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.NO;
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 _show_annotation_ref_source = true;
93 private boolean _abbreviate_scientific_names = false;
94 private boolean _color_labels_same_as_parent_branch = false;
95 private boolean _show_default_node_shapes_internal = false;
96 private boolean _show_default_node_shapes_external = false;
97 private NodeShape _default_node_shape = NodeShape.RECTANGLE;
98 private NodeFill _default_node_fill = NodeFill.SOLID;
99 private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
100 private boolean _taxonomy_colorize_node_shapes = false;
101 private int _default_bootstrap_samples = -1;
102 private File _path_to_local_mafft = null;
103 private File _path_to_local_fastme = null;
104 private File _path_to_local_raxml = null;
105 final static int display_as_phylogram = 0;
106 final static int show_node_names = 1;
107 final static int show_tax_code = 2;
108 final static int show_annotation = 3;
109 final static int write_confidence_values = 4;
110 final static int write_events = 5;
111 final static int color_according_to_species = 6;
112 final static int color_branches = 7;
113 final static int width_branches = 8;
114 final static int show_custom_node_shapes = 9;
115 final static int show_domain_architectures = 10;
116 final static int show_binary_characters = 11;
117 final static int show_binary_character_counts = 12;
118 final static int show_seq_names = 13;
119 final static int show_sequence_acc = 14;
120 final static int display_internal_data = 15;
121 final static int dynamically_hide_data = 16;
122 final static int show_taxonomy_scientific_names = 17;
123 final static int show_taxonomy_common_names = 18;
124 final static int color_according_to_annotation = 19;
125 final static int show_seq_symbols = 20;
126 final static int node_data_popup = 21;
127 final static int show_relation_confidence = 22;
128 final static int show_vector_data = 23;
129 final static int show_taxonomy_images = 24;
130 final static int show_properties = 25;
131 final static int show_gene_names = 26;
132 // ------------------
134 // ------------------
135 final static int display_node_data = 0;
136 final static int collapse_uncollapse = 1;
137 final static int reroot = 2;
138 final static int subtree = 3;
139 final static int swap = 4;
140 final static int color_subtree = 5;
141 final static int open_seq_web = 6;
142 final static int open_tax_web = 7;
143 final static int blast = 8;
144 final static int cut_subtree = 9;
145 final static int copy_subtree = 10;
146 final static int paste_subtree = 11;
147 final static int delete_subtree_or_node = 12;
148 final static int add_new_node = 13;
149 final static int edit_node_data = 14;
150 final static int sort_descendents = 15;
151 final static int get_ext_desc_data = 16;
152 final static int select_nodes = 17;
153 // ---------------------------
154 // Display options for trees
155 // ---------------------------
156 // ---------------------------------
157 // Pertaining to the config itself
158 // ---------------------------------
159 // Full path to config (may be URL)
160 String config_filename;
161 String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
162 final static String display_options[][] = {
163 { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
164 { "Seq Annotations", "nodisplay", "no" }, { "Confidence Values", "display", "?" },
165 { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "yes" },
166 { "Use Branch Colors", "display", "no" }, { "Use Branch Widths", "display", "no" },
167 { "Show Custom Nodes", "display", "yes" }, { "Protein Domains", "nodisplay", "no" },
168 { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
169 { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" },
170 { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
171 { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
172 { "Colorize by Annotation", "nodisplay", "no" }, { "Seq Symbol", "display", "yes" },
173 { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
174 { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
175 { "Properties", "nodisplay", "no" }, { "Gene Name", "display", "yes" } };
176 final static String clickto_options[][] = {
177 { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
178 { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" },
179 { "Colorize Subtree/Node(s)", "display" }, { "Open Sequence DB", "display" },
180 { "Open Taxonomy DB", "display" }, { "Blast", "display" }, { "Cut Subtree", "display" },
181 { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" },
182 { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Sort Descendants", "display" },
183 { "Return", "display" }, { "Select Node(s)", "display" } };
184 // This option is selected in the dropdown
185 int default_clickto = Configuration.display_node_data;
189 TreeColorSet tree_color_set;
193 TreeFontSet tree_font_set;
197 private static Hashtable<String, Color> _species_colors;
201 private static Hashtable<String, Color> _domain_colors;
205 private static Hashtable<String, Color> _annotation_colors;
206 boolean verbose = Constants.VERBOSE_DEFAULT;
207 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
208 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
209 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
210 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
211 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
212 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
213 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
214 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
215 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
216 private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
217 private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
218 private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
219 private String _label_for_get_ext_descendents_data = "";
