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;
37 import java.net.MalformedURLException;
39 import java.util.Arrays;
40 import java.util.Hashtable;
42 import java.util.SortedMap;
43 import java.util.StringTokenizer;
44 import java.util.TreeMap;
46 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
47 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
48 import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE;
49 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
50 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
51 import org.forester.phylogeny.data.NodeData.NODE_DATA;
52 import org.forester.phylogeny.data.NodeVisualization;
53 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
54 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
55 import org.forester.util.ForesterUtil;
57 public final class Configuration {
59 static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
60 private static final String WEB_LINK_KEY = "web_link";
61 private static final String DISPLAY_COLOR_KEY = "display_color";
62 private static final int DEPRECATED = -2;
63 private UI _ui = UI.UNKNOWN;
64 private boolean _use_tabbed_display = false;
65 private boolean _hide_controls_and_menus = false;
66 private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
67 private SortedMap<String, WebLink> _weblinks = null;
68 private SortedMap<String, Color> _display_colors = null;
69 private boolean _antialias_screen = true;
70 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
71 private String _base_font_family_name = "";
72 private int _base_font_size = -1;
73 private int _min_base_font_size = 2;
74 private int _max_base_font_size = 20;
75 private int _graphics_export_x = -1;
76 private int _graphics_export_y = -1;
77 private short _ov_max_width = 80;
78 private short _ov_max_height = 80;
79 private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
80 private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
81 private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
82 private boolean _show_scale = false;
83 private boolean _show_branch_length_values = false;
84 private boolean _show_overview = true;
85 private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
86 private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
87 private boolean _editable = true;
88 private boolean _nh_parsing_replace_underscores = false;
89 private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
90 private boolean _internal_number_are_confidence_for_nh_parsing = false;
91 private boolean _display_sequence_relations = false;
92 private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
93 private boolean _background_color_gradient = false;
94 private boolean _show_domain_labels = true;
95 private boolean _abbreviate_scientific_names = false;
96 private boolean _color_labels_same_as_parent_branch = false;
97 private boolean _show_default_node_shapes_internal = false;
98 private boolean _show_default_node_shapes_external = false;
99 private NodeShape _default_node_shape = NodeShape.CIRCLE;
100 private NodeFill _default_node_fill = NodeFill.GRADIENT;
101 private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
102 private boolean _taxonomy_colorize_node_shapes = false;
103 private int _default_bootstrap_samples = -1;
104 private File _path_to_local_mafft = null;
105 private File _path_to_local_fastme = null;
106 private File _path_to_local_raxml = null;
107 final static int display_as_phylogram = 0;
108 final static int show_node_names = 1;
109 final static int show_tax_code = 2;
110 final static int show_annotation = 3;
111 final static int write_confidence_values = 4;
112 final static int write_events = 5;
113 final static int color_according_to_species = 6;
114 final static int color_branches = 7;
115 final static int width_branches = 8;
116 final static int show_custom_node_shapes = 9;
117 final static int show_domain_architectures = 10;
118 final static int show_binary_characters = 11;
119 final static int show_binary_character_counts = 12;
120 final static int show_gene_names = 13;
121 final static int show_sequence_acc = 14;
122 final static int display_internal_data = 15;
123 final static int dynamically_hide_data = 16;
124 final static int show_taxonomy_scientific_names = 17;
125 final static int show_taxonomy_common_names = 18;
126 final static int color_according_to_annotation = 19;
127 final static int show_gene_symbols = 20;
128 final static int node_data_popup = 21;
129 final static int show_relation_confidence = 22;
130 final static int show_vector_data = 23;
131 final static int show_taxonomy_images = 24;
132 final static int show_properties = 25;
133 // ------------------
135 // ------------------
136 final static int display_node_data = 0;
137 final static int collapse_uncollapse = 1;
138 final static int reroot = 2;
139 final static int subtree = 3;
140 final static int swap = 4;
141 final static int color_subtree = 5;
142 final static int open_seq_web = 6;
143 final static int open_tax_web = 7;
144 final static int blast = 8;
145 final static int cut_subtree = 9;
146 final static int copy_subtree = 10;
147 final static int paste_subtree = 11;
148 final static int delete_subtree_or_node = 12;
149 final static int add_new_node = 13;
150 final static int edit_node_data = 14;
151 final static int sort_descendents = 15;
152 final static int get_ext_desc_data = 16;
153 final static int select_nodes = 17;
154 // ---------------------------
155 // Display options for trees
156 // ---------------------------
157 // ---------------------------------
158 // Pertaining to the config itself
159 // ---------------------------------
160 // Full path to config (may be URL)
161 String config_filename;
162 String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
163 final static String display_options[][] = {
164 { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
165 { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" },
166 { "Node Events", "display", "?" }, { "Taxonomy Colorize", "display", "yes" },
167 { "Colorize Branches", "display", "no" }, { "Use Branch-Widths", "display", "no" },
168 { "Show Custom Nodes", "display", "yes" }, { "Domains", "nodisplay", "no" },
169 { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
170 { "Seq Name", "display", "yes" }, { "Seq Acc", "display", "no" },
171 { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
172 { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
173 { "Annotation Colorize", "nodisplay", "no" }, { "Seq Symbol", "display", "yes" },
174 { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
175 { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
176 { "Properties", "nodisplay", "no" } };
177 final static String clickto_options[][] = {
178 { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
179 { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
180 { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Blast", "display" },
