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/Supertree", "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" } , { "Uncollapse All", "display" }, { "Order Subtree", "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 final static int uncollapse_all = 21;
118 final static int order_subtree = 22;
120 // ------------------
122 // ------------------
123 final static String display_options[][] = {
124 { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
125 { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" },
126 { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
127 { "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" },
128 { "Branch Widths", "display", "no" }, { "Domain Architectures", "display", "no" },
129 { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
130 { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" },
131 { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
132 { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
133 { "Colorize by Annotation", "display", "no" }, { "Seq Symbol", "display", "yes" },
134 { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
135 { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
136 { "Properties", "display", "no" }, { "Gene Name", "display", "yes" },
137 { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" }
138 , { "Taxonomy Rank", "display", "no" }};
139 final static int display_as_phylogram = 0;
140 final static int show_node_names = 1;
141 final static int show_tax_code = 2;
142 final static int show_annotation = 3;
143 final static int write_confidence_values = 4;
144 final static int write_events = 5;
145 final static int color_according_to_species = 6;
146 final static int color_according_to_sequence = 7;
147 final static int use_style = 8;
148 final static int width_branches = 9;
149 final static int show_domain_architectures = 10;
150 final static int show_binary_characters = 11;
151 final static int show_binary_character_counts = 12;
152 final static int show_seq_names = 13;
153 final static int show_sequence_acc = 14;
154 final static int display_internal_data = 15;
155 final static int dynamically_hide_data = 16;
156 final static int show_taxonomy_scientific_names = 17;
157 final static int show_taxonomy_common_names = 18;
158 final static int color_according_to_annotation = 19;
159 final static int show_seq_symbols = 20;
160 final static int node_data_popup = 21;
161 final static int show_relation_confidence = 22;
162 final static int show_vector_data = 23;
163 final static int show_taxonomy_images = 24;
164 final static int show_properties = 25;
165 final static int show_gene_names = 26;
166 final static int show_mol_seqs = 27;
167 final static int write_branch_length_values = 28;
168 final static int show_tax_rank = 29;
170 static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
171 private static Hashtable<String, Color> _sequence_colors;
172 private static Hashtable<String, Color> _annotation_colors;
173 private static Hashtable<String, Color> _domain_colors;
174 private static Hashtable<String, Color> _species_colors;
175 private static String DEFAULT_FONT_FAMILY = "";
176 private static final int DEPRECATED = -2;
177 private static final String DISPLAY_COLOR_KEY = "display_color";
178 // ---------------------------
179 // Display options for trees
180 // ---------------------------
181 // ---------------------------------
182 // Pertaining to the config itself
183 // ---------------------------------
184 // Full path to config (may be URL)
185 String config_filename;
186 // This option is selected in the dropdown
187 int default_clickto = Configuration.display_node_data;
188 String default_config_filename = AptxConstants.DEFAULT_CONFIGURATION_FILE_NAME;
192 TreeColorSet tree_color_set;
196 TreeFontSet tree_font_set;
197 boolean verbose = AptxConstants.VERBOSE_DEFAULT;
198 private boolean _abbreviate_scientific_names = false;
199 private boolean _antialias_screen = true;
200 private boolean _background_color_gradient = false;
201 private String _base_font_family_name = "";
202 private int _base_font_size = -1;
203 private CLADOGRAM_TYPE _cladogram_type = AptxConstants.CLADOGRAM_TYPE_DEFAULT;
204 private boolean _color_labels_same_as_parent_branch = false;
205 private int _default_bootstrap_samples = -1;
206 private NodeFill _default_node_fill = NodeFill.SOLID;
207 private NodeShape _default_node_shape = NodeShape.RECTANGLE;
208 private short _default_node_shape_size = AptxConstants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
209 private SortedMap<String, Color> _display_colors = null;
210 private boolean _display_sequence_relations = false;
211 private boolean _editable = true;
212 private NodeDataField _ext_desc_data_to_return = NodeDataField.UNKNOWN;
213 private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
214 private int _frame_x_size;
215 private int _frame_y_size;
216 private Color _gui_background_color = AptxConstants.GUI_BACKGROUND_DEFAULT;
217 private Color _gui_button_background_color = AptxConstants.BUTTON_BACKGROUND_COLOR_DEFAULT;
218 private Color _gui_button_border_color = AptxConstants.BUTTON_BORDER_COLOR_DEFAULT;
219 private Color _gui_button_text_color = AptxConstants.BUTTON_TEXT_COLOR_DEFAULT;
220 private Color _gui_checkbox_and_button_active_color = AptxConstants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
221 private Color _gui_checkbox_text_color = AptxConstants.CHECKBOX_TEXT_COLOR_DEFAULT;
222 private Color _gui_menu_background_color = AptxConstants.MENU_BACKGROUND_COLOR_DEFAULT;
223 private Color _gui_menu_text_color = AptxConstants.MENU_TEXT_COLOR_DEFAULT;
224 private boolean _hide_controls_and_menus = false;
225 private boolean _internal_number_are_confidence_for_nh_parsing = false;
226 private String _label_for_get_ext_descendents_data = "";
227 private int _max_base_font_size = 20;
228 private boolean _midpoint_root = false;
229 private int _min_base_font_size = 2;
230 private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
231 private boolean _nh_parsing_replace_underscores = false;
232 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
233 private short _number_of_digits_after_comma_for_branch_length_values = AptxConstants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
234 private short _number_of_digits_after_comma_for_confidence_values = AptxConstants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
235 private short _ov_max_height = 80;
236 private short _ov_max_width = 80;
237 private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
238 private File _path_to_local_fastme = null;
