2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
7 // Copyright (C) 2000-2001 Washington University School of Medicine
8 // and Howard Hughes Medical Institute
9 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
10 // All rights reserved
12 // This library is free software; you can redistribute it and/or
13 // modify it under the terms of the GNU Lesser General Public
14 // License as published by the Free Software Foundation; either
15 // version 2.1 of the License, or (at your option) any later version.
17 // This library is distributed in the hope that it will be useful,
18 // but WITHOUT ANY WARRANTY; without even the implied warranty of
19 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20 // Lesser General Public License for more details.
22 // You should have received a copy of the GNU Lesser General Public
23 // License along with this library; if not, write to the Free Software
24 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
26 // Contact: phylosoft @ gmail . com
27 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
29 package org.forester.archaeopteryx;
31 import java.awt.Color;
32 import java.io.BufferedReader;
34 import java.io.FileReader;
35 import java.io.IOException;
36 import java.io.InputStreamReader;
38 import java.util.Arrays;
39 import java.util.Hashtable;
41 import java.util.SortedMap;
42 import java.util.StringTokenizer;
43 import java.util.TreeMap;
45 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
46 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
47 import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE;
48 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
49 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
50 import org.forester.phylogeny.data.NodeData.NODE_DATA;
51 import org.forester.phylogeny.data.NodeVisualization;
52 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
53 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
54 import org.forester.util.ForesterUtil;
56 public final class Configuration {
58 static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
59 private static final String DISPLAY_COLOR_KEY = "display_color";
60 private static final int DEPRECATED = -2;
61 private UI _ui = UI.UNKNOWN;
62 private boolean _use_tabbed_display = false;
63 private boolean _hide_controls_and_menus = false;
64 private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
65 private SortedMap<String, Color> _display_colors = null;
66 private boolean _antialias_screen = true;
67 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
68 private String _base_font_family_name = "";
69 private int _base_font_size = -1;
70 private int _min_base_font_size = 2;
71 private int _max_base_font_size = 20;
72 private int _graphics_export_x = -1;
73 private int _graphics_export_y = -1;
74 private short _ov_max_width = 80;
75 private short _ov_max_height = 80;
76 private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
77 private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
78 private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
79 private boolean _show_scale = false;
80 private boolean _show_branch_length_values = false;
81 private boolean _show_overview = true;
82 private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
83 private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
84 private boolean _editable = true;
85 private boolean _nh_parsing_replace_underscores = false;
86 private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT;
87 private boolean _internal_number_are_confidence_for_nh_parsing = false;
88 private boolean _display_sequence_relations = false;
89 private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
90 private boolean _background_color_gradient = false;
91 private boolean _show_domain_labels = true;
92 private boolean _abbreviate_scientific_names = false;
93 private boolean _color_labels_same_as_parent_branch = false;
94 private boolean _show_default_node_shapes_internal = false;
95 private boolean _show_default_node_shapes_external = false;
96 private NodeShape _default_node_shape = NodeShape.RECTANGLE;
97 private NodeFill _default_node_fill = NodeFill.SOLID;
98 private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
99 private boolean _taxonomy_colorize_node_shapes = false;
100 private int _default_bootstrap_samples = -1;
101 private File _path_to_local_mafft = null;
102 private File _path_to_local_fastme = null;
103 private File _path_to_local_raxml = null;
104 final static int display_as_phylogram = 0;
105 final static int show_node_names = 1;
106 final static int show_tax_code = 2;
107 final static int show_annotation = 3;
108 final static int write_confidence_values = 4;
109 final static int write_events = 5;
110 final static int color_according_to_species = 6;
111 final static int color_branches = 7;
112 final static int width_branches = 8;
113 final static int show_custom_node_shapes = 9;
114 final static int show_domain_architectures = 10;
115 final static int show_binary_characters = 11;
116 final static int show_binary_character_counts = 12;
117 final static int show_gene_names = 13;
118 final static int show_sequence_acc = 14;
119 final static int display_internal_data = 15;
120 final static int dynamically_hide_data = 16;
121 final static int show_taxonomy_scientific_names = 17;
122 final static int show_taxonomy_common_names = 18;
123 final static int color_according_to_annotation = 19;
124 final static int show_gene_symbols = 20;
125 final static int node_data_popup = 21;
126 final static int show_relation_confidence = 22;
127 final static int show_vector_data = 23;
128 final static int show_taxonomy_images = 24;
129 final static int show_properties = 25;
130 // ------------------
132 // ------------------
133 final static int display_node_data = 0;
134 final static int collapse_uncollapse = 1;
135 final static int reroot = 2;
136 final static int subtree = 3;
137 final static int swap = 4;
138 final static int color_subtree = 5;
139 final static int open_seq_web = 6;
140 final static int open_tax_web = 7;
141 final static int blast = 8;
142 final static int cut_subtree = 9;
143 final static int copy_subtree = 10;
144 final static int paste_subtree = 11;
145 final static int delete_subtree_or_node = 12;
146 final static int add_new_node = 13;
147 final static int edit_node_data = 14;
148 final static int sort_descendents = 15;
149 final static int get_ext_desc_data = 16;
150 final static int select_nodes = 17;
151 // ---------------------------
152 // Display options for trees
153 // ---------------------------
154 // ---------------------------------
155 // Pertaining to the config itself
156 // ---------------------------------
157 // Full path to config (may be URL)
158 String config_filename;
159 String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
160 final static String display_options[][] = {
161 { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
162 { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" },
163 { "Node Events", "display", "?" }, { "Taxonomy Colorize", "display", "yes" },
164 { "Colorize Branches", "display", "no" }, { "Use Branch-Widths", "display", "no" },
165 { "Show Custom Nodes", "display", "yes" }, { "Domains", "nodisplay", "no" },
