2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
7 // Copyright (C) 2000-2001 Washington University School of Medicine
8 // and Howard Hughes Medical Institute
9 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
10 // All rights reserved
12 // This library is free software; you can redistribute it and/or
13 // modify it under the terms of the GNU Lesser General Public
14 // License as published by the Free Software Foundation; either
15 // version 2.1 of the License, or (at your option) any later version.
17 // This library is distributed in the hope that it will be useful,
18 // but WITHOUT ANY WARRANTY; without even the implied warranty of
19 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20 // Lesser General Public License for more details.
22 // You should have received a copy of the GNU Lesser General Public
23 // License along with this library; if not, write to the Free Software
24 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
26 // Contact: phylosoft @ gmail . com
27 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
29 package org.forester.archaeopteryx;
31 import java.awt.Color;
32 import java.io.BufferedReader;
34 import java.io.FileReader;
35 import java.io.IOException;
36 import java.io.InputStreamReader;
38 import java.util.Arrays;
39 import java.util.Hashtable;
41 import java.util.SortedMap;
42 import java.util.StringTokenizer;
43 import java.util.TreeMap;
45 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
46 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
47 import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE;
48 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
49 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
50 import org.forester.phylogeny.data.NodeDataField;
51 import org.forester.phylogeny.data.NodeVisualData;
52 import org.forester.phylogeny.data.NodeVisualData.NodeFill;
53 import org.forester.phylogeny.data.NodeVisualData.NodeShape;
54 import org.forester.util.ForesterUtil;
56 public final class Configuration {
58 public enum EXT_NODE_DATA_RETURN_ON {
59 BUFFER_ONLY, CONSOLE, WINODW;
63 CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN
69 final static String clickto_options[][] = {
70 { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
71 { "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "display" },
72 { "Colorize Node(s)", "display" }, { "Change Node Font(s)", "display" },
73 { "Colorize Subtree(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "display" },
74 { "Open Taxonomy DB", "display" }, { "Launch BLAST", "display" }, { "Cut Subtree", "display" },
75 { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" },
76 { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Sort Descendants", "display" },
77 { "List Node Data", "display" }, { "Select Node(s)", "display" } };
78 private final static String DEFAULT_SPECIES_COLORS[][] = {
79 { "BRAFL", "0x00FFFF" }, { "SPHGR", "0x9620F0" }, { "STRPU", "0x9620F0" }, { "CIOIN", "0xFF1CAE" },
80 { "CIOSA", "0xFF2CAE" }, { "BOVIN", "0x5C3317" }, { "CANFA", "0x8B2323" }, { "HUMAN", "0xFF2400" },
81 { "PANTR", "0xCC2400" }, { "MOUSE", "0xFF7F00" }, { "RAT", "0xFFEF00" }, { "MONDO", "0xEE9A49" },
82 { "ORNAN", "0xCD853F" }, { "XENLA", "0x6BAA23" }, { "XENTR", "0x6BAA23" }, { "CHICK", "0xFFC125" },
83 { "FUGRU", "0x0000FF" }, { "BRARE", "0x0000DD" }, { "DANRE", "0x0000BB" }, { "TETNG", "0x0000AA" },
84 { "ORYLA", "0x000088" }, { "GASAC", "0x000066" }, { "CAEEL", "0x666699" }, { "CAEBR", "0xB0B0B0" },
85 { "DROME", "0x663366" }, { "DROPS", "0x996699" }, { "APIME", "0x7A7700" }, { "AEDAE", "0x8C5900" },
86 { "TRICA", "0x918E00" }, { "NEMVE", "0x0066CC" }, { "HYDVU", "0x3399FF" }, { "LUBBA", "0xF7B5CB" },
87 { "GEOCY", "0xF5A0BD" }, { "AMPQE", "0x009966" }, { "SUBDO", "0xC790B9" }, { "MONBE", "0xFC0FC0" },
88 { "DICPU", "0xFFCC33" }, { "DICDI", "0xFFCC00" }, { "ENTHI", "0x5959AB" }, { "ARATH", "0x00FF00" },
89 { "POPTR", "0x006400" }, { "VITVI", "0x00CD00" }, { "GLYMA", "0x00FF7F" }, { "ORYSA", "0x008B00" },
90 { "ORYSJ", "0x008C00" }, { "SORBI", "0x00EE76" }, { "SELMO", "0x238E23" }, { "PHYPA", "0x09F911" },
91 { "OSTLU", "0x7FFF00" }, { "OSTTA", "0x7FFF00" }, { "OSTRC", "0x7FFF00" }, { "MICPU", "0x66CD00" },
92 { "MIC99", "0x66CD00" }, { "CHLRE", "0xB3EE3A" }, { "VOLCA", "0xC0FF3E" }, { "CHLSP", "0x6B8E23" },
93 { "CYAME", "0xD02090" }, { "YEAST", "0xAAAAAA" }, { "BACFR", "0xFF0000" }, { "BACTN", "0xFFFF00" },
94 { "MYXXD", "0x0000FF" }, { "STIAU", "0x00FFFF" }, { "BACOV", "0x8C5900" }, { "BACUN", "0x66CD00" },
95 { "PORGI", "0x918E00" } };
96 final static int display_node_data = 0;
97 final static int collapse_uncollapse = 1;
98 final static int reroot = 2;
99 final static int subtree = 3;
100 final static int swap = 4;
101 final static int color_node_font = 5;
102 final static int change_node_font = 6;
103 final static int color_subtree = 7;
104 final static int open_seq_web = 8;
105 final static int open_pdb_web = 9;
106 final static int open_tax_web = 10;
107 final static int blast = 11;
108 final static int cut_subtree = 12;
109 final static int copy_subtree = 13;
110 final static int paste_subtree = 14;
111 final static int delete_subtree_or_node = 15;
112 final static int add_new_node = 16;
113 final static int edit_node_data = 17;
114 final static int sort_descendents = 18;
115 final static int get_ext_desc_data = 19;
116 final static int select_nodes = 20;
117 // ------------------
119 // ------------------
120 final static String display_options[][] = {
121 { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
122 { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" },
123 { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
124 { "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" },
125 { "Branch Widths", "display", "no" }, { "Domain Architectures", "display", "no" },
126 { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
127 { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" },
128 { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
129 { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
130 { "Colorize by Annotation", "display", "no" }, { "Seq Symbol", "display", "yes" },
131 { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
132 { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
133 { "Properties", "display", "no" }, { "Gene Name", "display", "yes" },
134 { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" } };
135 final static int display_as_phylogram = 0;
136 final static int show_node_names = 1;
137 final static int show_tax_code = 2;
138 final static int show_annotation = 3;
139 final static int write_confidence_values = 4;
140 final static int write_events = 5;
141 final static int color_according_to_species = 6;
142 final static int color_according_to_sequence = 7;
143 final static int use_style = 8;
144 final static int width_branches = 9;
145 final static int show_domain_architectures = 10;
146 final static int show_binary_characters = 11;
147 final static int show_binary_character_counts = 12;
