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.NodeVisualization;
51 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
52 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
53 import org.forester.util.ForesterUtil;
55 public final class Configuration {
57 static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
58 private static final String WEB_LINK_KEY = "web_link";
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, WebLink> _weblinks = null;
66 private SortedMap<String, Color> _display_colors = null;
67 private boolean _antialias_screen = true;
68 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
69 private String _base_font_family_name = "";
70 private int _base_font_size = -1;
71 private int _graphics_export_x = -1;
72 private int _graphics_export_y = -1;
73 private short _ov_max_width = 80;
74 private short _ov_max_height = 80;
75 private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
76 private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
77 private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
78 private boolean _show_scale = false;
79 private boolean _show_branch_length_values = false;
80 private boolean _show_overview = true;
81 private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
82 private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
83 private boolean _editable = true;
84 private boolean _nh_parsing_replace_underscores = false;
85 private boolean _nh_parsing_extract_pfam_taxonomy_codes = false;
86 private boolean _internal_number_are_confidence_for_nh_parsing = false;
87 private boolean _display_sequence_relations = false;
88 private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
89 private boolean _background_color_gradient = false;
90 private boolean _show_domain_labels = true;
91 private boolean _abbreviate_scientific_names = false;
92 private boolean _color_labels_same_as_parent_branch = false;
93 private int _default_bootstrap_samples = -1;
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 final static int display_as_phylogram = 0;
100 final static int show_node_names = 1;
101 final static int show_tax_code = 2;
102 final static int show_annotation = 3;
103 final static int write_confidence_values = 4;
104 final static int write_events = 5;
105 final static int color_according_to_species = 6;
106 final static int color_branches = 7;
107 final static int width_branches = 8;
108 final static int show_custom_node_shapes = 9;
109 final static int show_domain_architectures = 10;
110 final static int show_binary_characters = 11;
111 final static int show_binary_character_counts = 12;
112 final static int show_gene_names = 13;
113 final static int show_sequence_acc = 14;
114 final static int display_internal_data = 15;
115 final static int dynamically_hide_data = 16;
116 final static int show_taxonomy_scientific_names = 17;
117 final static int show_taxonomy_common_names = 18;
118 final static int color_according_to_annotation = 19;
119 final static int show_gene_symbols = 20;
120 final static int node_data_popup = 21;
121 final static int show_relation_confidence = 22;
122 final static int show_vector_data = 23;
123 final static int show_taxonomy_images = 24;
124 final static int show_properties = 25;
125 // ------------------
127 // ------------------
128 final static int display_node_data = 0;
129 final static int collapse_uncollapse = 1;
130 final static int reroot = 2;
131 final static int subtree = 3;
132 final static int swap = 4;
133 final static int color_subtree = 5;
134 final static int open_seq_web = 6;
135 final static int open_tax_web = 7;
136 final static int cut_subtree = 8;
137 final static int copy_subtree = 9;
138 final static int paste_subtree = 10;
139 final static int delete_subtree_or_node = 11;
140 final static int add_new_node = 12;
141 final static int edit_node_data = 13;
142 final static int blast = 14;
143 final static int sort_descendents = 15;
146 // ---------------------------
147 // Display options for trees
148 // ---------------------------
149 // ---------------------------------
150 // Pertaining to the config itself
151 // ---------------------------------
152 // Full path to config (may be URL)
153 String config_filename;
154 String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
155 final static String display_options[][] = {
156 { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
157 { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, { "Event", "display", "?" },
158 { "Taxonomy Colorize", "display", "no" }, { "Colorize Branches", "display", "no" },
159 { "Use Branch-Widths", "display", "no" }, { "Show Custom Nodes", "display", "yes" },
160 { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" },
161 { "Binary Char Counts", "nodisplay", "no" }, { "Prot/Gene Name", "display", "yes" },
162 { "Prot/Gene Acc", "display", "no" }, { "Show Internal Data", "display", "yes" },
163 { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" },
164 { "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" },
165 { "Prot/Gene Symbol", "display", "yes" }, { "Rollover", "display", "yes" },
