.equals( "sort_descendants" ) ) {
405 index = Configuration.sort_descendents;
407 else if ( name.equals( "get_ext_descendents_data" ) ) {
408 index = Configuration.get_ext_desc_data;
410 else if ( name.equals( "display_sequences" ) ) {
412 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
415 else if ( name.equals( "open_seq_web" ) ) {
416 index = Configuration.open_seq_web;
418 else if ( name.equals( "open_pdb_web" ) ) {
419 index = Configuration.open_pdb_web;
421 else if ( name.equals( "open_tax_web" ) ) {
422 index = Configuration.open_tax_web;
424 else if ( name.equals( "blast" ) ) {
425 index = Configuration.blast;
427 else if ( name.equals( "cut_subtree" ) ) {
428 index = Configuration.cut_subtree;
430 else if ( name.equals( "copy_subtree" ) ) {
431 index = Configuration.copy_subtree;
433 else if ( name.equals( "paste_subtree" ) ) {
434 index = Configuration.paste_subtree;
436 else if ( name.equals( "delete" ) ) {
437 index = Configuration.delete_subtree_or_node;
439 else if ( name.equals( "add_new_node" ) ) {
440 index = Configuration.add_new_node;
442 else if ( name.equals( "edit_node_data" ) ) {
443 index = Configuration.edit_node_data;
445 else if ( name.equals( "select_nodes" ) ) {
446 index = Configuration.select_nodes;
448 else if ( name.equals( "display_node_popup" ) ) {
449 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
450 "configuration key [display_node_popup] is deprecated" );
453 else if ( name.equals( "custom_option" ) ) {
454 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
457 else if ( name.equals( "color_subtree" ) ) {
458 index = Configuration.color_subtree;
460 else if ( name.equals( "change_node_font" ) ) {
461 index = Configuration.change_node_font;
463 else if ( name.equals( "color_node_font" ) ) {
464 index = Configuration.color_node_font;
466 else if ( name.equals( "color_subtree" ) ) {
467 index = Configuration.color_subtree;
472 int getClickToOptionsCount() {
473 return clickto_options.length;
476 String getClickToTitle( final int which ) {
477 return clickto_options[ which ][ 0 ];
480 public int getDefaultBootstrapSamples() {
481 return _default_bootstrap_samples;
484 int getDefaultDisplayClicktoOption() {
485 return default_clickto;
488 public NodeFill getDefaultNodeFill() {
489 return _default_node_fill;
492 public NodeShape getDefaultNodeShape() {
493 return _default_node_shape;
496 public short getDefaultNodeShapeSize() {
497 return _default_node_shape_size;
500 SortedMap<String, Color> getDisplayColors() {
501 return _display_colors;
504 String getDisplayTitle( final int which ) {
505 return display_options[ which ][ 0 ];
508 Map<String, Color> getDomainColors() {
509 if ( _domain_colors == null ) {
510 _domain_colors = new Hashtable<String, Color>();
512 return _domain_colors;
515 public NODE_DATA getExtDescNodeDataToReturn() {
516 return _ext_desc_data_to_return;
519 public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
520 return _ext_node_data_return_on;
523 public int getFrameXSize() {
524 return _frame_x_size;
527 public int getFrameYSize() {
528 return _frame_y_size;
531 int getGraphicsExportX() {
532 return _graphics_export_x;
535 int getGraphicsExportY() {
536 return _graphics_export_y;
539 Color getGuiBackgroundColor() {
540 return _gui_background_color;
543 Color getGuiButtonBackgroundColor() {
544 return _gui_button_background_color;
547 Color getGuiButtonBorderColor() {
548 return _gui_button_border_color;
551 Color getGuiButtonTextColor() {
552 return _gui_button_text_color;
555 Color getGuiCheckboxAndButtonActiveColor() {
556 return _gui_checkbox_and_button_active_color;
559 Color getGuiCheckboxTextColor() {
560 return _gui_checkbox_text_color;
563 Color getGuiMenuBackgroundColor() {
564 return _gui_menu_background_color;
567 Color getGuiMenuTextColor() {
568 return _gui_menu_text_color;
571 public String getLabelForGetExtDescendentsData() {
572 return _label_for_get_ext_descendents_data;