166 { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
167 { "Seq Name", "display", "yes" }, { "Seq Acc", "display", "no" },
168 { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
169 { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
170 { "Annotation Colorize", "nodisplay", "no" }, { "Seq Symbol", "display", "yes" },
171 { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
172 { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
173 { "Properties", "nodisplay", "no" } };
174 final static String clickto_options[][] = {
175 { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
176 { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
177 { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Blast", "display" },
178 { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" },
179 { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" },
180 { "Sort Descendants", "display" }, { "Return", "display" }, { "Select Node(s)", "display" } };
181 // This option is selected in the dropdown
182 int default_clickto = Configuration.display_node_data;
186 TreeColorSet tree_color_set;
190 TreeFontSet tree_font_set;
194 private static Hashtable<String, Color> _species_colors;
198 private static Hashtable<String, Color> _domain_colors;
202 private static Hashtable<String, Color> _annotation_colors;
203 boolean verbose = Constants.VERBOSE_DEFAULT;
204 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
205 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
206 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
207 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
208 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
209 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
210 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
211 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
212 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
213 private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
214 private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
215 private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
216 private String _label_for_get_ext_descendents_data = "";
217 private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
218 private int _frame_x_size;
219 private int _frame_y_size;
220 private static String DEFAULT_FONT_FAMILY = "";
222 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
223 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
224 DEFAULT_FONT_FAMILY = font_name;
228 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
229 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
233 public Configuration() {
234 this( null, false, false, false );
237 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
238 if ( ForesterUtil.isEmpty( cf ) ) {
239 config_filename = default_config_filename;
242 config_filename = cf;
244 setDisplayColors( new TreeMap<String, Color>() );
245 config_filename = config_filename.trim();
248 // If URL, open accordingly
250 u = new URL( config_filename );
252 final InputStreamReader isr = new InputStreamReader( u.openStream() );
253 final BufferedReader bf = new BufferedReader( isr );
256 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
257 + config_filename + "]" );
259 catch ( final Exception e ) {
260 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
261 + config_filename + "]: " + e.getLocalizedMessage() );
264 catch ( final Exception e ) {
265 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
266 + config_filename + "]" );
270 // Otherwise, open as a file
271 File f = new File( config_filename );
273 f = new File( config_filename + ".txt" );
275 if ( f.exists() && f.canRead() ) {
277 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
281 catch ( final Exception e ) {
283 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
284 + config_filename + "]: " + e );
290 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
291 + config_filename + "]" );
297 public String getBaseFontFamilyName() {
298 return _base_font_family_name;
301 public int getDefaultBootstrapSamples() {
302 return _default_bootstrap_samples;
305 public NodeFill getDefaultNodeFill() {
306 return _default_node_fill;
309 public NodeShape getDefaultNodeShape() {
310 return _default_node_shape;
313 public short getDefaultNodeShapeSize() {
314 return _default_node_shape_size;
317 public Color getDomainStructureBaseColor() {
318 return _domain_structure_base_color;
321 public Color getDomainStructureFontColor() {
322 return _domain_structure_font_color;
325 public NODE_DATA getExtDescNodeDataToReturn() {
326 return _ext_desc_data_to_return;
329 public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
330 return _ext_node_data_return_on;
333 public int getFrameXSize() {
334 return _frame_x_size;
337 public int getFrameYSize() {
338 return _frame_y_size;
341 public String getLabelForGetExtDescendentsData() {
342 return _label_for_get_ext_descendents_data;
345 public File getPathToLocalFastme() {
346 return _path_to_local_fastme;
349 public File getpathToLocalMafft() {
350 return _path_to_local_mafft;
353 public File getPathToLocalRaxml() {
354 return _path_to_local_raxml;
357 public boolean isAbbreviateScientificTaxonNames() {
358 return _abbreviate_scientific_names;
361 public boolean isBackgroundColorGradient() {
362 return _background_color_gradient;
365 public boolean isColorLabelsSameAsParentBranch() {
366 return _color_labels_same_as_parent_branch;
369 public boolean isShowDefaultNodeShapesExternal() {
370 return _show_default_node_shapes_external;
373 public boolean isShowDefaultNodeShapesInternal() {
374 return _show_default_node_shapes_internal;
377 public boolean isShowDomainLabels() {
378 return _show_domain_labels;
381 public boolean isTaxonomyColorizeNodeShapes() {
382 return _taxonomy_colorize_node_shapes;
385 public void putDisplayColors( final String key, final Color color ) {
386 getDisplayColors().put( key, color );
389 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
390 _abbreviate_scientific_names = abbreviate_scientific_names;
393 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
394 _background_color_gradient = background_color_gradient;
397 public void setBaseFontFamilyName( final String base_font_family_name ) {
398 _base_font_family_name = base_font_family_name;
401 public void setBaseFontSize( final int base_font_size ) {
402 _base_font_size = base_font_size;
405 private void setMaxBaseFontSize( final int max_base_font_size ) {
406 _max_base_font_size = max_base_font_size;
409 private void setMinBaseFontSize( final int min_base_font_size ) {
410 _min_base_font_size = min_base_font_size;
413 public void setColorizeBranches( final boolean b ) {
414 display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
417 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
418 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
421 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
422 _default_node_fill = default_node_fill;
425 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
426 _default_node_shape = default_node_shape;
429 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
430 _default_node_shape_size = default_node_shape_size;
433 public void setDisplayAsPhylogram( final boolean b ) {