166 { "Relation Confidence", "display", "no" }, { "Vector Data", "display", "no" },
167 { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" } };
168 final static String clickto_options[][] = {
169 { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
170 { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
171 { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Cut Subtree", "display" },
172 { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" },
173 { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Blast", "nodisplay" }, { "Sort Descendants", "display" } };
174 // This option is selected in the dropdown
175 int default_clickto = Configuration.display_node_data;
179 TreeColorSet tree_color_set;
183 TreeFontSet tree_font_set;
187 private static Hashtable<String, Color> _species_colors;
191 private static Hashtable<String, Color> _domain_colors;
195 private static Hashtable<String, Color> _annotation_colors;
196 boolean verbose = Constants.VERBOSE_DEFAULT;
197 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
198 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
199 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
200 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
201 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
202 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
203 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
204 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
205 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
206 private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
207 private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
208 private static String DEFAULT_FONT_FAMILY = "";
210 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
211 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
212 DEFAULT_FONT_FAMILY = font_name;
216 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
217 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
221 public Configuration() {
222 this( null, false, false, false );
225 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
226 if ( ForesterUtil.isEmpty( cf ) ) {
227 config_filename = default_config_filename;
230 config_filename = cf;
232 setWebLinks( new TreeMap<String, WebLink>() );
233 setDisplayColors( new TreeMap<String, Color>() );
234 config_filename = config_filename.trim();
237 // If URL, open accordingly
239 u = new URL( config_filename );
241 final InputStreamReader isr = new InputStreamReader( u.openStream() );
242 final BufferedReader bf = new BufferedReader( isr );
245 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
246 + config_filename + "]" );
248 catch ( final Exception e ) {
249 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
250 + config_filename + "]: " + e.getLocalizedMessage() );
253 catch ( final Exception e ) {
254 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
255 + config_filename + "]" );
259 // Otherwise, open as a file
260 File f = new File( config_filename );
262 f = new File( config_filename + ".txt" );
264 if ( f.exists() && f.canRead() ) {
266 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
270 catch ( final Exception e ) {
272 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
273 + config_filename + "]: " + e );
279 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
280 + config_filename + "]" );
286 private void createWebLink( final String url_str, final String desc, final String source_identifier ) {
287 WebLink weblink = null;
290 weblink = new WebLink( new URL( url_str.trim() ), desc.trim(), source_identifier.trim() );
292 catch ( final MalformedURLException e ) {
293 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not create URL from [" + url_str + "]" );
296 if ( !ex && ( weblink != null ) ) {
297 getWebLinks().put( weblink.getSourceIdentifier().toLowerCase(), weblink );
301 boolean displaySequenceRelations() {
302 return _display_sequence_relations;
305 boolean doCheckOption( final int which ) {
306 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
307 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
310 boolean doDisplayClickToOption( final int which ) {
311 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
314 boolean doDisplayOption( final int which ) {
315 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
319 * Will attempt to use the phylogeny to determine whether to check
320 * this or not (e.g. phylogram)
323 boolean doGuessCheckOption( final int which ) {
324 return display_options[ which ][ 2 ].equals( "?" );
327 Map<String, Color> getAnnotationColors() {
328 if ( _annotation_colors == null ) {
329 _annotation_colors = new Hashtable<String, Color>();
331 return _annotation_colors;
334 public String getBaseFontFamilyName() {
335 return _base_font_family_name;
338 int getBaseFontSize() {
339 return _base_font_size;
342 CLADOGRAM_TYPE getCladogramType() {
343 return _cladogram_type;
346 private int getClickToIndex( final String name ) {
348 if ( name.equals( "edit_info" ) ) {
349 index = Configuration.display_node_data;
351 .printWarningMessage( Constants.PRG_NAME,
352 "configuration key [edit_info] is deprecated, use [display node data] instead" );