220 private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
221 private int _frame_x_size;
222 private int _frame_y_size;
223 private boolean _midpoint_root = false;
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 setDisplayColors( new TreeMap<String, Color>() );
249 config_filename = config_filename.trim();
252 // If URL, open accordingly
254 u = new URL( config_filename );
256 final InputStreamReader isr = new InputStreamReader( u.openStream() );
257 final BufferedReader bf = new BufferedReader( isr );
260 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
261 + config_filename + "]" );
263 catch ( final Exception e ) {
264 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
265 + config_filename + "]: " + e.getLocalizedMessage() );
268 catch ( final Exception e ) {
269 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
270 + config_filename + "]" );
274 // Otherwise, open as a file
275 File f = new File( config_filename );
277 f = new File( config_filename + ".txt" );
279 if ( f.exists() && f.canRead() ) {
281 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
285 catch ( final Exception e ) {
287 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
288 + config_filename + "]: " + e );
294 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
295 + config_filename + "]" );
301 public String getBaseFontFamilyName() {
302 return _base_font_family_name;
305 public int getDefaultBootstrapSamples() {
306 return _default_bootstrap_samples;
309 public NodeFill getDefaultNodeFill() {
310 return _default_node_fill;
313 public NodeShape getDefaultNodeShape() {
314 return _default_node_shape;
317 public short getDefaultNodeShapeSize() {
318 return _default_node_shape_size;
321 public Color getDomainStructureBaseColor() {
322 return _domain_structure_base_color;
325 public Color getDomainStructureFontColor() {
326 return _domain_structure_font_color;
329 public NODE_DATA getExtDescNodeDataToReturn() {
330 return _ext_desc_data_to_return;
333 public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
334 return _ext_node_data_return_on;
337 public int getFrameXSize() {
338 return _frame_x_size;
341 public int getFrameYSize() {
342 return _frame_y_size;
345 public String getLabelForGetExtDescendentsData() {
346 return _label_for_get_ext_descendents_data;
349 public File getPathToLocalFastme() {
350 return _path_to_local_fastme;
353 public File getpathToLocalMafft() {
354 return _path_to_local_mafft;
357 public File getPathToLocalRaxml() {
358 return _path_to_local_raxml;
361 public boolean isAbbreviateScientificTaxonNames() {
362 return _abbreviate_scientific_names;
365 public boolean isBackgroundColorGradient() {
366 return _background_color_gradient;
369 public boolean isColorLabelsSameAsParentBranch() {
370 return _color_labels_same_as_parent_branch;
373 public boolean isShowDefaultNodeShapesExternal() {
374 return _show_default_node_shapes_external;
377 public boolean isShowDefaultNodeShapesInternal() {
378 return _show_default_node_shapes_internal;
381 public boolean isShowDomainLabels() {
382 return _show_domain_labels;
385 public boolean isTaxonomyColorizeNodeShapes() {
386 return _taxonomy_colorize_node_shapes;
389 public void putDisplayColors( final String key, final Color color ) {
390 getDisplayColors().put( key, color );
393 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
394 _abbreviate_scientific_names = abbreviate_scientific_names;
397 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
398 _background_color_gradient = background_color_gradient;
401 public void setBaseFontFamilyName( final String base_font_family_name ) {
402 _base_font_family_name = base_font_family_name;
405 public void setBaseFontSize( final int base_font_size ) {
406 _base_font_size = base_font_size;
409 private void setMaxBaseFontSize( final int max_base_font_size ) {
410 _max_base_font_size = max_base_font_size;
413 private void setMinBaseFontSize( final int min_base_font_size ) {
414 _min_base_font_size = min_base_font_size;
417 public void setColorizeBranches( final boolean b ) {
418 display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
421 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
422 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
425 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
426 _default_node_fill = default_node_fill;
429 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
430 _default_node_shape = default_node_shape;
433 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
434 _default_node_shape_size = default_node_shape_size;
437 public void setDisplayAsPhylogram( final boolean b ) {
438 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
441 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
442 _display_colors = display_colors;
445 public void setDisplayConfidenceValues( final boolean b ) {
446 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
449 public void setDisplayInternalData( final boolean b ) {
450 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
453 public void setDisplayNodeNames( final boolean b ) {
454 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
457 public void setDisplaySequenceAcc( final boolean b ) {
458 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
461 public void setDisplaySequenceNames( final boolean b ) {
462 display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no";
465 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
466 _display_sequence_relations = display_sequence_relations;
469 public void setDisplaySequenceSymbols( final boolean b ) {
470 display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no";
473 public void setDisplayTaxonomyCode( final boolean b ) {
474 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
477 public void setDisplayTaxonomyCommonNames( final boolean b ) {
478 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
481 public void setDisplayTaxonomyImages( final boolean b ) {