434 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
437 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
438 _display_colors = display_colors;
441 public void setDisplayConfidenceValues( final boolean b ) {
442 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
445 public void setDisplayInternalData( final boolean b ) {
446 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
449 public void setDisplayNodeNames( final boolean b ) {
450 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
453 public void setDisplaySequenceAcc( final boolean b ) {
454 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
457 public void setDisplaySequenceNames( final boolean b ) {
458 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
461 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
462 _display_sequence_relations = display_sequence_relations;
465 public void setDisplaySequenceSymbols( final boolean b ) {
466 display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no";
469 public void setDisplayTaxonomyCode( final boolean b ) {
470 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
473 public void setDisplayTaxonomyCommonNames( final boolean b ) {
474 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
477 public void setDisplayTaxonomyImages( final boolean b ) {
478 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
481 public void setDisplayTaxonomyScientificNames( final boolean b ) {
482 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
485 public void setDynamicallyHideData( final boolean b ) {
486 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
489 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
490 _ext_desc_data_to_return = ext_desc_data_to_return;
493 public void setFrameXSize( final int frame_x_size ) {
494 _frame_x_size = frame_x_size;
497 public void setFrameYSize( final int frame_y_size ) {
498 _frame_y_size = frame_y_size;
501 public void setMinConfidenceValue( final double min_confidence_value ) {
502 _min_confidence_value = min_confidence_value;
505 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
506 _node_label_direction = node_label_direction;
509 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
510 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
513 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
514 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
517 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
518 _phylogeny_graphics_type = phylogeny_graphics_type;
521 public void setPrintLineWidth( final float print_line_width ) {
522 _print_line_width = print_line_width;
525 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
526 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
529 public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
530 _show_branch_length_values = show_branch_length_values;
533 public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
534 _show_default_node_shapes_external = show_default_node_shapes_external;
537 public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
538 _show_default_node_shapes_internal = show_default_node_shapes_internal;
541 public void setShowDomainLabels( final boolean show_domain_labels ) {
542 _show_domain_labels = show_domain_labels;
545 public void setShowScale( final boolean show_scale ) {
546 _show_scale = show_scale;
549 public void setTaxonomyColorize( final boolean b ) {
550 display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
553 public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
554 _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
557 public void setUseBranchesWidths( final boolean b ) {
558 display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
561 boolean displaySequenceRelations() {
562 return _display_sequence_relations;
565 boolean doCheckOption( final int which ) {
566 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
567 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
570 boolean doDisplayClickToOption( final int which ) {
571 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
574 boolean doDisplayOption( final int which ) {
575 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
579 * Will attempt to use the phylogeny to determine whether to check
580 * this or not (e.g. phylogram)
583 boolean doGuessCheckOption( final int which ) {
584 return display_options[ which ][ 2 ].equals( "?" );
587 Map<String, Color> getAnnotationColors() {
588 if ( _annotation_colors == null ) {
589 _annotation_colors = new Hashtable<String, Color>();
591 return _annotation_colors;
594 int getBaseFontSize() {
595 return _base_font_size;
598 int getMinBaseFontSize() {
599 return _min_base_font_size;
602 int getMaxBaseFontSize() {
603 return _max_base_font_size;
606 CLADOGRAM_TYPE getCladogramType() {
607 return _cladogram_type;
610 int getClickToOptionsCount() {
611 return clickto_options.length;
614 String getClickToTitle( final int which ) {
615 return clickto_options[ which ][ 0 ];
618 int getDefaultDisplayClicktoOption() {
619 return default_clickto;
622 SortedMap<String, Color> getDisplayColors() {
623 return _display_colors;
626 String getDisplayTitle( final int which ) {
627 return display_options[ which ][ 0 ];
630 Map<String, Color> getDomainColors() {
631 if ( _domain_colors == null ) {
632 _domain_colors = new Hashtable<String, Color>();
634 return _domain_colors;
637 int getGraphicsExportX() {
638 return _graphics_export_x;
641 int getGraphicsExportY() {
642 return _graphics_export_y;
645 Color getGuiBackgroundColor() {
646 return _gui_background_color;
649 Color getGuiButtonBackgroundColor() {
650 return _gui_button_background_color;
653 Color getGuiButtonBorderColor() {
654 return _gui_button_border_color;
657 Color getGuiButtonTextColor() {
658 return _gui_button_text_color;
661 Color getGuiCheckboxAndButtonActiveColor() {
662 return _gui_checkbox_and_button_active_color;
665 Color getGuiCheckboxTextColor() {
666 return _gui_checkbox_text_color;
669 Color getGuiMenuBackgroundColor() {
670 return _gui_menu_background_color;
673 Color getGuiMenuTextColor() {
674 return _gui_menu_text_color;
677 double getMinConfidenceValue() {
678 return _min_confidence_value;
681 NODE_LABEL_DIRECTION getNodeLabelDirection() {
682 return _node_label_direction;
685 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
686 return _number_of_digits_after_comma_for_branch_length_values;
689 short getNumberOfDigitsAfterCommaForConfidenceValues() {
690 return _number_of_digits_after_comma_for_confidence_values;
693 short getOvMaxHeight() {
694 return _ov_max_height;
697 short getOvMaxWidth() {
698 return _ov_max_width;
701 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
702 return _ov_placement;
705 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
706 return _phylogeny_graphics_type;
709 float getPrintLineWidth() {
710 return _print_line_width;
713 Hashtable<String, Color> getSpeciesColors() {
714 if ( _species_colors == null ) {
715 _species_colors = new Hashtable<String, Color>();
717 return _species_colors;
720 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
721 return _taxonomy_extraction;
724 boolean isAntialiasScreen() {
725 if ( AptxUtil.isMac() ) {
726 // Apple Macintosh graphics are slow, turn off anti-alias.
