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: www.phylosoft.org/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.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 WEB_LINK_KEY = "web_link";
60 private static final String DISPLAY_COLOR_KEY = "display_color";
61 private static final int DEPRECATED = -2;
62 private UI _ui = UI.UNKNOWN;
63 private boolean _use_tabbed_display = false;
64 private boolean _hide_controls_and_menus = false;
65 private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
66 private SortedMap<String, WebLink> _weblinks = null;
67 private SortedMap<String, Color> _display_colors = null;
68 private boolean _antialias_screen = true;
69 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
70 private String _base_font_family_name = "";
71 private int _base_font_size = -1;
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 boolean _nh_parsing_extract_pfam_taxonomy_codes = false;
87 private boolean _internal_number_are_confidence_for_nh_parsing = false;
88 private boolean _display_sequence_relations = false;
89 private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
90 private boolean _background_color_gradient = false;
91 private boolean _show_domain_labels = true;
92 private boolean _abbreviate_scientific_names = false;
93 private boolean _color_labels_same_as_parent_branch = false;
94 private boolean _show_default_node_shapes = false;
95 private NodeShape _default_node_shape = NodeShape.CIRCLE;
96 private NodeFill _default_node_fill = NodeFill.GRADIENT;
97 private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
98 private boolean _taxonomy_colorize_node_shapes = false;
99 private int _default_bootstrap_samples = -1;
100 private File _path_to_local_mafft = null;
101 private File _path_to_local_fastme = null;
102 private File _path_to_local_raxml = null;
103 private File _path_to_local_clustalo = null;
104 final static int display_as_phylogram = 0;
105 final static int show_node_names = 1;
106 final static int show_tax_code = 2;
107 final static int show_annotation = 3;
108 final static int write_confidence_values = 4;
109 final static int write_events = 5;
110 final static int color_according_to_species = 6;
111 final static int color_branches = 7;
112 final static int width_branches = 8;
113 final static int show_custom_node_shapes = 9;
114 final static int show_domain_architectures = 10;
115 final static int show_binary_characters = 11;
116 final static int show_binary_character_counts = 12;
117 final static int show_gene_names = 13;
118 final static int show_sequence_acc = 14;
119 final static int display_internal_data = 15;
120 final static int dynamically_hide_data = 16;
121 final static int show_taxonomy_scientific_names = 17;
122 final static int show_taxonomy_common_names = 18;
123 final static int color_according_to_annotation = 19;
124 final static int show_gene_symbols = 20;
125 final static int node_data_popup = 21;
126 final static int show_relation_confidence = 22;
127 final static int show_vector_data = 23;
128 final static int show_taxonomy_images = 24;
129 final static int show_properties = 25;
130 // ------------------
132 // ------------------
133 final static int display_node_data = 0;
134 final static int collapse_uncollapse = 1;
135 final static int reroot = 2;
136 final static int subtree = 3;
137 final static int swap = 4;
138 final static int color_subtree = 5;
139 final static int open_seq_web = 6;
140 final static int open_tax_web = 7;
141 final static int blast = 8;
142 final static int cut_subtree = 9;
143 final static int copy_subtree = 10;
144 final static int paste_subtree = 11;
145 final static int delete_subtree_or_node = 12;
146 final static int add_new_node = 13;
147 final static int edit_node_data = 14;
148 final static int sort_descendents = 15;
149 final static int get_ext_desc_data = 16;
150 // ---------------------------
151 // Display options for trees
152 // ---------------------------
153 // ---------------------------------
154 // Pertaining to the config itself
155 // ---------------------------------
156 // Full path to config (may be URL)
157 String config_filename;
158 String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
159 final static String display_options[][] = {
160 { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
161 { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, { "Event", "display", "?" },
162 { "Taxonomy Colorize", "display", "no" }, { "Colorize Branches", "display", "no" },
163 { "Use Branch-Widths", "display", "no" }, { "Show Custom Nodes", "display", "yes" },
164 { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" },
165 { "Binary Char Counts", "nodisplay", "no" }, { "Prot/Gene Name", "display", "yes" },
166 { "Prot/Gene Acc", "display", "no" }, { "Show Internal Data", "display", "yes" },
167 { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" },
168 { "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" },
169 { "Prot/Gene Symbol", "display", "yes" }, { "Rollover", "display", "yes" },
170 { "Relation Confidence", "display", "no" }, { "Vector Data", "display", "no" },
171 { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" } };
172 final static String clickto_options[][] = {
173 { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
174 { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
175 { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Blast", "display" },