239 private File _path_to_local_mafft = null;
240 private File _path_to_local_raxml = null;
241 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
242 private float _print_line_width = AptxConstants.PDF_LINE_WIDTH_DEFAULT;
243 private boolean _show_annotation_ref_source = true;
244 private boolean _show_default_node_shapes_external = false;
245 private boolean _show_default_node_shapes_for_marked_nodes = false;
246 private boolean _show_default_node_shapes_internal = false;
247 private boolean _show_domain_labels = true;
248 private boolean _show_overview = true;
249 private boolean _show_scale = false;
250 private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
251 private UI _ui = UI.UNKNOWN;
252 private boolean _use_tabbed_display = false;
253 private boolean _validate_against_phyloxml_xsd_schema = AptxConstants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
254 private Color _vector_data_min_color = Color.BLUE;
255 private Color _vector_data_max_color = Color.YELLOW;
256 private Color _vector_data_mean_color = Color.WHITE;
257 private double _vector_data_height = 12;
258 private int _vector_data_width = 120;
259 private boolean _line_up_renderable_node_data = true;
260 private boolean _right_align_domains = false;
261 private boolean _allow_thick_strokes = false;
262 private boolean _could_read_config_file = false;
264 for( final String font_name : AptxConstants.DEFAULT_FONT_CHOICES ) {
265 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
266 DEFAULT_FONT_FAMILY = font_name;
270 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
271 DEFAULT_FONT_FAMILY = AptxConstants.DEFAULT_FONT_CHOICES[ AptxConstants.DEFAULT_FONT_CHOICES.length - 1 ];
275 public Configuration() {
276 this( null, false, false, false );
279 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
280 if ( ForesterUtil.isEmpty( cf ) ) {
281 config_filename = default_config_filename;
284 config_filename = cf;
286 _could_read_config_file = false;
287 setDisplayColors( new TreeMap<String, Color>() );
288 config_filename = config_filename.trim();
291 // If URL, open accordingly
293 u = new URL( config_filename );
295 final InputStreamReader isr = new InputStreamReader( u.openStream() );
296 final BufferedReader bf = new BufferedReader( isr );
299 ForesterUtil.programMessage( AptxConstants.PRG_NAME, "successfully read from configuration url ["
300 + config_filename + "]" );
301 _could_read_config_file = true;
303 catch ( final Exception e ) {
304 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "failed to read configuration from ["
305 + config_filename + "]: " + e.getLocalizedMessage() );
308 catch ( final Exception e ) {
309 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "cannot find or open configuration url ["
310 + config_filename + "]" );
314 // Otherwise, open as a file
315 File f = new File( config_filename );
317 f = new File( config_filename + ".txt" );
319 if ( f.exists() && f.canRead() ) {
321 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
324 _could_read_config_file = true;
326 catch ( final Exception e ) {
328 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "failed to read configuration from ["
329 + config_filename + "]: " + e );
335 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "cannot find or open configuration file ["
336 + config_filename + "]" );
342 public String getBaseFontFamilyName() {
343 return _base_font_family_name;
346 public int getDefaultBootstrapSamples() {
347 return _default_bootstrap_samples;
350 public NodeFill getDefaultNodeFill() {
351 return _default_node_fill;
354 public NodeShape getDefaultNodeShape() {
355 return _default_node_shape;
358 public short getDefaultNodeShapeSize() {
359 return _default_node_shape_size;
362 public NodeDataField getExtDescNodeDataToReturn() {
363 return _ext_desc_data_to_return;
366 public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
367 return _ext_node_data_return_on;
370 public int getFrameXSize() {
371 return _frame_x_size;
374 public int getFrameYSize() {
375 return _frame_y_size;
378 public String getLabelForGetExtDescendentsData() {
379 return _label_for_get_ext_descendents_data;
382 public File getPathToLocalFastme() {
383 return _path_to_local_fastme;
386 public File getPathToLocalMafft() {
387 return _path_to_local_mafft;
390 public File getPathToLocalRaxml() {
391 return _path_to_local_raxml;
394 public double getVectorDataHeight() {
395 return _vector_data_height;
398 public Color getVectorDataMaxColor() {
399 return _vector_data_max_color;
402 public Color getVectorDataMeanColor() {
403 return _vector_data_mean_color;
406 public Color getVectorDataMinColor() {
407 return _vector_data_min_color;
410 public int getVectorDataWidth() {
411 return _vector_data_width;
414 public boolean isAbbreviateScientificTaxonNames() {
415 return _abbreviate_scientific_names;
418 public boolean isAllowThickStrokes() {
419 return _allow_thick_strokes;
422 public boolean isBackgroundColorGradient() {
423 return _background_color_gradient;
426 public boolean isColorByTaxonomicGroup() {
430 public boolean isColorLabelsSameAsParentBranch() {
431 return _color_labels_same_as_parent_branch;
434 final public boolean isLineUpRendarableNodeData() {
435 return _line_up_renderable_node_data;
438 public boolean isMidpointReroot() {
439 return _midpoint_root;
442 final public boolean isRightLineUpDomains() {
443 return _right_align_domains;
446 public boolean isShowAnnotationRefSource() {
447 return _show_annotation_ref_source;
450 public boolean isShowDefaultNodeShapesExternal() {
451 return _show_default_node_shapes_external;
454 public boolean isShowDefaultNodeShapesForMarkedNodes() {
455 return _show_default_node_shapes_for_marked_nodes;
458 public boolean isShowDefaultNodeShapesInternal() {
459 return _show_default_node_shapes_internal;
462 public boolean isShowDomainLabels() {
463 return _show_domain_labels;
466 public void putDisplayColors( final String key, final Color color ) {
467 getDisplayColors().put( key, color );
470 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
471 _abbreviate_scientific_names = abbreviate_scientific_names;
474 public void setAddTaxonomyImagesCB( final boolean b ) {
475 display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no";
478 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
479 _background_color_gradient = background_color_gradient;
482 public void setBaseFontFamilyName( final String base_font_family_name ) {
483 _base_font_family_name = base_font_family_name;
486 public void setBaseFontSize( final int base_font_size ) {
487 _base_font_size = base_font_size;