729 return _antialias_screen;
733 * Convenience method.
735 * @return true if value in configuration file was 'yes'
737 boolean isDrawAsPhylogram() {
738 return doCheckOption( display_as_phylogram );
741 boolean isEditable() {
746 * Only used by ArchaeoptryxE.
749 boolean isHideControlPanelAndMenubar() {
750 return _hide_controls_and_menus;
753 boolean isInternalNumberAreConfidenceForNhParsing() {
754 return _internal_number_are_confidence_for_nh_parsing;
757 boolean isReplaceUnderscoresInNhParsing() {
758 return _nh_parsing_replace_underscores;
761 boolean isShowBranchLengthValues() {
762 return _show_branch_length_values;
765 boolean isShowOverview() {
766 return _show_overview;
769 boolean isShowScale() {
773 final boolean isUseNativeUI() {
774 if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() ) {
777 return _ui == UI.NATIVE;
781 * Only used by ArchaeoptryxE.
784 boolean isUseTabbedDisplay() {
785 return _use_tabbed_display;
788 boolean isValidatePhyloXmlAgainstSchema() {
789 return _validate_against_phyloxml_xsd_schema;
792 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
793 _taxonomy_extraction = taxonomy_extraction;
796 private int getClickToIndex( final String name ) {
798 if ( name.equals( "edit_info" ) ) {
799 index = Configuration.display_node_data;
801 .printWarningMessage( Constants.PRG_NAME,
802 "configuration key [edit_info] is deprecated, use [display node data] instead" );
804 else if ( name.equals( "display_node_data" ) ) {
805 index = Configuration.display_node_data;
807 else if ( name.equals( "collapse_uncollapse" ) ) {
808 index = Configuration.collapse_uncollapse;
810 else if ( name.equals( "reroot" ) ) {
811 index = Configuration.reroot;
813 else if ( name.equals( "subtree" ) ) {
814 index = Configuration.subtree;
816 else if ( name.equals( "swap" ) ) {
817 index = Configuration.swap;
819 else if ( name.equals( "sort_descendants" ) ) {
820 index = Configuration.sort_descendents;
822 else if ( name.equals( "get_ext_descendents_data" ) ) {
823 index = Configuration.get_ext_desc_data;
825 else if ( name.equals( "display_sequences" ) ) {
827 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
830 else if ( name.equals( "open_seq_web" ) ) {
831 index = Configuration.open_seq_web;
833 else if ( name.equals( "open_tax_web" ) ) {
834 index = Configuration.open_tax_web;
836 else if ( name.equals( "blast" ) ) {
837 index = Configuration.blast;
839 else if ( name.equals( "cut_subtree" ) ) {
840 index = Configuration.cut_subtree;
842 else if ( name.equals( "copy_subtree" ) ) {
843 index = Configuration.copy_subtree;
845 else if ( name.equals( "paste_subtree" ) ) {
846 index = Configuration.paste_subtree;
848 else if ( name.equals( "delete" ) ) {
849 index = Configuration.delete_subtree_or_node;
851 else if ( name.equals( "add_new_node" ) ) {
852 index = Configuration.add_new_node;
854 else if ( name.equals( "edit_node_data" ) ) {
855 index = Configuration.edit_node_data;
857 else if ( name.equals( "select_nodes" ) ) {
858 index = Configuration.select_nodes;
860 else if ( name.equals( "display_node_popup" ) ) {
861 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
862 "configuration key [display_node_popup] is deprecated" );
865 else if ( name.equals( "custom_option" ) ) {
866 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
869 else if ( name.equals( "color_subtree" ) ) {
870 index = Configuration.color_subtree;
872 else if ( name.equals( "go_to_swiss_prot" ) ) {
873 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" );
879 private boolean parseBoolean( final String str ) {
880 final String my_str = str.trim().toLowerCase();
881 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
884 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
888 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
893 private double parseDouble( final String str ) {
896 d = Double.parseDouble( str.trim() );
898 catch ( final Exception e ) {
899 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
905 private float parseFloat( final String str ) {
908 f = Float.parseFloat( str.trim() );
910 catch ( final Exception e ) {
911 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
917 private int parseInt( final String str ) {
920 i = Integer.parseInt( str.trim() );
922 catch ( final Exception e ) {
923 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
929 private short parseShort( final String str ) {
932 i = Short.parseShort( str.trim() );
934 catch ( final Exception e ) {
935 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
941 private void processFontFamily( final StringTokenizer st ) {
942 setBaseFontFamilyName( "" );
943 final String font_str = ( ( String ) st.nextElement() ).trim();
944 final String[] fonts = font_str.split( ",+" );
945 for( String font : fonts ) {
946 font = font.replace( '_', ' ' ).trim();
947 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
948 setBaseFontFamilyName( font );
955 * read each line of config file, process non-comment lines
956 * @throws IOException
958 private void readConfig( final BufferedReader conf_in ) throws IOException {
961 line = conf_in.readLine();
962 if ( line != null ) {
964 // skip comments and blank lines
965 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
966 // convert runs of spaces to tabs
967 line = line.replaceAll( "\\s+", "\t" );
968 final StringTokenizer st = new StringTokenizer( line, "\t" );
972 } while ( line != null );
975 private void setAntialiasScreen( final boolean antialias_screen ) {
976 _antialias_screen = antialias_screen;
979 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
980 _cladogram_type = cladogram_type;
983 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
984 _default_bootstrap_samples = default_bootstrap_samples;
987 private void setEditable( final boolean editable ) {
988 _editable = editable;
991 private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
992 _ext_node_data_return_on = ext_node_data_return_on;