181 { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" },
182 { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" },
183 { "Sort Descendants", "display" }, { "Return", "display" }, { "Select Node(s)", "display" } };
184 // This option is selected in the dropdown
185 int default_clickto = Configuration.display_node_data;
189 TreeColorSet tree_color_set;
193 TreeFontSet tree_font_set;
197 private static Hashtable<String, Color> _species_colors;
201 private static Hashtable<String, Color> _domain_colors;
205 private static Hashtable<String, Color> _annotation_colors;
206 boolean verbose = Constants.VERBOSE_DEFAULT;
207 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
208 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
209 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
210 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
211 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
212 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
213 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
214 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
215 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
216 private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
217 private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
218 private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
219 private String _label_for_get_ext_descendents_data = "";
220 private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
221 private int _frame_x_size;
222 private int _frame_y_size;
223 private static String DEFAULT_FONT_FAMILY = "";
225 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
226 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
227 DEFAULT_FONT_FAMILY = font_name;
231 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
232 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
236 public Configuration() {
237 this( null, false, false, false );
240 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
241 if ( ForesterUtil.isEmpty( cf ) ) {
242 config_filename = default_config_filename;
245 config_filename = cf;
247 setWebLinks( new TreeMap<String, WebLink>() );
248 setDisplayColors( new TreeMap<String, Color>() );
249 config_filename = config_filename.trim();
252 // If URL, open accordingly
254 u = new URL( config_filename );
256 final InputStreamReader isr = new InputStreamReader( u.openStream() );
257 final BufferedReader bf = new BufferedReader( isr );
260 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
261 + config_filename + "]" );
263 catch ( final Exception e ) {
264 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
265 + config_filename + "]: " + e.getLocalizedMessage() );
268 catch ( final Exception e ) {
269 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
270 + config_filename + "]" );
274 // Otherwise, open as a file
275 File f = new File( config_filename );
277 f = new File( config_filename + ".txt" );
279 if ( f.exists() && f.canRead() ) {
281 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
285 catch ( final Exception e ) {
287 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
288 + config_filename + "]: " + e );
294 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
295 + config_filename + "]" );
301 public String getBaseFontFamilyName() {
302 return _base_font_family_name;
305 public int getDefaultBootstrapSamples() {
306 return _default_bootstrap_samples;
309 public NodeFill getDefaultNodeFill() {
310 return _default_node_fill;
313 public NodeShape getDefaultNodeShape() {
314 return _default_node_shape;
317 public short getDefaultNodeShapeSize() {
318 return _default_node_shape_size;
321 public Color getDomainStructureBaseColor() {
322 return _domain_structure_base_color;
325 public Color getDomainStructureFontColor() {
326 return _domain_structure_font_color;
329 public NODE_DATA getExtDescNodeDataToReturn() {
330 return _ext_desc_data_to_return;
333 public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
334 return _ext_node_data_return_on;
337 public int getFrameXSize() {
338 return _frame_x_size;
341 public int getFrameYSize() {
342 return _frame_y_size;
345 public String getLabelForGetExtDescendentsData() {
346 return _label_for_get_ext_descendents_data;
349 public File getPathToLocalFastme() {
350 return _path_to_local_fastme;
353 public File getpathToLocalMafft() {
354 return _path_to_local_mafft;
357 public File getPathToLocalRaxml() {
358 return _path_to_local_raxml;
361 public boolean isAbbreviateScientificTaxonNames() {
362 return _abbreviate_scientific_names;
365 public boolean isBackgroundColorGradient() {
366 return _background_color_gradient;
369 public boolean isColorLabelsSameAsParentBranch() {
370 return _color_labels_same_as_parent_branch;
373 public boolean isShowDefaultNodeShapesExternal() {
374 return _show_default_node_shapes_external;
377 public boolean isShowDefaultNodeShapesInternal() {
378 return _show_default_node_shapes_internal;
381 public boolean isShowDomainLabels() {
382 return _show_domain_labels;
385 public boolean isTaxonomyColorizeNodeShapes() {
386 return _taxonomy_colorize_node_shapes;
389 public void putDisplayColors( final String key, final Color color ) {
390 getDisplayColors().put( key, color );
393 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
394 _abbreviate_scientific_names = abbreviate_scientific_names;
397 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
398 _background_color_gradient = background_color_gradient;
401 public void setBaseFontFamilyName( final String base_font_family_name ) {
402 _base_font_family_name = base_font_family_name;
405 public void setBaseFontSize( final int base_font_size ) {
406 _base_font_size = base_font_size;
409 private void setMaxBaseFontSize( final int max_base_font_size ) {
410 _max_base_font_size = max_base_font_size;
413 private void setMinBaseFontSize( final int min_base_font_size ) {
414 _min_base_font_size = min_base_font_size;
417 public void setColorizeBranches( final boolean b ) {
418 display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
421 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
422 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
425 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
426 _default_node_fill = default_node_fill;
429 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
430 _default_node_shape = default_node_shape;
433 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
434 _default_node_shape_size = default_node_shape_size;
437 public void setDisplayAsPhylogram( final boolean b ) {
438 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
441 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
442 _display_colors = display_colors;
445 public void setDisplayConfidenceValues( final boolean b ) {
446 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
449 public void setDisplayInternalData( final boolean b ) {
450 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
