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 boolean _midpoint_root = false;
221 private static String DEFAULT_FONT_FAMILY = "";
223 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
224 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
225 DEFAULT_FONT_FAMILY = font_name;
229 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
230 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
234 public Configuration() {
235 this( null, false, false, false );
238 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
239 if ( ForesterUtil.isEmpty( cf ) ) {
240 config_filename = default_config_filename;
243 config_filename = cf;
245 setDisplayColors( new TreeMap<String, Color>() );
246 config_filename = config_filename.trim();
249 // If URL, open accordingly
251 u = new URL( config_filename );
253 final InputStreamReader isr = new InputStreamReader( u.openStream() );
254 final BufferedReader bf = new BufferedReader( isr );
257 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
258 + config_filename + "]" );
260 catch ( final Exception e ) {
261 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
262 + config_filename + "]: " + e.getLocalizedMessage() );
265 catch ( final Exception e ) {
266 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
267 + config_filename + "]" );
271 // Otherwise, open as a file
272 File f = new File( config_filename );
274 f = new File( config_filename + ".txt" );
276 if ( f.exists() && f.canRead() ) {
278 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
282 catch ( final Exception e ) {
284 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
285 + config_filename + "]: " + e );
291 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
292 + config_filename + "]" );
298 public String getBaseFontFamilyName() {
299 return _base_font_family_name;
302 public int getDefaultBootstrapSamples() {
303 return _default_bootstrap_samples;
306 public NodeFill getDefaultNodeFill() {
307 return _default_node_fill;
310 public NodeShape getDefaultNodeShape() {
311 return _default_node_shape;
314 public short getDefaultNodeShapeSize() {
315 return _default_node_shape_size;
318 public Color getDomainStructureBaseColor() {
319 return _domain_structure_base_color;
322 public Color getDomainStructureFontColor() {
323 return _domain_structure_font_color;
326 public NODE_DATA getExtDescNodeDataToReturn() {
327 return _ext_desc_data_to_return;
330 public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
331 return _ext_node_data_return_on;
334 public int getFrameXSize() {
335 return _frame_x_size;
338 public int getFrameYSize() {
339 return _frame_y_size;
342 public String getLabelForGetExtDescendentsData() {
343 return _label_for_get_ext_descendents_data;
346 public File getPathToLocalFastme() {
347 return _path_to_local_fastme;
350 public File getpathToLocalMafft() {
351 return _path_to_local_mafft;
354 public File getPathToLocalRaxml() {
355 return _path_to_local_raxml;
358 public boolean isAbbreviateScientificTaxonNames() {
359 return _abbreviate_scientific_names;
362 public boolean isBackgroundColorGradient() {
363 return _background_color_gradient;
366 public boolean isColorLabelsSameAsParentBranch() {
367 return _color_labels_same_as_parent_branch;
370 public boolean isShowDefaultNodeShapesExternal() {
371 return _show_default_node_shapes_external;
374 public boolean isShowDefaultNodeShapesInternal() {
375 return _show_default_node_shapes_internal;
378 public boolean isShowDomainLabels() {
379 return _show_domain_labels;
382 public boolean isTaxonomyColorizeNodeShapes() {
383 return _taxonomy_colorize_node_shapes;
386 public void putDisplayColors( final String key, final Color color ) {
387 getDisplayColors().put( key, color );
390 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
391 _abbreviate_scientific_names = abbreviate_scientific_names;
394 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
395 _background_color_gradient = background_color_gradient;
398 public void setBaseFontFamilyName( final String base_font_family_name ) {
399 _base_font_family_name = base_font_family_name;
402 public void setBaseFontSize( final int base_font_size ) {
403 _base_font_size = base_font_size;
406 private void setMaxBaseFontSize( final int max_base_font_size ) {
407 _max_base_font_size = max_base_font_size;
410 private void setMinBaseFontSize( final int min_base_font_size ) {
411 _min_base_font_size = min_base_font_size;
414 public void setColorizeBranches( final boolean b ) {
415 display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
418 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
419 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
422 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
423 _default_node_fill = default_node_fill;
426 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
427 _default_node_shape = default_node_shape;
430 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
431 _default_node_shape_size = default_node_shape_size;
434 public void setDisplayAsPhylogram( final boolean b ) {
435 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
438 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
439 _display_colors = display_colors;
442 public void setDisplayConfidenceValues( final boolean b ) {
443 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
446 public void setDisplayInternalData( final boolean b ) {