482 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
485 public void setDisplayTaxonomyScientificNames( final boolean b ) {
486 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
489 public void setDynamicallyHideData( final boolean b ) {
490 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
493 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
494 _ext_desc_data_to_return = ext_desc_data_to_return;
497 public void setFrameXSize( final int frame_x_size ) {
498 _frame_x_size = frame_x_size;
501 public void setFrameYSize( final int frame_y_size ) {
502 _frame_y_size = frame_y_size;
505 public void setMinConfidenceValue( final double min_confidence_value ) {
506 _min_confidence_value = min_confidence_value;
509 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
510 _node_label_direction = node_label_direction;
513 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
514 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
517 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
518 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
521 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
522 _phylogeny_graphics_type = phylogeny_graphics_type;
525 public void setPrintLineWidth( final float print_line_width ) {
526 _print_line_width = print_line_width;
529 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
530 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
533 public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
534 _show_branch_length_values = show_branch_length_values;
537 public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
538 _show_default_node_shapes_external = show_default_node_shapes_external;
541 public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
542 _show_default_node_shapes_internal = show_default_node_shapes_internal;
545 public void setShowDomainLabels( final boolean show_domain_labels ) {
546 _show_domain_labels = show_domain_labels;
549 public void setShowScale( final boolean show_scale ) {
550 _show_scale = show_scale;
553 public void setTaxonomyColorize( final boolean b ) {
554 display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
557 public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
558 _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
561 public void setUseBranchesWidths( final boolean b ) {
562 display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
565 boolean displaySequenceRelations() {
566 return _display_sequence_relations;
569 boolean doCheckOption( final int which ) {
570 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
571 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
574 boolean doDisplayClickToOption( final int which ) {
575 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
578 boolean doDisplayOption( final int which ) {
579 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
583 * Will attempt to use the phylogeny to determine whether to check
584 * this or not (e.g. phylogram)
587 boolean doGuessCheckOption( final int which ) {
588 return display_options[ which ][ 2 ].equals( "?" );
591 Map<String, Color> getAnnotationColors() {
592 if ( _annotation_colors == null ) {
593 _annotation_colors = new Hashtable<String, Color>();
595 return _annotation_colors;
598 int getBaseFontSize() {
599 return _base_font_size;
602 int getMinBaseFontSize() {
603 return _min_base_font_size;
606 int getMaxBaseFontSize() {
607 return _max_base_font_size;
610 CLADOGRAM_TYPE getCladogramType() {
611 return _cladogram_type;
614 int getClickToOptionsCount() {
615 return clickto_options.length;
618 String getClickToTitle( final int which ) {
619 return clickto_options[ which ][ 0 ];
622 int getDefaultDisplayClicktoOption() {
623 return default_clickto;
626 SortedMap<String, Color> getDisplayColors() {
627 return _display_colors;
630 String getDisplayTitle( final int which ) {
631 return display_options[ which ][ 0 ];
634 Map<String, Color> getDomainColors() {
635 if ( _domain_colors == null ) {
636 _domain_colors = new Hashtable<String, Color>();
638 return _domain_colors;
641 int getGraphicsExportX() {
642 return _graphics_export_x;
645 int getGraphicsExportY() {
646 return _graphics_export_y;
649 Color getGuiBackgroundColor() {
650 return _gui_background_color;
653 Color getGuiButtonBackgroundColor() {
654 return _gui_button_background_color;
657 Color getGuiButtonBorderColor() {
658 return _gui_button_border_color;
661 Color getGuiButtonTextColor() {
662 return _gui_button_text_color;
665 Color getGuiCheckboxAndButtonActiveColor() {
666 return _gui_checkbox_and_button_active_color;
669 Color getGuiCheckboxTextColor() {
670 return _gui_checkbox_text_color;
673 Color getGuiMenuBackgroundColor() {
674 return _gui_menu_background_color;
677 Color getGuiMenuTextColor() {
678 return _gui_menu_text_color;
681 double getMinConfidenceValue() {
682 return _min_confidence_value;
685 NODE_LABEL_DIRECTION getNodeLabelDirection() {
686 return _node_label_direction;
689 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
690 return _number_of_digits_after_comma_for_branch_length_values;
693 short getNumberOfDigitsAfterCommaForConfidenceValues() {
694 return _number_of_digits_after_comma_for_confidence_values;
697 short getOvMaxHeight() {
698 return _ov_max_height;
701 short getOvMaxWidth() {
702 return _ov_max_width;
705 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
706 return _ov_placement;
709 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
710 return _phylogeny_graphics_type;
713 float getPrintLineWidth() {
714 return _print_line_width;
717 Hashtable<String, Color> getSpeciesColors() {
718 if ( _species_colors == null ) {
719 _species_colors = new Hashtable<String, Color>();
721 return _species_colors;
724 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
725 return _taxonomy_extraction;
728 boolean isAntialiasScreen() {
729 if ( ForesterUtil.isMac() ) {
730 //Apple Macintosh graphics are slow, turn off anti-alias.