490 public void setColorizeBranches( final boolean b ) {
491 display_options[ use_style ][ 2 ] = b ? "yes" : "no";
494 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
495 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
498 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
499 _default_node_fill = default_node_fill;
502 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
503 _default_node_shape = default_node_shape;
506 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
507 _default_node_shape_size = default_node_shape_size;
510 public void setDisplayAsPhylogram( final boolean b ) {
511 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
514 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
515 _display_colors = display_colors;
518 public void setDisplayConfidenceValues( final boolean b ) {
519 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
522 public void setDisplayGeneNames( final boolean b ) {
523 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
526 public void setDisplayInternalData( final boolean b ) {
527 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
530 public void setDisplayMultipleSequenceAlignment( final boolean b ) {
531 display_options[ show_mol_seqs ][ 2 ] = b ? "yes" : "no";
534 public void setDisplayNodeNames( final boolean b ) {
535 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
538 public void setDisplaySequenceAcc( final boolean b ) {
539 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
542 public void setDisplaySequenceNames( final boolean b ) {
543 display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no";
546 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
547 _display_sequence_relations = display_sequence_relations;
550 public void setDisplaySequenceSymbols( final boolean b ) {
551 display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no";
554 public void setDisplayTaxonomyCode( final boolean b ) {
555 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
558 public void setDisplayTaxonomyRank( final boolean b ) {
559 display_options[ show_tax_rank ][ 2 ] = b ? "yes" : "no";
562 public void setDisplayTaxonomyCommonNames( final boolean b ) {
563 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
566 public void setDisplayTaxonomyImages( final boolean b ) {
567 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
570 public void setDisplayTaxonomyScientificNames( final boolean b ) {
571 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
574 public void setDynamicallyHideData( final boolean b ) {
575 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
578 public void setExtDescNodeDataToReturn( final NodeDataField ext_desc_data_to_return ) {
579 _ext_desc_data_to_return = ext_desc_data_to_return;
582 public void setFrameXSize( final int frame_x_size ) {
583 _frame_x_size = frame_x_size;
586 public void setFrameYSize( final int frame_y_size ) {
587 _frame_y_size = frame_y_size;
590 final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) {
591 _line_up_renderable_node_data = line_up_renderable_node_data;
594 public void setMidpointReroot( final boolean midpoint_root ) {
595 _midpoint_root = midpoint_root;
598 public void setMinConfidenceValue( final double min_confidence_value ) {
599 _min_confidence_value = min_confidence_value;
602 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
603 _node_label_direction = node_label_direction;
606 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
607 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
610 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
611 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
614 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
615 _phylogeny_graphics_type = phylogeny_graphics_type;
618 public void setPrintLineWidth( final float print_line_width ) {
619 _print_line_width = print_line_width;
622 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
623 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
626 final public void setRightLineUpDomains( final boolean right_align_domains ) {
627 _right_align_domains = right_align_domains;
630 public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
631 _show_default_node_shapes_external = show_default_node_shapes_external;
634 public void setShowDefaultNodeShapesForMarkedNodes( final boolean show_default_node_shapes_for_marked_nodes ) {
635 _show_default_node_shapes_for_marked_nodes = show_default_node_shapes_for_marked_nodes;
638 public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
639 _show_default_node_shapes_internal = show_default_node_shapes_internal;
642 public void setShowDomainLabels( final boolean show_domain_labels ) {
643 _show_domain_labels = show_domain_labels;
646 public void setShowScale( final boolean show_scale ) {
647 _show_scale = show_scale;
650 public void setUseStyle( final boolean b ) {
651 display_options[ use_style ][ 2 ] = b ? "yes" : "no";
654 private int getClickToIndex( final String name ) {
656 if ( name.equals( "edit_info" ) ) {
657 index = Configuration.display_node_data;
659 .printWarningMessage( AptxConstants.PRG_NAME,
660 "configuration key [edit_info] is deprecated, use [display node data] instead" );
662 else if ( name.equals( "display_node_data" ) ) {
663 index = Configuration.display_node_data;
665 else if ( name.equals( "collapse_uncollapse" ) ) {
666 index = Configuration.collapse_uncollapse;
668 else if ( name.equals( "uncollapse_all" ) ) {
669 index = Configuration.uncollapse_all;
671 else if ( name.equals( "reroot" ) ) {
672 index = Configuration.reroot;
674 else if ( name.equals( "subtree" ) ) {
675 index = Configuration.subtree;
677 else if ( name.equals( "swap" ) ) {
678 index = Configuration.swap;
680 else if ( name.equals( "order_subtree" ) ) {
681 index = Configuration.order_subtree;
683 else if ( name.equals( "sort_descendants" ) ) {
684 index = Configuration.sort_descendents;
686 else if ( name.equals( "get_ext_descendents_data" ) ) {
687 index = Configuration.get_ext_desc_data;
689 else if ( name.equals( "display_sequences" ) ) {
691 .printWarningMessage( AptxConstants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
694 else if ( name.equals( "open_seq_web" ) ) {
695 index = Configuration.open_seq_web;
697 else if ( name.equals( "open_pdb_web" ) ) {
698 index = Configuration.open_pdb_web;
700 else if ( name.equals( "open_tax_web" ) ) {
701 index = Configuration.open_tax_web;
703 else if ( name.equals( "blast" ) ) {
704 index = Configuration.blast;
706 else if ( name.equals( "cut_subtree" ) ) {
707 index = Configuration.cut_subtree;
709 else if ( name.equals( "copy_subtree" ) ) {
