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_STRICT;
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 if ( AptxUtil.isMac() ) {
738 // Apple Macintosh graphics are slow, turn off anti-alias.
741 return _antialias_screen;
745 * Convenience method.
747 * @return true if value in configuration file was 'yes'
749 boolean isDrawAsPhylogram() {
750 return doCheckOption( display_as_phylogram );
753 boolean isEditable() {
757 boolean isHasWebLink( final String source ) {
758 return getWebLinks().containsKey( source );
762 * Only used by ArchaeoptryxE.
765 boolean isHideControlPanelAndMenubar() {
766 return _hide_controls_and_menus;
769 boolean isInternalNumberAreConfidenceForNhParsing() {
770 return _internal_number_are_confidence_for_nh_parsing;
773 boolean isReplaceUnderscoresInNhParsing() {
774 return _nh_parsing_replace_underscores;
777 boolean isShowBranchLengthValues() {
778 return _show_branch_length_values;
781 boolean isShowOverview() {
782 return _show_overview;
785 boolean isShowScale() {
789 final boolean isUseNativeUI() {
790 if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() ) {
793 return _ui == UI.NATIVE;
797 * Only used by ArchaeoptryxE.
800 boolean isUseTabbedDisplay() {
801 return _use_tabbed_display;
804 boolean isValidatePhyloXmlAgainstSchema() {
805 return _validate_against_phyloxml_xsd_schema;
808 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
809 _taxonomy_extraction = taxonomy_extraction;
812 void setWebLinks( final SortedMap<String, WebLink> weblinks ) {
813 _weblinks = weblinks;
816 private void createWebLink( final String url_str, final String desc, final String source_identifier ) {
817 WebLink weblink = null;
820 weblink = new WebLink( new URL( url_str.trim() ), desc.trim(), source_identifier.trim() );
822 catch ( final MalformedURLException e ) {
823 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not create URL from [" + url_str + "]" );
826 if ( !ex && ( weblink != null ) ) {
827 getWebLinks().put( weblink.getSourceIdentifier().toLowerCase(), weblink );
831 private int getClickToIndex( final String name ) {
833 if ( name.equals( "edit_info" ) ) {
834 index = Configuration.display_node_data;
836 .printWarningMessage( Constants.PRG_NAME,
837 "configuration key [edit_info] is deprecated, use [display node data] instead" );
839 else if ( name.equals( "display_node_data" ) ) {
840 index = Configuration.display_node_data;
842 else if ( name.equals( "collapse_uncollapse" ) ) {
843 index = Configuration.collapse_uncollapse;
845 else if ( name.equals( "reroot" ) ) {
846 index = Configuration.reroot;
848 else if ( name.equals( "subtree" ) ) {
849 index = Configuration.subtree;
851 else if ( name.equals( "swap" ) ) {
852 index = Configuration.swap;
854 else if ( name.equals( "sort_descendants" ) ) {
855 index = Configuration.sort_descendents;
857 else if ( name.equals( "get_ext_descendents_data" ) ) {
858 index = Configuration.get_ext_desc_data;
860 else if ( name.equals( "display_sequences" ) ) {
862 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
865 else if ( name.equals( "open_seq_web" ) ) {
866 index = Configuration.open_seq_web;
868 else if ( name.equals( "open_tax_web" ) ) {
869 index = Configuration.open_tax_web;
871 else if ( name.equals( "blast" ) ) {
872 index = Configuration.blast;
874 else if ( name.equals( "cut_subtree" ) ) {
875 index = Configuration.cut_subtree;
877 else if ( name.equals( "copy_subtree" ) ) {
878 index = Configuration.copy_subtree;
880 else if ( name.equals( "paste_subtree" ) ) {
881 index = Configuration.paste_subtree;
883 else if ( name.equals( "delete" ) ) {
884 index = Configuration.delete_subtree_or_node;
886 else if ( name.equals( "add_new_node" ) ) {
887 index = Configuration.add_new_node;
889 else if ( name.equals( "edit_node_data" ) ) {
890 index = Configuration.edit_node_data;
892 else if ( name.equals( "select_nodes" ) ) {
893 index = Configuration.select_nodes;
895 else if ( name.equals( "display_node_popup" ) ) {
896 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
897 "configuration key [display_node_popup] is deprecated" );
900 else if ( name.equals( "custom_option" ) ) {
901 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
904 else if ( name.equals( "color_subtree" ) ) {
905 index = Configuration.color_subtree;
907 else if ( name.equals( "go_to_swiss_prot" ) ) {
908 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" );
914 private boolean parseBoolean( final String str ) {
915 final String my_str = str.trim().toLowerCase();
916 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
919 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
923 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
928 private double parseDouble( final String str ) {
931 d = Double.parseDouble( str.trim() );
933 catch ( final Exception e ) {
934 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
940 private float parseFloat( final String str ) {
943 f = Float.parseFloat( str.trim() );
945 catch ( final Exception e ) {
946 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
952 private int parseInt( final String str ) {
955 i = Integer.parseInt( str.trim() );
957 catch ( final Exception e ) {