148 final static int show_seq_names = 13;
149 final static int show_sequence_acc = 14;
150 final static int display_internal_data = 15;
151 final static int dynamically_hide_data = 16;
152 final static int show_taxonomy_scientific_names = 17;
153 final static int show_taxonomy_common_names = 18;
154 final static int color_according_to_annotation = 19;
155 final static int show_seq_symbols = 20;
156 final static int node_data_popup = 21;
157 final static int show_relation_confidence = 22;
158 final static int show_vector_data = 23;
159 final static int show_taxonomy_images = 24;
160 final static int show_properties = 25;
161 final static int show_gene_names = 26;
162 final static int show_mol_seqs = 27;
163 final static int write_branch_length_values = 28;
164 static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
165 private static Hashtable<String, Color> _sequence_colors;
166 private static Hashtable<String, Color> _annotation_colors;
167 private static Hashtable<String, Color> _domain_colors;
168 private static Hashtable<String, Color> _species_colors;
169 private static String DEFAULT_FONT_FAMILY = "";
170 private static final int DEPRECATED = -2;
171 private static final String DISPLAY_COLOR_KEY = "display_color";
172 // ---------------------------
173 // Display options for trees
174 // ---------------------------
175 // ---------------------------------
176 // Pertaining to the config itself
177 // ---------------------------------
178 // Full path to config (may be URL)
179 String config_filename;
180 // This option is selected in the dropdown
181 int default_clickto = Configuration.display_node_data;
182 String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
186 TreeColorSet tree_color_set;
190 TreeFontSet tree_font_set;
191 boolean verbose = Constants.VERBOSE_DEFAULT;
192 private boolean _abbreviate_scientific_names = false;
193 private boolean _antialias_screen = true;
194 private boolean _background_color_gradient = false;
195 private String _base_font_family_name = "";
196 private int _base_font_size = -1;
197 private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
198 private boolean _color_labels_same_as_parent_branch = false;
199 private int _default_bootstrap_samples = -1;
200 private NodeFill _default_node_fill = NodeFill.SOLID;
201 private NodeShape _default_node_shape = NodeShape.RECTANGLE;
202 private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
203 private SortedMap<String, Color> _display_colors = null;
204 private boolean _display_sequence_relations = false;
205 private boolean _editable = true;
206 private NodeDataField _ext_desc_data_to_return = NodeDataField.UNKNOWN;
207 private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
208 private int _frame_x_size;
209 private int _frame_y_size;
210 private int _graphics_export_x = -1;
211 private int _graphics_export_y = -1;
212 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
213 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
214 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
215 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
216 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
217 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
218 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
219 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
220 private boolean _hide_controls_and_menus = false;
221 private boolean _internal_number_are_confidence_for_nh_parsing = false;
222 private String _label_for_get_ext_descendents_data = "";
223 private int _max_base_font_size = 20;
224 private boolean _midpoint_root = false;
225 private int _min_base_font_size = 2;
226 private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
227 private boolean _nh_parsing_replace_underscores = false;
228 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
229 private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
230 private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
231 private short _ov_max_height = 80;
232 private short _ov_max_width = 80;
233 private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
234 private File _path_to_local_fastme = null;
235 private File _path_to_local_mafft = null;
236 private File _path_to_local_raxml = null;
237 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
238 private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
239 private boolean _show_annotation_ref_source = true;
240 private boolean _show_default_node_shapes_external = false;
241 private boolean _show_default_node_shapes_for_marked_nodes = false;
242 private boolean _show_default_node_shapes_internal = false;
243 private boolean _show_domain_labels = true;
244 private boolean _show_overview = true;
245 private boolean _show_scale = false;
246 private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
247 private UI _ui = UI.UNKNOWN;
248 private boolean _use_tabbed_display = false;
249 private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
250 private Color _vector_data_min_color = Color.BLUE;
251 private Color _vector_data_max_color = Color.YELLOW;
252 private Color _vector_data_mean_color = Color.WHITE;
253 private double _vector_data_height = 12;
254 private int _vector_data_width = 120;
255 private boolean _line_up_renderable_node_data = true;
256 private boolean _right_align_domains = false;
257 private boolean _allow_thick_strokes = false;
259 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
260 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
261 DEFAULT_FONT_FAMILY = font_name;
265 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
266 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
270 public Configuration() {
271 this( null, false, false, false );
274 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
275 if ( ForesterUtil.isEmpty( cf ) ) {
276 config_filename = default_config_filename;
279 config_filename = cf;
281 setDisplayColors( new TreeMap<String, Color>() );
282 config_filename = config_filename.trim();
285 // If URL, open accordingly
287 u = new URL( config_filename );
289 final InputStreamReader isr = new InputStreamReader( u.openStream() );
290 final BufferedReader bf = new BufferedReader( isr );
293 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
294 + config_filename + "]" );
296 catch ( final Exception e ) {
297 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
298 + config_filename + "]: " + e.getLocalizedMessage() );
301 catch ( final Exception e ) {
302 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
303 + config_filename + "]" );
307 // Otherwise, open as a file
308 File f = new File( config_filename );
310 f = new File( config_filename + ".txt" );
312 if ( f.exists() && f.canRead() ) {
314 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
318 catch ( final Exception e ) {
320 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
321 + config_filename + "]: " + e );
327 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
328 + config_filename + "]" );