447 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
450 public void setDisplayNodeNames( final boolean b ) {
451 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
454 public void setDisplaySequenceAcc( final boolean b ) {
455 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
458 public void setDisplaySequenceNames( final boolean b ) {
459 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
462 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
463 _display_sequence_relations = display_sequence_relations;
466 public void setDisplaySequenceSymbols( final boolean b ) {
467 display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no";
470 public void setDisplayTaxonomyCode( final boolean b ) {
471 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
474 public void setDisplayTaxonomyCommonNames( final boolean b ) {
475 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
478 public void setDisplayTaxonomyImages( final boolean b ) {
479 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
482 public void setDisplayTaxonomyScientificNames( final boolean b ) {
483 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
486 public void setDynamicallyHideData( final boolean b ) {
487 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
490 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
491 _ext_desc_data_to_return = ext_desc_data_to_return;
494 public void setFrameXSize( final int frame_x_size ) {
495 _frame_x_size = frame_x_size;
498 public void setFrameYSize( final int frame_y_size ) {
499 _frame_y_size = frame_y_size;
502 public void setMinConfidenceValue( final double min_confidence_value ) {
503 _min_confidence_value = min_confidence_value;
506 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
507 _node_label_direction = node_label_direction;
510 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
511 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
514 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
515 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
518 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
519 _phylogeny_graphics_type = phylogeny_graphics_type;
522 public void setPrintLineWidth( final float print_line_width ) {
523 _print_line_width = print_line_width;
526 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
527 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
530 public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
531 _show_branch_length_values = show_branch_length_values;
534 public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
535 _show_default_node_shapes_external = show_default_node_shapes_external;
538 public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
539 _show_default_node_shapes_internal = show_default_node_shapes_internal;
542 public void setShowDomainLabels( final boolean show_domain_labels ) {
543 _show_domain_labels = show_domain_labels;
546 public void setShowScale( final boolean show_scale ) {
547 _show_scale = show_scale;
550 public void setTaxonomyColorize( final boolean b ) {
551 display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
554 public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
555 _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
558 public void setUseBranchesWidths( final boolean b ) {
559 display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
562 boolean displaySequenceRelations() {
563 return _display_sequence_relations;
566 boolean doCheckOption( final int which ) {
567 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
568 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
571 boolean doDisplayClickToOption( final int which ) {
572 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
575 boolean doDisplayOption( final int which ) {
576 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
580 * Will attempt to use the phylogeny to determine whether to check
581 * this or not (e.g. phylogram)
584 boolean doGuessCheckOption( final int which ) {
585 return display_options[ which ][ 2 ].equals( "?" );
588 Map<String, Color> getAnnotationColors() {
589 if ( _annotation_colors == null ) {
590 _annotation_colors = new Hashtable<String, Color>();
592 return _annotation_colors;
595 int getBaseFontSize() {
596 return _base_font_size;
599 int getMinBaseFontSize() {
600 return _min_base_font_size;
603 int getMaxBaseFontSize() {
604 return _max_base_font_size;
607 CLADOGRAM_TYPE getCladogramType() {
608 return _cladogram_type;
611 int getClickToOptionsCount() {
612 return clickto_options.length;
615 String getClickToTitle( final int which ) {
616 return clickto_options[ which ][ 0 ];
619 int getDefaultDisplayClicktoOption() {
620 return default_clickto;
623 SortedMap<String, Color> getDisplayColors() {
624 return _display_colors;
627 String getDisplayTitle( final int which ) {
628 return display_options[ which ][ 0 ];
631 Map<String, Color> getDomainColors() {
632 if ( _domain_colors == null ) {
633 _domain_colors = new Hashtable<String, Color>();
635 return _domain_colors;
638 int getGraphicsExportX() {
639 return _graphics_export_x;
642 int getGraphicsExportY() {
643 return _graphics_export_y;
646 Color getGuiBackgroundColor() {
647 return _gui_background_color;
650 Color getGuiButtonBackgroundColor() {
651 return _gui_button_background_color;
654 Color getGuiButtonBorderColor() {
655 return _gui_button_border_color;
658 Color getGuiButtonTextColor() {