958 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
964 private short parseShort( final String str ) {
967 i = Short.parseShort( str.trim() );
969 catch ( final Exception e ) {
970 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
976 private void processFontFamily( final StringTokenizer st ) {
977 setBaseFontFamilyName( "" );
978 final String font_str = ( ( String ) st.nextElement() ).trim();
979 final String[] fonts = font_str.split( ",+" );
980 for( String font : fonts ) {
981 font = font.replace( '_', ' ' ).trim();
982 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
983 setBaseFontFamilyName( font );
990 * read each line of config file, process non-comment lines
991 * @throws IOException
993 private void readConfig( final BufferedReader conf_in ) throws IOException {
996 line = conf_in.readLine();
997 if ( line != null ) {
999 // skip comments and blank lines
1000 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
1001 // convert runs of spaces to tabs
1002 line = line.replaceAll( "\\s+", "\t" );
1003 final StringTokenizer st = new StringTokenizer( line, "\t" );
1007 } while ( line != null );
1010 private void setAntialiasScreen( final boolean antialias_screen ) {
1011 _antialias_screen = antialias_screen;
1014 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
1015 _cladogram_type = cladogram_type;
1018 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
1019 _default_bootstrap_samples = default_bootstrap_samples;
1022 private void setEditable( final boolean editable ) {
1023 _editable = editable;
1026 private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
1027 _ext_node_data_return_on = ext_node_data_return_on;
1030 private void setGraphicsExportX( final int graphics_export_x ) {
1031 _graphics_export_x = graphics_export_x;
1034 private void setGraphicsExportY( final int graphics_export_y ) {
1035 _graphics_export_y = graphics_export_y;
1038 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
1039 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
1043 * Set a key-value(s) tuple
1045 private void setKeyValue( final StringTokenizer st ) {
1046 final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
1047 if ( !st.hasMoreElements() ) {
1050 // Handle single value settings first:
1051 if ( key.equals( "default_click_to" ) ) {
1052 final String clickto_name = ( String ) st.nextElement();
1053 default_clickto = getClickToIndex( clickto_name );
1054 if ( default_clickto == -1 ) {
1055 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
1056 + "] for [default_click_to]" );
1057 default_clickto = 0;
1059 else if ( default_clickto == DEPRECATED ) {
1063 else if ( key.equals( "native_ui" ) ) {
1064 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
1065 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
1068 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
1069 _ui = UI.CROSSPLATFORM;
1071 else if ( my_str.equals( "?" ) ) {
1075 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
1080 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
1081 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
1083 else if ( key.equals( "antialias_screen" ) ) {
1084 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
1086 else if ( key.equals( "phylogeny_graphics_type" ) ) {
1087 final String type_str = ( ( String ) st.nextElement() ).trim();
1088 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
1089 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1091 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
1092 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1094 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
1095 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1097 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
1098 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1100 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
1101 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1103 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
1104 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1106 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
1107 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1109 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
1110 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1113 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1114 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1115 + "] for [phylogeny_graphics_type]" );
1118 else if ( key.equals( "min_confidence_value" ) ) {
1119 final String mcv_str = ( ( String ) st.nextElement() ).trim();
1120 final double d = parseDouble( mcv_str );
1121 setMinConfidenceValue( d );
1123 else if ( key.equals( "font_family" ) ) {
1124 processFontFamily( st );
1126 else if ( key.equals( "font_size" ) ) {
1127 final String size_str = ( ( String ) st.nextElement() ).trim();
1128 final int i = parseInt( size_str );
1130 setBaseFontSize( i );
1133 else if ( key.equals( "font_size_min" ) ) {
1134 final String size_str = ( ( String ) st.nextElement() ).trim();
1135 final int i = parseInt( size_str );
1137 setMinBaseFontSize( i );
1140 else if ( key.equals( "font_size_max" ) ) {
1141 final String size_str = ( ( String ) st.nextElement() ).trim();