733 return _antialias_screen;
737 * Convenience method.
739 * @return true if value in configuration file was 'yes'
741 boolean isDrawAsPhylogram() {
742 return doCheckOption( display_as_phylogram );
745 boolean isEditable() {
750 * Only used by ArchaeoptryxE.
753 boolean isHideControlPanelAndMenubar() {
754 return _hide_controls_and_menus;
757 boolean isInternalNumberAreConfidenceForNhParsing() {
758 return _internal_number_are_confidence_for_nh_parsing;
761 boolean isReplaceUnderscoresInNhParsing() {
762 return _nh_parsing_replace_underscores;
765 boolean isShowBranchLengthValues() {
766 return _show_branch_length_values;
769 boolean isShowOverview() {
770 return _show_overview;
773 boolean isShowScale() {
777 final boolean isUseNativeUI() {
778 if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
781 return _ui == UI.NATIVE;
785 * Only used by ArchaeoptryxE.
788 boolean isUseTabbedDisplay() {
789 return _use_tabbed_display;
792 boolean isValidatePhyloXmlAgainstSchema() {
793 return _validate_against_phyloxml_xsd_schema;
796 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
797 _taxonomy_extraction = taxonomy_extraction;
800 private int getClickToIndex( final String name ) {
802 if ( name.equals( "edit_info" ) ) {
803 index = Configuration.display_node_data;
805 .printWarningMessage( Constants.PRG_NAME,
806 "configuration key [edit_info] is deprecated, use [display node data] instead" );
808 else if ( name.equals( "display_node_data" ) ) {
809 index = Configuration.display_node_data;
811 else if ( name.equals( "collapse_uncollapse" ) ) {
812 index = Configuration.collapse_uncollapse;
814 else if ( name.equals( "reroot" ) ) {
815 index = Configuration.reroot;
817 else if ( name.equals( "subtree" ) ) {
818 index = Configuration.subtree;
820 else if ( name.equals( "swap" ) ) {
821 index = Configuration.swap;
823 else if ( name.equals( "sort_descendants" ) ) {
824 index = Configuration.sort_descendents;
826 else if ( name.equals( "get_ext_descendents_data" ) ) {
827 index = Configuration.get_ext_desc_data;
829 else if ( name.equals( "display_sequences" ) ) {
831 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
834 else if ( name.equals( "open_seq_web" ) ) {
835 index = Configuration.open_seq_web;
837 else if ( name.equals( "open_tax_web" ) ) {
838 index = Configuration.open_tax_web;
840 else if ( name.equals( "blast" ) ) {
841 index = Configuration.blast;
843 else if ( name.equals( "cut_subtree" ) ) {
844 index = Configuration.cut_subtree;
846 else if ( name.equals( "copy_subtree" ) ) {
847 index = Configuration.copy_subtree;
849 else if ( name.equals( "paste_subtree" ) ) {
850 index = Configuration.paste_subtree;
852 else if ( name.equals( "delete" ) ) {
853 index = Configuration.delete_subtree_or_node;
855 else if ( name.equals( "add_new_node" ) ) {
856 index = Configuration.add_new_node;
858 else if ( name.equals( "edit_node_data" ) ) {
859 index = Configuration.edit_node_data;
861 else if ( name.equals( "select_nodes" ) ) {
862 index = Configuration.select_nodes;
864 else if ( name.equals( "display_node_popup" ) ) {
865 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
866 "configuration key [display_node_popup] is deprecated" );
869 else if ( name.equals( "custom_option" ) ) {
870 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
873 else if ( name.equals( "color_subtree" ) ) {
874 index = Configuration.color_subtree;
879 private boolean parseBoolean( final String str ) {
880 final String my_str = str.trim().toLowerCase();
881 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
884 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
888 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
893 private double parseDouble( final String str ) {
896 d = Double.parseDouble( str.trim() );
898 catch ( final Exception e ) {
899 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
905 private float parseFloat( final String str ) {
908 f = Float.parseFloat( str.trim() );
910 catch ( final Exception e ) {
911 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
917 private int parseInt( final String str ) {
920 i = Integer.parseInt( str.trim() );
922 catch ( final Exception e ) {
923 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
929 private short parseShort( final String str ) {
932 i = Short.parseShort( str.trim() );
934 catch ( final Exception e ) {
935 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
941 private void processFontFamily( final StringTokenizer st ) {
942 setBaseFontFamilyName( "" );
943 final String font_str = ( ( String ) st.nextElement() ).trim();
944 final String[] fonts = font_str.split( ",+" );
945 for( String font : fonts ) {
946 font = font.replace( '_', ' ' ).trim();
947 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
948 setBaseFontFamilyName( font );
955 * read each line of config file, process non-comment lines
956 * @throws IOException
958 private void readConfig( final BufferedReader conf_in ) throws IOException {
961 line = conf_in.readLine();
962 if ( line != null ) {
964 // skip comments and blank lines
965 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
966 // convert runs of spaces to tabs
967 line = line.replaceAll( "\\s+", "\t" );
968 final StringTokenizer st = new StringTokenizer( line, "\t" );
972 } while ( line != null );
975 private void setAntialiasScreen( final boolean antialias_screen ) {
976 _antialias_screen = antialias_screen;
979 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
980 _cladogram_type = cladogram_type;
983 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
984 _default_bootstrap_samples = default_bootstrap_samples;
987 private void setEditable( final boolean editable ) {
988 _editable = editable;