176 { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" },
177 { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" },
178 { "Sort Descendants", "display" }, { "Get External Node Data", "display" } };
179 // This option is selected in the dropdown
180 int default_clickto = Configuration.display_node_data;
184 TreeColorSet tree_color_set;
188 TreeFontSet tree_font_set;
192 private static Hashtable<String, Color> _species_colors;
196 private static Hashtable<String, Color> _domain_colors;
200 private static Hashtable<String, Color> _annotation_colors;
201 boolean verbose = Constants.VERBOSE_DEFAULT;
202 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
203 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
204 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
205 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
206 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
207 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
208 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
209 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
210 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
211 private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
212 private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
213 private NODE_DATA _ext_desc_data_to_return;
214 private static String DEFAULT_FONT_FAMILY = "";
216 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
217 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
218 DEFAULT_FONT_FAMILY = font_name;
222 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
223 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
227 public Configuration() {
228 this( null, false, false, false );
231 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
232 if ( ForesterUtil.isEmpty( cf ) ) {
233 config_filename = default_config_filename;
236 config_filename = cf;
238 setWebLinks( new TreeMap<String, WebLink>() );
239 setDisplayColors( new TreeMap<String, Color>() );
240 config_filename = config_filename.trim();
243 // If URL, open accordingly
245 u = new URL( config_filename );
247 final InputStreamReader isr = new InputStreamReader( u.openStream() );
248 final BufferedReader bf = new BufferedReader( isr );
251 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
252 + config_filename + "]" );
254 catch ( final Exception e ) {
255 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
256 + config_filename + "]: " + e.getLocalizedMessage() );
259 catch ( final Exception e ) {
260 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
261 + config_filename + "]" );
265 // Otherwise, open as a file
266 File f = new File( config_filename );
268 f = new File( config_filename + ".txt" );
270 if ( f.exists() && f.canRead() ) {
272 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
276 catch ( final Exception e ) {
278 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
279 + config_filename + "]: " + e );
285 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
286 + config_filename + "]" );
292 private void createWebLink( final String url_str, final String desc, final String source_identifier ) {
293 WebLink weblink = null;
296 weblink = new WebLink( new URL( url_str.trim() ), desc.trim(), source_identifier.trim() );
298 catch ( final MalformedURLException e ) {
299 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not create URL from [" + url_str + "]" );
302 if ( !ex && ( weblink != null ) ) {
303 getWebLinks().put( weblink.getSourceIdentifier().toLowerCase(), weblink );
307 boolean displaySequenceRelations() {
308 return _display_sequence_relations;
311 boolean doCheckOption( final int which ) {
312 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
313 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
316 boolean doDisplayClickToOption( final int which ) {
317 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
320 boolean doDisplayOption( final int which ) {
321 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
325 * Will attempt to use the phylogeny to determine whether to check
326 * this or not (e.g. phylogram)
329 boolean doGuessCheckOption( final int which ) {
330 return display_options[ which ][ 2 ].equals( "?" );
333 Map<String, Color> getAnnotationColors() {
334 if ( _annotation_colors == null ) {
335 _annotation_colors = new Hashtable<String, Color>();
337 return _annotation_colors;
340 public String getBaseFontFamilyName() {
341 return _base_font_family_name;
344 int getBaseFontSize() {
345 return _base_font_size;
348 CLADOGRAM_TYPE getCladogramType() {
349 return _cladogram_type;
352 private int getClickToIndex( final String name ) {
354 if ( name.equals( "edit_info" ) ) {
355 index = Configuration.display_node_data;
357 .printWarningMessage( Constants.PRG_NAME,
358 "configuration key [edit_info] is deprecated, use [display node data] instead" );
360 else if ( name.equals( "display_node_data" ) ) {
361 index = Configuration.display_node_data;
363 else if ( name.equals( "collapse_uncollapse" ) ) {
364 index = Configuration.collapse_uncollapse;
366 else if ( name.equals( "reroot" ) ) {
367 index = Configuration.reroot;
369 else if ( name.equals( "subtree" ) ) {
370 index = Configuration.subtree;
372 else if ( name.equals( "swap" ) ) {
373 index = Configuration.swap;
375 else if ( name.equals( "sort_descendants" ) ) {
376 index = Configuration.sort_descendents;