995 private void setGraphicsExportX( final int graphics_export_x ) {
996 _graphics_export_x = graphics_export_x;
999 private void setGraphicsExportY( final int graphics_export_y ) {
1000 _graphics_export_y = graphics_export_y;
1003 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
1004 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
1008 * Set a key-value(s) tuple
1010 private void setKeyValue( final StringTokenizer st ) {
1011 final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
1012 if ( !st.hasMoreElements() ) {
1015 // Handle single value settings first:
1016 if ( key.equals( "default_click_to" ) ) {
1017 final String clickto_name = ( String ) st.nextElement();
1018 default_clickto = getClickToIndex( clickto_name );
1019 if ( default_clickto == -1 ) {
1020 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
1021 + "] for [default_click_to]" );
1022 default_clickto = 0;
1024 else if ( default_clickto == DEPRECATED ) {
1028 else if ( key.equals( "native_ui" ) ) {
1029 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
1030 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
1033 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
1034 _ui = UI.CROSSPLATFORM;
1036 else if ( my_str.equals( "?" ) ) {
1040 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
1045 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
1046 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
1048 else if ( key.equals( "antialias_screen" ) ) {
1049 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
1051 else if ( key.equals( "phylogeny_graphics_type" ) ) {
1052 final String type_str = ( ( String ) st.nextElement() ).trim();
1053 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
1054 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1056 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
1057 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1059 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
1060 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1062 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
1063 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1065 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
1066 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1068 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
1069 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1071 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
1072 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1074 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
1075 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1078 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1079 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1080 + "] for [phylogeny_graphics_type]" );
1083 else if ( key.equals( "min_confidence_value" ) ) {
1084 final String mcv_str = ( ( String ) st.nextElement() ).trim();
1085 final double d = parseDouble( mcv_str );
1086 setMinConfidenceValue( d );
1088 else if ( key.equals( "font_family" ) ) {
1089 processFontFamily( st );
1091 else if ( key.equals( "font_size" ) ) {
1092 final String size_str = ( ( String ) st.nextElement() ).trim();
1093 final int i = parseInt( size_str );
1095 setBaseFontSize( i );
1098 else if ( key.equals( "font_size_min" ) ) {
1099 final String size_str = ( ( String ) st.nextElement() ).trim();
1100 final int i = parseInt( size_str );
1102 setMinBaseFontSize( i );
1105 else if ( key.equals( "font_size_max" ) ) {
1106 final String size_str = ( ( String ) st.nextElement() ).trim();
1107 final int i = parseInt( size_str );
1109 setMaxBaseFontSize( i );
1112 else if ( key.equals( "graphics_export_x" ) ) {
1113 final String str = ( ( String ) st.nextElement() ).trim();
1114 final int i = parseInt( str );
1116 setGraphicsExportX( i );
1119 else if ( key.equals( "graphics_export_y" ) ) {
1120 final String str = ( ( String ) st.nextElement() ).trim();
1121 final int i = parseInt( str );
1123 setGraphicsExportY( i );
1126 else if ( key.equals( "pdf_export_line_width" ) ) {
1127 final String str = ( ( String ) st.nextElement() ).trim();
1128 final float f = parseFloat( str );
1130 setPrintLineWidth( f );
1133 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1134 "value for [pdf_export_line_width] cannot be zero or negative" );
1137 else if ( key.equals( "window_initial_size_x" ) ) {
1138 final String str = ( ( String ) st.nextElement() ).trim();
1139 final int i = parseInt( str );
1144 else if ( key.equals( "window_initial_size_y" ) ) {
1145 final String str = ( ( String ) st.nextElement() ).trim();
1146 final int i = parseInt( str );
1151 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1152 final String str = ( ( String ) st.nextElement() ).trim();
1153 final int i = parseInt( str );
1155 setDefaultBootstrapSamples( i );
1159 .printWarningMessage( Constants.PRG_NAME,
1160 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1163 else if ( key.equals( "mafft_local" ) ) {
1164 final String str = ( ( String ) st.nextElement() ).trim();
1165 if ( !ForesterUtil.isEmpty( str ) ) {
1166 setPathToLocalMafft( new File( str ) );
1169 else if ( key.equals( "fastme_local" ) ) {
1170 final String str = ( ( String ) st.nextElement() ).trim();
1171 if ( !ForesterUtil.isEmpty( str ) ) {
1172 setPathToLocalFastme( new File( str ) );
1175 else if ( key.equals( "raxml_local" ) ) {
1176 final String str = ( ( String ) st.nextElement() ).trim();
1177 if ( !ForesterUtil.isEmpty( str ) ) {
1178 setPathToLocalRaxml( new File( str ) );
1181 else if ( key.equals( "show_scale" ) ) {
1182 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1184 else if ( key.equals( "show_overview" ) ) {
1185 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1187 else if ( key.equals( "show_branch_length_values" ) ) {
1188 setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
1190 else if ( key.equals( "background_gradient" ) ) {
1191 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1193 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1194 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1196 else if ( key.equals( "show_domain_labels" ) ) {