991 private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
992 _ext_node_data_return_on = ext_node_data_return_on;
995 private void setGraphicsExportX( final int graphics_export_x ) {
996 _graphics_export_x = graphics_export_x;
999 private void setGraphicsExportY( final int graphics_export_y ) {
1000 _graphics_export_y = graphics_export_y;
1003 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
1004 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
1008 * Set a key-value(s) tuple
1010 private void setKeyValue( final StringTokenizer st ) {
1011 final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
1012 if ( !st.hasMoreElements() ) {
1015 // Handle single value settings first:
1016 if ( key.equals( "default_click_to" ) ) {
1017 final String clickto_name = ( String ) st.nextElement();
1018 default_clickto = getClickToIndex( clickto_name );
1019 if ( default_clickto == -1 ) {
1020 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
1021 + "] for [default_click_to]" );
1022 default_clickto = 0;
1024 else if ( default_clickto == DEPRECATED ) {
1028 else if ( key.equals( "native_ui" ) ) {
1029 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
1030 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
1033 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
1034 _ui = UI.CROSSPLATFORM;
1036 else if ( my_str.equals( "?" ) ) {
1040 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
1045 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
1046 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
1048 else if ( key.equals( "antialias_screen" ) ) {
1049 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
1051 else if ( key.equals( "phylogeny_graphics_type" ) ) {
1052 final String type_str = ( ( String ) st.nextElement() ).trim();
1053 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
1054 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1056 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
1057 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1059 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
1060 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1062 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
1063 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1065 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
1066 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1068 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
1069 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1071 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
1072 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1074 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
1075 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1078 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1079 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1080 + "] for [phylogeny_graphics_type]" );
1083 else if ( key.equals( "min_confidence_value" ) ) {
1084 final String mcv_str = ( ( String ) st.nextElement() ).trim();
1085 final double d = parseDouble( mcv_str );
1086 setMinConfidenceValue( d );
1088 else if ( key.equals( "font_family" ) ) {
1089 processFontFamily( st );
1091 else if ( key.equals( "font_size" ) ) {
1092 final String size_str = ( ( String ) st.nextElement() ).trim();
1093 final int i = parseInt( size_str );
1095 setBaseFontSize( i );
1098 else if ( key.equals( "font_size_min" ) ) {
1099 final String size_str = ( ( String ) st.nextElement() ).trim();
1100 final int i = parseInt( size_str );
1102 setMinBaseFontSize( i );
1105 else if ( key.equals( "font_size_max" ) ) {
1106 final String size_str = ( ( String ) st.nextElement() ).trim();
1107 final int i = parseInt( size_str );
1109 setMaxBaseFontSize( i );
1112 else if ( key.equals( "graphics_export_x" ) ) {
1113 final String str = ( ( String ) st.nextElement() ).trim();
1114 final int i = parseInt( str );
1116 setGraphicsExportX( i );
1119 else if ( key.equals( "graphics_export_y" ) ) {
1120 final String str = ( ( String ) st.nextElement() ).trim();
1121 final int i = parseInt( str );
1123 setGraphicsExportY( i );
1126 else if ( key.equals( "pdf_export_line_width" ) ) {
1127 final String str = ( ( String ) st.nextElement() ).trim();
1128 final float f = parseFloat( str );
1130 setPrintLineWidth( f );
1133 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1134 "value for [pdf_export_line_width] cannot be zero or negative" );
1137 else if ( key.equals( "window_initial_size_x" ) ) {
1138 final String str = ( ( String ) st.nextElement() ).trim();
1139 final int i = parseInt( str );
1144 else if ( key.equals( "window_initial_size_y" ) ) {
1145 final String str = ( ( String ) st.nextElement() ).trim();
1146 final int i = parseInt( str );
1151 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1152 final String str = ( ( String ) st.nextElement() ).trim();
1153 final int i = parseInt( str );
1155 setDefaultBootstrapSamples( i );
1159 .printWarningMessage( Constants.PRG_NAME,
1160 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1163 else if ( key.equals( "mafft_local" ) ) {
1164 final String str = ( ( String ) st.nextElement() ).trim();
1165 if ( !ForesterUtil.isEmpty( str ) ) {
1166 setPathToLocalMafft( new File( str ) );
1169 else if ( key.equals( "fastme_local" ) ) {
1170 final String str = ( ( String ) st.nextElement() ).trim();
1171 if ( !ForesterUtil.isEmpty( str ) ) {
1172 setPathToLocalFastme( new File( str ) );
1175 else if ( key.equals( "raxml_local" ) ) {
1176 final String str = ( ( String ) st.nextElement() ).trim();
1177 if ( !ForesterUtil.isEmpty( str ) ) {
1178 setPathToLocalRaxml( new File( str ) );
1181 else if ( key.equals( "show_scale" ) ) {
1182 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1184 else if ( key.equals( "show_overview" ) ) {