378 else if ( name.equals( "get_ext_descendents_data" ) ) {
379 index = Configuration.get_ext_desc_data;
381 else if ( name.equals( "display_sequences" ) ) {
383 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
386 else if ( name.equals( "open_seq_web" ) ) {
387 index = Configuration.open_seq_web;
389 else if ( name.equals( "open_tax_web" ) ) {
390 index = Configuration.open_tax_web;
392 else if ( name.equals( "blast" ) ) {
393 index = Configuration.blast;
395 else if ( name.equals( "cut_subtree" ) ) {
396 index = Configuration.cut_subtree;
398 else if ( name.equals( "copy_subtree" ) ) {
399 index = Configuration.copy_subtree;
401 else if ( name.equals( "paste_subtree" ) ) {
402 index = Configuration.paste_subtree;
404 else if ( name.equals( "delete" ) ) {
405 index = Configuration.delete_subtree_or_node;
407 else if ( name.equals( "add_new_node" ) ) {
408 index = Configuration.add_new_node;
410 else if ( name.equals( "edit_node_data" ) ) {
411 index = Configuration.edit_node_data;
413 else if ( name.equals( "display_node_popup" ) ) {
414 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
415 "configuration key [display_node_popup] is deprecated" );
418 else if ( name.equals( "custom_option" ) ) {
419 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
422 else if ( name.equals( "color_subtree" ) ) {
423 index = Configuration.color_subtree;
425 else if ( name.equals( "go_to_swiss_prot" ) ) {
426 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" );
432 int getClickToOptionsCount() {
433 return clickto_options.length;
436 String getClickToTitle( final int which ) {
437 return clickto_options[ which ][ 0 ];
440 public int getDefaultBootstrapSamples() {
441 return _default_bootstrap_samples;
444 public File getpathToLocalMafft() {
445 return _path_to_local_mafft;
448 public File getPathToLocalFastme() {
449 return _path_to_local_fastme;
452 public File getPathToLocalRaxml() {
453 return _path_to_local_raxml;
456 int getDefaultDisplayClicktoOption() {
457 return default_clickto;
460 public NodeFill getDefaultNodeFill() {
461 return _default_node_fill;
464 public NodeShape getDefaultNodeShape() {
465 return _default_node_shape;
468 public short getDefaultNodeShapeSize() {
469 return _default_node_shape_size;
472 SortedMap<String, Color> getDisplayColors() {
473 return _display_colors;
476 String getDisplayTitle( final int which ) {
477 return display_options[ which ][ 0 ];
480 Map<String, Color> getDomainColors() {
481 if ( _domain_colors == null ) {
482 _domain_colors = new Hashtable<String, Color>();
484 return _domain_colors;
487 public Color getDomainStructureBaseColor() {
488 return _domain_structure_base_color;
491 public Color getDomainStructureFontColor() {
492 return _domain_structure_font_color;
495 int getGraphicsExportX() {
496 return _graphics_export_x;
499 int getGraphicsExportY() {
500 return _graphics_export_y;
503 Color getGuiBackgroundColor() {
504 return _gui_background_color;
507 Color getGuiButtonBackgroundColor() {
508 return _gui_button_background_color;
511 Color getGuiButtonBorderColor() {
512 return _gui_button_border_color;
515 Color getGuiButtonTextColor() {
516 return _gui_button_text_color;
519 Color getGuiCheckboxAndButtonActiveColor() {
520 return _gui_checkbox_and_button_active_color;
523 Color getGuiCheckboxTextColor() {
524 return _gui_checkbox_text_color;
527 Color getGuiMenuBackgroundColor() {
528 return _gui_menu_background_color;
531 Color getGuiMenuTextColor() {
532 return _gui_menu_text_color;
535 double getMinConfidenceValue() {
536 return _min_confidence_value;
539 NODE_LABEL_DIRECTION getNodeLabelDirection() {
540 return _node_label_direction;
543 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
544 return _number_of_digits_after_comma_for_branch_length_values;
547 short getNumberOfDigitsAfterCommaForConfidenceValues() {
548 return _number_of_digits_after_comma_for_confidence_values;
551 short getOvMaxHeight() {
552 return _ov_max_height;
555 short getOvMaxWidth() {
556 return _ov_max_width;
559 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
560 return _ov_placement;
563 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
564 return _phylogeny_graphics_type;
567 float getPrintLineWidth() {
568 return _print_line_width;
571 Hashtable<String, Color> getSpeciesColors() {
572 if ( _species_colors == null ) {
573 _species_colors = new Hashtable<String, Color>();
575 return _species_colors;
578 TreeColorSet getTreeColorSet() {
582 TreeFontSet getTreeFontSet() {
586 WebLink getWebLink( final String source ) {
587 return getWebLinks().get( source );
590 Map<String, WebLink> getWebLinks() {
594 public boolean isAbbreviateScientificTaxonNames() {
595 return _abbreviate_scientific_names;
598 boolean isAntialiasScreen() {
599 return _antialias_screen;
602 public boolean isBackgroundColorGradient() {
603 return _background_color_gradient;
606 public boolean isColorLabelsSameAsParentBranch() {
607 return _color_labels_same_as_parent_branch;
611 * Convenience method.
613 * @return true if value in configuration file was 'yes'
615 boolean isDrawAsPhylogram() {
616 return doCheckOption( display_as_phylogram );
619 boolean isEditable() {
623 boolean isExtractPfamTaxonomyCodesInNhParsing() {
624 return _nh_parsing_extract_pfam_taxonomy_codes;
627 boolean isHasWebLink( final String source ) {
628 return getWebLinks().containsKey( source );
632 * Only used by ArchaeoptryxE.