334 public String getBaseFontFamilyName() {
335 return _base_font_family_name;
338 public int getDefaultBootstrapSamples() {
339 return _default_bootstrap_samples;
342 public NodeFill getDefaultNodeFill() {
343 return _default_node_fill;
346 public NodeShape getDefaultNodeShape() {
347 return _default_node_shape;
350 public short getDefaultNodeShapeSize() {
351 return _default_node_shape_size;
354 public NodeDataField getExtDescNodeDataToReturn() {
355 return _ext_desc_data_to_return;
358 public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
359 return _ext_node_data_return_on;
362 public int getFrameXSize() {
363 return _frame_x_size;
366 public int getFrameYSize() {
367 return _frame_y_size;
370 public String getLabelForGetExtDescendentsData() {
371 return _label_for_get_ext_descendents_data;
374 public File getPathToLocalFastme() {
375 return _path_to_local_fastme;
378 public File getPathToLocalMafft() {
379 return _path_to_local_mafft;
382 public File getPathToLocalRaxml() {
383 return _path_to_local_raxml;
386 public double getVectorDataHeight() {
387 return _vector_data_height;
390 public Color getVectorDataMaxColor() {
391 return _vector_data_max_color;
394 public Color getVectorDataMeanColor() {
395 return _vector_data_mean_color;
398 public Color getVectorDataMinColor() {
399 return _vector_data_min_color;
402 public int getVectorDataWidth() {
403 return _vector_data_width;
406 public boolean isAbbreviateScientificTaxonNames() {
407 return _abbreviate_scientific_names;
410 public boolean isAllowThickStrokes() {
411 return _allow_thick_strokes;
414 public boolean isBackgroundColorGradient() {
415 return _background_color_gradient;
418 public boolean isColorByTaxonomicGroup() {
422 public boolean isColorLabelsSameAsParentBranch() {
423 return _color_labels_same_as_parent_branch;
426 final public boolean isLineUpRendarableNodeData() {
427 return _line_up_renderable_node_data;
430 public boolean isMidpointReroot() {
431 return _midpoint_root;
434 final public boolean isRightLineUpDomains() {
435 return _right_align_domains;
438 public boolean isShowAnnotationRefSource() {
439 return _show_annotation_ref_source;
442 public boolean isShowDefaultNodeShapesExternal() {
443 return _show_default_node_shapes_external;
446 public boolean isShowDefaultNodeShapesForMarkedNodes() {
447 return _show_default_node_shapes_for_marked_nodes;
450 public boolean isShowDefaultNodeShapesInternal() {
451 return _show_default_node_shapes_internal;
454 public boolean isShowDomainLabels() {
455 return _show_domain_labels;
458 public void putDisplayColors( final String key, final Color color ) {
459 getDisplayColors().put( key, color );
462 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
463 _abbreviate_scientific_names = abbreviate_scientific_names;
466 public void setAddTaxonomyImagesCB( final boolean b ) {
467 display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no";
470 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
471 _background_color_gradient = background_color_gradient;
474 public void setBaseFontFamilyName( final String base_font_family_name ) {
475 _base_font_family_name = base_font_family_name;
478 public void setBaseFontSize( final int base_font_size ) {
479 _base_font_size = base_font_size;
482 public void setColorizeBranches( final boolean b ) {
483 display_options[ use_style ][ 2 ] = b ? "yes" : "no";
486 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
487 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
490 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
491 _default_node_fill = default_node_fill;
494 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
495 _default_node_shape = default_node_shape;
498 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
499 _default_node_shape_size = default_node_shape_size;
502 public void setDisplayAsPhylogram( final boolean b ) {
503 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
506 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
507 _display_colors = display_colors;
510 public void setDisplayConfidenceValues( final boolean b ) {
511 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
514 public void setDisplayGeneNames( final boolean b ) {
515 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
518 public void setDisplayInternalData( final boolean b ) {
519 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
522 public void setDisplayMultipleSequenceAlignment( final boolean b ) {
523 display_options[ show_mol_seqs ][ 2 ] = b ? "yes" : "no";
526 public void setDisplayNodeNames( final boolean b ) {
527 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
530 public void setDisplaySequenceAcc( final boolean b ) {
531 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
534 public void setDisplaySequenceNames( final boolean b ) {
535 display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no";
538 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
539 _display_sequence_relations = display_sequence_relations;
542 public void setDisplaySequenceSymbols( final boolean b ) {
543 display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no";
546 public void setDisplayTaxonomyCode( final boolean b ) {
547 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
550 public void setDisplayTaxonomyCommonNames( final boolean b ) {
551 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
554 public void setDisplayTaxonomyImages( final boolean b ) {
555 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
558 public void setDisplayTaxonomyScientificNames( final boolean b ) {
559 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
562 public void setDynamicallyHideData( final boolean b ) {
563 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
566 public void setExtDescNodeDataToReturn( final NodeDataField ext_desc_data_to_return ) {
567 _ext_desc_data_to_return = ext_desc_data_to_return;
570 public void setFrameXSize( final int frame_x_size ) {
571 _frame_x_size = frame_x_size;
574 public void setFrameYSize( final int frame_y_size ) {
575 _frame_y_size = frame_y_size;
578 final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) {
579 _line_up_renderable_node_data = line_up_renderable_node_data;
582 public void setMidpointReroot( final boolean midpoint_root ) {
583 _midpoint_root = midpoint_root;
586 public void setMinConfidenceValue( final double min_confidence_value ) {
587 _min_confidence_value = min_confidence_value;
590 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
591 _node_label_direction = node_label_direction;
594 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
595 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
598 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
599 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
602 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
603 _phylogeny_graphics_type = phylogeny_graphics_type;
606 public void setPrintLineWidth( final float print_line_width ) {
607 _print_line_width = print_line_width;