1185 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1187 else if ( key.equals( "show_branch_length_values" ) ) {
1188 setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
1190 else if ( key.equals( "background_gradient" ) ) {
1191 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1193 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1194 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1196 else if ( key.equals( "show_domain_labels" ) ) {
1197 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1199 else if ( key.equals( "show_seq_annotation_ref_sources" ) ) {
1200 setShowAnnotationRefSource( parseBoolean( ( String ) st.nextElement() ) );
1202 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1203 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1205 else if ( key.equals( "cladogram_type" ) ) {
1206 final String type_str = ( ( String ) st.nextElement() ).trim();
1207 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1208 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1210 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1211 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1213 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1214 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1217 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1218 + "] for [cladogram_type]" );
1221 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1223 .printWarningMessage( Constants.PRG_NAME,
1224 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1226 else if ( key.equals( "hide_controls_and_menus" ) ) {
1227 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1229 else if ( key.equals( "use_tabbed_display" ) ) {
1230 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1232 else if ( key.equals( "overview_width" ) ) {
1233 final short i = parseShort( ( ( String ) st.nextElement() ) );
1236 else if ( key.equals( "overview_height" ) ) {
1237 final short i = parseShort( ( ( String ) st.nextElement() ) );
1238 setOvMaxHeight( i );
1240 else if ( key.equals( "overview_placement_type" ) ) {
1241 final String type_str = ( ( String ) st.nextElement() ).trim();
1242 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1243 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1245 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1246 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1248 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1249 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1251 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1252 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1255 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1256 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1257 + "] for [overview_placement_type]" );
1260 else if ( key.equals( "node_label_direction" ) ) {
1261 final String type_str = ( ( String ) st.nextElement() ).trim();
1262 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1263 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1265 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1266 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1269 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1270 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1271 + "] for [node_label_direction]" );
1274 else if ( key.equals( "branch_length_value_digits" ) ) {
1275 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1277 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1280 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1281 + "] for [branch_length_value_digits]" );
1284 else if ( key.equals( "confidence_value_digits" ) ) {
1285 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1287 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1290 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1291 + "] for [confidence_value_digits]" );
1294 else if ( key.equals( "allow_editing" ) ) {
1295 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1297 else if ( key.equals( "display_sequence_relations" ) ) {
1298 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1300 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1301 final boolean r = parseBoolean( ( String ) st.nextElement() );
1302 if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
1304 .printWarningMessage( Constants.PRG_NAME,
1305 "attempt to extract taxonomies and replace underscores at the same time" );
1308 setReplaceUnderscoresInNhParsing( r );
1311 else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
1312 final String s = ( String ) st.nextElement();
1313 if ( s.equalsIgnoreCase( "no" ) ) {
1314 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1316 else if ( s.equalsIgnoreCase( "pfam_relaxed" ) ) {
1317 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1319 else if ( s.equalsIgnoreCase( "pfam_strict" ) ) {
1320 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1322 else if ( s.equalsIgnoreCase( "aggressive" ) ) {
1323 setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
1327 .printWarningMessage( Constants.PRG_NAME,
1328 "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
1330 + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
1332 if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
1334 .printWarningMessage( Constants.PRG_NAME,
1335 "attempt to extract taxonomies and replace underscores at the same time" );
1338 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1339 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1341 else if ( key.equals( "gui_background_color" ) ) {
1342 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1344 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1345 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1347 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1348 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1350 else if ( key.equals( "gui_button_text_color" ) ) {