453 public void setDisplayNodeNames( final boolean b ) {
454 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
457 public void setDisplaySequenceAcc( final boolean b ) {
458 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
461 public void setDisplaySequenceNames( final boolean b ) {
462 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
465 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
466 _display_sequence_relations = display_sequence_relations;
469 public void setDisplaySequenceSymbols( final boolean b ) {
470 display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no";
473 public void setDisplayTaxonomyCode( final boolean b ) {
474 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
477 public void setDisplayTaxonomyCommonNames( final boolean b ) {
478 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
481 public void setDisplayTaxonomyImages( final boolean b ) {
482 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
485 public void setDisplayTaxonomyScientificNames( final boolean b ) {
486 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
489 public void setDynamicallyHideData( final boolean b ) {
490 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
493 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
494 _ext_desc_data_to_return = ext_desc_data_to_return;
497 public void setFrameXSize( final int frame_x_size ) {
498 _frame_x_size = frame_x_size;
501 public void setFrameYSize( final int frame_y_size ) {
502 _frame_y_size = frame_y_size;
505 public void setMinConfidenceValue( final double min_confidence_value ) {
506 _min_confidence_value = min_confidence_value;
509 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
510 _node_label_direction = node_label_direction;
513 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
514 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
517 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
518 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
521 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
522 _phylogeny_graphics_type = phylogeny_graphics_type;
525 public void setPrintLineWidth( final float print_line_width ) {
526 _print_line_width = print_line_width;
529 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
530 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
533 public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
534 _show_branch_length_values = show_branch_length_values;
537 public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
538 _show_default_node_shapes_external = show_default_node_shapes_external;
541 public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
542 _show_default_node_shapes_internal = show_default_node_shapes_internal;
545 public void setShowDomainLabels( final boolean show_domain_labels ) {
546 _show_domain_labels = show_domain_labels;
549 public void setShowScale( final boolean show_scale ) {
550 _show_scale = show_scale;
553 public void setTaxonomyColorize( final boolean b ) {
554 display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
557 public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
558 _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
561 public void setUseBranchesWidths( final boolean b ) {
562 display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
565 boolean displaySequenceRelations() {
566 return _display_sequence_relations;
569 boolean doCheckOption( final int which ) {
570 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
571 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
574 boolean doDisplayClickToOption( final int which ) {
575 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
578 boolean doDisplayOption( final int which ) {
579 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
583 * Will attempt to use the phylogeny to determine whether to check
584 * this or not (e.g. phylogram)
587 boolean doGuessCheckOption( final int which ) {
588 return display_options[ which ][ 2 ].equals( "?" );
591 Map<String, Color> getAnnotationColors() {
592 if ( _annotation_colors == null ) {
593 _annotation_colors = new Hashtable<String, Color>();
595 return _annotation_colors;
598 int getBaseFontSize() {
599 return _base_font_size;
602 int getMinBaseFontSize() {
603 return _min_base_font_size;
606 int getMaxBaseFontSize() {
607 return _max_base_font_size;
610 CLADOGRAM_TYPE getCladogramType() {
611 return _cladogram_type;
614 int getClickToOptionsCount() {
615 return clickto_options.length;
618 String getClickToTitle( final int which ) {
619 return clickto_options[ which ][ 0 ];
622 int getDefaultDisplayClicktoOption() {
623 return default_clickto;
626 SortedMap<String, Color> getDisplayColors() {
627 return _display_colors;
630 String getDisplayTitle( final int which ) {
631 return display_options[ which ][ 0 ];
634 Map<String, Color> getDomainColors() {
635 if ( _domain_colors == null ) {
636 _domain_colors = new Hashtable<String, Color>();
638 return _domain_colors;
641 int getGraphicsExportX() {
642 return _graphics_export_x;
645 int getGraphicsExportY() {
646 return _graphics_export_y;
649 Color getGuiBackgroundColor() {
650 return _gui_background_color;
653 Color getGuiButtonBackgroundColor() {
654 return _gui_button_background_color;
657 Color getGuiButtonBorderColor() {
658 return _gui_button_border_color;
661 Color getGuiButtonTextColor() {
662 return _gui_button_text_color;
665 Color getGuiCheckboxAndButtonActiveColor() {
666 return _gui_checkbox_and_button_active_color;
669 Color getGuiCheckboxTextColor() {
670 return _gui_checkbox_text_color;
673 Color getGuiMenuBackgroundColor() {
674 return _gui_menu_background_color;
677 Color getGuiMenuTextColor() {
678 return _gui_menu_text_color;
681 double getMinConfidenceValue() {
682 return _min_confidence_value;
685 NODE_LABEL_DIRECTION getNodeLabelDirection() {
686 return _node_label_direction;
689 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
690 return _number_of_digits_after_comma_for_branch_length_values;
693 short getNumberOfDigitsAfterCommaForConfidenceValues() {
694 return _number_of_digits_after_comma_for_confidence_values;
697 short getOvMaxHeight() {
698 return _ov_max_height;
701 short getOvMaxWidth() {
702 return _ov_max_width;
705 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
706 return _ov_placement;
709 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
710 return _phylogeny_graphics_type;
713 float getPrintLineWidth() {
714 return _print_line_width;
717 Hashtable<String, Color> getSpeciesColors() {
718 if ( _species_colors == null ) {
719 _species_colors = new Hashtable<String, Color>();
721 return _species_colors;
724 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
725 return _taxonomy_extraction;
728 WebLink getWebLink( final String source ) {
729 return getWebLinks().get( source );
732 Map<String, WebLink> getWebLinks() {
736 boolean isAntialiasScreen() {
737 return _antialias_screen;
741 * Convenience method.
