2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
7 // Copyright (C) 2000-2001 Washington University School of Medicine
8 // and Howard Hughes Medical Institute
9 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
10 // All rights reserved
12 // This library is free software; you can redistribute it and/or
13 // modify it under the terms of the GNU Lesser General Public
14 // License as published by the Free Software Foundation; either
15 // version 2.1 of the License, or (at your option) any later version.
17 // This library is distributed in the hope that it will be useful,
18 // but WITHOUT ANY WARRANTY; without even the implied warranty of
19 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20 // Lesser General Public License for more details.
22 // You should have received a copy of the GNU Lesser General Public
23 // License along with this library; if not, write to the Free Software
24 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
26 // Contact: phylosoft @ gmail . com
27 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
29 package org.forester.archaeopteryx;
31 import java.awt.Color;
32 import java.io.BufferedReader;
34 import java.io.FileReader;
35 import java.io.IOException;
36 import java.io.InputStreamReader;
37 import java.net.MalformedURLException;
39 import java.util.Arrays;
40 import java.util.Hashtable;
42 import java.util.SortedMap;
43 import java.util.StringTokenizer;
44 import java.util.TreeMap;
46 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
47 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
48 import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE;
49 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
50 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
51 import org.forester.phylogeny.data.NodeData.NODE_DATA;
52 import org.forester.phylogeny.data.NodeVisualization;
53 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
54 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
55 import org.forester.util.ForesterUtil;
57 public final class Configuration {
59 static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
60 private static final String WEB_LINK_KEY = "web_link";
61 private static final String DISPLAY_COLOR_KEY = "display_color";
62 private static final int DEPRECATED = -2;
63 private UI _ui = UI.UNKNOWN;
64 private boolean _use_tabbed_display = false;
65 private boolean _hide_controls_and_menus = false;
66 private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
67 private SortedMap<String, WebLink> _weblinks = null;
68 private SortedMap<String, Color> _display_colors = null;
69 private boolean _antialias_screen = true;
70 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
71 private String _base_font_family_name = "";
72 private int _base_font_size = -1;
73 private int _min_base_font_size = 2;
74 private int _max_base_font_size = 20;
75 private int _graphics_export_x = -1;
76 private int _graphics_export_y = -1;
77 private short _ov_max_width = 80;
78 private short _ov_max_height = 80;
79 private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
80 private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
81 private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
82 private boolean _show_scale = false;
83 private boolean _show_branch_length_values = false;
84 private boolean _show_overview = true;
85 private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
86 private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
87 private boolean _editable = true;
88 private boolean _nh_parsing_replace_underscores = false;
89 private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
90 private boolean _internal_number_are_confidence_for_nh_parsing = false;
91 private boolean _display_sequence_relations = false;
92 private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
93 private boolean _background_color_gradient = false;
94 private boolean _show_domain_labels = true;
95 private boolean _abbreviate_scientific_names = false;
96 private boolean _color_labels_same_as_parent_branch = false;
97 private boolean _show_default_node_shapes_internal = false;
98 private boolean _show_default_node_shapes_external = false;
99 private NodeShape _default_node_shape = NodeShape.CIRCLE;
100 private NodeFill _default_node_fill = NodeFill.GRADIENT;
101 private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
102 private boolean _taxonomy_colorize_node_shapes = false;
103 private int _default_bootstrap_samples = -1;
104 private File _path_to_local_mafft = null;
105 private File _path_to_local_fastme = null;
106 private File _path_to_local_raxml = null;
107 private File _path_to_local_clustalo = null;
108 final static int display_as_phylogram = 0;
109 final static int show_node_names = 1;
110 final static int show_tax_code = 2;
111 final static int show_annotation = 3;
112 final static int write_confidence_values = 4;
113 final static int write_events = 5;
114 final static int color_according_to_species = 6;
115 final static int color_branches = 7;
116 final static int width_branches = 8;
117 final static int show_custom_node_shapes = 9;
118 final static int show_domain_architectures = 10;
119 final static int show_binary_characters = 11;
120 final static int show_binary_character_counts = 12;
121 final static int show_gene_names = 13;
122 final static int show_sequence_acc = 14;
123 final static int display_internal_data = 15;
124 final static int dynamically_hide_data = 16;
125 final static int show_taxonomy_scientific_names = 17;
126 final static int show_taxonomy_common_names = 18;
127 final static int color_according_to_annotation = 19;
128 final static int show_gene_symbols = 20;
129 final static int node_data_popup = 21;
130 final static int show_relation_confidence = 22;
131 final static int show_vector_data = 23;
132 final static int show_taxonomy_images = 24;
133 final static int show_properties = 25;
134 // ------------------
136 // ------------------
137 final static int display_node_data = 0;
138 final static int collapse_uncollapse = 1;
139 final static int reroot = 2;
140 final static int subtree = 3;
141 final static int swap = 4;
142 final static int color_subtree = 5;
143 final static int open_seq_web = 6;
144 final static int open_tax_web = 7;
145 final static int blast = 8;
146 final static int cut_subtree = 9;
147 final static int copy_subtree = 10;
148 final static int paste_subtree = 11;
149 final static int delete_subtree_or_node = 12;
150 final static int add_new_node = 13;
151 final static int edit_node_data = 14;
152 final static int sort_descendents = 15;
153 final static int get_ext_desc_data = 16;
154 final static int select_nodes = 17;
155 // ---------------------------
156 // Display options for trees
157 // ---------------------------
158 // ---------------------------------
159 // Pertaining to the config itself
160 // ---------------------------------
161 // Full path to config (may be URL)
162 String config_filename;
163 String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
164 final static String display_options[][] = {
165 { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
166 { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" },
167 { "Node Events", "display", "?" }, { "Taxonomy Colorize", "display", "yes" },
168 { "Colorize Branches", "display", "no" }, { "Use Branch-Widths", "display", "no" },
169 { "Show Custom Nodes", "display", "yes" }, { "Domains", "nodisplay", "no" },