635 boolean isHideControlPanelAndMenubar() {
636 return _hide_controls_and_menus;
639 boolean isInternalNumberAreConfidenceForNhParsing() {
640 return _internal_number_are_confidence_for_nh_parsing;
643 boolean isReplaceUnderscoresInNhParsing() {
644 return _nh_parsing_replace_underscores;
647 boolean isShowBranchLengthValues() {
648 return _show_branch_length_values;
651 public boolean isShowDefaultNodeShapes() {
652 return _show_default_node_shapes;
655 public boolean isShowDomainLabels() {
656 return _show_domain_labels;
659 boolean isShowOverview() {
660 return _show_overview;
663 boolean isShowScale() {
667 public boolean isTaxonomyColorizeNodeShapes() {
668 return _taxonomy_colorize_node_shapes;
671 final boolean isUseNativeUI() {
672 if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) {
675 return _ui == UI.NATIVE;
679 * Only used by ArchaeoptryxE.
682 boolean isUseTabbedDisplay() {
683 return _use_tabbed_display;
686 boolean isValidatePhyloXmlAgainstSchema() {
687 return _validate_against_phyloxml_xsd_schema;
690 private boolean parseBoolean( final String str ) {
691 final String my_str = str.trim().toLowerCase();
692 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
695 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
699 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
704 private double parseDouble( final String str ) {
707 d = Double.parseDouble( str );
709 catch ( final Exception e ) {
710 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
716 private float parseFloat( final String str ) {
719 f = Float.parseFloat( str );
721 catch ( final Exception e ) {
722 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
728 private int parseInt( final String str ) {
731 i = Integer.parseInt( str );
733 catch ( final Exception e ) {
734 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
740 private short parseShort( final String str ) {
743 i = Short.parseShort( str );
745 catch ( final Exception e ) {
746 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
752 private void processFontFamily( final StringTokenizer st ) {
753 setBaseFontFamilyName( "" );
754 final String font_str = ( ( String ) st.nextElement() ).trim();
755 final String[] fonts = font_str.split( ",+" );
756 for( String font : fonts ) {
757 font = font.replace( '_', ' ' ).trim();
758 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
759 setBaseFontFamilyName( font );
765 public void putDisplayColors( final String key, final Color color ) {
766 getDisplayColors().put( key, color );
770 * read each line of config file, process non-comment lines
771 * @throws IOException
773 private void readConfig( final BufferedReader conf_in ) throws IOException {
776 line = conf_in.readLine();
777 if ( line != null ) {
779 // skip comments and blank lines
780 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
781 // convert runs of spaces to tabs
782 line = line.replaceAll( "\\s+", "\t" );
783 final StringTokenizer st = new StringTokenizer( line, "\t" );
787 } while ( line != null );
790 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
791 _abbreviate_scientific_names = abbreviate_scientific_names;
794 private void setAntialiasScreen( final boolean antialias_screen ) {
795 _antialias_screen = antialias_screen;
798 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
799 _background_color_gradient = background_color_gradient;
802 public void setBaseFontFamilyName( final String base_font_family_name ) {
803 _base_font_family_name = base_font_family_name;
806 public void setBaseFontSize( final int base_font_size ) {
807 _base_font_size = base_font_size;
810 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
811 _cladogram_type = cladogram_type;
814 public void setColorizeBranches( final boolean b ) {
815 display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
818 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
819 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
822 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
823 _default_bootstrap_samples = default_bootstrap_samples;
826 private void setPathToLocalMafft( final File path_to_local_mafft ) {
827 _path_to_local_mafft = path_to_local_mafft;
830 private void setPathToLocalFastme( final File path_to_local_fastme ) {
831 _path_to_local_fastme = path_to_local_fastme;
834 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
835 _path_to_local_raxml = path_to_local_raxml;
838 public File getPathToLocalClustalOmega() {
839 return _path_to_local_clustalo;
842 public void setPathToLocalClustalOmega( final File path_to_local_clustalo ) {
843 _path_to_local_clustalo = path_to_local_clustalo;
846 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
847 _default_node_fill = default_node_fill;
850 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
851 _default_node_shape = default_node_shape;
854 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
855 _default_node_shape_size = default_node_shape_size;
858 public void setDisplayAsPhylogram( final boolean b ) {
859 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
862 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
863 _display_colors = display_colors;
866 public void setDisplayConfidenceValues( final boolean b ) {
867 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
870 public void setDisplayInternalData( final boolean b ) {
871 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
874 public void setDisplayNodeNames( final boolean b ) {
875 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
878 public void setDisplaySequenceAcc( final boolean b ) {
879 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
882 public void setDisplaySequenceNames( final boolean b ) {
883 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
886 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
887 _display_sequence_relations = display_sequence_relations;
890 public void setDisplaySequenceSymbols( final boolean b ) {
891 display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no";