743 * @return true if value in configuration file was 'yes'
745 boolean isDrawAsPhylogram() {
746 return doCheckOption( display_as_phylogram );
749 boolean isEditable() {
753 boolean isHasWebLink( final String source ) {
754 return getWebLinks().containsKey( source );
758 * Only used by ArchaeoptryxE.
761 boolean isHideControlPanelAndMenubar() {
762 return _hide_controls_and_menus;
765 boolean isInternalNumberAreConfidenceForNhParsing() {
766 return _internal_number_are_confidence_for_nh_parsing;
769 boolean isReplaceUnderscoresInNhParsing() {
770 return _nh_parsing_replace_underscores;
773 boolean isShowBranchLengthValues() {
774 return _show_branch_length_values;
777 boolean isShowOverview() {
778 return _show_overview;
781 boolean isShowScale() {
785 final boolean isUseNativeUI() {
786 if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) {
789 return _ui == UI.NATIVE;
793 * Only used by ArchaeoptryxE.
796 boolean isUseTabbedDisplay() {
797 return _use_tabbed_display;
800 boolean isValidatePhyloXmlAgainstSchema() {
801 return _validate_against_phyloxml_xsd_schema;
804 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
805 _taxonomy_extraction = taxonomy_extraction;
808 void setWebLinks( final SortedMap<String, WebLink> weblinks ) {
809 _weblinks = weblinks;
812 private void createWebLink( final String url_str, final String desc, final String source_identifier ) {
813 WebLink weblink = null;
816 weblink = new WebLink( new URL( url_str.trim() ), desc.trim(), source_identifier.trim() );
818 catch ( final MalformedURLException e ) {
819 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not create URL from [" + url_str + "]" );
822 if ( !ex && ( weblink != null ) ) {
823 getWebLinks().put( weblink.getSourceIdentifier().toLowerCase(), weblink );
827 private int getClickToIndex( final String name ) {
829 if ( name.equals( "edit_info" ) ) {
830 index = Configuration.display_node_data;
832 .printWarningMessage( Constants.PRG_NAME,
833 "configuration key [edit_info] is deprecated, use [display node data] instead" );
835 else if ( name.equals( "display_node_data" ) ) {
836 index = Configuration.display_node_data;
838 else if ( name.equals( "collapse_uncollapse" ) ) {
839 index = Configuration.collapse_uncollapse;
841 else if ( name.equals( "reroot" ) ) {
842 index = Configuration.reroot;
844 else if ( name.equals( "subtree" ) ) {
845 index = Configuration.subtree;
847 else if ( name.equals( "swap" ) ) {
848 index = Configuration.swap;
850 else if ( name.equals( "sort_descendants" ) ) {
851 index = Configuration.sort_descendents;
853 else if ( name.equals( "get_ext_descendents_data" ) ) {
854 index = Configuration.get_ext_desc_data;
856 else if ( name.equals( "display_sequences" ) ) {
858 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
861 else if ( name.equals( "open_seq_web" ) ) {
862 index = Configuration.open_seq_web;
864 else if ( name.equals( "open_tax_web" ) ) {
865 index = Configuration.open_tax_web;
867 else if ( name.equals( "blast" ) ) {
868 index = Configuration.blast;
870 else if ( name.equals( "cut_subtree" ) ) {
871 index = Configuration.cut_subtree;
873 else if ( name.equals( "copy_subtree" ) ) {
874 index = Configuration.copy_subtree;
876 else if ( name.equals( "paste_subtree" ) ) {
877 index = Configuration.paste_subtree;
879 else if ( name.equals( "delete" ) ) {
880 index = Configuration.delete_subtree_or_node;
882 else if ( name.equals( "add_new_node" ) ) {
883 index = Configuration.add_new_node;
885 else if ( name.equals( "edit_node_data" ) ) {
886 index = Configuration.edit_node_data;
888 else if ( name.equals( "select_nodes" ) ) {
889 index = Configuration.select_nodes;
891 else if ( name.equals( "display_node_popup" ) ) {
892 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
893 "configuration key [display_node_popup] is deprecated" );
896 else if ( name.equals( "custom_option" ) ) {
897 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
900 else if ( name.equals( "color_subtree" ) ) {
901 index = Configuration.color_subtree;
903 else if ( name.equals( "go_to_swiss_prot" ) ) {
904 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" );
910 private boolean parseBoolean( final String str ) {
911 final String my_str = str.trim().toLowerCase();
912 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
915 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
919 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
924 private double parseDouble( final String str ) {
927 d = Double.parseDouble( str.trim() );
929 catch ( final Exception e ) {
930 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
936 private float parseFloat( final String str ) {
939 f = Float.parseFloat( str.trim() );
941 catch ( final Exception e ) {
942 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
948 private int parseInt( final String str ) {
951 i = Integer.parseInt( str.trim() );
953 catch ( final Exception e ) {
954 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
960 private short parseShort( final String str ) {
963 i = Short.parseShort( str.trim() );
965 catch ( final Exception e ) {
966 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
972 private void processFontFamily( final StringTokenizer st ) {
973 setBaseFontFamilyName( "" );
974 final String font_str = ( ( String ) st.nextElement() ).trim();
975 final String[] fonts = font_str.split( ",+" );
976 for( String font : fonts ) {
977 font = font.replace( '_', ' ' ).trim();
978 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
979 setBaseFontFamilyName( font );
986 * read each line of config file, process non-comment lines
987 * @throws IOException
989 private void readConfig( final BufferedReader conf_in ) throws IOException {
992 line = conf_in.readLine();
993 if ( line != null ) {
995 // skip comments and blank lines
996 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
997 // convert runs of spaces to tabs
998 line = line.replaceAll( "\\s+", "\t" );
999 final StringTokenizer st = new StringTokenizer( line, "\t" );
1003 } while ( line != null );
1006 private void setAntialiasScreen( final boolean antialias_screen ) {
1007 _antialias_screen = antialias_screen;