1142 final int i = parseInt( size_str );
1144 setMaxBaseFontSize( i );
1147 else if ( key.equals( "graphics_export_x" ) ) {
1148 final String str = ( ( String ) st.nextElement() ).trim();
1149 final int i = parseInt( str );
1151 setGraphicsExportX( i );
1154 else if ( key.equals( "graphics_export_y" ) ) {
1155 final String str = ( ( String ) st.nextElement() ).trim();
1156 final int i = parseInt( str );
1158 setGraphicsExportY( i );
1161 else if ( key.equals( "pdf_export_line_width" ) ) {
1162 final String str = ( ( String ) st.nextElement() ).trim();
1163 final float f = parseFloat( str );
1165 setPrintLineWidth( f );
1168 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1169 "value for [pdf_export_line_width] cannot be zero or negative" );
1172 else if ( key.equals( "window_initial_size_x" ) ) {
1173 final String str = ( ( String ) st.nextElement() ).trim();
1174 final int i = parseInt( str );
1179 else if ( key.equals( "window_initial_size_y" ) ) {
1180 final String str = ( ( String ) st.nextElement() ).trim();
1181 final int i = parseInt( str );
1186 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1187 final String str = ( ( String ) st.nextElement() ).trim();
1188 final int i = parseInt( str );
1190 setDefaultBootstrapSamples( i );
1194 .printWarningMessage( Constants.PRG_NAME,
1195 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1198 else if ( key.equals( "mafft_local" ) ) {
1199 final String str = ( ( String ) st.nextElement() ).trim();
1200 if ( !ForesterUtil.isEmpty( str ) ) {
1201 setPathToLocalMafft( new File( str ) );
1204 else if ( key.equals( "fastme_local" ) ) {
1205 final String str = ( ( String ) st.nextElement() ).trim();
1206 if ( !ForesterUtil.isEmpty( str ) ) {
1207 setPathToLocalFastme( new File( str ) );
1210 else if ( key.equals( "raxml_local" ) ) {
1211 final String str = ( ( String ) st.nextElement() ).trim();
1212 if ( !ForesterUtil.isEmpty( str ) ) {
1213 setPathToLocalRaxml( new File( str ) );
1216 else if ( key.equals( "show_scale" ) ) {
1217 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1219 else if ( key.equals( "show_overview" ) ) {
1220 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1222 else if ( key.equals( "show_branch_length_values" ) ) {
1223 setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
1225 else if ( key.equals( "background_gradient" ) ) {
1226 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1228 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1229 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1231 else if ( key.equals( "show_domain_labels" ) ) {
1232 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1234 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1235 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1237 else if ( key.equals( "cladogram_type" ) ) {
1238 final String type_str = ( ( String ) st.nextElement() ).trim();
1239 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1240 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1242 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1243 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1245 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1246 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1249 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1250 + "] for [cladogram_type]" );
1253 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1255 .printWarningMessage( Constants.PRG_NAME,
1256 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1258 else if ( key.equals( "hide_controls_and_menus" ) ) {
1259 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1261 else if ( key.equals( "use_tabbed_display" ) ) {
1262 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1264 else if ( key.equals( "overview_width" ) ) {
1265 final short i = parseShort( ( ( String ) st.nextElement() ) );
1268 else if ( key.equals( "overview_height" ) ) {
1269 final short i = parseShort( ( ( String ) st.nextElement() ) );
1270 setOvMaxHeight( i );
1272 else if ( key.equals( "overview_placement_type" ) ) {
1273 final String type_str = ( ( String ) st.nextElement() ).trim();
1274 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1275 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1277 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1278 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1280 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1281 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1283 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1284 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1287 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1288 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1289 + "] for [overview_placement_type]" );
1292 else if ( key.equals( "node_label_direction" ) ) {
1293 final String type_str = ( ( String ) st.nextElement() ).trim();
1294 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1295 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1297 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1298 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1301 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1302 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1303 + "] for [node_label_direction]" );