170 { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
171 { "Seq Name", "display", "yes" }, { "Seq Acc", "display", "no" },
172 { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
173 { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
174 { "Annotation Colorize", "nodisplay", "no" }, { "Seq Symbol", "display", "yes" },
175 { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
176 { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
177 { "Properties", "nodisplay", "no" } };
178 final static String clickto_options[][] = {
179 { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
180 { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
181 { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Blast", "display" },
182 { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" },
183 { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" },
184 { "Sort Descendants", "display" }, { "Return", "display" }, { "Select Node(s)", "display" } };
185 // This option is selected in the dropdown
186 int default_clickto = Configuration.display_node_data;
190 TreeColorSet tree_color_set;
194 TreeFontSet tree_font_set;
198 private static Hashtable<String, Color> _species_colors;
202 private static Hashtable<String, Color> _domain_colors;
206 private static Hashtable<String, Color> _annotation_colors;
207 boolean verbose = Constants.VERBOSE_DEFAULT;
208 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
209 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
210 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
211 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
212 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
213 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
214 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
215 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
216 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
217 private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
218 private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
219 private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
220 private String _label_for_get_ext_descendents_data = "";
221 private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
222 private int _frame_x_size;
223 private int _frame_y_size;
224 private static String DEFAULT_FONT_FAMILY = "";
226 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
227 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
228 DEFAULT_FONT_FAMILY = font_name;
232 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
233 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
237 public Configuration() {
238 this( null, false, false, false );
241 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
242 if ( ForesterUtil.isEmpty( cf ) ) {
243 config_filename = default_config_filename;
246 config_filename = cf;
248 setWebLinks( new TreeMap<String, WebLink>() );
249 setDisplayColors( new TreeMap<String, Color>() );
250 config_filename = config_filename.trim();
253 // If URL, open accordingly
255 u = new URL( config_filename );
257 final InputStreamReader isr = new InputStreamReader( u.openStream() );
258 final BufferedReader bf = new BufferedReader( isr );
261 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
262 + config_filename + "]" );
264 catch ( final Exception e ) {
265 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
266 + config_filename + "]: " + e.getLocalizedMessage() );
269 catch ( final Exception e ) {
270 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
271 + config_filename + "]" );
275 // Otherwise, open as a file
276 File f = new File( config_filename );
278 f = new File( config_filename + ".txt" );
280 if ( f.exists() && f.canRead() ) {
282 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
286 catch ( final Exception e ) {
288 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
289 + config_filename + "]: " + e );
295 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
296 + config_filename + "]" );
302 public String getBaseFontFamilyName() {
303 return _base_font_family_name;
306 public int getDefaultBootstrapSamples() {
307 return _default_bootstrap_samples;
310 public NodeFill getDefaultNodeFill() {
311 return _default_node_fill;
314 public NodeShape getDefaultNodeShape() {
315 return _default_node_shape;
318 public short getDefaultNodeShapeSize() {
319 return _default_node_shape_size;
322 public Color getDomainStructureBaseColor() {
323 return _domain_structure_base_color;
326 public Color getDomainStructureFontColor() {
327 return _domain_structure_font_color;
330 public NODE_DATA getExtDescNodeDataToReturn() {
331 return _ext_desc_data_to_return;
334 public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
335 return _ext_node_data_return_on;
338 public int getFrameXSize() {
339 return _frame_x_size;
342 public int getFrameYSize() {
343 return _frame_y_size;
346 public String getLabelForGetExtDescendentsData() {
347 return _label_for_get_ext_descendents_data;
350 public File getPathToLocalClustalOmega() {
351 return _path_to_local_clustalo;
354 public File getPathToLocalFastme() {
355 return _path_to_local_fastme;
358 public File getpathToLocalMafft() {
359 return _path_to_local_mafft;
362 public File getPathToLocalRaxml() {
363 return _path_to_local_raxml;
366 public boolean isAbbreviateScientificTaxonNames() {
367 return _abbreviate_scientific_names;
370 public boolean isBackgroundColorGradient() {
371 return _background_color_gradient;
374 public boolean isColorLabelsSameAsParentBranch() {
375 return _color_labels_same_as_parent_branch;
378 public boolean isShowDefaultNodeShapesExternal() {
379 return _show_default_node_shapes_external;
382 public boolean isShowDefaultNodeShapesInternal() {
383 return _show_default_node_shapes_internal;
386 public boolean isShowDomainLabels() {
387 return _show_domain_labels;
390 public boolean isTaxonomyColorizeNodeShapes() {
391 return _taxonomy_colorize_node_shapes;
394 public void putDisplayColors( final String key, final Color color ) {
395 getDisplayColors().put( key, color );
398 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
399 _abbreviate_scientific_names = abbreviate_scientific_names;
402 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
403 _background_color_gradient = background_color_gradient;
406 public void setBaseFontFamilyName( final String base_font_family_name ) {
407 _base_font_family_name = base_font_family_name;
410 public void setBaseFontSize( final int base_font_size ) {
411 _base_font_size = base_font_size;
414 private void setMaxBaseFontSize( final int max_base_font_size ) {
415 _max_base_font_size = max_base_font_size;
418 private void setMinBaseFontSize( final int min_base_font_size ) {
419 _min_base_font_size = min_base_font_size;
422 public void setColorizeBranches( final boolean b ) {
423 display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
426 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
427 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
430 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
431 _default_node_fill = default_node_fill;
434 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
435 _default_node_shape = default_node_shape;
438 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
439 _default_node_shape_size = default_node_shape_size;
442 public void setDisplayAsPhylogram( final boolean b ) {
443 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