1010 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
1011 _cladogram_type = cladogram_type;
1014 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
1015 _default_bootstrap_samples = default_bootstrap_samples;
1018 private void setEditable( final boolean editable ) {
1019 _editable = editable;
1022 private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
1023 _ext_node_data_return_on = ext_node_data_return_on;
1026 private void setGraphicsExportX( final int graphics_export_x ) {
1027 _graphics_export_x = graphics_export_x;
1030 private void setGraphicsExportY( final int graphics_export_y ) {
1031 _graphics_export_y = graphics_export_y;
1034 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
1035 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
1039 * Set a key-value(s) tuple
1041 private void setKeyValue( final StringTokenizer st ) {
1042 final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
1043 if ( !st.hasMoreElements() ) {
1046 // Handle single value settings first:
1047 if ( key.equals( "default_click_to" ) ) {
1048 final String clickto_name = ( String ) st.nextElement();
1049 default_clickto = getClickToIndex( clickto_name );
1050 if ( default_clickto == -1 ) {
1051 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
1052 + "] for [default_click_to]" );
1053 default_clickto = 0;
1055 else if ( default_clickto == DEPRECATED ) {
1059 else if ( key.equals( "native_ui" ) ) {
1060 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
1061 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
1064 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
1065 _ui = UI.CROSSPLATFORM;
1067 else if ( my_str.equals( "?" ) ) {
1071 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
1076 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
1077 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
1079 else if ( key.equals( "antialias_screen" ) ) {
1080 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
1082 else if ( key.equals( "phylogeny_graphics_type" ) ) {
1083 final String type_str = ( ( String ) st.nextElement() ).trim();
1084 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
1085 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1087 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
1088 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1090 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
1091 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1093 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
1094 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1096 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
1097 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1099 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
1100 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1102 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
1103 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1105 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
1106 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1109 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1110 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1111 + "] for [phylogeny_graphics_type]" );
1114 else if ( key.equals( "min_confidence_value" ) ) {
1115 final String mcv_str = ( ( String ) st.nextElement() ).trim();
1116 final double d = parseDouble( mcv_str );
1117 setMinConfidenceValue( d );
1119 else if ( key.equals( "font_family" ) ) {
1120 processFontFamily( st );
1122 else if ( key.equals( "font_size" ) ) {
1123 final String size_str = ( ( String ) st.nextElement() ).trim();
1124 final int i = parseInt( size_str );
1126 setBaseFontSize( i );
1129 else if ( key.equals( "font_size_min" ) ) {
1130 final String size_str = ( ( String ) st.nextElement() ).trim();
1131 final int i = parseInt( size_str );
1133 setMinBaseFontSize( i );
1136 else if ( key.equals( "font_size_max" ) ) {
1137 final String size_str = ( ( String ) st.nextElement() ).trim();
1138 final int i = parseInt( size_str );
1140 setMaxBaseFontSize( i );
1143 else if ( key.equals( "graphics_export_x" ) ) {
1144 final String str = ( ( String ) st.nextElement() ).trim();
1145 final int i = parseInt( str );
1147 setGraphicsExportX( i );
1150 else if ( key.equals( "graphics_export_y" ) ) {
1151 final String str = ( ( String ) st.nextElement() ).trim();
1152 final int i = parseInt( str );
1154 setGraphicsExportY( i );
1157 else if ( key.equals( "pdf_export_line_width" ) ) {
1158 final String str = ( ( String ) st.nextElement() ).trim();
1159 final float f = parseFloat( str );
1161 setPrintLineWidth( f );
1164 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1165 "value for [pdf_export_line_width] cannot be zero or negative" );
1168 else if ( key.equals( "window_initial_size_x" ) ) {
1169 final String str = ( ( String ) st.nextElement() ).trim();
1170 final int i = parseInt( str );
1175 else if ( key.equals( "window_initial_size_y" ) ) {
1176 final String str = ( ( String ) st.nextElement() ).trim();
1177 final int i = parseInt( str );
1182 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1183 final String str = ( ( String ) st.nextElement() ).trim();
1184 final int i = parseInt( str );
1186 setDefaultBootstrapSamples( i );
1190 .printWarningMessage( Constants.PRG_NAME,
1191 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1194 else if ( key.equals( "mafft_local" ) ) {
1195 final String str = ( ( String ) st.nextElement() ).trim();
1196 if ( !ForesterUtil.isEmpty( str ) ) {
1197 setPathToLocalMafft( new File( str ) );
1200 else if ( key.equals( "fastme_local" ) ) {
1201 final String str = ( ( String ) st.nextElement() ).trim();
1202 if ( !ForesterUtil.isEmpty( str ) ) {
1203 setPathToLocalFastme( new File( str ) );
1206 else if ( key.equals( "raxml_local" ) ) {
1207 final String str = ( ( String ) st.nextElement() ).trim();
1208 if ( !ForesterUtil.isEmpty( str ) ) {
1209 setPathToLocalRaxml( new File( str ) );
1212 else if ( key.equals( "show_scale" ) ) {
1213 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1215 else if ( key.equals( "show_overview" ) ) {