1306 else if ( key.equals( "branch_length_value_digits" ) ) {
1307 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1309 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1312 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1313 + "] for [branch_length_value_digits]" );
1316 else if ( key.equals( "confidence_value_digits" ) ) {
1317 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1319 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1322 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1323 + "] for [confidence_value_digits]" );
1326 else if ( key.equals( "allow_editing" ) ) {
1327 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1329 else if ( key.equals( "display_sequence_relations" ) ) {
1330 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1332 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1333 final boolean r = parseBoolean( ( String ) st.nextElement() );
1334 if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
1336 .printWarningMessage( Constants.PRG_NAME,
1337 "attempt to extract taxonomies and replace underscores at the same time" );
1340 setReplaceUnderscoresInNhParsing( r );
1343 else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
1344 final String s = ( String ) st.nextElement();
1345 if ( s.equalsIgnoreCase( "no" ) ) {
1346 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1348 else if ( s.equalsIgnoreCase( "yes" ) ) {
1349 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1351 else if ( s.equalsIgnoreCase( "pfam" ) ) {
1352 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1355 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1356 "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + s );
1358 if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
1360 .printWarningMessage( Constants.PRG_NAME,
1361 "attempt to extract taxonomies and replace underscores at the same time" );
1364 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1365 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1367 else if ( key.equals( "gui_background_color" ) ) {
1368 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1370 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1371 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1373 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1374 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1376 else if ( key.equals( "gui_button_text_color" ) ) {
1377 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1379 else if ( key.equals( "gui_button_background_color" ) ) {
1380 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1382 else if ( key.equals( "gui_menu_background_color" ) ) {
1383 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1385 else if ( key.equals( "gui_menu_text_color" ) ) {
1386 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1388 else if ( key.equals( "gui_button_border_color" ) ) {
1389 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1391 else if ( key.equals( "domain_structure_font_color" ) ) {
1392 _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
1394 else if ( key.equals( "domain_structure_base_color" ) ) {
1395 _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
1397 else if ( key.equals( "show_default_node_shapes" ) ) {
1399 .printWarningMessage( Constants.PRG_NAME,
1400 "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" );
1401 final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() );
1402 setShowDefaultNodeShapesInternal( b );
1403 setShowDefaultNodeShapesExternal( b );
1405 else if ( key.equals( "show_default_node_shapes_internal" ) ) {
1406 setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1408 else if ( key.equals( "show_default_node_shapes_external" ) ) {
1409 setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1411 else if ( key.equals( "default_node_size" ) ) {
1412 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1413 setDefaultNodeShapeSize( i );
1415 else if ( key.equals( "default_node_fill" ) ) {
1416 final String fill_str = ( ( String ) st.nextElement() ).trim();
1417 if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.NONE.toString() ) ) {
1418 setDefaultNodeFill( NodeFill.NONE );
1420 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.GRADIENT.toString() ) ) {
1421 setDefaultNodeFill( NodeFill.GRADIENT );
1423 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.SOLID.toString() ) ) {
1424 setDefaultNodeFill( NodeFill.SOLID );
1427 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1428 + "] for [default_node_fill]" );
1431 else if ( key.equals( "default_node_shape" ) ) {
1432 final String shape_str = ( ( String ) st.nextElement() ).trim();
1433 if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.CIRCLE.toString() ) ) {
1434 setDefaultNodeShape( NodeShape.CIRCLE );
1436 else if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.RECTANGLE.toString() ) ) {
1437 setDefaultNodeShape( NodeShape.RECTANGLE );
1440 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1441 + "] for [default_node_shape]" );
1444 else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
1445 setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