610 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
611 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
614 final public void setRightLineUpDomains( final boolean right_align_domains ) {
615 _right_align_domains = right_align_domains;
618 public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
619 _show_default_node_shapes_external = show_default_node_shapes_external;
622 public void setShowDefaultNodeShapesForMarkedNodes( final boolean show_default_node_shapes_for_marked_nodes ) {
623 _show_default_node_shapes_for_marked_nodes = show_default_node_shapes_for_marked_nodes;
626 public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
627 _show_default_node_shapes_internal = show_default_node_shapes_internal;
630 public void setShowDomainLabels( final boolean show_domain_labels ) {
631 _show_domain_labels = show_domain_labels;
634 public void setShowScale( final boolean show_scale ) {
635 _show_scale = show_scale;
638 public void setUseStyle( final boolean b ) {
639 display_options[ use_style ][ 2 ] = b ? "yes" : "no";
642 private int getClickToIndex( final String name ) {
644 if ( name.equals( "edit_info" ) ) {
645 index = Configuration.display_node_data;
647 .printWarningMessage( Constants.PRG_NAME,
648 "configuration key [edit_info] is deprecated, use [display node data] instead" );
650 else if ( name.equals( "display_node_data" ) ) {
651 index = Configuration.display_node_data;
653 else if ( name.equals( "collapse_uncollapse" ) ) {
654 index = Configuration.collapse_uncollapse;
656 else if ( name.equals( "reroot" ) ) {
657 index = Configuration.reroot;
659 else if ( name.equals( "subtree" ) ) {
660 index = Configuration.subtree;
662 else if ( name.equals( "swap" ) ) {
663 index = Configuration.swap;
665 else if ( name.equals( "sort_descendants" ) ) {
666 index = Configuration.sort_descendents;
668 else if ( name.equals( "get_ext_descendents_data" ) ) {
669 index = Configuration.get_ext_desc_data;
671 else if ( name.equals( "display_sequences" ) ) {
673 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
676 else if ( name.equals( "open_seq_web" ) ) {
677 index = Configuration.open_seq_web;
679 else if ( name.equals( "open_pdb_web" ) ) {
680 index = Configuration.open_pdb_web;
682 else if ( name.equals( "open_tax_web" ) ) {
683 index = Configuration.open_tax_web;
685 else if ( name.equals( "blast" ) ) {
686 index = Configuration.blast;
688 else if ( name.equals( "cut_subtree" ) ) {
689 index = Configuration.cut_subtree;
691 else if ( name.equals( "copy_subtree" ) ) {
692 index = Configuration.copy_subtree;
694 else if ( name.equals( "paste_subtree" ) ) {
695 index = Configuration.paste_subtree;
697 else if ( name.equals( "delete" ) ) {
698 index = Configuration.delete_subtree_or_node;
700 else if ( name.equals( "add_new_node" ) ) {
701 index = Configuration.add_new_node;
703 else if ( name.equals( "edit_node_data" ) ) {
704 index = Configuration.edit_node_data;
706 else if ( name.equals( "select_nodes" ) ) {
707 index = Configuration.select_nodes;
709 else if ( name.equals( "display_node_popup" ) ) {
710 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
711 "configuration key [display_node_popup] is deprecated" );
714 else if ( name.equals( "custom_option" ) ) {
715 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
718 else if ( name.equals( "color_subtree" ) ) {
719 index = Configuration.color_subtree;
721 else if ( name.equals( "change_node_font" ) ) {
722 index = Configuration.change_node_font;
724 else if ( name.equals( "color_node_font" ) ) {
725 index = Configuration.color_node_font;
727 else if ( name.equals( "color_subtree" ) ) {
728 index = Configuration.color_subtree;
733 private final void initSpeciesColors() {
734 _species_colors = new Hashtable<String, Color>();
735 for( final String[] s : DEFAULT_SPECIES_COLORS ) {
736 _species_colors.put( s[ 0 ], Color.decode( s[ 1 ] ) );
740 private boolean parseBoolean( final String str ) {
741 final String my_str = str.trim().toLowerCase();
742 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
745 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
749 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
754 private double parseDouble( final String str ) {
757 d = Double.parseDouble( str.trim() );
759 catch ( final Exception e ) {
760 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
766 private float parseFloat( final String str ) {
769 f = Float.parseFloat( str.trim() );
771 catch ( final Exception e ) {
772 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
778 private int parseInt( final String str ) {
781 i = Integer.parseInt( str.trim() );
783 catch ( final Exception e ) {
784 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
790 private short parseShort( final String str ) {
793 i = Short.parseShort( str.trim() );
795 catch ( final Exception e ) {
796 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
802 private void processFontFamily( final StringTokenizer st ) {
803 setBaseFontFamilyName( "" );
804 final String font_str = ( ( String ) st.nextElement() ).trim();
805 final String[] fonts = font_str.split( ",+" );
806 for( String font : fonts ) {
807 font = font.replace( '_', ' ' ).trim();
808 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
809 setBaseFontFamilyName( font );
816 * read each line of config file, process non-comment lines
817 * @throws IOException
819 private void readConfig( final BufferedReader conf_in ) throws IOException {
822 line = conf_in.readLine();
823 if ( line != null ) {
825 // skip comments and blank lines
826 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
827 // convert runs of spaces to tabs
828 line = line.replaceAll( "\\s+", "\t" );
829 final StringTokenizer st = new StringTokenizer( line, "\t" );
833 } while ( line != null );
836 private void setAntialiasScreen( final boolean antialias_screen ) {
837 _antialias_screen = antialias_screen;
840 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
841 _cladogram_type = cladogram_type;
844 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
845 _default_bootstrap_samples = default_bootstrap_samples;
848 private void setEditable( final boolean editable ) {
849 _editable = editable;
852 private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
853 _ext_node_data_return_on = ext_node_data_return_on;
856 private void setGraphicsExportX( final int graphics_export_x ) {
857 _graphics_export_x = graphics_export_x;
860 private void setGraphicsExportY( final int graphics_export_y ) {
861 _graphics_export_y = graphics_export_y;
864 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
865 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
869 * Set a key-value(s) tuple
871 private void setKeyValue( final StringTokenizer st ) {
872 final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
873 if ( !st.hasMoreElements() ) {
876 // Handle single value settings first:
877 if ( key.equals( "default_click_to" ) ) {
878 final String clickto_name = ( String ) st.nextElement();
879 default_clickto = getClickToIndex( clickto_name );