1216 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1218 else if ( key.equals( "show_branch_length_values" ) ) {
1219 setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
1221 else if ( key.equals( "background_gradient" ) ) {
1222 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1224 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1225 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1227 else if ( key.equals( "show_domain_labels" ) ) {
1228 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1230 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1231 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1233 else if ( key.equals( "cladogram_type" ) ) {
1234 final String type_str = ( ( String ) st.nextElement() ).trim();
1235 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1236 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1238 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1239 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1241 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1242 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1245 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1246 + "] for [cladogram_type]" );
1249 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1251 .printWarningMessage( Constants.PRG_NAME,
1252 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1254 else if ( key.equals( "hide_controls_and_menus" ) ) {
1255 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1257 else if ( key.equals( "use_tabbed_display" ) ) {
1258 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1260 else if ( key.equals( "overview_width" ) ) {
1261 final short i = parseShort( ( ( String ) st.nextElement() ) );
1264 else if ( key.equals( "overview_height" ) ) {
1265 final short i = parseShort( ( ( String ) st.nextElement() ) );
1266 setOvMaxHeight( i );
1268 else if ( key.equals( "overview_placement_type" ) ) {
1269 final String type_str = ( ( String ) st.nextElement() ).trim();
1270 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1271 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1273 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1274 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1276 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1277 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1279 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1280 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1283 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1284 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1285 + "] for [overview_placement_type]" );
1288 else if ( key.equals( "node_label_direction" ) ) {
1289 final String type_str = ( ( String ) st.nextElement() ).trim();
1290 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1291 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1293 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1294 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1297 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1298 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1299 + "] for [node_label_direction]" );
1302 else if ( key.equals( "branch_length_value_digits" ) ) {
1303 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1305 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1308 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1309 + "] for [branch_length_value_digits]" );
1312 else if ( key.equals( "confidence_value_digits" ) ) {
1313 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1315 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1318 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1319 + "] for [confidence_value_digits]" );
1322 else if ( key.equals( "allow_editing" ) ) {
1323 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1325 else if ( key.equals( "display_sequence_relations" ) ) {
1326 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1328 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1329 final boolean r = parseBoolean( ( String ) st.nextElement() );
1330 if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
1332 .printWarningMessage( Constants.PRG_NAME,
1333 "attempt to extract taxonomies and replace underscores at the same time" );
1336 setReplaceUnderscoresInNhParsing( r );
1339 else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
1340 final String s = ( String ) st.nextElement();
1341 if ( s.equalsIgnoreCase( "no" ) ) {
1342 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1344 else if ( s.equalsIgnoreCase( "yes" ) ) {
1345 setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES );
1347 else if ( s.equalsIgnoreCase( "pfam" ) ) {
1348 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
1351 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1352 "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + s );
1354 if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
1356 .printWarningMessage( Constants.PRG_NAME,
1357 "attempt to extract taxonomies and replace underscores at the same time" );
1360 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1361 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1363 else if ( key.equals( "gui_background_color" ) ) {
1364 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1366 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1367 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1369 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1370 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1372 else if ( key.equals( "gui_button_text_color" ) ) {
1373 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1375 else if ( key.equals( "gui_button_background_color" ) ) {
1376 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1378 else if ( key.equals( "gui_menu_background_color" ) ) {
1379 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1381 else if ( key.equals( "gui_menu_text_color" ) ) {
1382 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1384 else if ( key.equals( "gui_button_border_color" ) ) {
1385 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1387 else if ( key.equals( "domain_structure_font_color" ) ) {
1388 _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