1197 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1199 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1200 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1202 else if ( key.equals( "cladogram_type" ) ) {
1203 final String type_str = ( ( String ) st.nextElement() ).trim();
1204 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1205 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1207 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1208 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1210 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1211 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1214 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1215 + "] for [cladogram_type]" );
1218 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1220 .printWarningMessage( Constants.PRG_NAME,
1221 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1223 else if ( key.equals( "hide_controls_and_menus" ) ) {
1224 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1226 else if ( key.equals( "use_tabbed_display" ) ) {
1227 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1229 else if ( key.equals( "overview_width" ) ) {
1230 final short i = parseShort( ( ( String ) st.nextElement() ) );
1233 else if ( key.equals( "overview_height" ) ) {
1234 final short i = parseShort( ( ( String ) st.nextElement() ) );
1235 setOvMaxHeight( i );
1237 else if ( key.equals( "overview_placement_type" ) ) {
1238 final String type_str = ( ( String ) st.nextElement() ).trim();
1239 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1240 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1242 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1243 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1245 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1246 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1248 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1249 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1252 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1253 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1254 + "] for [overview_placement_type]" );
1257 else if ( key.equals( "node_label_direction" ) ) {
1258 final String type_str = ( ( String ) st.nextElement() ).trim();
1259 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1260 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1262 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1263 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1266 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1267 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1268 + "] for [node_label_direction]" );
1271 else if ( key.equals( "branch_length_value_digits" ) ) {
1272 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1274 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1277 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1278 + "] for [branch_length_value_digits]" );
1281 else if ( key.equals( "confidence_value_digits" ) ) {
1282 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1284 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1287 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1288 + "] for [confidence_value_digits]" );
1291 else if ( key.equals( "allow_editing" ) ) {
1292 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1294 else if ( key.equals( "display_sequence_relations" ) ) {
1295 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1297 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1298 final boolean r = parseBoolean( ( String ) st.nextElement() );
1299 if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
1301 .printWarningMessage( Constants.PRG_NAME,
1302 "attempt to extract taxonomies and replace underscores at the same time" );
1305 setReplaceUnderscoresInNhParsing( r );
1308 else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
1309 final String s = ( String ) st.nextElement();
1310 if ( s.equalsIgnoreCase( "no" ) ) {
1311 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1313 else if ( s.equalsIgnoreCase( "yes" ) ) {
1314 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1316 else if ( s.equalsIgnoreCase( "pfam" ) ) {
1317 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1320 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1321 "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + s );
1323 if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
1325 .printWarningMessage( Constants.PRG_NAME,
1326 "attempt to extract taxonomies and replace underscores at the same time" );
1329 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1330 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1332 else if ( key.equals( "gui_background_color" ) ) {
1333 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1335 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1336 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1338 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1339 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1341 else if ( key.equals( "gui_button_text_color" ) ) {
1342 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1344 else if ( key.equals( "gui_button_background_color" ) ) {
1345 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1347 else if ( key.equals( "gui_menu_background_color" ) ) {
1348 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1350 else if ( key.equals( "gui_menu_text_color" ) ) {
1351 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1353 else if ( key.equals( "gui_button_border_color" ) ) {
1354 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1356 else if ( key.equals( "domain_structure_font_color" ) ) {
1357 _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
1359 else if ( key.equals( "domain_structure_base_color" ) ) {
1360 _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
1362 else if ( key.equals( "show_default_node_shapes" ) ) {