880 if ( default_clickto == -1 ) {
881 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
882 + "] for [default_click_to]" );
885 else if ( default_clickto == DEPRECATED ) {
889 else if ( key.equals( "native_ui" ) ) {
890 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
891 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
894 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
895 _ui = UI.CROSSPLATFORM;
897 else if ( my_str.equals( "?" ) ) {
901 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
906 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
907 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
909 else if ( key.equals( "antialias_screen" ) ) {
910 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
912 else if ( key.equals( "phylogeny_graphics_type" ) ) {
913 final String type_str = ( ( String ) st.nextElement() ).trim();
914 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
915 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
917 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
918 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
920 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
921 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
923 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
924 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
926 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
927 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
929 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
930 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
932 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
933 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
935 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
936 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
939 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
940 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
941 + "] for [phylogeny_graphics_type]" );
944 else if ( key.equals( "min_confidence_value" ) ) {
945 final String mcv_str = ( ( String ) st.nextElement() ).trim();
946 final double d = parseDouble( mcv_str );
947 setMinConfidenceValue( d );
949 else if ( key.equals( "font_family" ) ) {
950 processFontFamily( st );
952 else if ( key.equals( "font_size" ) ) {
953 final String size_str = ( ( String ) st.nextElement() ).trim();
954 final int i = parseInt( size_str );
956 setBaseFontSize( i );
959 else if ( key.equals( "font_size_min" ) ) {
960 final String size_str = ( ( String ) st.nextElement() ).trim();
961 final int i = parseInt( size_str );
963 setMinBaseFontSize( i );
966 else if ( key.equals( "font_size_max" ) ) {
967 final String size_str = ( ( String ) st.nextElement() ).trim();
968 final int i = parseInt( size_str );
970 setMaxBaseFontSize( i );
973 else if ( key.equals( "graphics_export_x" ) ) {
974 final String str = ( ( String ) st.nextElement() ).trim();
975 final int i = parseInt( str );
977 setGraphicsExportX( i );
980 else if ( key.equals( "graphics_export_y" ) ) {
981 final String str = ( ( String ) st.nextElement() ).trim();
982 final int i = parseInt( str );
984 setGraphicsExportY( i );
987 else if ( key.equals( "pdf_export_line_width" ) ) {
988 final String str = ( ( String ) st.nextElement() ).trim();
989 final float f = parseFloat( str );
991 setPrintLineWidth( f );
994 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
995 "value for [pdf_export_line_width] cannot be zero or negative" );
998 else if ( key.equals( "window_initial_size_x" ) ) {
999 final String str = ( ( String ) st.nextElement() ).trim();
1000 final int i = parseInt( str );
1005 else if ( key.equals( "window_initial_size_y" ) ) {
1006 final String str = ( ( String ) st.nextElement() ).trim();
1007 final int i = parseInt( str );
1012 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1013 final String str = ( ( String ) st.nextElement() ).trim();
1014 final int i = parseInt( str );
1016 setDefaultBootstrapSamples( i );
1020 .printWarningMessage( Constants.PRG_NAME,
1021 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1024 else if ( key.equals( "mafft_local" ) ) {
1025 final String str = ( ( String ) st.nextElement() ).trim();
1026 if ( !ForesterUtil.isEmpty( str ) ) {
1027 setPathToLocalMafft( new File( str ) );
1030 else if ( key.equals( "fastme_local" ) ) {
1031 final String str = ( ( String ) st.nextElement() ).trim();
1032 if ( !ForesterUtil.isEmpty( str ) ) {
1033 setPathToLocalFastme( new File( str ) );
1036 else if ( key.equals( "raxml_local" ) ) {
1037 final String str = ( ( String ) st.nextElement() ).trim();
1038 if ( !ForesterUtil.isEmpty( str ) ) {
1039 setPathToLocalRaxml( new File( str ) );
1042 else if ( key.equals( "show_scale" ) ) {
1043 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1045 else if ( key.equals( "show_overview" ) ) {
1046 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1048 else if ( key.equals( "background_gradient" ) ) {
1049 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1051 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1052 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1054 else if ( key.equals( "show_domain_labels" ) ) {
1055 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1057 else if ( key.equals( "show_seq_annotation_ref_sources" ) ) {
1058 setShowAnnotationRefSource( parseBoolean( ( String ) st.nextElement() ) );
1060 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1061 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1063 else if ( key.equals( "cladogram_type" ) ) {
1064 final String type_str = ( ( String ) st.nextElement() ).trim();
1065 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1066 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1068 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1069 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1071 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1072 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1075 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1076 + "] for [cladogram_type]" );
1079 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1081 .printWarningMessage( Constants.PRG_NAME,
1082 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1084 else if ( key.equals( "hide_controls_and_menus" ) ) {
1085 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1087 else if ( key.equals( "use_tabbed_display" ) ) {
1088 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1090 else if ( key.equals( "overview_width" ) ) {
1091 final short i = parseShort( ( ( String ) st.nextElement() ) );
1094 else if ( key.equals( "overview_height" ) ) {
1095 final short i = parseShort( ( ( String ) st.nextElement() ) );
1096 setOvMaxHeight( i );
1098 else if ( key.equals( "overview_placement_type" ) ) {
1099 final String type_str = ( ( String ) st.nextElement() ).trim();