659 return _gui_button_text_color;
662 Color getGuiCheckboxAndButtonActiveColor() {
663 return _gui_checkbox_and_button_active_color;
666 Color getGuiCheckboxTextColor() {
667 return _gui_checkbox_text_color;
670 Color getGuiMenuBackgroundColor() {
671 return _gui_menu_background_color;
674 Color getGuiMenuTextColor() {
675 return _gui_menu_text_color;
678 double getMinConfidenceValue() {
679 return _min_confidence_value;
682 NODE_LABEL_DIRECTION getNodeLabelDirection() {
683 return _node_label_direction;
686 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
687 return _number_of_digits_after_comma_for_branch_length_values;
690 short getNumberOfDigitsAfterCommaForConfidenceValues() {
691 return _number_of_digits_after_comma_for_confidence_values;
694 short getOvMaxHeight() {
695 return _ov_max_height;
698 short getOvMaxWidth() {
699 return _ov_max_width;
702 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
703 return _ov_placement;
706 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
707 return _phylogeny_graphics_type;
710 float getPrintLineWidth() {
711 return _print_line_width;
714 Hashtable<String, Color> getSpeciesColors() {
715 if ( _species_colors == null ) {
716 _species_colors = new Hashtable<String, Color>();
718 return _species_colors;
721 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
722 return _taxonomy_extraction;
725 boolean isAntialiasScreen() {
726 if ( AptxUtil.isMac() ) {
727 // Apple Macintosh graphics are slow, turn off anti-alias.
730 return _antialias_screen;
734 * Convenience method.
736 * @return true if value in configuration file was 'yes'
738 boolean isDrawAsPhylogram() {
739 return doCheckOption( display_as_phylogram );
742 boolean isEditable() {
747 * Only used by ArchaeoptryxE.
750 boolean isHideControlPanelAndMenubar() {
751 return _hide_controls_and_menus;
754 boolean isInternalNumberAreConfidenceForNhParsing() {
755 return _internal_number_are_confidence_for_nh_parsing;
758 boolean isReplaceUnderscoresInNhParsing() {
759 return _nh_parsing_replace_underscores;
762 boolean isShowBranchLengthValues() {
763 return _show_branch_length_values;
766 boolean isShowOverview() {
767 return _show_overview;
770 boolean isShowScale() {
774 final boolean isUseNativeUI() {
775 if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() ) {
778 return _ui == UI.NATIVE;
782 * Only used by ArchaeoptryxE.
785 boolean isUseTabbedDisplay() {
786 return _use_tabbed_display;
789 boolean isValidatePhyloXmlAgainstSchema() {
790 return _validate_against_phyloxml_xsd_schema;
793 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
794 _taxonomy_extraction = taxonomy_extraction;
797 private int getClickToIndex( final String name ) {
799 if ( name.equals( "edit_info" ) ) {
800 index = Configuration.display_node_data;
802 .printWarningMessage( Constants.PRG_NAME,
803 "configuration key [edit_info] is deprecated, use [display node data] instead" );
805 else if ( name.equals( "display_node_data" ) ) {
806 index = Configuration.display_node_data;
808 else if ( name.equals( "collapse_uncollapse" ) ) {
809 index = Configuration.collapse_uncollapse;
811 else if ( name.equals( "reroot" ) ) {
812 index = Configuration.reroot;
814 else if ( name.equals( "subtree" ) ) {
815 index = Configuration.subtree;
817 else if ( name.equals( "swap" ) ) {
818 index = Configuration.swap;
820 else if ( name.equals( "sort_descendants" ) ) {
821 index = Configuration.sort_descendents;
823 else if ( name.equals( "get_ext_descendents_data" ) ) {
824 index = Configuration.get_ext_desc_data;
826 else if ( name.equals( "display_sequences" ) ) {
828 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
831 else if ( name.equals( "open_seq_web" ) ) {
832 index = Configuration.open_seq_web;
834 else if ( name.equals( "open_tax_web" ) ) {
835 index = Configuration.open_tax_web;
837 else if ( name.equals( "blast" ) ) {
838 index = Configuration.blast;
840 else if ( name.equals( "cut_subtree" ) ) {
841 index = Configuration.cut_subtree;
843 else if ( name.equals( "copy_subtree" ) ) {
844 index = Configuration.copy_subtree;
846 else if ( name.equals( "paste_subtree" ) ) {
847 index = Configuration.paste_subtree;
849 else if ( name.equals( "delete" ) ) {
850 index = Configuration.delete_subtree_or_node;
852 else if ( name.equals( "add_new_node" ) ) {
853 index = Configuration.add_new_node;
855 else if ( name.equals( "edit_node_data" ) ) {
856 index = Configuration.edit_node_data;
858 else if ( name.equals( "select_nodes" ) ) {
859 index = Configuration.select_nodes;
861 else if ( name.equals( "display_node_popup" ) ) {
862 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
863 "configuration key [display_node_popup] is deprecated" );
866 else if ( name.equals( "custom_option" ) ) {
867 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
870 else if ( name.equals( "color_subtree" ) ) {
871 index = Configuration.color_subtree;
876 private boolean parseBoolean( final String str ) {
877 final String my_str = str.trim().toLowerCase();
878 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
881 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
885 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
890 private double parseDouble( final String str ) {
893 d = Double.parseDouble( str.trim() );
895 catch ( final Exception e ) {
896 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