446 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
447 _display_colors = display_colors;
450 public void setDisplayConfidenceValues( final boolean b ) {
451 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
454 public void setDisplayInternalData( final boolean b ) {
455 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
458 public void setDisplayNodeNames( final boolean b ) {
459 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
462 public void setDisplaySequenceAcc( final boolean b ) {
463 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
466 public void setDisplaySequenceNames( final boolean b ) {
467 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
470 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
471 _display_sequence_relations = display_sequence_relations;
474 public void setDisplaySequenceSymbols( final boolean b ) {
475 display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no";
478 public void setDisplayTaxonomyCode( final boolean b ) {
479 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
482 public void setDisplayTaxonomyCommonNames( final boolean b ) {
483 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
486 public void setDisplayTaxonomyImages( final boolean b ) {
487 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
490 public void setDisplayTaxonomyScientificNames( final boolean b ) {
491 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
494 public void setDynamicallyHideData( final boolean b ) {
495 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
498 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
499 _ext_desc_data_to_return = ext_desc_data_to_return;
502 public void setFrameXSize( final int frame_x_size ) {
503 _frame_x_size = frame_x_size;
506 public void setFrameYSize( final int frame_y_size ) {
507 _frame_y_size = frame_y_size;
510 public void setMinConfidenceValue( final double min_confidence_value ) {
511 _min_confidence_value = min_confidence_value;
514 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
515 _node_label_direction = node_label_direction;
518 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
519 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
522 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
523 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
526 public void setPathToLocalClustalOmega( final File path_to_local_clustalo ) {
527 _path_to_local_clustalo = path_to_local_clustalo;
530 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
531 _phylogeny_graphics_type = phylogeny_graphics_type;
534 public void setPrintLineWidth( final float print_line_width ) {
535 _print_line_width = print_line_width;
538 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
539 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
542 public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
543 _show_branch_length_values = show_branch_length_values;
546 public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
547 _show_default_node_shapes_external = show_default_node_shapes_external;
550 public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
551 _show_default_node_shapes_internal = show_default_node_shapes_internal;
554 public void setShowDomainLabels( final boolean show_domain_labels ) {
555 _show_domain_labels = show_domain_labels;
558 public void setShowScale( final boolean show_scale ) {
559 _show_scale = show_scale;
562 public void setTaxonomyColorize( final boolean b ) {
563 display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
566 public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
567 _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
570 public void setUseBranchesWidths( final boolean b ) {
571 display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
574 boolean displaySequenceRelations() {
575 return _display_sequence_relations;
578 boolean doCheckOption( final int which ) {
579 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
580 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
583 boolean doDisplayClickToOption( final int which ) {
584 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
587 boolean doDisplayOption( final int which ) {
588 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
592 * Will attempt to use the phylogeny to determine whether to check
593 * this or not (e.g. phylogram)
596 boolean doGuessCheckOption( final int which ) {
597 return display_options[ which ][ 2 ].equals( "?" );
600 Map<String, Color> getAnnotationColors() {
601 if ( _annotation_colors == null ) {
602 _annotation_colors = new Hashtable<String, Color>();
604 return _annotation_colors;
607 int getBaseFontSize() {
608 return _base_font_size;
611 int getMinBaseFontSize() {
612 return _min_base_font_size;
615 int getMaxBaseFontSize() {
616 return _max_base_font_size;
619 CLADOGRAM_TYPE getCladogramType() {
620 return _cladogram_type;
623 int getClickToOptionsCount() {
624 return clickto_options.length;
627 String getClickToTitle( final int which ) {
628 return clickto_options[ which ][ 0 ];
631 int getDefaultDisplayClicktoOption() {
632 return default_clickto;
635 SortedMap<String, Color> getDisplayColors() {
636 return _display_colors;
639 String getDisplayTitle( final int which ) {
640 return display_options[ which ][ 0 ];
643 Map<String, Color> getDomainColors() {
644 if ( _domain_colors == null ) {
645 _domain_colors = new Hashtable<String, Color>();
647 return _domain_colors;
650 int getGraphicsExportX() {
651 return _graphics_export_x;
654 int getGraphicsExportY() {
655 return _graphics_export_y;
658 Color getGuiBackgroundColor() {
659 return _gui_background_color;
662 Color getGuiButtonBackgroundColor() {
663 return _gui_button_background_color;
666 Color getGuiButtonBorderColor() {
667 return _gui_button_border_color;
670 Color getGuiButtonTextColor() {
671 return _gui_button_text_color;
674 Color getGuiCheckboxAndButtonActiveColor() {
675 return _gui_checkbox_and_button_active_color;
678 Color getGuiCheckboxTextColor() {
679 return _gui_checkbox_text_color;
682 Color getGuiMenuBackgroundColor() {
683 return _gui_menu_background_color;
686 Color getGuiMenuTextColor() {
687 return _gui_menu_text_color;
690 double getMinConfidenceValue() {
691 return _min_confidence_value;
694 NODE_LABEL_DIRECTION getNodeLabelDirection() {
695 return _node_label_direction;
698 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
699 return _number_of_digits_after_comma_for_branch_length_values;
702 short getNumberOfDigitsAfterCommaForConfidenceValues() {
703 return _number_of_digits_after_comma_for_confidence_values;
706 short getOvMaxHeight() {
707 return _ov_max_height;
710 short getOvMaxWidth() {
711 return _ov_max_width;
714 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
715 return _ov_placement;
718 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
719 return _phylogeny_graphics_type;
722 float getPrintLineWidth() {
723 return _print_line_width;
726 Hashtable<String, Color> getSpeciesColors() {
727 if ( _species_colors == null ) {
728 _species_colors = new Hashtable<String, Color>();
730 return _species_colors;
733 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
734 return _taxonomy_extraction;
737 WebLink getWebLink( final String source ) {
738 return getWebLinks().get( source );
741 Map<String, WebLink> getWebLinks() {
745 boolean isAntialiasScreen() {
746 return _antialias_screen;
750 * Convenience method.