1100 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1101 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1103 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1104 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1106 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1107 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1109 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1110 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1113 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1114 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1115 + "] for [overview_placement_type]" );
1118 else if ( key.equals( "node_label_direction" ) ) {
1119 final String type_str = ( ( String ) st.nextElement() ).trim();
1120 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1121 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1123 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1124 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1127 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1128 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1129 + "] for [node_label_direction]" );
1132 else if ( key.equals( "branch_length_value_digits" ) ) {
1133 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1135 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1138 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1139 + "] for [branch_length_value_digits]" );
1142 else if ( key.equals( "confidence_value_digits" ) ) {
1143 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1145 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1148 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1149 + "] for [confidence_value_digits]" );
1152 else if ( key.equals( "allow_editing" ) ) {
1153 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1155 else if ( key.equals( "display_sequence_relations" ) ) {
1156 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1158 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1159 final boolean r = parseBoolean( ( String ) st.nextElement() );
1160 if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
1162 .printWarningMessage( Constants.PRG_NAME,
1163 "attempt to extract taxonomies and replace underscores at the same time" );
1166 setReplaceUnderscoresInNhParsing( r );
1169 else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
1170 final String s = ( String ) st.nextElement();
1171 if ( s.equalsIgnoreCase( "no" ) ) {
1172 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1174 else if ( s.equalsIgnoreCase( "pfam_relaxed" ) ) {
1175 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1177 else if ( s.equalsIgnoreCase( "pfam_strict" ) ) {
1178 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1180 else if ( s.equalsIgnoreCase( "aggressive" ) ) {
1181 setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
1185 .printWarningMessage( Constants.PRG_NAME,
1186 "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
1188 + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
1190 if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
1192 .printWarningMessage( Constants.PRG_NAME,
1193 "attempt to extract taxonomies and replace underscores at the same time" );
1196 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1197 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1199 else if ( key.equals( "gui_background_color" ) ) {
1200 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1202 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1203 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1205 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1206 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1208 else if ( key.equals( "gui_button_text_color" ) ) {
1209 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1211 else if ( key.equals( "gui_button_background_color" ) ) {
1212 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1214 else if ( key.equals( "gui_menu_background_color" ) ) {
1215 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1217 else if ( key.equals( "gui_menu_text_color" ) ) {
1218 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1220 else if ( key.equals( "gui_button_border_color" ) ) {
1221 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1223 else if ( key.equals( "show_default_node_shapes_internal" ) ) {
1224 setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1226 else if ( key.equals( "show_default_node_shapes_external" ) ) {
1227 setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1229 else if ( key.equals( "show_node_shapes_for_nodes_with_vis_data" ) ) {
1230 setShowDefaultNodeShapesForMarkedNodes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1232 else if ( key.equals( "default_node_size" ) ) {
1233 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1234 setDefaultNodeShapeSize( i );
1236 else if ( key.equals( "default_node_fill" ) ) {
1237 final String fill_str = ( ( String ) st.nextElement() ).trim();
1238 if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.NONE.toString() ) ) {
1239 setDefaultNodeFill( NodeFill.NONE );
1241 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.GRADIENT.toString() ) ) {
1242 setDefaultNodeFill( NodeFill.GRADIENT );
1244 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.SOLID.toString() ) ) {
1245 setDefaultNodeFill( NodeFill.SOLID );
1248 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1249 + "] for [default_node_fill]" );
1252 else if ( key.equals( "default_node_shape" ) ) {
1253 final String shape_str = ( ( String ) st.nextElement() ).trim();
1254 if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.CIRCLE.toString() ) ) {
1255 setDefaultNodeShape( NodeShape.CIRCLE );
1257 else if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.RECTANGLE.toString() ) ) {
1258 setDefaultNodeShape( NodeShape.RECTANGLE );
1261 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1262 + "] for [default_node_shape]" );
1265 else if ( key.equals( "midpoint_reroot" ) ) {
1266 setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) );
1268 else if ( key.equals( "list_node_data_field" ) || key.equals( "ext_descendents_data_to_return" ) ) {
1269 final String s = ( ( String ) st.nextElement() ).trim();
1270 if ( s.equalsIgnoreCase( "node_name" ) ) {
1271 setExtDescNodeDataToReturn( NodeDataField.NODE_NAME );
1273 else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
1274 setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_ACC );
1276 else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) {
1277 setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );
1279 else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
1280 setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_NAME );
1282 else if ( s.equalsIgnoreCase( "gene_name" ) ) {
1283 setExtDescNodeDataToReturn( NodeDataField.GENE_NAME );
1285 else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
1286 setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_SYMBOL );
1288 else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
1289 setExtDescNodeDataToReturn( NodeDataField.TAXONOMY_SCIENTIFIC_NAME );
1291 else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
1292 setExtDescNodeDataToReturn( NodeDataField.TAXONOMY_CODE );