354 else if ( name.equals( "display_node_data" ) ) {
355 index = Configuration.display_node_data;
357 else if ( name.equals( "collapse_uncollapse" ) ) {
358 index = Configuration.collapse_uncollapse;
360 else if ( name.equals( "reroot" ) ) {
361 index = Configuration.reroot;
363 else if ( name.equals( "subtree" ) ) {
364 index = Configuration.subtree;
366 else if ( name.equals( "swap" ) ) {
367 index = Configuration.swap;
369 else if ( name.equals( "sort_descendants" ) ) {
370 index = Configuration.sort_descendents;
372 else if ( name.equals( "display_sequences" ) ) {
374 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
377 else if ( name.equals( "open_seq_web" ) ) {
378 index = Configuration.open_seq_web;
380 else if ( name.equals( "open_tax_web" ) ) {
381 index = Configuration.open_tax_web;
383 else if ( name.equals( "cut_subtree" ) ) {
384 index = Configuration.cut_subtree;
386 else if ( name.equals( "copy_subtree" ) ) {
387 index = Configuration.copy_subtree;
389 else if ( name.equals( "paste_subtree" ) ) {
390 index = Configuration.paste_subtree;
392 else if ( name.equals( "delete" ) ) {
393 index = Configuration.delete_subtree_or_node;
395 else if ( name.equals( "add_new_node" ) ) {
396 index = Configuration.add_new_node;
398 else if ( name.equals( "edit_node_data" ) ) {
399 index = Configuration.edit_node_data;
401 else if ( name.equals( "display_node_popup" ) ) {
402 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
403 "configuration key [display_node_popup] is deprecated" );
406 else if ( name.equals( "custom_option" ) ) {
407 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
410 else if ( name.equals( "color_subtree" ) ) {
411 index = Configuration.color_subtree;
413 else if ( name.equals( "go_to_swiss_prot" ) ) {
414 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" );
420 int getClickToOptionsCount() {
421 return clickto_options.length;
424 String getClickToTitle( final int which ) {
425 return clickto_options[ which ][ 0 ];
428 public int getDefaultBootstrapSamples() {
429 return _default_bootstrap_samples;
432 int getDefaultDisplayClicktoOption() {
433 return default_clickto;
436 public NodeFill getDefaultNodeFill() {
437 return _default_node_fill;
440 public NodeShape getDefaultNodeShape() {
441 return _default_node_shape;
444 public short getDefaultNodeShapeSize() {
445 return _default_node_shape_size;
448 SortedMap<String, Color> getDisplayColors() {
449 return _display_colors;
452 String getDisplayTitle( final int which ) {
453 return display_options[ which ][ 0 ];
456 Map<String, Color> getDomainColors() {
457 if ( _domain_colors == null ) {
458 _domain_colors = new Hashtable<String, Color>();
460 return _domain_colors;
463 public Color getDomainStructureBaseColor() {
464 return _domain_structure_base_color;
467 public Color getDomainStructureFontColor() {
468 return _domain_structure_font_color;
471 int getGraphicsExportX() {
472 return _graphics_export_x;
475 int getGraphicsExportY() {
476 return _graphics_export_y;
479 Color getGuiBackgroundColor() {
480 return _gui_background_color;
483 Color getGuiButtonBackgroundColor() {
484 return _gui_button_background_color;
487 Color getGuiButtonBorderColor() {
488 return _gui_button_border_color;
491 Color getGuiButtonTextColor() {
492 return _gui_button_text_color;
495 Color getGuiCheckboxAndButtonActiveColor() {
496 return _gui_checkbox_and_button_active_color;
499 Color getGuiCheckboxTextColor() {
500 return _gui_checkbox_text_color;
503 Color getGuiMenuBackgroundColor() {
504 return _gui_menu_background_color;
507 Color getGuiMenuTextColor() {
508 return _gui_menu_text_color;
511 double getMinConfidenceValue() {
512 return _min_confidence_value;
515 NODE_LABEL_DIRECTION getNodeLabelDirection() {
516 return _node_label_direction;
519 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
520 return _number_of_digits_after_comma_for_branch_length_values;
523 short getNumberOfDigitsAfterCommaForConfidenceValues() {
524 return _number_of_digits_after_comma_for_confidence_values;
527 short getOvMaxHeight() {
528 return _ov_max_height;
531 short getOvMaxWidth() {
532 return _ov_max_width;
535 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
536 return _ov_placement;
539 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
540 return _phylogeny_graphics_type;
543 float getPrintLineWidth() {
544 return _print_line_width;
547 Hashtable<String, Color> getSpeciesColors() {
548 if ( _species_colors == null ) {
549 _species_colors = new Hashtable<String, Color>();
551 return _species_colors;
554 TreeColorSet getTreeColorSet() {
558 TreeFontSet getTreeFontSet() {
562 WebLink getWebLink( final String source ) {
563 return getWebLinks().get( source );
566 Map<String, WebLink> getWebLinks() {
570 public boolean isAbbreviateScientificTaxonNames() {
571 return _abbreviate_scientific_names;
574 boolean isAntialiasScreen() {
575 return _antialias_screen;
578 public boolean isBackgroundColorGradient() {
579 return _background_color_gradient;
582 public boolean isColorLabelsSameAsParentBranch() {
583 return _color_labels_same_as_parent_branch;
587 * Convenience method.