710 index = Configuration.copy_subtree;
712 else if ( name.equals( "paste_subtree" ) ) {
713 index = Configuration.paste_subtree;
715 else if ( name.equals( "delete" ) ) {
716 index = Configuration.delete_subtree_or_node;
718 else if ( name.equals( "add_new_node" ) ) {
719 index = Configuration.add_new_node;
721 else if ( name.equals( "edit_node_data" ) ) {
722 index = Configuration.edit_node_data;
724 else if ( name.equals( "select_nodes" ) ) {
725 index = Configuration.select_nodes;
727 else if ( name.equals( "display_node_popup" ) ) {
728 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME,
729 "configuration key [display_node_popup] is deprecated" );
732 else if ( name.equals( "custom_option" ) ) {
733 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "configuration key [custom_option] is deprecated" );
736 else if ( name.equals( "color_subtree" ) ) {
737 index = Configuration.color_subtree;
739 else if ( name.equals( "change_node_font" ) ) {
740 index = Configuration.change_node_font;
742 else if ( name.equals( "color_node_font" ) ) {
743 index = Configuration.color_node_font;
745 else if ( name.equals( "color_subtree" ) ) {
746 index = Configuration.color_subtree;
751 private final void initSpeciesColors() {
752 _species_colors = new Hashtable<String, Color>();
753 for( final String[] s : DEFAULT_SPECIES_COLORS ) {
754 _species_colors.put( s[ 0 ], Color.decode( s[ 1 ] ) );
758 private boolean parseBoolean( final String str ) {
759 final String my_str = str.trim().toLowerCase();
760 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
763 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
767 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
772 private double parseDouble( final String str ) {
775 d = Double.parseDouble( str.trim() );
777 catch ( final Exception e ) {
778 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse double from [" + str + "]" );
784 private float parseFloat( final String str ) {
787 f = Float.parseFloat( str.trim() );
789 catch ( final Exception e ) {
790 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse float from [" + str + "]" );
796 private int parseInt( final String str ) {
799 i = Integer.parseInt( str.trim() );
801 catch ( final Exception e ) {
802 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse integer from [" + str + "]" );
808 private short parseShort( final String str ) {
811 i = Short.parseShort( str.trim() );
813 catch ( final Exception e ) {
814 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse short from [" + str + "]" );
820 private void processFontFamily( final StringTokenizer st ) {
821 setBaseFontFamilyName( "" );
822 final String font_str = ( ( String ) st.nextElement() ).trim();
823 final String[] fonts = font_str.split( ",+" );
824 for( String font : fonts ) {
825 font = font.replace( '_', ' ' ).trim();
826 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
827 setBaseFontFamilyName( font );
834 * read each line of config file, process non-comment lines
835 * @throws IOException
837 private void readConfig( final BufferedReader conf_in ) throws IOException {
840 line = conf_in.readLine();
841 if ( line != null ) {
843 // skip comments and blank lines
844 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
845 // convert runs of spaces to tabs
846 line = line.replaceAll( "\\s+", "\t" );
847 final StringTokenizer st = new StringTokenizer( line, "\t" );
851 } while ( line != null );
854 private void setAntialiasScreen( final boolean antialias_screen ) {
855 _antialias_screen = antialias_screen;
858 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
859 _cladogram_type = cladogram_type;
862 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
863 _default_bootstrap_samples = default_bootstrap_samples;
866 private void setEditable( final boolean editable ) {
867 _editable = editable;
870 private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
871 _ext_node_data_return_on = ext_node_data_return_on;
874 //private void setGraphicsExportX( final int graphics_export_x ) {
875 // _graphics_export_x = graphics_export_x;
878 //private void setGraphicsExportY( final int graphics_export_y ) {
879 // _graphics_export_y = graphics_export_y;
882 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
883 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
887 * Set a key-value(s) tuple
889 private void setKeyValue( final StringTokenizer st ) {
890 final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
891 if ( !st.hasMoreElements() ) {
894 // Handle single value settings first:
895 if ( key.equals( "default_click_to" ) ) {
896 final String clickto_name = ( String ) st.nextElement();
897 default_clickto = getClickToIndex( clickto_name );
898 if ( default_clickto == -1 ) {
899 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "invalid value [" + clickto_name
900 + "] for [default_click_to]" );
903 else if ( default_clickto == DEPRECATED ) {
907 else if ( key.equals( "native_ui" ) ) {
908 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
909 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
912 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
913 _ui = UI.CROSSPLATFORM;
915 else if ( my_str.equals( "?" ) ) {
919 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
924 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
925 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
927 else if ( key.equals( "antialias_screen" ) ) {
928 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
930 else if ( key.equals( "phylogeny_graphics_type" ) ) {
931 final String type_str = ( ( String ) st.nextElement() ).trim();
932 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
933 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
935 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
936 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
938 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
939 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
941 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
942 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
944 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
945 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
947 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
948 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
950 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
951 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
953 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
954 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
957 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