894 public void setDisplayTaxonomyCode( final boolean b ) {
895 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
898 public void setDisplayTaxonomyCommonNames( final boolean b ) {
899 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
902 public void setDisplayTaxonomyImages( final boolean b ) {
903 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
906 public void setDisplayTaxonomyScientificNames( final boolean b ) {
907 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
910 public void setDynamicallyHideData( final boolean b ) {
911 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
914 private void setEditable( final boolean editable ) {
915 _editable = editable;
918 public void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) {
919 _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes;
922 private void setGraphicsExportX( final int graphics_export_x ) {
923 _graphics_export_x = graphics_export_x;
926 private void setGraphicsExportY( final int graphics_export_y ) {
927 _graphics_export_y = graphics_export_y;
930 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
931 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
935 * Set a key-value(s) tuple
937 private void setKeyValue( final StringTokenizer st ) {
938 String key = ( String ) st.nextElement();
939 key = key.replace( ':', ' ' );
941 key = key.toLowerCase();
942 // Handle single value settings first:
943 if ( key.equals( "default_click_to" ) ) {
944 final String clickto_name = ( String ) st.nextElement();
945 default_clickto = getClickToIndex( clickto_name );
946 if ( default_clickto == -1 ) {
947 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
948 + "] for [default_click_to]" );
951 else if ( default_clickto == DEPRECATED ) {
955 else if ( key.equals( "native_ui" ) ) {
956 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
957 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
960 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
961 _ui = UI.CROSSPLATFORM;
963 else if ( my_str.equals( "?" ) ) {
967 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
972 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
973 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
975 else if ( key.equals( "antialias_screen" ) ) {
976 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
978 else if ( key.equals( "phylogeny_graphics_type" ) ) {
979 final String type_str = ( ( String ) st.nextElement() ).trim();
980 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
981 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
983 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
984 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
986 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
987 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
989 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
990 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
992 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
993 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
995 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
996 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
998 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
999 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1001 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
1002 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1005 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1006 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1007 + "] for [phylogeny_graphics_type]" );
1010 else if ( key.equals( "min_confidence_value" ) ) {
1011 final String mcv_str = ( ( String ) st.nextElement() ).trim();
1012 final double d = parseDouble( mcv_str );
1013 setMinConfidenceValue( d );
1015 else if ( key.equals( "font_family" ) ) {
1016 processFontFamily( st );
1018 else if ( key.equals( "font_size" ) ) {
1019 final String size_str = ( ( String ) st.nextElement() ).trim();
1020 final int i = parseInt( size_str );
1021 setBaseFontSize( i );
1023 else if ( key.equals( "graphics_export_x" ) ) {
1024 final String str = ( ( String ) st.nextElement() ).trim();
1025 final int i = parseInt( str );
1026 setGraphicsExportX( i );
1028 else if ( key.equals( "graphics_export_y" ) ) {
1029 final String str = ( ( String ) st.nextElement() ).trim();
1030 final int i = parseInt( str );
1031 setGraphicsExportY( i );
1033 else if ( key.equals( "pdf_export_line_width" ) ) {
1034 final String str = ( ( String ) st.nextElement() ).trim();
1035 final float f = parseFloat( str );
1037 setPrintLineWidth( f );
1040 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1041 "value for [pdf_export_line_width] cannot be zero or negative" );
1044 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1045 final String str = ( ( String ) st.nextElement() ).trim();
1046 final int i = parseInt( str );
1048 setDefaultBootstrapSamples( i );
1052 .printWarningMessage( Constants.PRG_NAME,
1053 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1056 else if ( key.equals( "clustalo_local" ) ) {
1057 final String str = ( ( String ) st.nextElement() ).trim();
1058 if ( !ForesterUtil.isEmpty( str ) ) {
1059 setPathToLocalClustalOmega( new File( str ) );
1062 else if ( key.equals( "mafft_local" ) ) {
1063 final String str = ( ( String ) st.nextElement() ).trim();
1064 if ( !ForesterUtil.isEmpty( str ) ) {
1065 setPathToLocalMafft( new File( str ) );
1068 else if ( key.equals( "fastme_local" ) ) {
1069 final String str = ( ( String ) st.nextElement() ).trim();
1070 if ( !ForesterUtil.isEmpty( str ) ) {
1071 setPathToLocalFastme( new File( str ) );
1074 else if ( key.equals( "raxml_local" ) ) {
1075 final String str = ( ( String ) st.nextElement() ).trim();
1076 if ( !ForesterUtil.isEmpty( str ) ) {
1077 setPathToLocalRaxml( new File( str ) );
1080 else if ( key.equals( "show_scale" ) ) {
1081 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1083 else if ( key.equals( "show_overview" ) ) {