752 * @return true if value in configuration file was 'yes'
754 boolean isDrawAsPhylogram() {
755 return doCheckOption( display_as_phylogram );
758 boolean isEditable() {
762 boolean isHasWebLink( final String source ) {
763 return getWebLinks().containsKey( source );
767 * Only used by ArchaeoptryxE.
770 boolean isHideControlPanelAndMenubar() {
771 return _hide_controls_and_menus;
774 boolean isInternalNumberAreConfidenceForNhParsing() {
775 return _internal_number_are_confidence_for_nh_parsing;
778 boolean isReplaceUnderscoresInNhParsing() {
779 return _nh_parsing_replace_underscores;
782 boolean isShowBranchLengthValues() {
783 return _show_branch_length_values;
786 boolean isShowOverview() {
787 return _show_overview;
790 boolean isShowScale() {
794 final boolean isUseNativeUI() {
795 if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) {
798 return _ui == UI.NATIVE;
802 * Only used by ArchaeoptryxE.
805 boolean isUseTabbedDisplay() {
806 return _use_tabbed_display;
809 boolean isValidatePhyloXmlAgainstSchema() {
810 return _validate_against_phyloxml_xsd_schema;
813 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
814 _taxonomy_extraction = taxonomy_extraction;
817 void setWebLinks( final SortedMap<String, WebLink> weblinks ) {
818 _weblinks = weblinks;
821 private void createWebLink( final String url_str, final String desc, final String source_identifier ) {
822 WebLink weblink = null;
825 weblink = new WebLink( new URL( url_str.trim() ), desc.trim(), source_identifier.trim() );
827 catch ( final MalformedURLException e ) {
828 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not create URL from [" + url_str + "]" );
831 if ( !ex && ( weblink != null ) ) {
832 getWebLinks().put( weblink.getSourceIdentifier().toLowerCase(), weblink );
836 private int getClickToIndex( final String name ) {
838 if ( name.equals( "edit_info" ) ) {
839 index = Configuration.display_node_data;
841 .printWarningMessage( Constants.PRG_NAME,
842 "configuration key [edit_info] is deprecated, use [display node data] instead" );
844 else if ( name.equals( "display_node_data" ) ) {
845 index = Configuration.display_node_data;
847 else if ( name.equals( "collapse_uncollapse" ) ) {
848 index = Configuration.collapse_uncollapse;
850 else if ( name.equals( "reroot" ) ) {
851 index = Configuration.reroot;
853 else if ( name.equals( "subtree" ) ) {
854 index = Configuration.subtree;
856 else if ( name.equals( "swap" ) ) {
857 index = Configuration.swap;
859 else if ( name.equals( "sort_descendants" ) ) {
860 index = Configuration.sort_descendents;
862 else if ( name.equals( "get_ext_descendents_data" ) ) {
863 index = Configuration.get_ext_desc_data;
865 else if ( name.equals( "display_sequences" ) ) {
867 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
870 else if ( name.equals( "open_seq_web" ) ) {
871 index = Configuration.open_seq_web;
873 else if ( name.equals( "open_tax_web" ) ) {
874 index = Configuration.open_tax_web;
876 else if ( name.equals( "blast" ) ) {
877 index = Configuration.blast;
879 else if ( name.equals( "cut_subtree" ) ) {
880 index = Configuration.cut_subtree;
882 else if ( name.equals( "copy_subtree" ) ) {
883 index = Configuration.copy_subtree;
885 else if ( name.equals( "paste_subtree" ) ) {
886 index = Configuration.paste_subtree;
888 else if ( name.equals( "delete" ) ) {
889 index = Configuration.delete_subtree_or_node;
891 else if ( name.equals( "add_new_node" ) ) {
892 index = Configuration.add_new_node;
894 else if ( name.equals( "edit_node_data" ) ) {
895 index = Configuration.edit_node_data;
897 else if ( name.equals( "select_nodes" ) ) {
898 index = Configuration.select_nodes;
900 else if ( name.equals( "display_node_popup" ) ) {
901 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
902 "configuration key [display_node_popup] is deprecated" );
905 else if ( name.equals( "custom_option" ) ) {
906 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
909 else if ( name.equals( "color_subtree" ) ) {
910 index = Configuration.color_subtree;
912 else if ( name.equals( "go_to_swiss_prot" ) ) {
913 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" );
919 private boolean parseBoolean( final String str ) {
920 final String my_str = str.trim().toLowerCase();
921 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
924 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
928 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
933 private double parseDouble( final String str ) {
936 d = Double.parseDouble( str.trim() );
938 catch ( final Exception e ) {
939 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
945 private float parseFloat( final String str ) {
948 f = Float.parseFloat( str.trim() );
950 catch ( final Exception e ) {
951 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
957 private int parseInt( final String str ) {
960 i = Integer.parseInt( str.trim() );
962 catch ( final Exception e ) {
963 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
969 private short parseShort( final String str ) {
972 i = Short.parseShort( str.trim() );
974 catch ( final Exception e ) {
975 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
981 private void processFontFamily( final StringTokenizer st ) {
982 setBaseFontFamilyName( "" );
983 final String font_str = ( ( String ) st.nextElement() ).trim();
984 final String[] fonts = font_str.split( ",+" );
985 for( String font : fonts ) {
986 font = font.replace( '_', ' ' ).trim();
987 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
988 setBaseFontFamilyName( font );
995 * read each line of config file, process non-comment lines
996 * @throws IOException
998 private void readConfig( final BufferedReader conf_in ) throws IOException {
1001 line = conf_in.readLine();
1002 if ( line != null ) {
1004 // skip comments and blank lines
1005 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
1006 // convert runs of spaces to tabs
1007 line = line.replaceAll( "\\s+", "\t" );
1008 final StringTokenizer st = new StringTokenizer( line, "\t" );
1012 } while ( line != null );
1015 private void setAntialiasScreen( final boolean antialias_screen ) {
1016 _antialias_screen = antialias_screen;