902 private float parseFloat( final String str ) {
905 f = Float.parseFloat( str.trim() );
907 catch ( final Exception e ) {
908 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
914 private int parseInt( final String str ) {
917 i = Integer.parseInt( str.trim() );
919 catch ( final Exception e ) {
920 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
926 private short parseShort( final String str ) {
929 i = Short.parseShort( str.trim() );
931 catch ( final Exception e ) {
932 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
938 private void processFontFamily( final StringTokenizer st ) {
939 setBaseFontFamilyName( "" );
940 final String font_str = ( ( String ) st.nextElement() ).trim();
941 final String[] fonts = font_str.split( ",+" );
942 for( String font : fonts ) {
943 font = font.replace( '_', ' ' ).trim();
944 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
945 setBaseFontFamilyName( font );
952 * read each line of config file, process non-comment lines
953 * @throws IOException
955 private void readConfig( final BufferedReader conf_in ) throws IOException {
958 line = conf_in.readLine();
959 if ( line != null ) {
961 // skip comments and blank lines
962 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
963 // convert runs of spaces to tabs
964 line = line.replaceAll( "\\s+", "\t" );
965 final StringTokenizer st = new StringTokenizer( line, "\t" );
969 } while ( line != null );
972 private void setAntialiasScreen( final boolean antialias_screen ) {
973 _antialias_screen = antialias_screen;
976 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
977 _cladogram_type = cladogram_type;
980 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
981 _default_bootstrap_samples = default_bootstrap_samples;
984 private void setEditable( final boolean editable ) {
985 _editable = editable;
988 private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
989 _ext_node_data_return_on = ext_node_data_return_on;
992 private void setGraphicsExportX( final int graphics_export_x ) {
993 _graphics_export_x = graphics_export_x;
996 private void setGraphicsExportY( final int graphics_export_y ) {
997 _graphics_export_y = graphics_export_y;
1000 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
1001 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
1005 * Set a key-value(s) tuple
1007 private void setKeyValue( final StringTokenizer st ) {
1008 final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
1009 if ( !st.hasMoreElements() ) {
1012 // Handle single value settings first:
1013 if ( key.equals( "default_click_to" ) ) {
1014 final String clickto_name = ( String ) st.nextElement();
1015 default_clickto = getClickToIndex( clickto_name );
1016 if ( default_clickto == -1 ) {
1017 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
1018 + "] for [default_click_to]" );
1019 default_clickto = 0;
1021 else if ( default_clickto == DEPRECATED ) {
1025 else if ( key.equals( "native_ui" ) ) {
1026 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
1027 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
1030 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
1031 _ui = UI.CROSSPLATFORM;
1033 else if ( my_str.equals( "?" ) ) {
1037 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
1042 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
1043 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
1045 else if ( key.equals( "antialias_screen" ) ) {
1046 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
1048 else if ( key.equals( "phylogeny_graphics_type" ) ) {
1049 final String type_str = ( ( String ) st.nextElement() ).trim();
1050 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
1051 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1053 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
1054 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1056 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
1057 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1059 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
1060 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1062 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
1063 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1065 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
1066 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1068 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
1069 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1071 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
1072 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1075 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1076 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1077 + "] for [phylogeny_graphics_type]" );
1080 else if ( key.equals( "min_confidence_value" ) ) {
1081 final String mcv_str = ( ( String ) st.nextElement() ).trim();
1082 final double d = parseDouble( mcv_str );
1083 setMinConfidenceValue( d );
1085 else if ( key.equals( "font_family" ) ) {
1086 processFontFamily( st );
1088 else if ( key.equals( "font_size" ) ) {
1089 final String size_str = ( ( String ) st.nextElement() ).trim();
1090 final int i = parseInt( size_str );
1092 setBaseFontSize( i );
1095 else if ( key.equals( "font_size_min" ) ) {
1096 final String size_str = ( ( String ) st.nextElement() ).trim();
1097 final int i = parseInt( size_str );
1099 setMinBaseFontSize( i );