1447 else if ( key.equals( "ext_descendents_data_to_return" ) ) {
1448 final String s = ( ( String ) st.nextElement() ).trim();
1449 if ( s.equalsIgnoreCase( "node_name" ) ) {
1450 setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
1452 else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
1453 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
1455 else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) {
1456 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ_FASTA );
1458 else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
1459 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
1461 else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
1462 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
1464 else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
1465 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
1467 else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
1468 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME );
1470 else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
1471 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
1473 else if ( s.equalsIgnoreCase( "user_selected" ) ) {
1474 setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
1477 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1478 + "] for [ext_descendents_data_to_return]" );
1481 else if ( key.equals( "label_for_get_ext_descendents_data" ) ) {
1482 final String s = ( ( String ) st.nextElement() ).trim();
1483 if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) {
1484 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s
1485 + "] for [label_for_get_ext_descendents_data]" );
1488 setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
1491 else if ( key.equals( "ext_descendents_data_to_return_on" ) ) {
1492 final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
1493 if ( s.equals( "console" ) ) {
1494 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
1496 else if ( s.equals( "window" ) ) {
1497 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
1499 else if ( s.equals( "buffer_only" ) ) {
1500 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
1503 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1504 + "] for [ext_descendents_data_to_return_on]" );
1507 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1510 if ( key.equals( "use_real_br_lengths" ) || key.equals( "phylogram" ) ) {
1511 key_index = Configuration.display_as_phylogram;
1512 if ( key.equals( "use_real_br_lengths" ) ) {
1514 .printWarningMessage( Constants.PRG_NAME,
1515 "configuration key [use_real_br_lengths] is deprecated, use [phylogram] instead" );
1518 else if ( key.equals( "rollover" ) ) {
1519 key_index = Configuration.node_data_popup;
1521 else if ( key.equals( "color_according_to_species" ) ) {
1522 key_index = Configuration.color_according_to_species;
1524 else if ( key.equals( "show_node_names" ) ) {
1525 key_index = Configuration.show_node_names;
1527 else if ( key.equals( "show_taxonomy" ) || key.equals( "show_taxonomy_code" ) ) {
1528 key_index = Configuration.show_tax_code;
1529 if ( key.equals( "show_taxonomy" ) ) {
1531 .printWarningMessage( Constants.PRG_NAME,
1532 "configuration key [show_taxonomy] is deprecated, use [show_taxonomy_code] instead" );
1535 else if ( key.equals( "write_br_length_values" ) ) {
1536 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1537 "configuration key [write_br_length_values] is deprecated" );
1538 key_index = DEPRECATED;
1540 else if ( key.equals( "write_bootstrap_values" ) || key.equals( "write_confidence_values" ) ) {
1541 key_index = Configuration.write_confidence_values;
1542 if ( key.equals( "write_bootstrap_values" ) ) {
1544 .printWarningMessage( Constants.PRG_NAME,
1545 "configuration key [write_bootstrap_values] is deprecated, use [write_confidence_values] instead" );
1548 else if ( key.equals( "write_events" ) || key.equals( "write_dup_spec" ) ) {
1549 key_index = Configuration.write_events;
1550 if ( key.equals( "write_dup_spec" ) ) {
1552 .printWarningMessage( Constants.PRG_NAME,
1553 "configuration key [write_dup_spec] is deprecated, use [write_events] instead" );
1556 else if ( key.equals( "color_branches" ) ) {
1557 key_index = Configuration.color_branches;
1559 else if ( key.equals( "width_branches" ) ) {
1560 key_index = Configuration.width_branches;
1562 else if ( key.equals( "color_orthologous" ) ) {
1563 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1564 "configuration key [color_orthologous] is deprecated" );
1566 else if ( key.equals( "color_subtree_neighbors" ) ) {
1567 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1568 "configuration key [color_subtree_neighbors] is deprecated" );
1570 else if ( key.equals( "color_super_orthologous" ) ) {
1571 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1572 "configuration key [color_super_orthologous] is deprecated" );
1574 else if ( key.equals( "mark_nodes_with_box" ) ) {
1575 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1576 "configuration key [mark_nodes_with_box] is deprecated" );
1577 key_index = DEPRECATED;
1579 else if ( key.equals( "show_domain_architectures" ) ) {
1580 key_index = Configuration.show_domain_architectures;