589 * @return true if value in configuration file was 'yes'
591 boolean isDrawAsPhylogram() {
592 return doCheckOption( display_as_phylogram );
595 boolean isEditable() {
599 boolean isExtractPfamTaxonomyCodesInNhParsing() {
600 return _nh_parsing_extract_pfam_taxonomy_codes;
603 boolean isHasWebLink( final String source ) {
604 return getWebLinks().containsKey( source );
608 * Only used by ArchaeoptryxE.
611 boolean isHideControlPanelAndMenubar() {
612 return _hide_controls_and_menus;
615 boolean isInternalNumberAreConfidenceForNhParsing() {
616 return _internal_number_are_confidence_for_nh_parsing;
619 boolean isReplaceUnderscoresInNhParsing() {
620 return _nh_parsing_replace_underscores;
623 boolean isShowBranchLengthValues() {
624 return _show_branch_length_values;
627 public boolean isShowDefaultNodeShapes() {
628 return _show_default_node_shapes;
631 public boolean isShowDomainLabels() {
632 return _show_domain_labels;
635 boolean isShowOverview() {
636 return _show_overview;
639 boolean isShowScale() {
643 public boolean isTaxonomyColorizeNodeShapes() {
644 return _taxonomy_colorize_node_shapes;
647 final boolean isUseNativeUI() {
648 if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) {
651 return _ui == UI.NATIVE;
655 * Only used by ArchaeoptryxE.
658 boolean isUseTabbedDisplay() {
659 return _use_tabbed_display;
662 boolean isValidatePhyloXmlAgainstSchema() {
663 return _validate_against_phyloxml_xsd_schema;
666 private boolean parseBoolean( final String str ) {
667 final String my_str = str.trim().toLowerCase();
668 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
671 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
675 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
680 private double parseDouble( final String str ) {
683 d = Double.parseDouble( str );
685 catch ( final Exception e ) {
686 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
692 private float parseFloat( final String str ) {
695 f = Float.parseFloat( str );
697 catch ( final Exception e ) {
698 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
704 private int parseInt( final String str ) {
707 i = Integer.parseInt( str );
709 catch ( final Exception e ) {
710 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
716 private short parseShort( final String str ) {
719 i = Short.parseShort( str );
721 catch ( final Exception e ) {
722 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
728 private void processFontFamily( final StringTokenizer st ) {
729 setBaseFontFamilyName( "" );
730 final String font_str = ( ( String ) st.nextElement() ).trim();
731 final String[] fonts = font_str.split( ",+" );
732 for( String font : fonts ) {
733 font = font.replace( '_', ' ' ).trim();
734 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
735 setBaseFontFamilyName( font );
741 public void putDisplayColors( final String key, final Color color ) {
742 getDisplayColors().put( key, color );
746 * read each line of config file, process non-comment lines
747 * @throws IOException
749 private void readConfig( final BufferedReader conf_in ) throws IOException {
752 line = conf_in.readLine();
753 if ( line != null ) {
755 // skip comments and blank lines
756 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
757 // convert runs of spaces to tabs
758 line = line.replaceAll( "\\s+", "\t" );
759 final StringTokenizer st = new StringTokenizer( line, "\t" );
763 } while ( line != null );
766 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
767 _abbreviate_scientific_names = abbreviate_scientific_names;
770 private void setAntialiasScreen( final boolean antialias_screen ) {
771 _antialias_screen = antialias_screen;
774 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
775 _background_color_gradient = background_color_gradient;
778 public void setBaseFontFamilyName( final String base_font_family_name ) {
779 _base_font_family_name = base_font_family_name;
782 public void setBaseFontSize( final int base_font_size ) {
783 _base_font_size = base_font_size;
786 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
787 _cladogram_type = cladogram_type;
790 public void setColorizeBranches( final boolean b ) {
791 display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
794 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
795 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
798 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
799 _default_bootstrap_samples = default_bootstrap_samples;
802 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
803 _default_node_fill = default_node_fill;
806 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
807 _default_node_shape = default_node_shape;
810 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
811 _default_node_shape_size = default_node_shape_size;
814 public void setDisplayAsPhylogram( final boolean b ) {
815 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
818 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
819 _display_colors = display_colors;
822 public void setDisplayConfidenceValues( final boolean b ) {
823 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
826 public void setDisplayInternalData( final boolean b ) {
827 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
830 public void setDisplayNodeNames( final boolean b ) {
831 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
834 public void setDisplaySequenceAcc( final boolean b ) {
835 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
838 public void setDisplaySequenceNames( final boolean b ) {
839 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