1102 else if ( key.equals( "font_size_max" ) ) {
1103 final String size_str = ( ( String ) st.nextElement() ).trim();
1104 final int i = parseInt( size_str );
1106 setMaxBaseFontSize( i );
1109 else if ( key.equals( "graphics_export_x" ) ) {
1110 final String str = ( ( String ) st.nextElement() ).trim();
1111 final int i = parseInt( str );
1113 setGraphicsExportX( i );
1116 else if ( key.equals( "graphics_export_y" ) ) {
1117 final String str = ( ( String ) st.nextElement() ).trim();
1118 final int i = parseInt( str );
1120 setGraphicsExportY( i );
1123 else if ( key.equals( "pdf_export_line_width" ) ) {
1124 final String str = ( ( String ) st.nextElement() ).trim();
1125 final float f = parseFloat( str );
1127 setPrintLineWidth( f );
1130 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1131 "value for [pdf_export_line_width] cannot be zero or negative" );
1134 else if ( key.equals( "window_initial_size_x" ) ) {
1135 final String str = ( ( String ) st.nextElement() ).trim();
1136 final int i = parseInt( str );
1141 else if ( key.equals( "window_initial_size_y" ) ) {
1142 final String str = ( ( String ) st.nextElement() ).trim();
1143 final int i = parseInt( str );
1148 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1149 final String str = ( ( String ) st.nextElement() ).trim();
1150 final int i = parseInt( str );
1152 setDefaultBootstrapSamples( i );
1156 .printWarningMessage( Constants.PRG_NAME,
1157 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1160 else if ( key.equals( "mafft_local" ) ) {
1161 final String str = ( ( String ) st.nextElement() ).trim();
1162 if ( !ForesterUtil.isEmpty( str ) ) {
1163 setPathToLocalMafft( new File( str ) );
1166 else if ( key.equals( "fastme_local" ) ) {
1167 final String str = ( ( String ) st.nextElement() ).trim();
1168 if ( !ForesterUtil.isEmpty( str ) ) {
1169 setPathToLocalFastme( new File( str ) );
1172 else if ( key.equals( "raxml_local" ) ) {
1173 final String str = ( ( String ) st.nextElement() ).trim();
1174 if ( !ForesterUtil.isEmpty( str ) ) {
1175 setPathToLocalRaxml( new File( str ) );
1178 else if ( key.equals( "show_scale" ) ) {
1179 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1181 else if ( key.equals( "show_overview" ) ) {
1182 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1184 else if ( key.equals( "show_branch_length_values" ) ) {
1185 setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
1187 else if ( key.equals( "background_gradient" ) ) {
1188 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1190 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1191 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1193 else if ( key.equals( "show_domain_labels" ) ) {
1194 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1196 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1197 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1199 else if ( key.equals( "cladogram_type" ) ) {
1200 final String type_str = ( ( String ) st.nextElement() ).trim();
1201 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1202 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1204 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1205 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1207 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1208 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1211 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1212 + "] for [cladogram_type]" );
1215 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1217 .printWarningMessage( Constants.PRG_NAME,
1218 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1220 else if ( key.equals( "hide_controls_and_menus" ) ) {
1221 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1223 else if ( key.equals( "use_tabbed_display" ) ) {
1224 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1226 else if ( key.equals( "overview_width" ) ) {
1227 final short i = parseShort( ( ( String ) st.nextElement() ) );
1230 else if ( key.equals( "overview_height" ) ) {
1231 final short i = parseShort( ( ( String ) st.nextElement() ) );
1232 setOvMaxHeight( i );
1234 else if ( key.equals( "overview_placement_type" ) ) {
1235 final String type_str = ( ( String ) st.nextElement() ).trim();
1236 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1237 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1239 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1240 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1242 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1243 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1245 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1246 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1249 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1250 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1251 + "] for [overview_placement_type]" );
1254 else if ( key.equals( "node_label_direction" ) ) {
1255 final String type_str = ( ( String ) st.nextElement() ).trim();
1256 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1257 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1259 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1260 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1263 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1264 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1265 + "] for [node_label_direction]" );
1268 else if ( key.equals( "branch_length_value_digits" ) ) {