1351 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1353 else if ( key.equals( "gui_button_background_color" ) ) {
1354 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1356 else if ( key.equals( "gui_menu_background_color" ) ) {
1357 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1359 else if ( key.equals( "gui_menu_text_color" ) ) {
1360 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1362 else if ( key.equals( "gui_button_border_color" ) ) {
1363 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1365 else if ( key.equals( "domain_structure_font_color" ) ) {
1366 _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
1368 else if ( key.equals( "domain_structure_base_color" ) ) {
1369 _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
1371 else if ( key.equals( "show_default_node_shapes" ) ) {
1373 .printWarningMessage( Constants.PRG_NAME,
1374 "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" );
1375 final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() );
1376 setShowDefaultNodeShapesInternal( b );
1377 setShowDefaultNodeShapesExternal( b );
1379 else if ( key.equals( "show_default_node_shapes_internal" ) ) {
1380 setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1382 else if ( key.equals( "show_default_node_shapes_external" ) ) {
1383 setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1385 else if ( key.equals( "default_node_size" ) ) {
1386 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1387 setDefaultNodeShapeSize( i );
1389 else if ( key.equals( "default_node_fill" ) ) {
1390 final String fill_str = ( ( String ) st.nextElement() ).trim();
1391 if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.NONE.toString() ) ) {
1392 setDefaultNodeFill( NodeFill.NONE );
1394 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.GRADIENT.toString() ) ) {
1395 setDefaultNodeFill( NodeFill.GRADIENT );
1397 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.SOLID.toString() ) ) {
1398 setDefaultNodeFill( NodeFill.SOLID );
1401 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1402 + "] for [default_node_fill]" );
1405 else if ( key.equals( "default_node_shape" ) ) {
1406 final String shape_str = ( ( String ) st.nextElement() ).trim();
1407 if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.CIRCLE.toString() ) ) {
1408 setDefaultNodeShape( NodeShape.CIRCLE );
1410 else if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.RECTANGLE.toString() ) ) {
1411 setDefaultNodeShape( NodeShape.RECTANGLE );
1414 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1415 + "] for [default_node_shape]" );
1418 else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
1419 setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
1421 else if ( key.equals( "midpoint_reroot" ) ) {
1422 setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) );
1424 else if ( key.equals( "ext_descendents_data_to_return" ) ) {
1425 final String s = ( ( String ) st.nextElement() ).trim();
1426 if ( s.equalsIgnoreCase( "node_name" ) ) {
1427 setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
1429 else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
1430 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
1432 else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) {
1433 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ_FASTA );
1435 else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
1436 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
1438 else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
1439 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
1441 else if ( s.equalsIgnoreCase( "gene_name" ) ) {
1442 setExtDescNodeDataToReturn( NODE_DATA.GENE_NAME );
1444 else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
1445 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
1447 else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
1448 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME );
1450 else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
1451 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
1453 else if ( s.equalsIgnoreCase( "taxonomy_common_name" ) ) {
1454 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_COMM0N_NAME );
1456 else if ( s.equalsIgnoreCase( "user_selected" ) ) {
1457 setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
1460 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1461 + "] for [ext_descendents_data_to_return]" );
1464 else if ( key.equals( "label_for_get_ext_descendents_data" ) ) {
1465 final String s = ( ( String ) st.nextElement() ).trim();
1466 if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) {
1467 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s
1468 + "] for [label_for_get_ext_descendents_data]" );
1471 setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
1474 else if ( key.equals( "ext_descendents_data_to_return_on" ) ) {
1475 final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
1476 if ( s.equals( "console" ) ) {
1477 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
1479 else if ( s.equals( "window" ) ) {
1480 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
1482 else if ( s.equals( "buffer_only" ) ) {
1483 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
1486 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1487 + "] for [ext_descendents_data_to_return_on]" );
1490 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1493 if ( key.equals( "phylogram" ) ) {
1494 key_index = Configuration.display_as_phylogram;
1496 else if ( key.equals( "rollover" ) ) {
1497 key_index = Configuration.node_data_popup;
1499 else if ( key.equals( "color_according_to_species" ) ) {