842 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
843 _display_sequence_relations = display_sequence_relations;
846 public void setDisplaySequenceSymbols( final boolean b ) {
847 display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no";
850 public void setDisplayTaxonomyCode( final boolean b ) {
851 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
854 public void setDisplayTaxonomyCommonNames( final boolean b ) {
855 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
858 public void setDisplayTaxonomyImages( final boolean b ) {
859 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
862 public void setDisplayTaxonomyScientificNames( final boolean b ) {
863 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
866 public void setDynamicallyHideData( final boolean b ) {
867 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
870 private void setEditable( final boolean editable ) {
871 _editable = editable;
874 public void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) {
875 _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes;
878 private void setGraphicsExportX( final int graphics_export_x ) {
879 _graphics_export_x = graphics_export_x;
882 private void setGraphicsExportY( final int graphics_export_y ) {
883 _graphics_export_y = graphics_export_y;
886 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
887 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
891 * Set a key-value(s) tuple
893 private void setKeyValue( final StringTokenizer st ) {
894 String key = ( String ) st.nextElement();
895 key = key.replace( ':', ' ' );
897 key = key.toLowerCase();
898 // Handle single value settings first:
899 if ( key.equals( "default_click_to" ) ) {
900 final String clickto_name = ( String ) st.nextElement();
901 default_clickto = getClickToIndex( clickto_name );
902 if ( default_clickto == -1 ) {
903 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
904 + "] for [default_click_to]" );
907 else if ( default_clickto == DEPRECATED ) {
911 else if ( key.equals( "native_ui" ) ) {
912 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
913 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
916 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
917 _ui = UI.CROSSPLATFORM;
919 else if ( my_str.equals( "?" ) ) {
923 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
928 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
929 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
931 else if ( key.equals( "antialias_screen" ) ) {
932 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
934 else if ( key.equals( "phylogeny_graphics_type" ) ) {
935 final String type_str = ( ( String ) st.nextElement() ).trim();
936 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
937 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
939 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
940 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
942 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
943 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
945 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
946 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
948 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
949 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
951 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
952 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
954 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
955 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
957 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
958 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
961 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
962 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
963 + "] for [phylogeny_graphics_type]" );
966 else if ( key.equals( "min_confidence_value" ) ) {
967 final String mcv_str = ( ( String ) st.nextElement() ).trim();
968 final double d = parseDouble( mcv_str );
969 setMinConfidenceValue( d );
971 else if ( key.equals( "font_family" ) ) {
972 processFontFamily( st );
974 else if ( key.equals( "font_size" ) ) {
975 final String size_str = ( ( String ) st.nextElement() ).trim();
976 final int i = parseInt( size_str );
977 setBaseFontSize( i );
979 else if ( key.equals( "graphics_export_x" ) ) {
980 final String str = ( ( String ) st.nextElement() ).trim();
981 final int i = parseInt( str );
982 setGraphicsExportX( i );
984 else if ( key.equals( "graphics_export_y" ) ) {
985 final String str = ( ( String ) st.nextElement() ).trim();
986 final int i = parseInt( str );
987 setGraphicsExportY( i );
989 else if ( key.equals( "pdf_export_line_width" ) ) {
990 final String str = ( ( String ) st.nextElement() ).trim();
991 final float f = parseFloat( str );
993 setPrintLineWidth( f );
996 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
997 "value for [pdf_export_line_width] cannot be zero or negative" );
1000 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1001 final String str = ( ( String ) st.nextElement() ).trim();
1002 final int i = parseInt( str );
1004 setDefaultBootstrapSamples( i );
1008 .printWarningMessage( Constants.PRG_NAME,
1009 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1012 else if ( key.equals( "show_scale" ) ) {
1013 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1015 else if ( key.equals( "show_overview" ) ) {
1016 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1018 else if ( key.equals( "show_branch_length_values" ) ) {
1019 setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
1021 else if ( key.equals( "background_gradient" ) ) {