1084 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1086 else if ( key.equals( "show_branch_length_values" ) ) {
1087 setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
1089 else if ( key.equals( "background_gradient" ) ) {
1090 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1092 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1093 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1095 else if ( key.equals( "show_domain_labels" ) ) {
1096 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1098 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1099 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1101 else if ( key.equals( "cladogram_type" ) ) {
1102 final String type_str = ( ( String ) st.nextElement() ).trim();
1103 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1104 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1106 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1107 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1109 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1110 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1113 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1114 + "] for [cladogram_type]" );
1117 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1119 .printWarningMessage( Constants.PRG_NAME,
1120 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1122 else if ( key.equals( "hide_controls_and_menus" ) ) {
1123 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1125 else if ( key.equals( "use_tabbed_display" ) ) {
1126 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1128 else if ( key.equals( "overview_width" ) ) {
1129 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1132 else if ( key.equals( "overview_height" ) ) {
1133 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1134 setOvMaxHeight( i );
1136 else if ( key.equals( "overview_placement_type" ) ) {
1137 final String type_str = ( ( String ) st.nextElement() ).trim();
1138 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1139 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1141 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1142 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1144 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1145 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1147 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1148 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1151 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1152 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1153 + "] for [overview_placement_type]" );
1156 else if ( key.equals( "node_label_direction" ) ) {
1157 final String type_str = ( ( String ) st.nextElement() ).trim();
1158 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1159 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1161 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1162 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1165 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1166 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1167 + "] for [node_label_direction]" );
1170 else if ( key.equals( "branch_length_value_digits" ) ) {
1171 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1173 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1176 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1177 + "] for [branch_length_value_digits]" );
1180 else if ( key.equals( "confidence_value_digits" ) ) {
1181 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1183 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1186 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1187 + "] for [confidence_value_digits]" );
1190 else if ( key.equals( "allow_editing" ) ) {
1191 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1193 else if ( key.equals( "display_sequence_relations" ) ) {
1194 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1196 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1197 final boolean r = parseBoolean( ( String ) st.nextElement() );
1198 if ( r && isExtractPfamTaxonomyCodesInNhParsing() ) {
1200 .printWarningMessage( Constants.PRG_NAME,
1201 "attempt to extract taxonomies and replace underscores at the same time" );
1204 setReplaceUnderscoresInNhParsing( r );
1207 else if ( key.equals( "extract_taxonomy_codes_in_nh_parsing" ) ) {
1208 final boolean e = parseBoolean( ( String ) st.nextElement() );
1209 if ( e && isReplaceUnderscoresInNhParsing() ) {
1211 .printWarningMessage( Constants.PRG_NAME,
1212 "attempt to extract taxonomies and replace underscores at the same time" );
1215 setExtractPfamTaxonomyCodesInNhParsing( e );
1218 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1219 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1221 else if ( key.equals( "gui_background_color" ) ) {
1222 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1224 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1225 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1227 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1228 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1230 else if ( key.equals( "gui_button_text_color" ) ) {
1231 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1233 else if ( key.equals( "gui_button_background_color" ) ) {
1234 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1236 else if ( key.equals( "gui_menu_background_color" ) ) {
1237 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1239 else if ( key.equals( "gui_menu_text_color" ) ) {
1240 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1242 else if ( key.equals( "gui_button_border_color" ) ) {
1243 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1245 else if ( key.equals( "domain_structure_font_color" ) ) {
1246 _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
1248 else if ( key.equals( "domain_structure_base_color" ) ) {
1249 _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
1251 else if ( key.equals( "show_default_node_shapes" ) ) {
1252 setShowDefaultNodeShapes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1254 else if ( key.equals( "default_node_size" ) ) {