1294 else if ( s.equalsIgnoreCase( "user_selected" ) ) {
1295 setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
1297 else if ( s.equalsIgnoreCase( "domains" ) ) {
1298 setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );
1300 else if ( s.equalsIgnoreCase( "domains_collapsed" ) ) {
1301 setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );
1303 else if ( s.equalsIgnoreCase( "seq_annotations" ) ) {
1304 setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );
1306 else if ( s.equalsIgnoreCase( "go_term_ids" ) ) {
1307 setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );
1310 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1311 + "] for [ext_descendents_data_to_return]" );
1314 else if ( key.equals( "list_node_data_custom_label" ) || key.equals( "label_for_get_ext_descendents_data" ) ) {
1315 final String s = ( ( String ) st.nextElement() ).trim();
1316 if ( !ForesterUtil.isEmpty( s ) && ( s.length() > 1 ) ) {
1317 setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
1320 else if ( key.equals( "list_node_data_in" ) || key.equals( "ext_descendents_data_to_return_on" ) ) {
1321 final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
1322 if ( s.equals( "console" ) ) {
1323 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
1325 else if ( s.equals( "window" ) ) {
1326 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
1328 else if ( s.equals( "buffer_only" ) ) {
1329 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
1332 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1333 + "] for [ext_descendents_data_to_return_on]" );
1336 else if ( key.equals( "vector_data_min_color" ) ) {
1337 _vector_data_min_color = Color.decode( ( String ) st.nextElement() );
1339 else if ( key.equals( "vector_data_max_color" ) ) {
1340 _vector_data_max_color = Color.decode( ( String ) st.nextElement() );
1342 else if ( key.equals( "vector_data_mean_color" ) ) {
1343 _vector_data_mean_color = Color.decode( ( String ) st.nextElement() );
1345 else if ( key.equals( "vector_data_width" ) ) {
1346 _vector_data_width = parseShort( ( String ) st.nextElement() );
1347 if ( _vector_data_width < 1 ) {
1348 _vector_data_width = 120;
1351 else if ( key.equals( "vector_data_height" ) ) {
1352 _vector_data_height = parseShort( ( String ) st.nextElement() );
1353 if ( _vector_data_height < 1 ) {
1354 _vector_data_height = 12;
1357 else if ( key.equals( "line_up_renderable_data" ) ) {
1358 setLineUpRendarableNodeData( parseBoolean( ( String ) st.nextElement() ) );
1360 else if ( key.equals( "right_align_domain_architectures" ) ) {
1361 setRightLineUpDomains( parseBoolean( ( String ) st.nextElement() ) );
1363 else if ( key.equals( "allow_thick_strokes" ) ) {
1364 _allow_thick_strokes = parseBoolean( ( String ) st.nextElement() );
1366 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1369 if ( key.equals( "phylogram" ) ) {
1370 key_index = Configuration.display_as_phylogram;
1372 else if ( key.equals( "rollover" ) ) {
1373 key_index = Configuration.node_data_popup;
1375 else if ( key.equals( "color_according_to_species" ) ) {
1376 key_index = Configuration.color_according_to_species;
1378 else if ( key.equals( "color_according_to_sequence" ) ) {
1379 key_index = Configuration.color_according_to_sequence;
1381 else if ( key.equals( "show_node_names" ) ) {
1382 key_index = Configuration.show_node_names;
1384 else if ( key.equals( "show_taxonomy_code" ) ) {
1385 key_index = Configuration.show_tax_code;
1387 else if ( key.equals( "write_confidence_values" ) ) {
1388 key_index = Configuration.write_confidence_values;
1390 else if ( key.equals( "write_branch_length_values" ) ) {
1391 key_index = Configuration.write_branch_length_values;
1393 else if ( key.equals( "write_events" ) ) {
1394 key_index = Configuration.write_events;
1396 else if ( key.equals( "use_visual_styles" ) ) {
1397 key_index = Configuration.use_style;
1399 else if ( key.equals( "color_branches" ) ) {
1400 key_index = Configuration.use_style;
1402 .printWarningMessage( Constants.PRG_NAME,
1403 "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" );
1405 else if ( key.equals( "width_branches" ) ) {
1406 key_index = Configuration.width_branches;
1408 else if ( key.equals( "show_domain_architectures" ) ) {
1409 key_index = Configuration.show_domain_architectures;
1411 else if ( key.equals( "show_msa" ) ) {
1412 key_index = Configuration.show_mol_seqs;
1414 else if ( key.equals( "show_annotations" ) ) {
1415 key_index = Configuration.show_annotation;
1417 else if ( key.equals( "show_binary_characters" ) ) {
1418 key_index = Configuration.show_binary_characters;
1420 else if ( key.equals( "show_binary_character_counts" ) ) {
1421 key_index = Configuration.show_binary_character_counts;
1423 else if ( key.equals( "show_seq_names" ) ) {
1424 key_index = Configuration.show_seq_names;
1426 else if ( key.equals( "show_gene_names" ) ) {
1427 key_index = Configuration.show_gene_names;
1429 else if ( key.equals( "show_seq_symbols" ) ) {
1430 key_index = Configuration.show_seq_symbols;
1432 else if ( key.equals( "show_seq_acc" ) ) {
1433 key_index = Configuration.show_sequence_acc;
1435 else if ( key.equals( "display_internal_data" ) ) {
1436 key_index = Configuration.display_internal_data;
1438 else if ( key.equals( "dynamically_hide_data" ) ) {
1439 key_index = Configuration.dynamically_hide_data;
1441 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1442 key_index = Configuration.show_taxonomy_scientific_names;
1444 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1445 key_index = Configuration.show_taxonomy_common_names;
1447 else if ( key.equals( "show_taxonomy_images" ) ) {
1448 key_index = Configuration.show_taxonomy_images;
1450 else if ( key.equals( "color_according_to_annotation" ) ) {
1451 key_index = Configuration.color_according_to_annotation;
1453 else if ( key.equals( "show_vector_data" ) ) {
1454 key_index = Configuration.show_vector_data;
1456 else if ( key.equals( "show_properties" ) ) {
1457 key_index = Configuration.show_properties;
1459 else if ( key.equals( "show_relation_confidence" ) ) {
1460 key_index = Configuration.show_relation_confidence;
1462 // If we've found the key, set the values
1463 if ( key_index >= 0 ) {
1464 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1465 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1466 // otherwise, keep looking
1469 if ( key_index == DEPRECATED ) {
1472 else if ( key.equals( "click_to" ) ) {
1473 final String click_to_name = ( String ) st.nextElement();
1474 key_index = getClickToIndex( click_to_name );
1475 if ( key_index >= 0 ) {
1476 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1478 else if ( key_index == DEPRECATED ) {
1482 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1486 else if ( key.equals( "species_color" ) ) {
1487 getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
1488 Color.decode( ( String ) st.nextElement() ) );
1490 else if ( key.equals( "sequence_color" ) ) {