1022 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1024 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1025 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1027 else if ( key.equals( "show_domain_labels" ) ) {
1028 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1030 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1031 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1033 else if ( key.equals( "cladogram_type" ) ) {
1034 final String type_str = ( ( String ) st.nextElement() ).trim();
1035 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1036 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1038 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1039 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1041 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1042 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1045 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1046 + "] for [cladogram_type]" );
1049 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1051 .printWarningMessage( Constants.PRG_NAME,
1052 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1054 else if ( key.equals( "hide_controls_and_menus" ) ) {
1055 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1057 else if ( key.equals( "use_tabbed_display" ) ) {
1058 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1060 else if ( key.equals( "overview_width" ) ) {
1061 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1064 else if ( key.equals( "overview_height" ) ) {
1065 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1066 setOvMaxHeight( i );
1068 else if ( key.equals( "overview_placement_type" ) ) {
1069 final String type_str = ( ( String ) st.nextElement() ).trim();
1070 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1071 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1073 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1074 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1076 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1077 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1079 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1080 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1083 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1084 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1085 + "] for [overview_placement_type]" );
1088 else if ( key.equals( "node_label_direction" ) ) {
1089 final String type_str = ( ( String ) st.nextElement() ).trim();
1090 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1091 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1093 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1094 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1097 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1098 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1099 + "] for [node_label_direction]" );
1102 else if ( key.equals( "branch_length_value_digits" ) ) {
1103 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1105 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1108 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1109 + "] for [branch_length_value_digits]" );
1112 else if ( key.equals( "confidence_value_digits" ) ) {
1113 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1115 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1118 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1119 + "] for [confidence_value_digits]" );
1122 else if ( key.equals( "allow_editing" ) ) {
1123 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1125 else if ( key.equals( "display_sequence_relations" ) ) {
1126 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1128 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1129 final boolean r = parseBoolean( ( String ) st.nextElement() );
1130 if ( r && isExtractPfamTaxonomyCodesInNhParsing() ) {
1132 .printWarningMessage( Constants.PRG_NAME,
1133 "attempt to extract taxonomies and replace underscores at the same time" );
1136 setReplaceUnderscoresInNhParsing( r );
1139 else if ( key.equals( "extract_taxonomy_codes_in_nh_parsing" ) ) {
1140 final boolean e = parseBoolean( ( String ) st.nextElement() );
1141 if ( e && isReplaceUnderscoresInNhParsing() ) {
1143 .printWarningMessage( Constants.PRG_NAME,
1144 "attempt to extract taxonomies and replace underscores at the same time" );
1147 setExtractPfamTaxonomyCodesInNhParsing( e );
1150 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1151 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1153 else if ( key.equals( "gui_background_color" ) ) {
1154 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1156 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1157 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1159 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1160 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1162 else if ( key.equals( "gui_button_text_color" ) ) {
1163 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1165 else if ( key.equals( "gui_button_background_color" ) ) {
1166 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1168 else if ( key.equals( "gui_menu_background_color" ) ) {
1169 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1171 else if ( key.equals( "gui_menu_text_color" ) ) {
1172 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1174 else if ( key.equals( "gui_button_border_color" ) ) {
1175 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1177 else if ( key.equals( "domain_structure_font_color" ) ) {
1178 _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