575 int getMaxBaseFontSize() {
576 return _max_base_font_size;
579 int getMinBaseFontSize() {
580 return _min_base_font_size;
583 double getMinConfidenceValue() {
584 return _min_confidence_value;
587 NODE_LABEL_DIRECTION getNodeLabelDirection() {
588 return _node_label_direction;
591 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
592 return _number_of_digits_after_comma_for_branch_length_values;
595 short getNumberOfDigitsAfterCommaForConfidenceValues() {
596 return _number_of_digits_after_comma_for_confidence_values;
599 short getOvMaxHeight() {
600 return _ov_max_height;
603 short getOvMaxWidth() {
604 return _ov_max_width;
607 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
608 return _ov_placement;
611 public File getPathToLocalFastme() {
612 return _path_to_local_fastme;
615 public File getPathToLocalMafft() {
616 return _path_to_local_mafft;
619 public File getPathToLocalRaxml() {
620 return _path_to_local_raxml;
623 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
624 return _phylogeny_graphics_type;
627 float getPrintLineWidth() {
628 return _print_line_width;
631 Hashtable<String, Color> getSequenceColors() {
632 if ( _sequence_colors == null ) {
633 _sequence_colors = new Hashtable<String, Color>();
635 return _sequence_colors;
638 Hashtable<String, Color> getSpeciesColors() {
639 if ( _species_colors == null ) {
642 return _species_colors;
645 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
646 return _taxonomy_extraction;
649 public double getVectorDataHeight() {
650 return _vector_data_height;
653 public Color getVectorDataMaxColor() {
654 return _vector_data_max_color;
657 public Color getVectorDataMeanColor() {
658 return _vector_data_mean_color;
661 public Color getVectorDataMinColor() {
662 return _vector_data_min_color;
665 public int getVectorDataWidth() {
666 return _vector_data_width;
669 private final void initSpeciesColors() {
670 _species_colors = new Hashtable<String, Color>();
671 for( final String[] s : DEFAULT_SPECIES_COLORS ) {
672 _species_colors.put( s[ 0 ], Color.decode( s[ 1 ] ) );
676 public boolean isAbbreviateScientificTaxonNames() {
677 return _abbreviate_scientific_names;
680 boolean isAntialiasScreen() {
681 if ( ForesterUtil.isMac() ) {
682 //Apple Macintosh graphics are slow, turn off anti-alias.
685 return _antialias_screen;
688 public boolean isBackgroundColorGradient() {
689 return _background_color_gradient;
692 public boolean isColorByTaxonomicGroup() {
696 public boolean isColorLabelsSameAsParentBranch() {
697 return _color_labels_same_as_parent_branch;
701 * Convenience method.
703 * @return true if value in configuration file was 'yes'
705 boolean isDrawAsPhylogram() {
706 return doCheckOption( display_as_phylogram );
709 boolean isEditable() {
714 * Only used by ArchaeoptryxE.
717 boolean isHideControlPanelAndMenubar() {
718 return _hide_controls_and_menus;
721 boolean isInternalNumberAreConfidenceForNhParsing() {
722 return _internal_number_are_confidence_for_nh_parsing;
725 final public boolean isLineUpRendarableNodeData() {
726 return _line_up_renderable_node_data;
729 public boolean isMidpointReroot() {
730 return _midpoint_root;
733 boolean isReplaceUnderscoresInNhParsing() {
734 return _nh_parsing_replace_underscores;
737 final public boolean isRightLineUpDomains() {
738 return _right_align_domains;
741 public boolean isShowAnnotationRefSource() {
742 return _show_annotation_ref_source;
745 public boolean isShowDefaultNodeShapesExternal() {
746 return _show_default_node_shapes_external;
749 public boolean isShowDefaultNodeShapesInternal() {
750 return _show_default_node_shapes_internal;
753 public boolean isShowDomainLabels() {
754 return _show_domain_labels;
757 boolean isShowOverview() {
758 return _show_overview;
761 boolean isShowScale() {
765 final boolean isUseNativeUI() {
766 if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
769 return _ui == UI.NATIVE;
773 * Only used by ArchaeoptryxE.