1255 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1256 setDefaultNodeShapeSize( i );
1258 else if ( key.equals( "default_node_fill" ) ) {
1259 final String fill_str = ( ( String ) st.nextElement() ).trim();
1260 if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.NONE.toString() ) ) {
1261 setDefaultNodeFill( NodeFill.NONE );
1263 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.GRADIENT.toString() ) ) {
1264 setDefaultNodeFill( NodeFill.GRADIENT );
1266 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.SOLID.toString() ) ) {
1267 setDefaultNodeFill( NodeFill.SOLID );
1270 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1271 + "] for [default_node_fill]" );
1274 else if ( key.equals( "default_node_shape" ) ) {
1275 final String shape_str = ( ( String ) st.nextElement() ).trim();
1276 if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.CIRCLE.toString() ) ) {
1277 setDefaultNodeShape( NodeShape.CIRCLE );
1279 else if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.RECTANGLE.toString() ) ) {
1280 setDefaultNodeShape( NodeShape.RECTANGLE );
1283 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1284 + "] for [default_node_shape]" );
1287 else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
1288 setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
1290 else if ( key.equals( "ext_descendents_data_to_return" ) ) {
1291 final String s = ( ( String ) st.nextElement() ).trim();
1292 if ( s.equalsIgnoreCase( "node_name" ) ) {
1293 setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
1295 else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
1296 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
1298 else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
1299 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
1301 else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
1302 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
1304 else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
1305 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
1308 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1309 + "] for [ext_descendents_data_to_return]" );
1312 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1315 if ( key.equals( "use_real_br_lengths" ) || key.equals( "phylogram" ) ) {
1316 key_index = Configuration.display_as_phylogram;
1317 if ( key.equals( "use_real_br_lengths" ) ) {
1319 .printWarningMessage( Constants.PRG_NAME,
1320 "configuration key [use_real_br_lengths] is deprecated, use [phylogram] instead" );
1323 else if ( key.equals( "rollover" ) ) {
1324 key_index = Configuration.node_data_popup;
1326 else if ( key.equals( "color_according_to_species" ) ) {
1327 key_index = Configuration.color_according_to_species;
1329 else if ( key.equals( "show_node_names" ) ) {
1330 key_index = Configuration.show_node_names;
1332 else if ( key.equals( "show_taxonomy" ) || key.equals( "show_taxonomy_code" ) ) {
1333 key_index = Configuration.show_tax_code;
1334 if ( key.equals( "show_taxonomy" ) ) {
1336 .printWarningMessage( Constants.PRG_NAME,
1337 "configuration key [show_taxonomy] is deprecated, use [show_taxonomy_code] instead" );
1340 else if ( key.equals( "write_br_length_values" ) ) {
1341 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1342 "configuration key [write_br_length_values] is deprecated" );
1343 key_index = DEPRECATED;
1345 else if ( key.equals( "write_bootstrap_values" ) || key.equals( "write_confidence_values" ) ) {
1346 key_index = Configuration.write_confidence_values;
1347 if ( key.equals( "write_bootstrap_values" ) ) {
1349 .printWarningMessage( Constants.PRG_NAME,
1350 "configuration key [write_bootstrap_values] is deprecated, use [write_confidence_values] instead" );
1353 else if ( key.equals( "write_events" ) || key.equals( "write_dup_spec" ) ) {
1354 key_index = Configuration.write_events;
1355 if ( key.equals( "write_dup_spec" ) ) {
1357 .printWarningMessage( Constants.PRG_NAME,
1358 "configuration key [write_dup_spec] is deprecated, use [write_events] instead" );
1361 else if ( key.equals( "color_branches" ) ) {
1362 key_index = Configuration.color_branches;
1364 else if ( key.equals( "width_branches" ) ) {
1365 key_index = Configuration.width_branches;
1367 else if ( key.equals( "color_orthologous" ) ) {
1368 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1369 "configuration key [color_orthologous] is deprecated" );
1371 else if ( key.equals( "color_subtree_neighbors" ) ) {
1372 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1373 "configuration key [color_subtree_neighbors] is deprecated" );
1375 else if ( key.equals( "color_super_orthologous" ) ) {
1376 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1377 "configuration key [color_super_orthologous] is deprecated" );
1379 else if ( key.equals( "mark_nodes_with_box" ) ) {
1380 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1381 "configuration key [mark_nodes_with_box] is deprecated" );
1382 key_index = DEPRECATED;
1384 else if ( key.equals( "show_domain_architectures" ) ) {
1385 key_index = Configuration.show_domain_architectures;
1387 else if ( key.equals( "show_annotations" ) ) {
1388 key_index = Configuration.show_annotation;
1390 else if ( key.equals( "show_binary_characters" ) ) {
1391 key_index = Configuration.show_binary_characters;
1393 else if ( key.equals( "show_binary_character_counts" ) ) {
1394 key_index = Configuration.show_binary_character_counts;
1396 else if ( key.equals( "show_gene_names" ) ) {
1397 key_index = Configuration.show_gene_names;
1399 else if ( key.equals( "show_gene_symbols" ) ) {
1400 key_index = Configuration.show_gene_symbols;
1402 else if ( key.equals( "show_sequence_acc" ) ) {
1403 key_index = Configuration.show_sequence_acc;
1405 else if ( key.equals( "show_node_ids" ) ) {
1407 .printWarningMessage( Constants.PRG_NAME, "configuration key [show_node_ids] is deprecated" );
1408 key_index = DEPRECATED;