1019 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
1020 _cladogram_type = cladogram_type;
1023 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
1024 _default_bootstrap_samples = default_bootstrap_samples;
1027 private void setEditable( final boolean editable ) {
1028 _editable = editable;
1031 private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
1032 _ext_node_data_return_on = ext_node_data_return_on;
1035 private void setGraphicsExportX( final int graphics_export_x ) {
1036 _graphics_export_x = graphics_export_x;
1039 private void setGraphicsExportY( final int graphics_export_y ) {
1040 _graphics_export_y = graphics_export_y;
1043 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
1044 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
1048 * Set a key-value(s) tuple
1050 private void setKeyValue( final StringTokenizer st ) {
1051 final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
1052 if ( !st.hasMoreElements() ) {
1055 // Handle single value settings first:
1056 if ( key.equals( "default_click_to" ) ) {
1057 final String clickto_name = ( String ) st.nextElement();
1058 default_clickto = getClickToIndex( clickto_name );
1059 if ( default_clickto == -1 ) {
1060 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
1061 + "] for [default_click_to]" );
1062 default_clickto = 0;
1064 else if ( default_clickto == DEPRECATED ) {
1068 else if ( key.equals( "native_ui" ) ) {
1069 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
1070 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
1073 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
1074 _ui = UI.CROSSPLATFORM;
1076 else if ( my_str.equals( "?" ) ) {
1080 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
1085 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
1086 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
1088 else if ( key.equals( "antialias_screen" ) ) {
1089 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
1091 else if ( key.equals( "phylogeny_graphics_type" ) ) {
1092 final String type_str = ( ( String ) st.nextElement() ).trim();
1093 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
1094 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1096 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
1097 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1099 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
1100 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1102 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
1103 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1105 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
1106 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1108 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
1109 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1111 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
1112 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1114 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
1115 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1118 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1119 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1120 + "] for [phylogeny_graphics_type]" );
1123 else if ( key.equals( "min_confidence_value" ) ) {
1124 final String mcv_str = ( ( String ) st.nextElement() ).trim();
1125 final double d = parseDouble( mcv_str );
1126 setMinConfidenceValue( d );
1128 else if ( key.equals( "font_family" ) ) {
1129 processFontFamily( st );
1131 else if ( key.equals( "font_size" ) ) {
1132 final String size_str = ( ( String ) st.nextElement() ).trim();
1133 final int i = parseInt( size_str );
1135 setBaseFontSize( i );
1138 else if ( key.equals( "font_size_min" ) ) {
1139 final String size_str = ( ( String ) st.nextElement() ).trim();
1140 final int i = parseInt( size_str );
1142 setMinBaseFontSize( i );
1145 else if ( key.equals( "font_size_max" ) ) {
1146 final String size_str = ( ( String ) st.nextElement() ).trim();
1147 final int i = parseInt( size_str );
1149 setMaxBaseFontSize( i );
1152 else if ( key.equals( "graphics_export_x" ) ) {
1153 final String str = ( ( String ) st.nextElement() ).trim();
1154 final int i = parseInt( str );
1156 setGraphicsExportX( i );
1159 else if ( key.equals( "graphics_export_y" ) ) {
1160 final String str = ( ( String ) st.nextElement() ).trim();
1161 final int i = parseInt( str );
1163 setGraphicsExportY( i );
1166 else if ( key.equals( "pdf_export_line_width" ) ) {
1167 final String str = ( ( String ) st.nextElement() ).trim();
1168 final float f = parseFloat( str );
1170 setPrintLineWidth( f );
1173 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1174 "value for [pdf_export_line_width] cannot be zero or negative" );
1177 else if ( key.equals( "window_initial_size_x" ) ) {
1178 final String str = ( ( String ) st.nextElement() ).trim();
1179 final int i = parseInt( str );
1184 else if ( key.equals( "window_initial_size_y" ) ) {
1185 final String str = ( ( String ) st.nextElement() ).trim();
1186 final int i = parseInt( str );
1191 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1192 final String str = ( ( String ) st.nextElement() ).trim();
1193 final int i = parseInt( str );
1195 setDefaultBootstrapSamples( i );
1199 .printWarningMessage( Constants.PRG_NAME,
1200 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1203 else if ( key.equals( "clustalo_local" ) ) {
1204 final String str = ( ( String ) st.nextElement() ).trim();
1205 if ( !ForesterUtil.isEmpty( str ) ) {
1206 setPathToLocalClustalOmega( new File( str ) );
1209 else if ( key.equals( "mafft_local" ) ) {
1210 final String str = ( ( String ) st.nextElement() ).trim();
1211 if ( !ForesterUtil.isEmpty( str ) ) {
1212 setPathToLocalMafft( new File( str ) );
1215 else if ( key.equals( "fastme_local" ) ) {
1216 final String str = ( ( String ) st.nextElement() ).trim();
1217 if ( !ForesterUtil.isEmpty( str ) ) {
1218 setPathToLocalFastme( new File( str ) );
1221 else if ( key.equals( "raxml_local" ) ) {
1222 final String str = ( ( String ) st.nextElement() ).trim();
1223 if ( !ForesterUtil.isEmpty( str ) ) {
1224 setPathToLocalRaxml( new File( str ) );
1227 else if ( key.equals( "show_scale" ) ) {