1269 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1271 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1274 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1275 + "] for [branch_length_value_digits]" );
1278 else if ( key.equals( "confidence_value_digits" ) ) {
1279 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1281 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1284 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1285 + "] for [confidence_value_digits]" );
1288 else if ( key.equals( "allow_editing" ) ) {
1289 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1291 else if ( key.equals( "display_sequence_relations" ) ) {
1292 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1294 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1295 final boolean r = parseBoolean( ( String ) st.nextElement() );
1296 if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
1298 .printWarningMessage( Constants.PRG_NAME,
1299 "attempt to extract taxonomies and replace underscores at the same time" );
1302 setReplaceUnderscoresInNhParsing( r );
1305 else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
1306 final String s = ( String ) st.nextElement();
1307 if ( s.equalsIgnoreCase( "no" ) ) {
1308 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1310 else if ( s.equalsIgnoreCase( "yes" ) ) {
1311 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1313 else if ( s.equalsIgnoreCase( "pfam" ) ) {
1314 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1317 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1318 "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + s );
1320 if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
1322 .printWarningMessage( Constants.PRG_NAME,
1323 "attempt to extract taxonomies and replace underscores at the same time" );
1326 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1327 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1329 else if ( key.equals( "gui_background_color" ) ) {
1330 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1332 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1333 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1335 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1336 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1338 else if ( key.equals( "gui_button_text_color" ) ) {
1339 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1341 else if ( key.equals( "gui_button_background_color" ) ) {
1342 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1344 else if ( key.equals( "gui_menu_background_color" ) ) {
1345 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1347 else if ( key.equals( "gui_menu_text_color" ) ) {
1348 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1350 else if ( key.equals( "gui_button_border_color" ) ) {
1351 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1353 else if ( key.equals( "domain_structure_font_color" ) ) {
1354 _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
1356 else if ( key.equals( "domain_structure_base_color" ) ) {
1357 _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
1359 else if ( key.equals( "show_default_node_shapes" ) ) {
1361 .printWarningMessage( Constants.PRG_NAME,
1362 "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" );
1363 final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() );
1364 setShowDefaultNodeShapesInternal( b );
1365 setShowDefaultNodeShapesExternal( b );
1367 else if ( key.equals( "show_default_node_shapes_internal" ) ) {
1368 setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1370 else if ( key.equals( "show_default_node_shapes_external" ) ) {
1371 setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1373 else if ( key.equals( "default_node_size" ) ) {
1374 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1375 setDefaultNodeShapeSize( i );
1377 else if ( key.equals( "default_node_fill" ) ) {
1378 final String fill_str = ( ( String ) st.nextElement() ).trim();
1379 if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.NONE.toString() ) ) {
1380 setDefaultNodeFill( NodeFill.NONE );
1382 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.GRADIENT.toString() ) ) {
1383 setDefaultNodeFill( NodeFill.GRADIENT );
1385 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.SOLID.toString() ) ) {
1386 setDefaultNodeFill( NodeFill.SOLID );
1389 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1390 + "] for [default_node_fill]" );
1393 else if ( key.equals( "default_node_shape" ) ) {
1394 final String shape_str = ( ( String ) st.nextElement() ).trim();
1395 if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.CIRCLE.toString() ) ) {
1396 setDefaultNodeShape( NodeShape.CIRCLE );
1398 else if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.RECTANGLE.toString() ) ) {
1399 setDefaultNodeShape( NodeShape.RECTANGLE );
1402 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1403 + "] for [default_node_shape]" );
1406 else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
1407 setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
1409 else if ( key.equals( "midpoint_reroot" ) ) {
1410 setMidpointReroot( 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
1710 public boolean isMidpointReroot() {
1711 return _midpoint_root;
1714 public void setMidpointReroot( final boolean midpoint_root ) {
1715 _midpoint_root = midpoint_root;