958 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str
959 + "] for [phylogeny_graphics_type]" );
962 else if ( key.equals( "min_confidence_value" ) ) {
963 final String mcv_str = ( ( String ) st.nextElement() ).trim();
964 final double d = parseDouble( mcv_str );
965 setMinConfidenceValue( d );
967 else if ( key.equals( "font_family" ) ) {
968 processFontFamily( st );
970 else if ( key.equals( "font_size" ) ) {
971 final String size_str = ( ( String ) st.nextElement() ).trim();
972 final int i = parseInt( size_str );
974 setBaseFontSize( i );
977 else if ( key.equals( "font_size_min" ) ) {
978 final String size_str = ( ( String ) st.nextElement() ).trim();
979 final int i = parseInt( size_str );
981 setMinBaseFontSize( i );
984 else if ( key.equals( "font_size_max" ) ) {
985 final String size_str = ( ( String ) st.nextElement() ).trim();
986 final int i = parseInt( size_str );
988 setMaxBaseFontSize( i );
991 else if ( key.equals( "graphics_export_x" ) ) {
992 // final String str = ( ( String ) st.nextElement() ).trim();
993 // final int i = parseInt( str );
995 // setGraphicsExportX( i );
998 else if ( key.equals( "graphics_export_y" ) ) {
999 //final String str = ( ( String ) st.nextElement() ).trim();
1000 // final int i = parseInt( str );
1002 // setGraphicsExportY( i );
1005 else if ( key.equals( "pdf_export_line_width" ) ) {
1006 final String str = ( ( String ) st.nextElement() ).trim();
1007 final float f = parseFloat( str );
1009 setPrintLineWidth( f );
1012 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME,
1013 "value for [pdf_export_line_width] cannot be zero or negative" );
1016 else if ( key.equals( "window_initial_size_x" ) ) {
1017 final String str = ( ( String ) st.nextElement() ).trim();
1018 final int i = parseInt( str );
1023 else if ( key.equals( "window_initial_size_y" ) ) {
1024 final String str = ( ( String ) st.nextElement() ).trim();
1025 final int i = parseInt( str );
1030 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1031 final String str = ( ( String ) st.nextElement() ).trim();
1032 final int i = parseInt( str );
1034 setDefaultBootstrapSamples( i );
1038 .printWarningMessage( AptxConstants.PRG_NAME,
1039 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1042 else if ( key.equals( "mafft_local" ) ) {
1043 final String str = ( ( String ) st.nextElement() ).trim();
1044 if ( !ForesterUtil.isEmpty( str ) ) {
1045 setPathToLocalMafft( new File( str ) );
1048 else if ( key.equals( "fastme_local" ) ) {
1049 final String str = ( ( String ) st.nextElement() ).trim();
1050 if ( !ForesterUtil.isEmpty( str ) ) {
1051 setPathToLocalFastme( new File( str ) );
1054 else if ( key.equals( "raxml_local" ) ) {
1055 final String str = ( ( String ) st.nextElement() ).trim();
1056 if ( !ForesterUtil.isEmpty( str ) ) {
1057 setPathToLocalRaxml( new File( str ) );
1060 else if ( key.equals( "show_scale" ) ) {
1061 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1063 else if ( key.equals( "show_overview" ) ) {
1064 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1066 else if ( key.equals( "background_gradient" ) ) {
1067 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1069 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1070 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1072 else if ( key.equals( "show_domain_labels" ) ) {
1073 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1075 else if ( key.equals( "show_seq_annotation_ref_sources" ) ) {
1076 setShowAnnotationRefSource( parseBoolean( ( String ) st.nextElement() ) );
1078 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1079 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1081 else if ( key.equals( "cladogram_type" ) ) {
1082 final String type_str = ( ( String ) st.nextElement() ).trim();
1083 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1084 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1086 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1087 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1089 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1090 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1093 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str
1094 + "] for [cladogram_type]" );
1097 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1099 .printWarningMessage( AptxConstants.PRG_NAME,
1100 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1102 else if ( key.equals( "hide_controls_and_menus" ) ) {
1103 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1105 else if ( key.equals( "use_tabbed_display" ) ) {
1106 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1108 else if ( key.equals( "overview_width" ) ) {
1109 final short i = parseShort( ( ( String ) st.nextElement() ) );
1112 else if ( key.equals( "overview_height" ) ) {
1113 final short i = parseShort( ( ( String ) st.nextElement() ) );
1114 setOvMaxHeight( i );
1116 else if ( key.equals( "overview_placement_type" ) ) {
1117 final String type_str = ( ( String ) st.nextElement() ).trim();
1118 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1119 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1121 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1122 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1124 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1125 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1127 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1128 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1131 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1132 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str
1133 + "] for [overview_placement_type]" );
1136 else if ( key.equals( "node_label_direction" ) ) {
1137 final String type_str = ( ( String ) st.nextElement() ).trim();
1138 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1139 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1141 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1142 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1145 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1146 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str
1147 + "] for [node_label_direction]" );
1150 else if ( key.equals( "branch_length_value_digits" ) ) {
1151 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1153 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1156 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "illegal value [" + i
1157 + "] for [branch_length_value_digits]" );
1160 else if ( key.equals( "confidence_value_digits" ) ) {