1410 else if ( key.equals( "display_internal_data" ) ) {
1411 key_index = Configuration.display_internal_data;
1413 else if ( key.equals( "dynamically_hide_data" ) ) {
1414 key_index = Configuration.dynamically_hide_data;
1416 else if ( key.equals( "show_taxonomy_names" ) ) {
1417 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1418 "configuration key [show_taxonomy_names] is deprecated" );
1419 key_index = DEPRECATED;
1421 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1422 key_index = Configuration.show_taxonomy_scientific_names;
1424 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1425 key_index = Configuration.show_taxonomy_common_names;
1427 else if ( key.equals( "show_taxonomy_images" ) ) {
1428 key_index = Configuration.show_taxonomy_images;
1430 else if ( key.equals( "color_according_to_annotation" ) ) {
1431 key_index = Configuration.color_according_to_annotation;
1433 else if ( key.equals( "show_vector_data" ) ) {
1434 key_index = Configuration.show_vector_data;
1436 else if ( key.equals( "show_properties" ) ) {
1437 key_index = Configuration.show_properties;
1439 else if ( key.equals( "show_relation_confidence" ) ) {
1440 key_index = Configuration.show_relation_confidence;
1442 else if ( key.equals( "show_custom_node_shapes" ) ) {
1443 key_index = Configuration.show_custom_node_shapes;
1445 // If we've found the key, set the values
1446 if ( key_index >= 0 ) {
1447 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1448 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1449 // otherwise, keep looking
1452 if ( key_index == DEPRECATED ) {
1455 else if ( key.equals( "click_to" ) ) {
1456 final String click_to_name = ( String ) st.nextElement();
1457 key_index = getClickToIndex( click_to_name );
1458 if ( key_index >= 0 ) {
1459 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1461 else if ( key_index == DEPRECATED ) {
1465 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1469 else if ( key.equals( "species_color" ) ) {
1470 getSpeciesColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1472 else if ( key.equals( "domain_color" ) ) {
1473 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1475 else if ( key.equals( "annotation_color" ) ) {
1476 getAnnotationColors()
1477 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1479 else if ( key.equals( "function_color" ) ) {
1480 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1481 "configuration key [function_color] is deprecated" );
1483 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1484 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1486 else if ( key.equals( WEB_LINK_KEY ) ) {
1487 if ( st.countTokens() == 3 ) {
1488 createWebLink( ( String ) st.nextElement(),
1489 ( String ) st.nextElement(),
1490 ( String ) st.nextElement() );
1493 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1494 "illegal format in configuration file for key [" + key + "]" );
1498 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1499 + "] in: " + config_filename );
1504 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1505 + config_filename );
1509 public void setMinConfidenceValue( final double min_confidence_value ) {
1510 _min_confidence_value = min_confidence_value;
1513 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
1514 _node_label_direction = node_label_direction;
1517 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short _number_of_digits_after_comma_for_branch_length_values ) {
1518 this._number_of_digits_after_comma_for_branch_length_values = _number_of_digits_after_comma_for_branch_length_values;
1521 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short _number_of_digits_after_comma_for_confidence_values ) {
1522 this._number_of_digits_after_comma_for_confidence_values = _number_of_digits_after_comma_for_confidence_values;
1525 private void setOvMaxHeight( final short ov_max_height ) {
1526 _ov_max_height = ov_max_height;
1529 private void setOvMaxWidth( final short ov_max_width ) {
1530 _ov_max_width = ov_max_width;
1533 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1534 _ov_placement = ov_placement;
1537 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
1538 _phylogeny_graphics_type = phylogeny_graphics_type;
1541 public void setPrintLineWidth( final float print_line_width ) {
1542 _print_line_width = print_line_width;
1545 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
1546 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
1549 public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
1550 _show_branch_length_values = show_branch_length_values;
1553 public void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
1554 _show_default_node_shapes = show_default_node_shapes;
1557 public void setShowDomainLabels( final boolean show_domain_labels ) {
1558 _show_domain_labels = show_domain_labels;
1561 private void setShowOverview( final boolean show_overview ) {
1562 _show_overview = show_overview;
1565 public void setShowScale( final boolean show_scale ) {
1566 _show_scale = show_scale;
1569 public void setTaxonomyColorize( final boolean b ) {
1570 display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
1573 public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
1574 _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
1577 public void setUseBranchesWidths( final boolean b ) {
1578 display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
1581 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1582 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1585 void setWebLinks( final SortedMap<String, WebLink> weblinks ) {
1586 _weblinks = weblinks;
1589 static String getDefaultFontFamilyName() {
1590 return DEFAULT_FONT_FAMILY;
1593 static enum TRIPLET {
1594 TRUE, FALSE, UNKNOWN
1598 NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN
1601 public NODE_DATA getExtDescNodeDataToReturn() {
1602 return _ext_desc_data_to_return;
1605 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
1606 _ext_desc_data_to_return = ext_desc_data_to_return;