1228 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1230 else if ( key.equals( "show_overview" ) ) {
1231 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1233 else if ( key.equals( "show_branch_length_values" ) ) {
1234 setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
1236 else if ( key.equals( "background_gradient" ) ) {
1237 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1239 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1240 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1242 else if ( key.equals( "show_domain_labels" ) ) {
1243 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1245 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1246 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1248 else if ( key.equals( "cladogram_type" ) ) {
1249 final String type_str = ( ( String ) st.nextElement() ).trim();
1250 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1251 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1253 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1254 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1256 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1257 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1260 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1261 + "] for [cladogram_type]" );
1264 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1266 .printWarningMessage( Constants.PRG_NAME,
1267 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1269 else if ( key.equals( "hide_controls_and_menus" ) ) {
1270 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1272 else if ( key.equals( "use_tabbed_display" ) ) {
1273 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1275 else if ( key.equals( "overview_width" ) ) {
1276 final short i = parseShort( ( ( String ) st.nextElement() ) );
1279 else if ( key.equals( "overview_height" ) ) {
1280 final short i = parseShort( ( ( String ) st.nextElement() ) );
1281 setOvMaxHeight( i );
1283 else if ( key.equals( "overview_placement_type" ) ) {
1284 final String type_str = ( ( String ) st.nextElement() ).trim();
1285 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1286 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1288 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1289 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1291 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1292 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1294 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1295 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1298 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1299 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1300 + "] for [overview_placement_type]" );
1303 else if ( key.equals( "node_label_direction" ) ) {
1304 final String type_str = ( ( String ) st.nextElement() ).trim();
1305 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1306 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1308 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1309 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1312 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1313 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1314 + "] for [node_label_direction]" );
1317 else if ( key.equals( "branch_length_value_digits" ) ) {
1318 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1320 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1323 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1324 + "] for [branch_length_value_digits]" );
1327 else if ( key.equals( "confidence_value_digits" ) ) {
1328 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1330 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1333 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1334 + "] for [confidence_value_digits]" );
1337 else if ( key.equals( "allow_editing" ) ) {
1338 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1340 else if ( key.equals( "display_sequence_relations" ) ) {
1341 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1343 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1344 final boolean r = parseBoolean( ( String ) st.nextElement() );
1345 if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
1347 .printWarningMessage( Constants.PRG_NAME,
1348 "attempt to extract taxonomies and replace underscores at the same time" );
1351 setReplaceUnderscoresInNhParsing( r );
1354 else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
1355 final String s = ( String ) st.nextElement();
1356 if ( s.equalsIgnoreCase( "no" ) ) {
1357 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1359 else if ( s.equalsIgnoreCase( "yes" ) ) {
1360 setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES );
1362 else if ( s.equalsIgnoreCase( "pfam" ) ) {
1363 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
1366 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1367 "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + s );
1369 if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
1371 .printWarningMessage( Constants.PRG_NAME,
1372 "attempt to extract taxonomies and replace underscores at the same time" );
1375 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1376 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1378 else if ( key.equals( "gui_background_color" ) ) {
1379 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1381 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1382 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1384 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1385 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1387 else if ( key.equals( "gui_button_text_color" ) ) {
1388 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1390 else if ( key.equals( "gui_button_background_color" ) ) {
1391 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1393 else if ( key.equals( "gui_menu_background_color" ) ) {
1394 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1396 else if ( key.equals( "gui_menu_text_color" ) ) {
1397 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1399 else if ( key.equals( "gui_button_border_color" ) ) {
1400 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1402 else if ( key.equals( "domain_structure_font_color" ) ) {