1161 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1163 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1166 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "illegal value [" + i
1167 + "] for [confidence_value_digits]" );
1170 else if ( key.equals( "allow_editing" ) ) {
1171 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1173 else if ( key.equals( "display_sequence_relations" ) ) {
1174 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1176 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1177 final boolean r = parseBoolean( ( String ) st.nextElement() );
1178 if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
1180 .printWarningMessage( AptxConstants.PRG_NAME,
1181 "attempt to extract taxonomies and replace underscores at the same time" );
1184 setReplaceUnderscoresInNhParsing( r );
1187 else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
1188 final String s = ( String ) st.nextElement();
1189 if ( s.equalsIgnoreCase( "no" ) ) {
1190 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1192 else if ( s.equalsIgnoreCase( "pfam_relaxed" ) ) {
1193 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1195 else if ( s.equalsIgnoreCase( "pfam_strict" ) ) {
1196 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1198 else if ( s.equalsIgnoreCase( "aggressive" ) ) {
1199 setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
1203 .printWarningMessage( AptxConstants.PRG_NAME,
1204 "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
1206 + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
1208 if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
1210 .printWarningMessage( AptxConstants.PRG_NAME,
1211 "attempt to extract taxonomies and replace underscores at the same time" );
1214 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1215 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1217 else if ( key.equals( "gui_background_color" ) ) {
1218 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1220 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1221 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1223 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1224 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1226 else if ( key.equals( "gui_button_text_color" ) ) {
1227 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1229 else if ( key.equals( "gui_button_background_color" ) ) {
1230 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1232 else if ( key.equals( "gui_menu_background_color" ) ) {
1233 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1235 else if ( key.equals( "gui_menu_text_color" ) ) {
1236 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1238 else if ( key.equals( "gui_button_border_color" ) ) {
1239 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1241 else if ( key.equals( "show_default_node_shapes_internal" ) ) {
1242 setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1244 else if ( key.equals( "show_default_node_shapes_external" ) ) {
1245 setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1247 else if ( key.equals( "show_node_shapes_for_nodes_with_vis_data" ) ) {
1248 setShowDefaultNodeShapesForMarkedNodes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1250 else if ( key.equals( "default_node_size" ) ) {
1251 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1252 setDefaultNodeShapeSize( i );
1254 else if ( key.equals( "default_node_fill" ) ) {
1255 final String fill_str = ( ( String ) st.nextElement() ).trim();
1256 if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.NONE.toString() ) ) {
1257 setDefaultNodeFill( NodeFill.NONE );
1259 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.GRADIENT.toString() ) ) {
1260 setDefaultNodeFill( NodeFill.GRADIENT );
1262 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.SOLID.toString() ) ) {
1263 setDefaultNodeFill( NodeFill.SOLID );
1266 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + fill_str
1267 + "] for [default_node_fill]" );
1270 else if ( key.equals( "default_node_shape" ) ) {
1271 final String shape_str = ( ( String ) st.nextElement() ).trim();
1272 if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.CIRCLE.toString() ) ) {
1273 setDefaultNodeShape( NodeShape.CIRCLE );
1275 else if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.RECTANGLE.toString() ) ) {
1276 setDefaultNodeShape( NodeShape.RECTANGLE );
1279 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + shape_str
1280 + "] for [default_node_shape]" );
1283 else if ( key.equals( "midpoint_reroot" ) ) {
1284 setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) );
1286 else if ( key.equals( "list_node_data_field" ) || key.equals( "ext_descendents_data_to_return" ) ) {
1287 final String s = ( ( String ) st.nextElement() ).trim();
1288 if ( s.equalsIgnoreCase( "node_name" ) ) {
1289 setExtDescNodeDataToReturn( NodeDataField.NODE_NAME );
1291 else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
1292 setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_ACC );
1294 else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) {
1295 setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );
1297 else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
1298 setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_NAME );
1300 else if ( s.equalsIgnoreCase( "gene_name" ) ) {
1301 setExtDescNodeDataToReturn( NodeDataField.GENE_NAME );
1303 else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
1304 setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_SYMBOL );
1306 else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
1307 setExtDescNodeDataToReturn( NodeDataField.TAXONOMY_SCIENTIFIC_NAME );
1309 else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
1310 setExtDescNodeDataToReturn( NodeDataField.TAXONOMY_CODE );
1312 else if ( s.equalsIgnoreCase( "user_selected" ) ) {
1313 setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
1315 else if ( s.equalsIgnoreCase( "domains" ) ) {
1316 setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );
1318 else if ( s.equalsIgnoreCase( "domains_collapsed" ) ) {
1319 setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );
1321 else if ( s.equalsIgnoreCase( "seq_annotations" ) ) {
1322 setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );
1324 else if ( s.equalsIgnoreCase( "go_term_ids" ) ) {
1325 setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );
1328 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + s
1329 + "] for [ext_descendents_data_to_return]" );
1332 else if ( key.equals( "list_node_data_custom_label" ) || key.equals( "label_for_get_ext_descendents_data" ) ) {
1333 final String s = ( ( String ) st.nextElement() ).trim();
1334 if ( !ForesterUtil.isEmpty( s ) && ( s.length() > 1 ) ) {
1335 setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
1338 else if ( key.equals( "list_node_data_in" ) || key.equals( "ext_descendents_data_to_return_on" ) ) {
1339 final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
1340 if ( s.equals( "console" ) ) {
1341 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
1343 else if ( s.equals( "window" ) ) {
1344 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
1346 else if ( s.equals( "buffer_only" ) ) {
1347 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
1350 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + s
1351 + "] for [ext_descendents_data_to_return_on]" );
1354 else if ( key.equals( "vector_data_min_color" ) ) {
1355 _vector_data_min_color = Color.decode( ( String ) st.nextElement() );
1357 else if ( key.equals( "vector_data_max_color" ) ) {
1358 _vector_data_max_color = Color.decode( ( String ) st.nextElement() );
1360 else if ( key.equals( "vector_data_mean_color" ) ) {
1361 _vector_data_mean_color = Color.decode( ( String ) st.nextElement() );
1363 else if ( key.equals( "vector_data_width" ) ) {
1364 _vector_data_width = parseShort( ( String ) st.nextElement() );
1365 if ( _vector_data_width < 1 ) {
1366 _vector_data_width = 120;
1369 else if ( key.equals( "vector_data_height" ) ) {
1370 _vector_data_height = parseShort( ( String ) st.nextElement() );
1371 if ( _vector_data_height < 1 ) {
1372 _vector_data_height = 12;
1375 else if ( key.equals( "line_up_renderable_data" ) ) {
1376 setLineUpRendarableNodeData( parseBoolean( ( String ) st.nextElement() ) );
1378 else if ( key.equals( "right_align_domain_architectures" ) ) {
1379 setRightLineUpDomains( parseBoolean( ( String ) st.nextElement() ) );
1381 else if ( key.equals( "allow_thick_strokes" ) ) {
1382 _allow_thick_strokes = parseBoolean( ( String ) st.nextElement() );
1384 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1387 if ( key.equals( "phylogram" ) ) {
1388 key_index = Configuration.display_as_phylogram;
1390 else if ( key.equals( "rollover" ) ) {
1391 key_index = Configuration.node_data_popup;
1393 else if ( key.equals( "color_according_to_species" ) ) {
1394 key_index = Configuration.color_according_to_species;
1396 else if ( key.equals( "color_according_to_sequence" ) ) {
1397 key_index = Configuration.color_according_to_sequence;
1399 else if ( key.equals( "show_node_names" ) ) {
1400 key_index = Configuration.show_node_names;
1402 else if ( key.equals( "show_taxonomy_code" ) ) {
1403 key_index = Configuration.show_tax_code;
1405 else if ( key.equals( "show_taxonomy_rank" ) ) {
1406 key_index = Configuration.show_tax_rank;
1408 else if ( key.equals( "write_confidence_values" ) ) {
1409 key_index = Configuration.write_confidence_values;
1411 else if ( key.equals( "write_branch_length_values" ) ) {
1412 key_index = Configuration.write_branch_length_values;
1414 else if ( key.equals( "write_events" ) ) {
1415 key_index = Configuration.write_events;
1417 else if ( key.equals( "use_visual_styles" ) ) {
1418 key_index = Configuration.use_style;
1420 else if ( key.equals( "color_branches" ) ) {
1421 key_index = Configuration.use_style;
1423 .printWarningMessage( AptxConstants.PRG_NAME,
1424 "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" );
1426 else if ( key.equals( "width_branches" ) ) {
1427 key_index = Configuration.width_branches;
1429 else if ( key.equals( "show_domain_architectures" ) ) {
1430 key_index = Configuration.show_domain_architectures;
1432 else if ( key.equals( "show_msa" ) ) {
1433 key_index = Configuration.show_mol_seqs;
1435 else if ( key.equals( "show_annotations" ) ) {
1436 key_index = Configuration.show_annotation;
1438 else if ( key.equals( "show_binary_characters" ) ) {
1439 key_index = Configuration.show_binary_characters;
1441 else if ( key.equals( "show_binary_character_counts" ) ) {
1442 key_index = Configuration.show_binary_character_counts;
1444 else if ( key.equals( "show_seq_names" ) ) {
1445 key_index = Configuration.show_seq_names;
1447 else if ( key.equals( "show_gene_names" ) ) {
1448 key_index = Configuration.show_gene_names;
1450 else if ( key.equals( "show_seq_symbols" ) ) {
1451 key_index = Configuration.show_seq_symbols;
1453 else if ( key.equals( "show_seq_acc" ) ) {
1454 key_index = Configuration.show_sequence_acc;
1456 else if ( key.equals( "display_internal_data" ) ) {
1457 key_index = Configuration.display_internal_data;
1459 else if ( key.equals( "dynamically_hide_data" ) ) {
1460 key_index = Configuration.dynamically_hide_data;
1462 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1463 key_index = Configuration.show_taxonomy_scientific_names;
1465 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1466 key_index = Configuration.show_taxonomy_common_names;
1468 else if ( key.equals( "show_taxonomy_images" ) ) {
1469 key_index = Configuration.show_taxonomy_images;
1471 else if ( key.equals( "color_according_to_annotation" ) ) {
1472 key_index = Configuration.color_according_to_annotation;
1474 else if ( key.equals( "show_vector_data" ) ) {
1475 key_index = Configuration.show_vector_data;
1477 else if ( key.equals( "show_properties" ) ) {
1478 key_index = Configuration.show_properties;
1480 else if ( key.equals( "show_relation_confidence" ) ) {
1481 key_index = Configuration.show_relation_confidence;
1483 // If we've found the key, set the values
1484 if ( key_index >= 0 ) {
1485 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1486 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1487 // otherwise, keep looking
1490 if ( key_index == DEPRECATED ) {
1493 else if ( key.equals( "click_to" ) ) {
1494 final String click_to_name = ( String ) st.nextElement();
1495 key_index = getClickToIndex( click_to_name );
1496 if ( key_index >= 0 ) {
1497 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1499 else if ( key_index == DEPRECATED ) {
1503 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown click-to option: "
1507 else if ( key.equals( "species_color" ) ) {
1508 getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
1509 Color.decode( ( String ) st.nextElement() ) );
1511 else if ( key.equals( "sequence_color" ) ) {
1512 getSequenceColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
1513 Color.decode( ( String ) st.nextElement() ) );
1515 else if ( key.equals( "domain_color" ) ) {
1516 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1518 else if ( key.equals( "annotation_color" ) ) {
1519 getAnnotationColors()
1520 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1522 else if ( key.equals( "function_color" ) ) {