1364 .printWarningMessage( Constants.PRG_NAME,
1365 "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" );
1366 final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() );
1367 setShowDefaultNodeShapesInternal( b );
1368 setShowDefaultNodeShapesExternal( b );
1370 else if ( key.equals( "show_default_node_shapes_internal" ) ) {
1371 setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1373 else if ( key.equals( "show_default_node_shapes_external" ) ) {
1374 setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1376 else if ( key.equals( "default_node_size" ) ) {
1377 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1378 setDefaultNodeShapeSize( i );
1380 else if ( key.equals( "default_node_fill" ) ) {
1381 final String fill_str = ( ( String ) st.nextElement() ).trim();
1382 if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.NONE.toString() ) ) {
1383 setDefaultNodeFill( NodeFill.NONE );
1385 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.GRADIENT.toString() ) ) {
1386 setDefaultNodeFill( NodeFill.GRADIENT );
1388 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.SOLID.toString() ) ) {
1389 setDefaultNodeFill( NodeFill.SOLID );
1392 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1393 + "] for [default_node_fill]" );
1396 else if ( key.equals( "default_node_shape" ) ) {
1397 final String shape_str = ( ( String ) st.nextElement() ).trim();
1398 if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.CIRCLE.toString() ) ) {
1399 setDefaultNodeShape( NodeShape.CIRCLE );
1401 else if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.RECTANGLE.toString() ) ) {
1402 setDefaultNodeShape( NodeShape.RECTANGLE );
1405 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1406 + "] for [default_node_shape]" );
1409 else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
1410 setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
1412 else if ( key.equals( "ext_descendents_data_to_return" ) ) {
1413 final String s = ( ( String ) st.nextElement() ).trim();
1414 if ( s.equalsIgnoreCase( "node_name" ) ) {
1415 setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
1417 else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
1418 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
1420 else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) {
1421 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ_FASTA );
1423 else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
1424 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
1426 else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
1427 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
1429 else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
1430 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
1432 else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
1433 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME );
1435 else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
1436 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
1438 else if ( s.equalsIgnoreCase( "user_selected" ) ) {
1439 setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
1442 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1443 + "] for [ext_descendents_data_to_return]" );
1446 else if ( key.equals( "label_for_get_ext_descendents_data" ) ) {
1447 final String s = ( ( String ) st.nextElement() ).trim();
1448 if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) {
1449 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s
1450 + "] for [label_for_get_ext_descendents_data]" );
1453 setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
1456 else if ( key.equals( "ext_descendents_data_to_return_on" ) ) {
1457 final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
1458 if ( s.equals( "console" ) ) {
1459 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
1461 else if ( s.equals( "window" ) ) {
1462 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
1464 else if ( s.equals( "buffer_only" ) ) {
1465 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
1468 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1469 + "] for [ext_descendents_data_to_return_on]" );
1472 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1475 if ( key.equals( "use_real_br_lengths" ) || key.equals( "phylogram" ) ) {
1476 key_index = Configuration.display_as_phylogram;
1477 if ( key.equals( "use_real_br_lengths" ) ) {
1479 .printWarningMessage( Constants.PRG_NAME,
1480 "configuration key [use_real_br_lengths] is deprecated, use [phylogram] instead" );
1483 else if ( key.equals( "rollover" ) ) {
1484 key_index = Configuration.node_data_popup;
1486 else if ( key.equals( "color_according_to_species" ) ) {
1487 key_index = Configuration.color_according_to_species;
1489 else if ( key.equals( "show_node_names" ) ) {
1490 key_index = Configuration.show_node_names;
1492 else if ( key.equals( "show_taxonomy" ) || key.equals( "show_taxonomy_code" ) ) {
1493 key_index = Configuration.show_tax_code;
1494 if ( key.equals( "show_taxonomy" ) ) {
1496 .printWarningMessage( Constants.PRG_NAME,
1497 "configuration key [show_taxonomy] is deprecated, use [show_taxonomy_code] instead" );
1500 else if ( key.equals( "write_br_length_values" ) ) {
1501 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1502 "configuration key [write_br_length_values] is deprecated" );
1503 key_index = DEPRECATED;
1505 else if ( key.equals( "write_bootstrap_values" ) || key.equals( "write_confidence_values" ) ) {
1506 key_index = Configuration.write_confidence_values;
1507 if ( key.equals( "write_bootstrap_values" ) ) {
1509 .printWarningMessage( Constants.PRG_NAME,
1510 "configuration key [write_bootstrap_values] is deprecated, use [write_confidence_values] instead" );
1513 else if ( key.equals( "write_events" ) || key.equals( "write_dup_spec" ) ) {
1514 key_index = Configuration.write_events;
1515 if ( key.equals( "write_dup_spec" ) ) {
1517 .printWarningMessage( Constants.PRG_NAME,