1403 _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
1405 else if ( key.equals( "domain_structure_base_color" ) ) {
1406 _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
1408 else if ( key.equals( "show_default_node_shapes" ) ) {
1410 .printWarningMessage( Constants.PRG_NAME,
1411 "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" );
1412 final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() );
1413 setShowDefaultNodeShapesInternal( b );
1414 setShowDefaultNodeShapesExternal( b );
1416 else if ( key.equals( "show_default_node_shapes_internal" ) ) {
1417 setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1419 else if ( key.equals( "show_default_node_shapes_external" ) ) {
1420 setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1422 else if ( key.equals( "default_node_size" ) ) {
1423 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1424 setDefaultNodeShapeSize( i );
1426 else if ( key.equals( "default_node_fill" ) ) {
1427 final String fill_str = ( ( String ) st.nextElement() ).trim();
1428 if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.NONE.toString() ) ) {
1429 setDefaultNodeFill( NodeFill.NONE );
1431 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.GRADIENT.toString() ) ) {
1432 setDefaultNodeFill( NodeFill.GRADIENT );
1434 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.SOLID.toString() ) ) {
1435 setDefaultNodeFill( NodeFill.SOLID );
1438 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1439 + "] for [default_node_fill]" );
1442 else if ( key.equals( "default_node_shape" ) ) {
1443 final String shape_str = ( ( String ) st.nextElement() ).trim();
1444 if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.CIRCLE.toString() ) ) {
1445 setDefaultNodeShape( NodeShape.CIRCLE );
1447 else if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.RECTANGLE.toString() ) ) {
1448 setDefaultNodeShape( NodeShape.RECTANGLE );
1451 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1452 + "] for [default_node_shape]" );
1455 else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
1456 setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
1458 else if ( key.equals( "ext_descendents_data_to_return" ) ) {
1459 final String s = ( ( String ) st.nextElement() ).trim();
1460 if ( s.equalsIgnoreCase( "node_name" ) ) {
1461 setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
1463 else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
1464 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
1466 else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
1467 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
1469 else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
1470 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
1472 else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
1473 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
1475 else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
1476 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME );
1478 else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
1479 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
1481 else if ( s.equalsIgnoreCase( "user_selected" ) ) {
1482 setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
1485 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1486 + "] for [ext_descendents_data_to_return]" );
1489 else if ( key.equals( "label_for_get_ext_descendents_data" ) ) {
1490 final String s = ( ( String ) st.nextElement() ).trim();
1491 if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) {
1492 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s
1493 + "] for [label_for_get_ext_descendents_data]" );
1496 setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
1499 else if ( key.equals( "ext_descendents_data_to_return_on" ) ) {
1500 final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
1501 if ( s.equals( "console" ) ) {
1502 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
1504 else if ( s.equals( "window" ) ) {
1505 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
1507 else if ( s.equals( "buffer_only" ) ) {
1508 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
1511 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1512 + "] for [ext_descendents_data_to_return_on]" );
1515 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1518 if ( key.equals( "use_real_br_lengths" ) || key.equals( "phylogram" ) ) {
1519 key_index = Configuration.display_as_phylogram;
1520 if ( key.equals( "use_real_br_lengths" ) ) {
1522 .printWarningMessage( Constants.PRG_NAME,
1523 "configuration key [use_real_br_lengths] is deprecated, use [phylogram] instead" );
1526 else if ( key.equals( "rollover" ) ) {
1527 key_index = Configuration.node_data_popup;
1529 else if ( key.equals( "color_according_to_species" ) ) {
1530 key_index = Configuration.color_according_to_species;
1532 else if ( key.equals( "show_node_names" ) ) {
1533 key_index = Configuration.show_node_names;
1535 else if ( key.equals( "show_taxonomy" ) || key.equals( "show_taxonomy_code" ) ) {
1536 key_index = Configuration.show_tax_code;
1537 if ( key.equals( "show_taxonomy" ) ) {
1539 .printWarningMessage( Constants.PRG_NAME,
1540 "configuration key [show_taxonomy] is deprecated, use [show_taxonomy_code] instead" );
1543 else if ( key.equals( "write_br_length_values" ) ) {
1544 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1545 "configuration key [write_br_length_values] is deprecated" );
1546 key_index = DEPRECATED;
1548 else if ( key.equals( "write_bootstrap_values" ) || key.equals( "write_confidence_values" ) ) {
1549 key_index = Configuration.write_confidence_values;
1550 if ( key.equals( "write_bootstrap_values" ) ) {
1552 .printWarningMessage( Constants.PRG_NAME,
1553 "configuration key [write_bootstrap_values] is deprecated, use [write_confidence_values] instead" );
1556 else if ( key.equals( "write_events" ) || key.equals( "write_dup_spec" ) ) {
1557 key_index = Configuration.write_events;
1558 if ( key.equals( "write_dup_spec" ) ) {
1560 .printWarningMessage( Constants.PRG_NAME,
1561 "configuration key [write_dup_spec] is deprecated, use [write_events] instead" );
1564 else if ( key.equals( "color_branches" ) ) {