1500 key_index = Configuration.color_according_to_species;
1502 else if ( key.equals( "show_node_names" ) ) {
1503 key_index = Configuration.show_node_names;
1505 else if ( key.equals( "show_taxonomy_code" ) ) {
1506 key_index = Configuration.show_tax_code;
1508 else if ( key.equals( "write_confidence_values" ) ) {
1509 key_index = Configuration.write_confidence_values;
1511 else if ( key.equals( "write_events" ) ) {
1512 key_index = Configuration.write_events;
1514 else if ( key.equals( "color_branches" ) ) {
1515 key_index = Configuration.color_branches;
1517 else if ( key.equals( "width_branches" ) ) {
1518 key_index = Configuration.width_branches;
1520 else if ( key.equals( "show_domain_architectures" ) ) {
1521 key_index = Configuration.show_domain_architectures;
1523 else if ( key.equals( "show_annotations" ) ) {
1524 key_index = Configuration.show_annotation;
1526 else if ( key.equals( "show_binary_characters" ) ) {
1527 key_index = Configuration.show_binary_characters;
1529 else if ( key.equals( "show_binary_character_counts" ) ) {
1530 key_index = Configuration.show_binary_character_counts;
1532 else if ( key.equals( "show_seq_names" ) ) {
1533 key_index = Configuration.show_seq_names;
1535 else if ( key.equals( "show_gene_names" ) ) {
1536 key_index = Configuration.show_gene_names;
1538 else if ( key.equals( "show_seq_symbols" ) ) {
1539 key_index = Configuration.show_seq_symbols;
1541 else if ( key.equals( "show_seq_acc" ) ) {
1542 key_index = Configuration.show_sequence_acc;
1544 else if ( key.equals( "display_internal_data" ) ) {
1545 key_index = Configuration.display_internal_data;
1547 else if ( key.equals( "dynamically_hide_data" ) ) {
1548 key_index = Configuration.dynamically_hide_data;
1550 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1551 key_index = Configuration.show_taxonomy_scientific_names;
1553 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1554 key_index = Configuration.show_taxonomy_common_names;
1556 else if ( key.equals( "show_taxonomy_images" ) ) {
1557 key_index = Configuration.show_taxonomy_images;
1559 else if ( key.equals( "color_according_to_annotation" ) ) {
1560 key_index = Configuration.color_according_to_annotation;
1562 else if ( key.equals( "show_vector_data" ) ) {
1563 key_index = Configuration.show_vector_data;
1565 else if ( key.equals( "show_properties" ) ) {
1566 key_index = Configuration.show_properties;
1568 else if ( key.equals( "show_relation_confidence" ) ) {
1569 key_index = Configuration.show_relation_confidence;
1571 else if ( key.equals( "show_custom_node_shapes" ) ) {
1572 key_index = Configuration.show_custom_node_shapes;
1574 // If we've found the key, set the values
1575 if ( key_index >= 0 ) {
1576 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1577 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1578 // otherwise, keep looking
1581 if ( key_index == DEPRECATED ) {
1584 else if ( key.equals( "click_to" ) ) {
1585 final String click_to_name = ( String ) st.nextElement();
1586 key_index = getClickToIndex( click_to_name );
1587 if ( key_index >= 0 ) {
1588 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1590 else if ( key_index == DEPRECATED ) {
1594 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1598 else if ( key.equals( "species_color" ) ) {
1599 getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
1600 Color.decode( ( String ) st.nextElement() ) );
1602 else if ( key.equals( "domain_color" ) ) {
1603 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1605 else if ( key.equals( "annotation_color" ) ) {
1606 getAnnotationColors()
1607 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1609 else if ( key.equals( "function_color" ) ) {
1610 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1611 "configuration key [function_color] is deprecated" );
1613 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1614 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1617 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1618 + "] in: " + config_filename );
1623 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1624 + config_filename );
1628 private void setShowAnnotationRefSource( final boolean b ) {
1629 _show_annotation_ref_source = b;
1632 private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
1633 _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
1636 private void setOvMaxHeight( final short ov_max_height ) {
1637 _ov_max_height = ov_max_height;
1640 private void setOvMaxWidth( final short ov_max_width ) {
1641 _ov_max_width = ov_max_width;
1644 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1645 _ov_placement = ov_placement;
1648 private void setPathToLocalFastme( final File path_to_local_fastme ) {
1649 _path_to_local_fastme = path_to_local_fastme;
1652 private void setPathToLocalMafft( final File path_to_local_mafft ) {
1653 _path_to_local_mafft = path_to_local_mafft;
1656 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
1657 _path_to_local_raxml = path_to_local_raxml;
1660 private void setShowOverview( final boolean show_overview ) {
1661 _show_overview = show_overview;
1664 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1665 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1668 static String getDefaultFontFamilyName() {
1669 return DEFAULT_FONT_FAMILY;
1672 public enum EXT_NODE_DATA_RETURN_ON {
1673 CONSOLE, WINODW, BUFFER_ONLY;
1677 NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN
1680 static enum TRIPLET {
1681 TRUE, FALSE, UNKNOWN
1684 public boolean isMidpointReroot() {
1685 return _midpoint_root;
1688 public void setMidpointReroot( final boolean midpoint_root ) {
1689 _midpoint_root = midpoint_root;
1692 public boolean isShowAnnotationRefSource() {
1693 return _show_annotation_ref_source;