1518 "configuration key [write_dup_spec] is deprecated, use [write_events] instead" );
1521 else if ( key.equals( "color_branches" ) ) {
1522 key_index = Configuration.color_branches;
1524 else if ( key.equals( "width_branches" ) ) {
1525 key_index = Configuration.width_branches;
1527 else if ( key.equals( "color_orthologous" ) ) {
1528 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1529 "configuration key [color_orthologous] is deprecated" );
1531 else if ( key.equals( "color_subtree_neighbors" ) ) {
1532 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1533 "configuration key [color_subtree_neighbors] is deprecated" );
1535 else if ( key.equals( "color_super_orthologous" ) ) {
1536 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1537 "configuration key [color_super_orthologous] is deprecated" );
1539 else if ( key.equals( "mark_nodes_with_box" ) ) {
1540 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1541 "configuration key [mark_nodes_with_box] is deprecated" );
1542 key_index = DEPRECATED;
1544 else if ( key.equals( "show_domain_architectures" ) ) {
1545 key_index = Configuration.show_domain_architectures;
1547 else if ( key.equals( "show_annotations" ) ) {
1548 key_index = Configuration.show_annotation;
1550 else if ( key.equals( "show_binary_characters" ) ) {
1551 key_index = Configuration.show_binary_characters;
1553 else if ( key.equals( "show_binary_character_counts" ) ) {
1554 key_index = Configuration.show_binary_character_counts;
1556 else if ( key.equals( "show_gene_names" ) ) {
1557 key_index = Configuration.show_gene_names;
1559 else if ( key.equals( "show_gene_symbols" ) ) {
1560 key_index = Configuration.show_gene_symbols;
1562 else if ( key.equals( "show_sequence_acc" ) ) {
1563 key_index = Configuration.show_sequence_acc;
1565 else if ( key.equals( "show_node_ids" ) ) {
1567 .printWarningMessage( Constants.PRG_NAME, "configuration key [show_node_ids] is deprecated" );
1568 key_index = DEPRECATED;
1570 else if ( key.equals( "display_internal_data" ) ) {
1571 key_index = Configuration.display_internal_data;
1573 else if ( key.equals( "dynamically_hide_data" ) ) {
1574 key_index = Configuration.dynamically_hide_data;
1576 else if ( key.equals( "show_taxonomy_names" ) ) {
1577 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1578 "configuration key [show_taxonomy_names] is deprecated" );
1579 key_index = DEPRECATED;
1581 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1582 key_index = Configuration.show_taxonomy_scientific_names;
1584 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1585 key_index = Configuration.show_taxonomy_common_names;
1587 else if ( key.equals( "show_taxonomy_images" ) ) {
1588 key_index = Configuration.show_taxonomy_images;
1590 else if ( key.equals( "color_according_to_annotation" ) ) {
1591 key_index = Configuration.color_according_to_annotation;
1593 else if ( key.equals( "show_vector_data" ) ) {
1594 key_index = Configuration.show_vector_data;
1596 else if ( key.equals( "show_properties" ) ) {
1597 key_index = Configuration.show_properties;
1599 else if ( key.equals( "show_relation_confidence" ) ) {
1600 key_index = Configuration.show_relation_confidence;
1602 else if ( key.equals( "show_custom_node_shapes" ) ) {
1603 key_index = Configuration.show_custom_node_shapes;
1605 // If we've found the key, set the values
1606 if ( key_index >= 0 ) {
1607 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1608 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1609 // otherwise, keep looking
1612 if ( key_index == DEPRECATED ) {
1615 else if ( key.equals( "click_to" ) ) {
1616 final String click_to_name = ( String ) st.nextElement();
1617 key_index = getClickToIndex( click_to_name );
1618 if ( key_index >= 0 ) {
1619 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1621 else if ( key_index == DEPRECATED ) {
1625 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1629 else if ( key.equals( "species_color" ) ) {
1630 getSpeciesColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1632 else if ( key.equals( "domain_color" ) ) {
1633 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1635 else if ( key.equals( "annotation_color" ) ) {
1636 getAnnotationColors()
1637 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1639 else if ( key.equals( "function_color" ) ) {
1640 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1641 "configuration key [function_color] is deprecated" );
1643 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1644 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1647 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1648 + "] in: " + config_filename );
1653 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1654 + config_filename );
1658 private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
1659 _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
1662 private void setOvMaxHeight( final short ov_max_height ) {
1663 _ov_max_height = ov_max_height;
1666 private void setOvMaxWidth( final short ov_max_width ) {
1667 _ov_max_width = ov_max_width;
1670 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1671 _ov_placement = ov_placement;
1674 private void setPathToLocalFastme( final File path_to_local_fastme ) {
1675 _path_to_local_fastme = path_to_local_fastme;
1678 private void setPathToLocalMafft( final File path_to_local_mafft ) {
1679 _path_to_local_mafft = path_to_local_mafft;
1682 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
1683 _path_to_local_raxml = path_to_local_raxml;
1686 private void setShowOverview( final boolean show_overview ) {
1687 _show_overview = show_overview;
1690 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1691 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1694 static String getDefaultFontFamilyName() {
1695 return DEFAULT_FONT_FAMILY;
1698 public enum EXT_NODE_DATA_RETURN_ON {
1699 CONSOLE, WINODW, BUFFER_ONLY;
1703 NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN
1706 static enum TRIPLET {
1707 TRUE, FALSE, UNKNOWN