776 boolean isUseTabbedDisplay() {
777 return _use_tabbed_display;
780 boolean isValidatePhyloXmlAgainstSchema() {
781 return _validate_against_phyloxml_xsd_schema;
784 private boolean parseBoolean( final String str ) {
785 final String my_str = str.trim().toLowerCase();
786 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
789 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
793 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
798 private double parseDouble( final String str ) {
801 d = Double.parseDouble( str.trim() );
803 catch ( final Exception e ) {
804 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
810 private float parseFloat( final String str ) {
813 f = Float.parseFloat( str.trim() );
815 catch ( final Exception e ) {
816 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
822 private int parseInt( final String str ) {
825 i = Integer.parseInt( str.trim() );
827 catch ( final Exception e ) {
828 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
834 private short parseShort( final String str ) {
837 i = Short.parseShort( str.trim() );
839 catch ( final Exception e ) {
840 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
846 private void processFontFamily( final StringTokenizer st ) {
847 setBaseFontFamilyName( "" );
848 final String font_str = ( ( String ) st.nextElement() ).trim();
849 final String[] fonts = font_str.split( ",+" );
850 for( String font : fonts ) {
851 font = font.replace( '_', ' ' ).trim();
852 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
853 setBaseFontFamilyName( font );
859 public void putDisplayColors( final String key, final Color color ) {
860 getDisplayColors().put( key, color );
864 * read each line of config file, process non-comment lines
865 * @throws IOException
867 private void readConfig( final BufferedReader conf_in ) throws IOException {
870 line = conf_in.readLine();
871 if ( line != null ) {
873 // skip comments and blank lines
874 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
875 // convert runs of spaces to tabs
876 line = line.replaceAll( "\\s+", "\t" );
877 final StringTokenizer st = new StringTokenizer( line, "\t" );
881 } while ( line != null );
884 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
885 _abbreviate_scientific_names = abbreviate_scientific_names;
888 public void setAddTaxonomyImagesCB( final boolean b ) {
889 display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no";
892 private void setAntialiasScreen( final boolean antialias_screen ) {
893 _antialias_screen = antialias_screen;
896 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
897 _background_color_gradient = background_color_gradient;
900 public void setBaseFontFamilyName( final String base_font_family_name ) {
901 _base_font_family_name = base_font_family_name;
904 public void setBaseFontSize( final int base_font_size ) {
905 _base_font_size = base_font_size;
908 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
909 _cladogram_type = cladogram_type;
912 public void setColorizeBranches( final boolean b ) {
913 display_options[ use_style ][ 2 ] = b ? "yes" : "no";
916 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
917 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
920 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
921 _default_bootstrap_samples = default_bootstrap_samples;
924 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
925 _default_node_fill = default_node_fill;
928 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
929 _default_node_shape = default_node_shape;
932 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
933 _default_node_shape_size = default_node_shape_size;
936 public void setDisplayAsPhylogram( final boolean b ) {
937 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
940 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
941 _display_colors = display_colors;
944 public void setDisplayConfidenceValues( final boolean b ) {
945 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
948 public void setDisplayGeneNames( final boolean b ) {
949 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
952 public void setDisplayInternalData( final boolean b ) {
953 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
956 public void setDisplayNodeNames( final boolean b ) {
957 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
960 public void setDisplaySequenceAcc( final boolean b ) {
961 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
964 public void setDisplaySequenceNames( final boolean b ) {
965 display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no";
968 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
969 _display_sequence_relations = display_sequence_relations;
972 public void setDisplaySequenceSymbols( final boolean b ) {
973 display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no";
976 public void setDisplayTaxonomyCode( final boolean b ) {
977 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
980 public void setDisplayTaxonomyCommonNames( final boolean b ) {
981 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
984 public void setDisplayTaxonomyImages( final boolean b ) {
985 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
988 public void setDisplayTaxonomyScientificNames( final boolean b ) {
989 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
992 public void setDynamicallyHideData( final boolean b ) {
993 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
996 private void setEditable( final boolean editable ) {
997 _editable = editable;
1000 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
1001 _ext_desc_data_to_return = ext_desc_data_to_return;
1004 private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
1005 _ext_node_data_return_on = ext_node_data_return_on;
1008 public void setFrameXSize( final int frame_x_size ) {
1009 _frame_x_size = frame_x_size;
1012 public void setFrameYSize( final int frame_y_size ) {
1013 _frame_y_size = frame_y_size;
1016 private void setGraphicsExportX( final int graphics_export_x ) {
1017 _graphics_export_x = graphics_export_x;
1020 private void setGraphicsExportY( final int graphics_export_y ) {
1021 _graphics_export_y = graphics_export_y;
1024 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
1025 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
1029 * Set a key-value(s) tuple
1031 private void setKeyValue( final StringTokenizer st ) {