1565 key_index = Configuration.color_branches;
1567 else if ( key.equals( "width_branches" ) ) {
1568 key_index = Configuration.width_branches;
1570 else if ( key.equals( "color_orthologous" ) ) {
1571 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1572 "configuration key [color_orthologous] is deprecated" );
1574 else if ( key.equals( "color_subtree_neighbors" ) ) {
1575 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1576 "configuration key [color_subtree_neighbors] is deprecated" );
1578 else if ( key.equals( "color_super_orthologous" ) ) {
1579 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1580 "configuration key [color_super_orthologous] is deprecated" );
1582 else if ( key.equals( "mark_nodes_with_box" ) ) {
1583 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1584 "configuration key [mark_nodes_with_box] is deprecated" );
1585 key_index = DEPRECATED;
1587 else if ( key.equals( "show_domain_architectures" ) ) {
1588 key_index = Configuration.show_domain_architectures;
1590 else if ( key.equals( "show_annotations" ) ) {
1591 key_index = Configuration.show_annotation;
1593 else if ( key.equals( "show_binary_characters" ) ) {
1594 key_index = Configuration.show_binary_characters;
1596 else if ( key.equals( "show_binary_character_counts" ) ) {
1597 key_index = Configuration.show_binary_character_counts;
1599 else if ( key.equals( "show_gene_names" ) ) {
1600 key_index = Configuration.show_gene_names;
1602 else if ( key.equals( "show_gene_symbols" ) ) {
1603 key_index = Configuration.show_gene_symbols;
1605 else if ( key.equals( "show_sequence_acc" ) ) {
1606 key_index = Configuration.show_sequence_acc;
1608 else if ( key.equals( "show_node_ids" ) ) {
1610 .printWarningMessage( Constants.PRG_NAME, "configuration key [show_node_ids] is deprecated" );
1611 key_index = DEPRECATED;
1613 else if ( key.equals( "display_internal_data" ) ) {
1614 key_index = Configuration.display_internal_data;
1616 else if ( key.equals( "dynamically_hide_data" ) ) {
1617 key_index = Configuration.dynamically_hide_data;
1619 else if ( key.equals( "show_taxonomy_names" ) ) {
1620 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1621 "configuration key [show_taxonomy_names] is deprecated" );
1622 key_index = DEPRECATED;
1624 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1625 key_index = Configuration.show_taxonomy_scientific_names;
1627 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1628 key_index = Configuration.show_taxonomy_common_names;
1630 else if ( key.equals( "show_taxonomy_images" ) ) {
1631 key_index = Configuration.show_taxonomy_images;
1633 else if ( key.equals( "color_according_to_annotation" ) ) {
1634 key_index = Configuration.color_according_to_annotation;
1636 else if ( key.equals( "show_vector_data" ) ) {
1637 key_index = Configuration.show_vector_data;
1639 else if ( key.equals( "show_properties" ) ) {
1640 key_index = Configuration.show_properties;
1642 else if ( key.equals( "show_relation_confidence" ) ) {
1643 key_index = Configuration.show_relation_confidence;
1645 else if ( key.equals( "show_custom_node_shapes" ) ) {
1646 key_index = Configuration.show_custom_node_shapes;
1648 // If we've found the key, set the values
1649 if ( key_index >= 0 ) {
1650 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1651 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1652 // otherwise, keep looking
1655 if ( key_index == DEPRECATED ) {
1658 else if ( key.equals( "click_to" ) ) {
1659 final String click_to_name = ( String ) st.nextElement();
1660 key_index = getClickToIndex( click_to_name );
1661 if ( key_index >= 0 ) {
1662 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1664 else if ( key_index == DEPRECATED ) {
1668 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1672 else if ( key.equals( "species_color" ) ) {
1673 getSpeciesColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1675 else if ( key.equals( "domain_color" ) ) {
1676 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1678 else if ( key.equals( "annotation_color" ) ) {
1679 getAnnotationColors()
1680 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1682 else if ( key.equals( "function_color" ) ) {
1683 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1684 "configuration key [function_color] is deprecated" );
1686 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1687 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1689 else if ( key.equals( WEB_LINK_KEY ) ) {
1690 if ( st.countTokens() == 3 ) {
1691 createWebLink( ( String ) st.nextElement(),
1692 ( String ) st.nextElement(),
1693 ( String ) st.nextElement() );
1696 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1697 "illegal format in configuration file for key [" + key + "]" );
1701 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1702 + "] in: " + config_filename );
1707 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1708 + config_filename );
1712 private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
1713 _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
1716 private void setOvMaxHeight( final short ov_max_height ) {
1717 _ov_max_height = ov_max_height;
1720 private void setOvMaxWidth( final short ov_max_width ) {
1721 _ov_max_width = ov_max_width;
1724 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1725 _ov_placement = ov_placement;
1728 private void setPathToLocalFastme( final File path_to_local_fastme ) {
1729 _path_to_local_fastme = path_to_local_fastme;
1732 private void setPathToLocalMafft( final File path_to_local_mafft ) {
1733 _path_to_local_mafft = path_to_local_mafft;
1736 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
1737 _path_to_local_raxml = path_to_local_raxml;
1740 private void setShowOverview( final boolean show_overview ) {
1741 _show_overview = show_overview;
1744 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1745 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1748 static String getDefaultFontFamilyName() {
1749 return DEFAULT_FONT_FAMILY;
1752 public enum EXT_NODE_DATA_RETURN_ON {
1753 CONSOLE, WINODW, BUFFER_ONLY;
1757 NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN
1760 static enum TRIPLET {
1761 TRUE, FALSE, UNKNOWN