1390 else if ( key.equals( "domain_structure_base_color" ) ) {
1391 _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
1393 else if ( key.equals( "show_default_node_shapes" ) ) {
1395 .printWarningMessage( Constants.PRG_NAME,
1396 "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" );
1397 final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() );
1398 setShowDefaultNodeShapesInternal( b );
1399 setShowDefaultNodeShapesExternal( b );
1401 else if ( key.equals( "show_default_node_shapes_internal" ) ) {
1402 setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1404 else if ( key.equals( "show_default_node_shapes_external" ) ) {
1405 setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1407 else if ( key.equals( "default_node_size" ) ) {
1408 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1409 setDefaultNodeShapeSize( i );
1411 else if ( key.equals( "default_node_fill" ) ) {
1412 final String fill_str = ( ( String ) st.nextElement() ).trim();
1413 if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.NONE.toString() ) ) {
1414 setDefaultNodeFill( NodeFill.NONE );
1416 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.GRADIENT.toString() ) ) {
1417 setDefaultNodeFill( NodeFill.GRADIENT );
1419 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.SOLID.toString() ) ) {
1420 setDefaultNodeFill( NodeFill.SOLID );
1423 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1424 + "] for [default_node_fill]" );
1427 else if ( key.equals( "default_node_shape" ) ) {
1428 final String shape_str = ( ( String ) st.nextElement() ).trim();
1429 if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.CIRCLE.toString() ) ) {
1430 setDefaultNodeShape( NodeShape.CIRCLE );
1432 else if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.RECTANGLE.toString() ) ) {
1433 setDefaultNodeShape( NodeShape.RECTANGLE );
1436 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1437 + "] for [default_node_shape]" );
1440 else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
1441 setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
1443 else if ( key.equals( "ext_descendents_data_to_return" ) ) {
1444 final String s = ( ( String ) st.nextElement() ).trim();
1445 if ( s.equalsIgnoreCase( "node_name" ) ) {
1446 setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
1448 else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
1449 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
1451 else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
1452 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
1454 else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
1455 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
1457 else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
1458 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
1460 else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
1461 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME );
1463 else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
1464 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
1466 else if ( s.equalsIgnoreCase( "user_selected" ) ) {
1467 setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
1470 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1471 + "] for [ext_descendents_data_to_return]" );
1474 else if ( key.equals( "label_for_get_ext_descendents_data" ) ) {
1475 final String s = ( ( String ) st.nextElement() ).trim();
1476 if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) {
1477 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s
1478 + "] for [label_for_get_ext_descendents_data]" );
1481 setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
1484 else if ( key.equals( "ext_descendents_data_to_return_on" ) ) {
1485 final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
1486 if ( s.equals( "console" ) ) {
1487 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
1489 else if ( s.equals( "window" ) ) {
1490 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
1492 else if ( s.equals( "buffer_only" ) ) {
1493 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
1496 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1497 + "] for [ext_descendents_data_to_return_on]" );
1500 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1503 if ( key.equals( "use_real_br_lengths" ) || key.equals( "phylogram" ) ) {
1504 key_index = Configuration.display_as_phylogram;
1505 if ( key.equals( "use_real_br_lengths" ) ) {
1507 .printWarningMessage( Constants.PRG_NAME,
1508 "configuration key [use_real_br_lengths] is deprecated, use [phylogram] instead" );
1511 else if ( key.equals( "rollover" ) ) {
1512 key_index = Configuration.node_data_popup;
1514 else if ( key.equals( "color_according_to_species" ) ) {
1515 key_index = Configuration.color_according_to_species;
1517 else if ( key.equals( "show_node_names" ) ) {
1518 key_index = Configuration.show_node_names;
1520 else if ( key.equals( "show_taxonomy" ) || key.equals( "show_taxonomy_code" ) ) {
1521 key_index = Configuration.show_tax_code;
1522 if ( key.equals( "show_taxonomy" ) ) {
1524 .printWarningMessage( Constants.PRG_NAME,
1525 "configuration key [show_taxonomy] is deprecated, use [show_taxonomy_code] instead" );
1528 else if ( key.equals( "write_br_length_values" ) ) {
1529 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1530 "configuration key [write_br_length_values] is deprecated" );
1531 key_index = DEPRECATED;
1533 else if ( key.equals( "write_bootstrap_values" ) || key.equals( "write_confidence_values" ) ) {
1534 key_index = Configuration.write_confidence_values;
1535 if ( key.equals( "write_bootstrap_values" ) ) {
1537 .printWarningMessage( Constants.PRG_NAME,
1538 "configuration key [write_bootstrap_values] is deprecated, use [write_confidence_values] instead" );
1541 else if ( key.equals( "write_events" ) || key.equals( "write_dup_spec" ) ) {
1542 key_index = Configuration.write_events;
1543 if ( key.equals( "write_dup_spec" ) ) {
1545 .printWarningMessage( Constants.PRG_NAME,
1546 "configuration key [write_dup_spec] is deprecated, use [write_events] instead" );
1549 else if ( key.equals( "color_branches" ) ) {
1550 key_index = Configuration.color_branches;