1582 else if ( key.equals( "show_annotations" ) ) {
1583 key_index = Configuration.show_annotation;
1585 else if ( key.equals( "show_binary_characters" ) ) {
1586 key_index = Configuration.show_binary_characters;
1588 else if ( key.equals( "show_binary_character_counts" ) ) {
1589 key_index = Configuration.show_binary_character_counts;
1591 else if ( key.equals( "show_gene_names" ) ) {
1592 key_index = Configuration.show_gene_names;
1594 else if ( key.equals( "show_gene_symbols" ) ) {
1595 key_index = Configuration.show_gene_symbols;
1597 else if ( key.equals( "show_sequence_acc" ) ) {
1598 key_index = Configuration.show_sequence_acc;
1600 else if ( key.equals( "show_node_ids" ) ) {
1602 .printWarningMessage( Constants.PRG_NAME, "configuration key [show_node_ids] is deprecated" );
1603 key_index = DEPRECATED;
1605 else if ( key.equals( "display_internal_data" ) ) {
1606 key_index = Configuration.display_internal_data;
1608 else if ( key.equals( "dynamically_hide_data" ) ) {
1609 key_index = Configuration.dynamically_hide_data;
1611 else if ( key.equals( "show_taxonomy_names" ) ) {
1612 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1613 "configuration key [show_taxonomy_names] is deprecated" );
1614 key_index = DEPRECATED;
1616 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1617 key_index = Configuration.show_taxonomy_scientific_names;
1619 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1620 key_index = Configuration.show_taxonomy_common_names;
1622 else if ( key.equals( "show_taxonomy_images" ) ) {
1623 key_index = Configuration.show_taxonomy_images;
1625 else if ( key.equals( "color_according_to_annotation" ) ) {
1626 key_index = Configuration.color_according_to_annotation;
1628 else if ( key.equals( "show_vector_data" ) ) {
1629 key_index = Configuration.show_vector_data;
1631 else if ( key.equals( "show_properties" ) ) {
1632 key_index = Configuration.show_properties;
1634 else if ( key.equals( "show_relation_confidence" ) ) {
1635 key_index = Configuration.show_relation_confidence;
1637 else if ( key.equals( "show_custom_node_shapes" ) ) {
1638 key_index = Configuration.show_custom_node_shapes;
1640 // If we've found the key, set the values
1641 if ( key_index >= 0 ) {
1642 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1643 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1644 // otherwise, keep looking
1647 if ( key_index == DEPRECATED ) {
1650 else if ( key.equals( "click_to" ) ) {
1651 final String click_to_name = ( String ) st.nextElement();
1652 key_index = getClickToIndex( click_to_name );
1653 if ( key_index >= 0 ) {
1654 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1656 else if ( key_index == DEPRECATED ) {
1660 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1664 else if ( key.equals( "species_color" ) ) {
1665 getSpeciesColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1667 else if ( key.equals( "domain_color" ) ) {
1668 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1670 else if ( key.equals( "annotation_color" ) ) {
1671 getAnnotationColors()
1672 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1674 else if ( key.equals( "function_color" ) ) {
1675 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1676 "configuration key [function_color] is deprecated" );
1678 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1679 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1681 else if ( key.equals( WEB_LINK_KEY ) ) {
1682 if ( st.countTokens() == 3 ) {
1683 createWebLink( ( String ) st.nextElement(),
1684 ( String ) st.nextElement(),
1685 ( String ) st.nextElement() );
1688 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1689 "illegal format in configuration file for key [" + key + "]" );
1693 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1694 + "] in: " + config_filename );
1699 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1700 + config_filename );
1704 private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
1705 _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
1708 private void setOvMaxHeight( final short ov_max_height ) {
1709 _ov_max_height = ov_max_height;
1712 private void setOvMaxWidth( final short ov_max_width ) {
1713 _ov_max_width = ov_max_width;
1716 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1717 _ov_placement = ov_placement;
1720 private void setPathToLocalFastme( final File path_to_local_fastme ) {
1721 _path_to_local_fastme = path_to_local_fastme;
1724 private void setPathToLocalMafft( final File path_to_local_mafft ) {
1725 _path_to_local_mafft = path_to_local_mafft;
1728 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
1729 _path_to_local_raxml = path_to_local_raxml;
1732 private void setShowOverview( final boolean show_overview ) {
1733 _show_overview = show_overview;
1736 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1737 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1740 static String getDefaultFontFamilyName() {
1741 return DEFAULT_FONT_FAMILY;
1744 public enum EXT_NODE_DATA_RETURN_ON {
1745 CONSOLE, WINODW, BUFFER_ONLY;
1749 NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN
1752 static enum TRIPLET {
1753 TRUE, FALSE, UNKNOWN