1523 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME,
1524 "configuration key [function_color] is deprecated" );
1526 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1527 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1530 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown configuration key [" + key
1531 + "] in: " + config_filename );
1536 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1537 + config_filename );
1541 private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
1542 _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
1545 private void setMaxBaseFontSize( final int max_base_font_size ) {
1546 _max_base_font_size = max_base_font_size;
1549 private void setMinBaseFontSize( final int min_base_font_size ) {
1550 _min_base_font_size = min_base_font_size;
1553 private void setOvMaxHeight( final short ov_max_height ) {
1554 _ov_max_height = ov_max_height;
1557 private void setOvMaxWidth( final short ov_max_width ) {
1558 _ov_max_width = ov_max_width;
1561 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1562 _ov_placement = ov_placement;
1565 private void setPathToLocalFastme( final File path_to_local_fastme ) {
1566 _path_to_local_fastme = path_to_local_fastme;
1569 private void setPathToLocalMafft( final File path_to_local_mafft ) {
1570 _path_to_local_mafft = path_to_local_mafft;
1573 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
1574 _path_to_local_raxml = path_to_local_raxml;
1577 private void setShowAnnotationRefSource( final boolean b ) {
1578 _show_annotation_ref_source = b;
1581 private void setShowOverview( final boolean show_overview ) {
1582 _show_overview = show_overview;
1585 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1586 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1589 boolean displaySequenceRelations() {
1590 return _display_sequence_relations;
1593 boolean doCheckOption( final int which ) {
1594 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
1595 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
1598 boolean doDisplayClickToOption( final int which ) {
1599 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
1602 boolean doDisplayOption( final int which ) {
1603 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
1607 * Will attempt to use the phylogeny to determine whether to check
1608 * this or not (e.g. phylogram)
1611 boolean doGuessCheckOption( final int which ) {
1612 return display_options[ which ][ 2 ].equals( "?" );
1615 Map<String, Color> getAnnotationColors() {
1616 if ( _annotation_colors == null ) {
1617 _annotation_colors = new Hashtable<String, Color>();
1619 return _annotation_colors;
1622 int getBaseFontSize() {
1623 return _base_font_size;
1626 CLADOGRAM_TYPE getCladogramType() {
1627 return _cladogram_type;
1630 int getClickToOptionsCount() {
1631 return clickto_options.length;
1634 String getClickToTitle( final int which ) {
1635 return clickto_options[ which ][ 0 ];
1638 int getDefaultDisplayClicktoOption() {
1639 return default_clickto;
1642 SortedMap<String, Color> getDisplayColors() {
1643 return _display_colors;
1646 String getDisplayTitle( final int which ) {
1647 return display_options[ which ][ 0 ];
1650 Map<String, Color> getDomainColors() {
1651 if ( _domain_colors == null ) {
1652 _domain_colors = new Hashtable<String, Color>();
1654 return _domain_colors;
1658 Color getGuiBackgroundColor() {
1659 return _gui_background_color;
1662 Color getGuiButtonBackgroundColor() {
1663 return _gui_button_background_color;
1666 Color getGuiButtonBorderColor() {
1667 return _gui_button_border_color;
1670 Color getGuiButtonTextColor() {
1671 return _gui_button_text_color;
1674 Color getGuiCheckboxAndButtonActiveColor() {
1675 return _gui_checkbox_and_button_active_color;
1678 Color getGuiCheckboxTextColor() {
1679 return _gui_checkbox_text_color;
1682 Color getGuiMenuBackgroundColor() {
1683 return _gui_menu_background_color;
1686 Color getGuiMenuTextColor() {
1687 return _gui_menu_text_color;
1690 int getMaxBaseFontSize() {
1691 return _max_base_font_size;
1694 int getMinBaseFontSize() {
1695 return _min_base_font_size;
1698 double getMinConfidenceValue() {
1699 return _min_confidence_value;
1702 NODE_LABEL_DIRECTION getNodeLabelDirection() {
1703 return _node_label_direction;
1706 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
1707 return _number_of_digits_after_comma_for_branch_length_values;
1710 short getNumberOfDigitsAfterCommaForConfidenceValues() {
1711 return _number_of_digits_after_comma_for_confidence_values;
1714 short getOvMaxHeight() {
1715 return _ov_max_height;
1718 short getOvMaxWidth() {
1719 return _ov_max_width;
1722 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
1723 return _ov_placement;
1726 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
1727 return _phylogeny_graphics_type;
1730 float getPrintLineWidth() {
1731 return _print_line_width;
1734 Hashtable<String, Color> getSequenceColors() {
1735 if ( _sequence_colors == null ) {
1736 _sequence_colors = new Hashtable<String, Color>();
1738 return _sequence_colors;
1741 Hashtable<String, Color> getSpeciesColors() {
1742 if ( _species_colors == null ) {
1743 initSpeciesColors();
1745 return _species_colors;
1748 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
1749 return _taxonomy_extraction;
1752 boolean isAntialiasScreen() {
1753 return _antialias_screen;
1757 * Convenience method.
1759 * @return true if value in configuration file was 'yes'
1761 boolean isDrawAsPhylogram() {
1762 return doCheckOption( display_as_phylogram );
1765 boolean isEditable() {
1770 * Only used by ArchaeoptryxE.
1773 boolean isHideControlPanelAndMenubar() {
1774 return _hide_controls_and_menus;
1777 boolean isInternalNumberAreConfidenceForNhParsing() {
1778 return _internal_number_are_confidence_for_nh_parsing;
1781 boolean isReplaceUnderscoresInNhParsing() {
1782 return _nh_parsing_replace_underscores;
1785 boolean isShowOverview() {
1786 return _show_overview;
1789 boolean isShowScale() {
1793 final boolean isUseNativeUI() {
1794 if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
1797 return _ui == UI.NATIVE;
1801 * Only used by ArchaeoptryxE.
1804 boolean isUseTabbedDisplay() {
1805 return _use_tabbed_display;
1808 boolean isValidatePhyloXmlAgainstSchema() {
1809 return _validate_against_phyloxml_xsd_schema;
1812 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
1813 _taxonomy_extraction = taxonomy_extraction;
1816 static String getDefaultFontFamilyName() {
1817 return DEFAULT_FONT_FAMILY;
1820 public boolean isCouldReadConfigFile() {
1821 return _could_read_config_file;