1180 else if ( key.equals( "domain_structure_base_color" ) ) {
1181 _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
1183 else if ( key.equals( "show_default_node_shapes" ) ) {
1184 setShowDefaultNodeShapes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1186 else if ( key.equals( "default_node_size" ) ) {
1187 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1188 setDefaultNodeShapeSize( i );
1190 else if ( key.equals( "default_node_fill" ) ) {
1191 final String fill_str = ( ( String ) st.nextElement() ).trim();
1192 if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.NONE.toString() ) ) {
1193 setDefaultNodeFill( NodeFill.NONE );
1195 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.GRADIENT.toString() ) ) {
1196 setDefaultNodeFill( NodeFill.GRADIENT );
1198 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.SOLID.toString() ) ) {
1199 setDefaultNodeFill( NodeFill.SOLID );
1202 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1203 + "] for [default_node_fill]" );
1206 else if ( key.equals( "default_node_shape" ) ) {
1207 final String shape_str = ( ( String ) st.nextElement() ).trim();
1208 if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.CIRCLE.toString() ) ) {
1209 setDefaultNodeShape( NodeShape.CIRCLE );
1211 else if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.RECTANGLE.toString() ) ) {
1212 setDefaultNodeShape( NodeShape.RECTANGLE );
1215 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1216 + "] for [default_node_shape]" );
1219 else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
1220 setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
1222 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1225 if ( key.equals( "use_real_br_lengths" ) || key.equals( "phylogram" ) ) {
1226 key_index = Configuration.display_as_phylogram;
1227 if ( key.equals( "use_real_br_lengths" ) ) {
1229 .printWarningMessage( Constants.PRG_NAME,
1230 "configuration key [use_real_br_lengths] is deprecated, use [phylogram] instead" );
1233 else if ( key.equals( "rollover" ) ) {
1234 key_index = Configuration.node_data_popup;
1236 else if ( key.equals( "color_according_to_species" ) ) {
1237 key_index = Configuration.color_according_to_species;
1239 else if ( key.equals( "show_node_names" ) ) {
1240 key_index = Configuration.show_node_names;
1242 else if ( key.equals( "show_taxonomy" ) || key.equals( "show_taxonomy_code" ) ) {
1243 key_index = Configuration.show_tax_code;
1244 if ( key.equals( "show_taxonomy" ) ) {
1246 .printWarningMessage( Constants.PRG_NAME,
1247 "configuration key [show_taxonomy] is deprecated, use [show_taxonomy_code] instead" );
1250 else if ( key.equals( "write_br_length_values" ) ) {
1251 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1252 "configuration key [write_br_length_values] is deprecated" );
1253 key_index = DEPRECATED;
1255 else if ( key.equals( "write_bootstrap_values" ) || key.equals( "write_confidence_values" ) ) {
1256 key_index = Configuration.write_confidence_values;
1257 if ( key.equals( "write_bootstrap_values" ) ) {
1259 .printWarningMessage( Constants.PRG_NAME,
1260 "configuration key [write_bootstrap_values] is deprecated, use [write_confidence_values] instead" );
1263 else if ( key.equals( "write_events" ) || key.equals( "write_dup_spec" ) ) {
1264 key_index = Configuration.write_events;
1265 if ( key.equals( "write_dup_spec" ) ) {
1267 .printWarningMessage( Constants.PRG_NAME,
1268 "configuration key [write_dup_spec] is deprecated, use [write_events] instead" );
1271 else if ( key.equals( "color_branches" ) ) {
1272 key_index = Configuration.color_branches;
1274 else if ( key.equals( "width_branches" ) ) {
1275 key_index = Configuration.width_branches;
1277 else if ( key.equals( "color_orthologous" ) ) {
1278 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1279 "configuration key [color_orthologous] is deprecated" );
1281 else if ( key.equals( "color_subtree_neighbors" ) ) {
1282 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1283 "configuration key [color_subtree_neighbors] is deprecated" );
1285 else if ( key.equals( "color_super_orthologous" ) ) {
1286 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1287 "configuration key [color_super_orthologous] is deprecated" );
1289 else if ( key.equals( "mark_nodes_with_box" ) ) {
1290 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1291 "configuration key [mark_nodes_with_box] is deprecated" );
1292 key_index = DEPRECATED;
1294 else if ( key.equals( "show_domain_architectures" ) ) {
1295 key_index = Configuration.show_domain_architectures;
1297 else if ( key.equals( "show_annotations" ) ) {
1298 key_index = Configuration.show_annotation;
1300 else if ( key.equals( "show_binary_characters" ) ) {
1301 key_index = Configuration.show_binary_characters;
1303 else if ( key.equals( "show_binary_character_counts" ) ) {
1304 key_index = Configuration.show_binary_character_counts;
1306 else if ( key.equals( "show_gene_names" ) ) {
1307 key_index = Configuration.show_gene_names;
1309 else if ( key.equals( "show_gene_symbols" ) ) {
1310 key_index = Configuration.show_gene_symbols;
1312 else if ( key.equals( "show_sequence_acc" ) ) {
1313 key_index = Configuration.show_sequence_acc;
1315 else if ( key.equals( "show_node_ids" ) ) {
1317 .printWarningMessage( Constants.PRG_NAME, "configuration key [show_node_ids] is deprecated" );
1318 key_index = DEPRECATED;
1320 else if ( key.equals( "display_internal_data" ) ) {
1321 key_index = Configuration.display_internal_data;
1323 else if ( key.equals( "dynamically_hide_data" ) ) {
1324 key_index = Configuration.dynamically_hide_data;