1032 final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
1033 if ( !st.hasMoreElements() ) {
1036 // Handle single value settings first:
1037 if ( key.equals( "default_click_to" ) ) {
1038 final String clickto_name = ( String ) st.nextElement();
1039 default_clickto = getClickToIndex( clickto_name );
1040 if ( default_clickto == -1 ) {
1041 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
1042 + "] for [default_click_to]" );
1043 default_clickto = 0;
1045 else if ( default_clickto == DEPRECATED ) {
1049 else if ( key.equals( "native_ui" ) ) {
1050 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
1051 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
1054 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
1055 _ui = UI.CROSSPLATFORM;
1057 else if ( my_str.equals( "?" ) ) {
1061 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
1066 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
1067 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
1069 else if ( key.equals( "antialias_screen" ) ) {
1070 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
1072 else if ( key.equals( "phylogeny_graphics_type" ) ) {
1073 final String type_str = ( ( String ) st.nextElement() ).trim();
1074 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
1075 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1077 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
1078 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1080 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
1081 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1083 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
1084 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1086 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
1087 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1089 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
1090 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1092 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
1093 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1095 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
1096 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1099 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1100 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1101 + "] for [phylogeny_graphics_type]" );
1104 else if ( key.equals( "min_confidence_value" ) ) {
1105 final String mcv_str = ( ( String ) st.nextElement() ).trim();
1106 final double d = parseDouble( mcv_str );
1107 setMinConfidenceValue( d );
1109 else if ( key.equals( "font_family" ) ) {
1110 processFontFamily( st );
1112 else if ( key.equals( "font_size" ) ) {
1113 final String size_str = ( ( String ) st.nextElement() ).trim();
1114 final int i = parseInt( size_str );
1116 setBaseFontSize( i );
1119 else if ( key.equals( "font_size_min" ) ) {
1120 final String size_str = ( ( String ) st.nextElement() ).trim();
1121 final int i = parseInt( size_str );
1123 setMinBaseFontSize( i );
1126 else if ( key.equals( "font_size_max" ) ) {
1127 final String size_str = ( ( String ) st.nextElement() ).trim();
1128 final int i = parseInt( size_str );
1130 setMaxBaseFontSize( i );
1133 else if ( key.equals( "graphics_export_x" ) ) {
1134 final String str = ( ( String ) st.nextElement() ).trim();
1135 final int i = parseInt( str );
1137 setGraphicsExportX( i );
1140 else if ( key.equals( "graphics_export_y" ) ) {
1141 final String str = ( ( String ) st.nextElement() ).trim();
1142 final int i = parseInt( str );
1144 setGraphicsExportY( i );
1147 else if ( key.equals( "pdf_export_line_width" ) ) {
1148 final String str = ( ( String ) st.nextElement() ).trim();
1149 final float f = parseFloat( str );
1151 setPrintLineWidth( f );
1154 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1155 "value for [pdf_export_line_width] cannot be zero or negative" );
1158 else if ( key.equals( "window_initial_size_x" ) ) {
1159 final String str = ( ( String ) st.nextElement() ).trim();
1160 final int i = parseInt( str );
1165 else if ( key.equals( "window_initial_size_y" ) ) {
1166 final String str = ( ( String ) st.nextElement() ).trim();
1167 final int i = parseInt( str );
1172 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1173 final String str = ( ( String ) st.nextElement() ).trim();
1174 final int i = parseInt( str );
1176 setDefaultBootstrapSamples( i );
1180 .printWarningMessage( Constants.PRG_NAME,
1181 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1184 else if ( key.equals( "mafft_local" ) ) {
1185 final String str = ( ( String ) st.nextElement() ).trim();
1186 if ( !ForesterUtil.isEmpty( str ) ) {
1187 setPathToLocalMafft( new File( str ) );
1190 else if ( key.equals( "fastme_local" ) ) {
1191 final String str = ( ( String ) st.nextElement() ).trim();
1192 if ( !ForesterUtil.isEmpty( str ) ) {
1193 setPathToLocalFastme( new File( str ) );
1196 else if ( key.equals( "raxml_local" ) ) {
1197 final String str = ( ( String ) st.nextElement() ).trim();
1198 if ( !ForesterUtil.isEmpty( str ) ) {
1199 setPathToLocalRaxml( new File( str ) );
1202 else if ( key.equals( "show_scale" ) ) {
1203 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1205 else if ( key.equals( "show_overview" ) ) {
1206 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1208 else if ( key.equals( "background_gradient" ) ) {
1209 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1211 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1212 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1214 else if ( key.equals( "show_domain_labels" ) ) {
1215 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1217 else if ( key.equals( "show_seq_annotation_ref_sources" ) ) {
1218 setShowAnnotationRefSource( parseBoolean( ( String ) st.nextElement() ) );
1220 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1221 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1223 else if ( key.equals( "cladogram_type" ) ) {
1224 final String type_str = ( ( String ) st.nextElement() ).trim();
1225 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1226 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1228 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1229 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1231 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1232 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1235 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1236 + "] for [cladogram_type]" );
1239 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1241 .printWarningMessage( Constants.PRG_NAME,
1242 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1244 else if ( key.equals( "hide_controls_and_menus" ) ) {
1245 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1247 else if ( key.equals( "use_tabbed_display" ) ) {
1248 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1250 else if ( key.equals( "overview_width" ) ) {
1251 final short i = parseShort( ( ( String ) st.nextElement() ) );
1254 else if ( key.equals( "overview_height" ) ) {
1255 final short i = parseShort( ( ( String ) st.nextElement() ) );
1256 setOvMaxHeight( i );
1258 else if ( key.equals( "overview_placement_type" ) ) {
1259 final String type_str = ( ( String ) st.nextElement() ).trim();
1260 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1261 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1263 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1264 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1266 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1267 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1269 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1270 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1273 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1274 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1275 + "] for [overview_placement_type]" );
1278 else if ( key.equals( "node_label_direction" ) ) {
1279 final String type_str = ( ( String ) st.nextElement() ).trim();
1280 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1281 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1283 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1284 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1287 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1288 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1289 + "] for [node_label_direction]" );
1292 else if ( key.equals( "branch_length_value_digits" ) ) {
1293 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1295 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1298 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1299 + "] for [branch_length_value_digits]" );
1302 else if ( key.equals( "confidence_value_digits" ) ) {
1303 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1305 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1308 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1309 + "] for [confidence_value_digits]" );
1312 else if ( key.equals( "allow_editing" ) ) {
1313 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1315 else if ( key.equals( "display_sequence_relations" ) ) {
1316 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1318 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1319 final boolean r = parseBoolean( ( String ) st.nextElement() );
1320 if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
1322 .printWarningMessage( Constants.PRG_NAME,
1323 "attempt to extract taxonomies and replace underscores at the same time" );
1326 setReplaceUnderscoresInNhParsing( r );
1329 else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
1330 final String s = ( String ) st.nextElement();
1331 if ( s.equalsIgnoreCase( "no" ) ) {
1332 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1334 else if ( s.equalsIgnoreCase( "pfam_relaxed" ) ) {
1335 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1337 else if ( s.equalsIgnoreCase( "pfam_strict" ) ) {
1338 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1340 else if ( s.equalsIgnoreCase( "aggressive" ) ) {
1341 setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
1345 .printWarningMessage( Constants.PRG_NAME,
1346 "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
1348 + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
1350 if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
1352 .printWarningMessage( Constants.PRG_NAME,
1353 "attempt to extract taxonomies and replace underscores at the same time" );
1356 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1357 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1359 else if ( key.equals( "gui_background_color" ) ) {
1360 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1362 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1363 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1365 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1366 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1368 else if ( key.equals( "gui_button_text_color" ) ) {
1369 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1371 else if ( key.equals( "gui_button_background_color" ) ) {
1372 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1374 else if ( key.equals( "gui_menu_background_color" ) ) {
1375 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1377 else if ( key.equals( "gui_menu_text_color" ) ) {
1378 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1380 else if ( key.equals( "gui_button_border_color" ) ) {
1381 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1383 else if ( key.equals( "show_default_node_shapes" ) ) {
1385 .printWarningMessage( Constants.PRG_NAME,
1386 "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" );
1387 final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() );
1388 setShowDefaultNodeShapesInternal( b );
1389 setShowDefaultNodeShapesExternal( b );
1391 else if ( key.equals( "show_default_node_shapes_internal" ) ) {
1392 setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1394 else if ( key.equals( "show_default_node_shapes_external" ) ) {
1395 setShowDefaultNodeShapesExternal( 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 setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
1765 _show_default_node_shapes_internal = show_default_node_shapes_internal;
1768 public void setShowDomainLabels( final boolean show_domain_labels ) {
1769 _show_domain_labels = show_domain_labels;
1772 private void setShowOverview( final boolean show_overview ) {
1773 _show_overview = show_overview;
1776 public void setShowScale( final boolean show_scale ) {
1777 _show_scale = show_scale;
1780 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
1781 _taxonomy_extraction = taxonomy_extraction;
1784 public void setUseStyle( final boolean b ) {
1785 display_options[ use_style ][ 2 ] = b ? "yes" : "no";
1788 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1789 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;