1491 getSequenceColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
1492 Color.decode( ( String ) st.nextElement() ) );
1494 else if ( key.equals( "domain_color" ) ) {
1495 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1497 else if ( key.equals( "annotation_color" ) ) {
1498 getAnnotationColors()
1499 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1501 else if ( key.equals( "function_color" ) ) {
1502 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1503 "configuration key [function_color] is deprecated" );
1505 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1506 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1509 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1510 + "] in: " + config_filename );
1515 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1516 + config_filename );
1520 private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
1521 _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
1524 private void setMaxBaseFontSize( final int max_base_font_size ) {
1525 _max_base_font_size = max_base_font_size;
1528 private void setMinBaseFontSize( final int min_base_font_size ) {
1529 _min_base_font_size = min_base_font_size;
1532 private void setOvMaxHeight( final short ov_max_height ) {
1533 _ov_max_height = ov_max_height;
1536 private void setOvMaxWidth( final short ov_max_width ) {
1537 _ov_max_width = ov_max_width;
1540 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1541 _ov_placement = ov_placement;
1544 private void setPathToLocalFastme( final File path_to_local_fastme ) {
1545 _path_to_local_fastme = path_to_local_fastme;
1548 private void setPathToLocalMafft( final File path_to_local_mafft ) {
1549 _path_to_local_mafft = path_to_local_mafft;
1552 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
1553 _path_to_local_raxml = path_to_local_raxml;
1556 private void setShowAnnotationRefSource( final boolean b ) {
1557 _show_annotation_ref_source = b;
1560 private void setShowOverview( final boolean show_overview ) {
1561 _show_overview = show_overview;
1564 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1565 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1568 boolean displaySequenceRelations() {
1569 return _display_sequence_relations;
1572 boolean doCheckOption( final int which ) {
1573 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
1574 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
1577 boolean doDisplayClickToOption( final int which ) {
1578 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
1581 boolean doDisplayOption( final int which ) {
1582 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
1586 * Will attempt to use the phylogeny to determine whether to check
1587 * this or not (e.g. phylogram)
1590 boolean doGuessCheckOption( final int which ) {
1591 return display_options[ which ][ 2 ].equals( "?" );
1594 Map<String, Color> getAnnotationColors() {
1595 if ( _annotation_colors == null ) {
1596 _annotation_colors = new Hashtable<String, Color>();
1598 return _annotation_colors;
1601 int getBaseFontSize() {
1602 return _base_font_size;
1605 CLADOGRAM_TYPE getCladogramType() {
1606 return _cladogram_type;
1609 int getClickToOptionsCount() {
1610 return clickto_options.length;
1613 String getClickToTitle( final int which ) {
1614 return clickto_options[ which ][ 0 ];
1617 int getDefaultDisplayClicktoOption() {
1618 return default_clickto;
1621 SortedMap<String, Color> getDisplayColors() {
1622 return _display_colors;
1625 String getDisplayTitle( final int which ) {
1626 return display_options[ which ][ 0 ];
1629 Map<String, Color> getDomainColors() {
1630 if ( _domain_colors == null ) {
1631 _domain_colors = new Hashtable<String, Color>();
1633 return _domain_colors;
1636 int getGraphicsExportX() {
1637 return _graphics_export_x;
1640 int getGraphicsExportY() {
1641 return _graphics_export_y;
1644 Color getGuiBackgroundColor() {
1645 return _gui_background_color;
1648 Color getGuiButtonBackgroundColor() {
1649 return _gui_button_background_color;
1652 Color getGuiButtonBorderColor() {
1653 return _gui_button_border_color;
1656 Color getGuiButtonTextColor() {
1657 return _gui_button_text_color;
1660 Color getGuiCheckboxAndButtonActiveColor() {
1661 return _gui_checkbox_and_button_active_color;
1664 Color getGuiCheckboxTextColor() {
1665 return _gui_checkbox_text_color;
1668 Color getGuiMenuBackgroundColor() {
1669 return _gui_menu_background_color;
1672 Color getGuiMenuTextColor() {
1673 return _gui_menu_text_color;
1676 int getMaxBaseFontSize() {
1677 return _max_base_font_size;
1680 int getMinBaseFontSize() {
1681 return _min_base_font_size;
1684 double getMinConfidenceValue() {
1685 return _min_confidence_value;
1688 NODE_LABEL_DIRECTION getNodeLabelDirection() {
1689 return _node_label_direction;
1692 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
1693 return _number_of_digits_after_comma_for_branch_length_values;
1696 short getNumberOfDigitsAfterCommaForConfidenceValues() {
1697 return _number_of_digits_after_comma_for_confidence_values;
1700 short getOvMaxHeight() {
1701 return _ov_max_height;
1704 short getOvMaxWidth() {
1705 return _ov_max_width;
1708 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
1709 return _ov_placement;
1712 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
1713 return _phylogeny_graphics_type;
1716 float getPrintLineWidth() {
1717 return _print_line_width;
1720 Hashtable<String, Color> getSequenceColors() {
1721 if ( _sequence_colors == null ) {
1722 _sequence_colors = new Hashtable<String, Color>();
1724 return _sequence_colors;
1727 Hashtable<String, Color> getSpeciesColors() {
1728 if ( _species_colors == null ) {
1729 initSpeciesColors();
1731 return _species_colors;
1734 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
1735 return _taxonomy_extraction;
1738 boolean isAntialiasScreen() {
1739 return _antialias_screen;
1743 * Convenience method.
1745 * @return true if value in configuration file was 'yes'
1747 boolean isDrawAsPhylogram() {
1748 return doCheckOption( display_as_phylogram );
1751 boolean isEditable() {
1756 * Only used by ArchaeoptryxE.
1759 boolean isHideControlPanelAndMenubar() {
1760 return _hide_controls_and_menus;
1763 boolean isInternalNumberAreConfidenceForNhParsing() {
1764 return _internal_number_are_confidence_for_nh_parsing;
1767 boolean isReplaceUnderscoresInNhParsing() {
1768 return _nh_parsing_replace_underscores;
1771 boolean isShowOverview() {
1772 return _show_overview;
1775 boolean isShowScale() {
1779 final boolean isUseNativeUI() {
1780 if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
1783 return _ui == UI.NATIVE;
1787 * Only used by ArchaeoptryxE.
1790 boolean isUseTabbedDisplay() {
1791 return _use_tabbed_display;
1794 boolean isValidatePhyloXmlAgainstSchema() {
1795 return _validate_against_phyloxml_xsd_schema;
1798 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
1799 _taxonomy_extraction = taxonomy_extraction;
1802 static String getDefaultFontFamilyName() {
1803 return DEFAULT_FONT_FAMILY;