1552 else if ( key.equals( "width_branches" ) ) {
1553 key_index = Configuration.width_branches;
1555 else if ( key.equals( "color_orthologous" ) ) {
1556 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1557 "configuration key [color_orthologous] is deprecated" );
1559 else if ( key.equals( "color_subtree_neighbors" ) ) {
1560 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1561 "configuration key [color_subtree_neighbors] is deprecated" );
1563 else if ( key.equals( "color_super_orthologous" ) ) {
1564 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1565 "configuration key [color_super_orthologous] is deprecated" );
1567 else if ( key.equals( "mark_nodes_with_box" ) ) {
1568 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1569 "configuration key [mark_nodes_with_box] is deprecated" );
1570 key_index = DEPRECATED;
1572 else if ( key.equals( "show_domain_architectures" ) ) {
1573 key_index = Configuration.show_domain_architectures;
1575 else if ( key.equals( "show_annotations" ) ) {
1576 key_index = Configuration.show_annotation;
1578 else if ( key.equals( "show_binary_characters" ) ) {
1579 key_index = Configuration.show_binary_characters;
1581 else if ( key.equals( "show_binary_character_counts" ) ) {
1582 key_index = Configuration.show_binary_character_counts;
1584 else if ( key.equals( "show_gene_names" ) ) {
1585 key_index = Configuration.show_gene_names;
1587 else if ( key.equals( "show_gene_symbols" ) ) {
1588 key_index = Configuration.show_gene_symbols;
1590 else if ( key.equals( "show_sequence_acc" ) ) {
1591 key_index = Configuration.show_sequence_acc;
1593 else if ( key.equals( "show_node_ids" ) ) {
1595 .printWarningMessage( Constants.PRG_NAME, "configuration key [show_node_ids] is deprecated" );
1596 key_index = DEPRECATED;
1598 else if ( key.equals( "display_internal_data" ) ) {
1599 key_index = Configuration.display_internal_data;
1601 else if ( key.equals( "dynamically_hide_data" ) ) {
1602 key_index = Configuration.dynamically_hide_data;
1604 else if ( key.equals( "show_taxonomy_names" ) ) {
1605 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1606 "configuration key [show_taxonomy_names] is deprecated" );
1607 key_index = DEPRECATED;
1609 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1610 key_index = Configuration.show_taxonomy_scientific_names;
1612 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1613 key_index = Configuration.show_taxonomy_common_names;
1615 else if ( key.equals( "show_taxonomy_images" ) ) {
1616 key_index = Configuration.show_taxonomy_images;
1618 else if ( key.equals( "color_according_to_annotation" ) ) {
1619 key_index = Configuration.color_according_to_annotation;
1621 else if ( key.equals( "show_vector_data" ) ) {
1622 key_index = Configuration.show_vector_data;
1624 else if ( key.equals( "show_properties" ) ) {
1625 key_index = Configuration.show_properties;
1627 else if ( key.equals( "show_relation_confidence" ) ) {
1628 key_index = Configuration.show_relation_confidence;
1630 else if ( key.equals( "show_custom_node_shapes" ) ) {
1631 key_index = Configuration.show_custom_node_shapes;
1633 // If we've found the key, set the values
1634 if ( key_index >= 0 ) {
1635 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1636 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1637 // otherwise, keep looking
1640 if ( key_index == DEPRECATED ) {
1643 else if ( key.equals( "click_to" ) ) {
1644 final String click_to_name = ( String ) st.nextElement();
1645 key_index = getClickToIndex( click_to_name );
1646 if ( key_index >= 0 ) {
1647 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1649 else if ( key_index == DEPRECATED ) {
1653 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1657 else if ( key.equals( "species_color" ) ) {
1658 getSpeciesColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1660 else if ( key.equals( "domain_color" ) ) {
1661 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1663 else if ( key.equals( "annotation_color" ) ) {
1664 getAnnotationColors()
1665 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1667 else if ( key.equals( "function_color" ) ) {
1668 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1669 "configuration key [function_color] is deprecated" );
1671 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1672 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1674 else if ( key.equals( WEB_LINK_KEY ) ) {
1675 if ( st.countTokens() == 3 ) {
1676 createWebLink( ( String ) st.nextElement(),
1677 ( String ) st.nextElement(),
1678 ( String ) st.nextElement() );
1681 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1682 "illegal format in configuration file for key [" + key + "]" );
1686 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1687 + "] in: " + config_filename );
1692 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1693 + config_filename );
1697 private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
1698 _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
1701 private void setOvMaxHeight( final short ov_max_height ) {
1702 _ov_max_height = ov_max_height;
1705 private void setOvMaxWidth( final short ov_max_width ) {
1706 _ov_max_width = ov_max_width;
1709 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1710 _ov_placement = ov_placement;
1713 private void setPathToLocalFastme( final File path_to_local_fastme ) {
1714 _path_to_local_fastme = path_to_local_fastme;
1717 private void setPathToLocalMafft( final File path_to_local_mafft ) {
1718 _path_to_local_mafft = path_to_local_mafft;
1721 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
1722 _path_to_local_raxml = path_to_local_raxml;
1725 private void setShowOverview( final boolean show_overview ) {
1726 _show_overview = show_overview;
1729 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1730 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1733 static String getDefaultFontFamilyName() {
1734 return DEFAULT_FONT_FAMILY;
1737 public enum EXT_NODE_DATA_RETURN_ON {
1738 CONSOLE, WINODW, BUFFER_ONLY;
1742 NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN
1745 static enum TRIPLET {
1746 TRUE, FALSE, UNKNOWN