1326 else if ( key.equals( "show_taxonomy_names" ) ) {
1327 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1328 "configuration key [show_taxonomy_names] is deprecated" );
1329 key_index = DEPRECATED;
1331 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1332 key_index = Configuration.show_taxonomy_scientific_names;
1334 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1335 key_index = Configuration.show_taxonomy_common_names;
1337 else if ( key.equals( "show_taxonomy_images" ) ) {
1338 key_index = Configuration.show_taxonomy_images;
1340 else if ( key.equals( "color_according_to_annotation" ) ) {
1341 key_index = Configuration.color_according_to_annotation;
1343 else if ( key.equals( "show_vector_data" ) ) {
1344 key_index = Configuration.show_vector_data;
1346 else if ( key.equals( "show_properties" ) ) {
1347 key_index = Configuration.show_properties;
1349 else if ( key.equals( "show_relation_confidence" ) ) {
1350 key_index = Configuration.show_relation_confidence;
1352 else if ( key.equals( "show_custom_node_shapes" ) ) {
1353 key_index = Configuration.show_custom_node_shapes;
1355 // If we've found the key, set the values
1356 if ( key_index >= 0 ) {
1357 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1358 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1359 // otherwise, keep looking
1362 if ( key_index == DEPRECATED ) {
1365 else if ( key.equals( "click_to" ) ) {
1366 final String click_to_name = ( String ) st.nextElement();
1367 key_index = getClickToIndex( click_to_name );
1368 if ( key_index >= 0 ) {
1369 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1371 else if ( key_index == DEPRECATED ) {
1375 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1379 else if ( key.equals( "species_color" ) ) {
1380 getSpeciesColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1382 else if ( key.equals( "domain_color" ) ) {
1383 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1385 else if ( key.equals( "annotation_color" ) ) {
1386 getAnnotationColors()
1387 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1389 else if ( key.equals( "function_color" ) ) {
1390 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1391 "configuration key [function_color] is deprecated" );
1393 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1394 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1396 else if ( key.equals( WEB_LINK_KEY ) ) {
1397 if ( st.countTokens() == 3 ) {
1398 createWebLink( ( String ) st.nextElement(),
1399 ( String ) st.nextElement(),
1400 ( String ) st.nextElement() );
1403 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1404 "illegal format in configuration file for key [" + key + "]" );
1408 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1409 + "] in: " + config_filename );
1414 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1415 + config_filename );
1419 public void setMinConfidenceValue( final double min_confidence_value ) {
1420 _min_confidence_value = min_confidence_value;
1423 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
1424 _node_label_direction = node_label_direction;
1427 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short _number_of_digits_after_comma_for_branch_length_values ) {
1428 this._number_of_digits_after_comma_for_branch_length_values = _number_of_digits_after_comma_for_branch_length_values;
1431 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short _number_of_digits_after_comma_for_confidence_values ) {
1432 this._number_of_digits_after_comma_for_confidence_values = _number_of_digits_after_comma_for_confidence_values;
1435 private void setOvMaxHeight( final short ov_max_height ) {
1436 _ov_max_height = ov_max_height;
1439 private void setOvMaxWidth( final short ov_max_width ) {
1440 _ov_max_width = ov_max_width;
1443 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1444 _ov_placement = ov_placement;
1447 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
1448 _phylogeny_graphics_type = phylogeny_graphics_type;
1451 public void setPrintLineWidth( final float print_line_width ) {
1452 _print_line_width = print_line_width;
1455 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
1456 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
1459 public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
1460 _show_branch_length_values = show_branch_length_values;
1463 public void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
1464 _show_default_node_shapes = show_default_node_shapes;
1467 public void setShowDomainLabels( final boolean show_domain_labels ) {
1468 _show_domain_labels = show_domain_labels;
1471 private void setShowOverview( final boolean show_overview ) {
1472 _show_overview = show_overview;
1475 public void setShowScale( final boolean show_scale ) {
1476 _show_scale = show_scale;
1479 public void setTaxonomyColorize( final boolean b ) {
1480 display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
1483 public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
1484 _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
1487 public void setUseBranchesWidths( final boolean b ) {
1488 display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
1491 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1492 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1495 void setWebLinks( final SortedMap<String, WebLink> weblinks ) {
1496 _weblinks = weblinks;
1499 static String getDefaultFontFamilyName() {
1500 return DEFAULT_FONT_FAMILY;
1503 static enum TRIPLET {
1504 TRUE, FALSE, UNKNOWN
1508 NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN