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 blast = 8;
137 final static int cut_subtree = 9;
138 final static int copy_subtree = 10;
139 final static int paste_subtree = 11;
140 final static int delete_subtree_or_node = 12;
141 final static int add_new_node = 13;
142 final static int edit_node_data = 14;
143 final static int sort_descendents = 15;
144 // ---------------------------
145 // Display options for trees
146 // ---------------------------
147 // ---------------------------------
148 // Pertaining to the config itself
149 // ---------------------------------
150 // Full path to config (may be URL)
151 String config_filename;
152 String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
153 final static String display_options[][] = {
154 { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
155 { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, { "Event", "display", "?" },
156 { "Taxonomy Colorize", "display", "no" }, { "Colorize Branches", "display", "no" },
157 { "Use Branch-Widths", "display", "no" }, { "Show Custom Nodes", "display", "yes" },
158 { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" },
159 { "Binary Char Counts", "nodisplay", "no" }, { "Prot/Gene Name", "display", "yes" },
160 { "Prot/Gene Acc", "display", "no" }, { "Show Internal Data", "display", "yes" },
161 { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" },
162 { "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" },
163 { "Prot/Gene Symbol", "display", "yes" }, { "Rollover", "display", "yes" },
164 { "Relation Confidence", "display", "no" }, { "Vector Data", "display", "no" },
165 { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" } };
166 final static String clickto_options[][] = {
167 { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
168 { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
169 { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Blast", "display" },
170 { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" },
171 { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" },
172 { "Sort Descendants", "display" } };
173 // This option is selected in the dropdown
174 int default_clickto = Configuration.display_node_data;
178 TreeColorSet tree_color_set;
182 TreeFontSet tree_font_set;
186 private static Hashtable<String, Color> _species_colors;
190 private static Hashtable<String, Color> _domain_colors;
194 private static Hashtable<String, Color> _annotation_colors;
195 boolean verbose = Constants.VERBOSE_DEFAULT;
196 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
197 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
198 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
199 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
200 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
201 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
202 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
203 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
204 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
205 private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
206 private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
207 private static String DEFAULT_FONT_FAMILY = "";
209 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
210 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
211 DEFAULT_FONT_FAMILY = font_name;
215 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
216 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
220 public Configuration() {
221 this( null, false, false, false );
224 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
225 if ( ForesterUtil.isEmpty( cf ) ) {
226 config_filename = default_config_filename;
229 config_filename = cf;
231 setWebLinks( new TreeMap<String, WebLink>() );
232 setDisplayColors( new TreeMap<String, Color>() );
233 config_filename = config_filename.trim();
236 // If URL, open accordingly
238 u = new URL( config_filename );
240 final InputStreamReader isr = new InputStreamReader( u.openStream() );
241 final BufferedReader bf = new BufferedReader( isr );
244 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
245 + config_filename + "]" );
247 catch ( final Exception e ) {
248 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
249 + config_filename + "]: " + e.getLocalizedMessage() );
252 catch ( final Exception e ) {
253 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
254 + config_filename + "]" );
258 // Otherwise, open as a file
259 File f = new File( config_filename );
261 f = new File( config_filename + ".txt" );
263 if ( f.exists() && f.canRead() ) {
265 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
269 catch ( final Exception e ) {
271 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
272 + config_filename + "]: " + e );
278 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
279 + config_filename + "]" );
285 private void createWebLink( final String url_str, final String desc, final String source_identifier ) {
286 WebLink weblink = null;
289 weblink = new WebLink( new URL( url_str.trim() ), desc.trim(), source_identifier.trim() );
291 catch ( final MalformedURLException e ) {
292 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not create URL from [" + url_str + "]" );
295 if ( !ex && ( weblink != null ) ) {
296 getWebLinks().put( weblink.getSourceIdentifier().toLowerCase(), weblink );
300 boolean displaySequenceRelations() {
301 return _display_sequence_relations;
304 boolean doCheckOption( final int which ) {
305 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
306 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
309 boolean doDisplayClickToOption( final int which ) {
310 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
313 boolean doDisplayOption( final int which ) {
314 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
318 * Will attempt to use the phylogeny to determine whether to check
319 * this or not (e.g. phylogram)
322 boolean doGuessCheckOption( final int which ) {
323 return display_options[ which ][ 2 ].equals( "?" );
326 Map<String, Color> getAnnotationColors() {
327 if ( _annotation_colors == null ) {
328 _annotation_colors = new Hashtable<String, Color>();
330 return _annotation_colors;
333 public String getBaseFontFamilyName() {
334 return _base_font_family_name;
337 int getBaseFontSize() {
338 return _base_font_size;
341 CLADOGRAM_TYPE getCladogramType() {
342 return _cladogram_type;
345 private int getClickToIndex( final String name ) {
347 if ( name.equals( "edit_info" ) ) {
348 index = Configuration.display_node_data;
350 .printWarningMessage( Constants.PRG_NAME,
351 "configuration key [edit_info] is deprecated, use [display node data] instead" );
353 else if ( name.equals( "display_node_data" ) ) {
354 index = Configuration.display_node_data;
356 else if ( name.equals( "collapse_uncollapse" ) ) {
357 index = Configuration.collapse_uncollapse;
359 else if ( name.equals( "reroot" ) ) {
360 index = Configuration.reroot;
362 else if ( name.equals( "subtree" ) ) {
363 index = Configuration.subtree;
365 else if ( name.equals( "swap" ) ) {
366 index = Configuration.swap;
368 else if ( name.equals( "sort_descendants" ) ) {
369 index = Configuration.sort_descendents;
371 else if ( name.equals( "display_sequences" ) ) {
373 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
376 else if ( name.equals( "open_seq_web" ) ) {
377 index = Configuration.open_seq_web;
379 else if ( name.equals( "open_tax_web" ) ) {
380 index = Configuration.open_tax_web;
382 else if ( name.equals( "blast" ) ) {
383 index = Configuration.blast;
385 else if ( name.equals( "cut_subtree" ) ) {
386 index = Configuration.cut_subtree;
388 else if ( name.equals( "copy_subtree" ) ) {
389 index = Configuration.copy_subtree;
391 else if ( name.equals( "paste_subtree" ) ) {
392 index = Configuration.paste_subtree;
394 else if ( name.equals( "delete" ) ) {
395 index = Configuration.delete_subtree_or_node;
397 else if ( name.equals( "add_new_node" ) ) {
398 index = Configuration.add_new_node;
400 else if ( name.equals( "edit_node_data" ) ) {
401 index = Configuration.edit_node_data;
403 else if ( name.equals( "display_node_popup" ) ) {
404 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
405 "configuration key [display_node_popup] is deprecated" );
408 else if ( name.equals( "custom_option" ) ) {
409 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
412 else if ( name.equals( "color_subtree" ) ) {
413 index = Configuration.color_subtree;
415 else if ( name.equals( "go_to_swiss_prot" ) ) {
416 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" );
422 int getClickToOptionsCount() {
423 return clickto_options.length;
426 String getClickToTitle( final int which ) {
427 return clickto_options[ which ][ 0 ];
430 public int getDefaultBootstrapSamples() {
431 return _default_bootstrap_samples;
434 int getDefaultDisplayClicktoOption() {
435 return default_clickto;
438 public NodeFill getDefaultNodeFill() {
439 return _default_node_fill;
442 public NodeShape getDefaultNodeShape() {
443 return _default_node_shape;
446 public short getDefaultNodeShapeSize() {
447 return _default_node_shape_size;
450 SortedMap<String, Color> getDisplayColors() {
451 return _display_colors;
454 String getDisplayTitle( final int which ) {
455 return display_options[ which ][ 0 ];
458 Map<String, Color> getDomainColors() {
459 if ( _domain_colors == null ) {
460 _domain_colors = new Hashtable<String, Color>();
462 return _domain_colors;
465 public Color getDomainStructureBaseColor() {
466 return _domain_structure_base_color;
469 public Color getDomainStructureFontColor() {
470 return _domain_structure_font_color;
473 int getGraphicsExportX() {
474 return _graphics_export_x;
477 int getGraphicsExportY() {
478 return _graphics_export_y;
481 Color getGuiBackgroundColor() {
482 return _gui_background_color;
485 Color getGuiButtonBackgroundColor() {
486 return _gui_button_background_color;
489 Color getGuiButtonBorderColor() {
490 return _gui_button_border_color;
493 Color getGuiButtonTextColor() {
494 return _gui_button_text_color;
497 Color getGuiCheckboxAndButtonActiveColor() {
498 return _gui_checkbox_and_button_active_color;
501 Color getGuiCheckboxTextColor() {
502 return _gui_checkbox_text_color;
505 Color getGuiMenuBackgroundColor() {
506 return _gui_menu_background_color;
509 Color getGuiMenuTextColor() {
510 return _gui_menu_text_color;
513 double getMinConfidenceValue() {
514 return _min_confidence_value;
517 NODE_LABEL_DIRECTION getNodeLabelDirection() {
518 return _node_label_direction;
521 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
522 return _number_of_digits_after_comma_for_branch_length_values;
525 short getNumberOfDigitsAfterCommaForConfidenceValues() {
526 return _number_of_digits_after_comma_for_confidence_values;
529 short getOvMaxHeight() {
530 return _ov_max_height;
533 short getOvMaxWidth() {
534 return _ov_max_width;
537 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
538 return _ov_placement;
541 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
542 return _phylogeny_graphics_type;
545 float getPrintLineWidth() {
546 return _print_line_width;
549 Hashtable<String, Color> getSpeciesColors() {
550 if ( _species_colors == null ) {
551 _species_colors = new Hashtable<String, Color>();
553 return _species_colors;
556 TreeColorSet getTreeColorSet() {
560 TreeFontSet getTreeFontSet() {
564 WebLink getWebLink( final String source ) {
565 return getWebLinks().get( source );
568 Map<String, WebLink> getWebLinks() {
572 public boolean isAbbreviateScientificTaxonNames() {
573 return _abbreviate_scientific_names;
576 boolean isAntialiasScreen() {
577 return _antialias_screen;
580 public boolean isBackgroundColorGradient() {
581 return _background_color_gradient;
584 public boolean isColorLabelsSameAsParentBranch() {
585 return _color_labels_same_as_parent_branch;
589 * Convenience method.
591 * @return true if value in configuration file was 'yes'
593 boolean isDrawAsPhylogram() {
594 return doCheckOption( display_as_phylogram );
597 boolean isEditable() {
601 boolean isExtractPfamTaxonomyCodesInNhParsing() {
602 return _nh_parsing_extract_pfam_taxonomy_codes;
605 boolean isHasWebLink( final String source ) {
606 return getWebLinks().containsKey( source );
610 * Only used by ArchaeoptryxE.
613 boolean isHideControlPanelAndMenubar() {
614 return _hide_controls_and_menus;
617 boolean isInternalNumberAreConfidenceForNhParsing() {
618 return _internal_number_are_confidence_for_nh_parsing;
621 boolean isReplaceUnderscoresInNhParsing() {
622 return _nh_parsing_replace_underscores;
625 boolean isShowBranchLengthValues() {
626 return _show_branch_length_values;
629 public boolean isShowDefaultNodeShapes() {
630 return _show_default_node_shapes;
633 public boolean isShowDomainLabels() {
634 return _show_domain_labels;
637 boolean isShowOverview() {
638 return _show_overview;
641 boolean isShowScale() {
645 public boolean isTaxonomyColorizeNodeShapes() {
646 return _taxonomy_colorize_node_shapes;
649 final boolean isUseNativeUI() {
650 if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) {
653 return _ui == UI.NATIVE;
657 * Only used by ArchaeoptryxE.
660 boolean isUseTabbedDisplay() {
661 return _use_tabbed_display;
664 boolean isValidatePhyloXmlAgainstSchema() {
665 return _validate_against_phyloxml_xsd_schema;
668 private boolean parseBoolean( final String str ) {
669 final String my_str = str.trim().toLowerCase();
670 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
673 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
677 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
682 private double parseDouble( final String str ) {
685 d = Double.parseDouble( str );
687 catch ( final Exception e ) {
688 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
694 private float parseFloat( final String str ) {
697 f = Float.parseFloat( str );
699 catch ( final Exception e ) {
700 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
706 private int parseInt( final String str ) {
709 i = Integer.parseInt( str );
711 catch ( final Exception e ) {
712 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
718 private short parseShort( final String str ) {
721 i = Short.parseShort( str );
723 catch ( final Exception e ) {
724 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
730 private void processFontFamily( final StringTokenizer st ) {
731 setBaseFontFamilyName( "" );
732 final String font_str = ( ( String ) st.nextElement() ).trim();
733 final String[] fonts = font_str.split( ",+" );
734 for( String font : fonts ) {
735 font = font.replace( '_', ' ' ).trim();
736 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
737 setBaseFontFamilyName( font );
743 public void putDisplayColors( final String key, final Color color ) {
744 getDisplayColors().put( key, color );
748 * read each line of config file, process non-comment lines
749 * @throws IOException
751 private void readConfig( final BufferedReader conf_in ) throws IOException {
754 line = conf_in.readLine();
755 if ( line != null ) {
757 // skip comments and blank lines
758 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
759 // convert runs of spaces to tabs
760 line = line.replaceAll( "\\s+", "\t" );
761 final StringTokenizer st = new StringTokenizer( line, "\t" );
765 } while ( line != null );
768 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
769 _abbreviate_scientific_names = abbreviate_scientific_names;
772 private void setAntialiasScreen( final boolean antialias_screen ) {
773 _antialias_screen = antialias_screen;
776 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
777 _background_color_gradient = background_color_gradient;
780 public void setBaseFontFamilyName( final String base_font_family_name ) {
781 _base_font_family_name = base_font_family_name;
784 public void setBaseFontSize( final int base_font_size ) {
785 _base_font_size = base_font_size;
788 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
789 _cladogram_type = cladogram_type;
792 public void setColorizeBranches( final boolean b ) {
793 display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
796 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
797 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
800 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
801 _default_bootstrap_samples = default_bootstrap_samples;
804 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
805 _default_node_fill = default_node_fill;
808 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
809 _default_node_shape = default_node_shape;
812 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
813 _default_node_shape_size = default_node_shape_size;
816 public void setDisplayAsPhylogram( final boolean b ) {
817 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
820 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
821 _display_colors = display_colors;
824 public void setDisplayConfidenceValues( final boolean b ) {
825 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
828 public void setDisplayInternalData( final boolean b ) {
829 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
832 public void setDisplayNodeNames( final boolean b ) {
833 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
836 public void setDisplaySequenceAcc( final boolean b ) {
837 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
840 public void setDisplaySequenceNames( final boolean b ) {
841 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
844 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
845 _display_sequence_relations = display_sequence_relations;
848 public void setDisplaySequenceSymbols( final boolean b ) {
849 display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no";
852 public void setDisplayTaxonomyCode( final boolean b ) {
853 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
856 public void setDisplayTaxonomyCommonNames( final boolean b ) {
857 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
860 public void setDisplayTaxonomyImages( final boolean b ) {
861 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
864 public void setDisplayTaxonomyScientificNames( final boolean b ) {
865 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
868 public void setDynamicallyHideData( final boolean b ) {
869 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
872 private void setEditable( final boolean editable ) {
873 _editable = editable;
876 public void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) {
877 _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes;
880 private void setGraphicsExportX( final int graphics_export_x ) {
881 _graphics_export_x = graphics_export_x;
884 private void setGraphicsExportY( final int graphics_export_y ) {
885 _graphics_export_y = graphics_export_y;
888 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
889 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
893 * Set a key-value(s) tuple
895 private void setKeyValue( final StringTokenizer st ) {
896 String key = ( String ) st.nextElement();
897 key = key.replace( ':', ' ' );
899 key = key.toLowerCase();
900 // Handle single value settings first:
901 if ( key.equals( "default_click_to" ) ) {
902 final String clickto_name = ( String ) st.nextElement();
903 default_clickto = getClickToIndex( clickto_name );
904 if ( default_clickto == -1 ) {
905 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
906 + "] for [default_click_to]" );
909 else if ( default_clickto == DEPRECATED ) {
913 else if ( key.equals( "native_ui" ) ) {
914 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
915 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
918 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
919 _ui = UI.CROSSPLATFORM;
921 else if ( my_str.equals( "?" ) ) {
925 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
930 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
931 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
933 else if ( key.equals( "antialias_screen" ) ) {
934 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
936 else if ( key.equals( "phylogeny_graphics_type" ) ) {
937 final String type_str = ( ( String ) st.nextElement() ).trim();
938 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
939 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
941 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
942 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
944 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
945 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
947 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
948 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
950 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
951 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
953 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
954 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
956 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
957 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
959 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
960 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
963 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
964 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
965 + "] for [phylogeny_graphics_type]" );
968 else if ( key.equals( "min_confidence_value" ) ) {
969 final String mcv_str = ( ( String ) st.nextElement() ).trim();
970 final double d = parseDouble( mcv_str );
971 setMinConfidenceValue( d );
973 else if ( key.equals( "font_family" ) ) {
974 processFontFamily( st );
976 else if ( key.equals( "font_size" ) ) {
977 final String size_str = ( ( String ) st.nextElement() ).trim();
978 final int i = parseInt( size_str );
979 setBaseFontSize( i );
981 else if ( key.equals( "graphics_export_x" ) ) {
982 final String str = ( ( String ) st.nextElement() ).trim();
983 final int i = parseInt( str );
984 setGraphicsExportX( i );
986 else if ( key.equals( "graphics_export_y" ) ) {
987 final String str = ( ( String ) st.nextElement() ).trim();
988 final int i = parseInt( str );
989 setGraphicsExportY( i );
991 else if ( key.equals( "pdf_export_line_width" ) ) {
992 final String str = ( ( String ) st.nextElement() ).trim();
993 final float f = parseFloat( str );
995 setPrintLineWidth( f );
998 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
999 "value for [pdf_export_line_width] cannot be zero or negative" );
1002 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1003 final String str = ( ( String ) st.nextElement() ).trim();
1004 final int i = parseInt( str );
1006 setDefaultBootstrapSamples( i );
1010 .printWarningMessage( Constants.PRG_NAME,
1011 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1014 else if ( key.equals( "show_scale" ) ) {
1015 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1017 else if ( key.equals( "show_overview" ) ) {
1018 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1020 else if ( key.equals( "show_branch_length_values" ) ) {
1021 setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
1023 else if ( key.equals( "background_gradient" ) ) {
1024 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1026 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1027 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1029 else if ( key.equals( "show_domain_labels" ) ) {
1030 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1032 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1033 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1035 else if ( key.equals( "cladogram_type" ) ) {
1036 final String type_str = ( ( String ) st.nextElement() ).trim();
1037 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1038 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1040 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1041 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1043 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1044 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1047 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1048 + "] for [cladogram_type]" );
1051 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1053 .printWarningMessage( Constants.PRG_NAME,
1054 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1056 else if ( key.equals( "hide_controls_and_menus" ) ) {
1057 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1059 else if ( key.equals( "use_tabbed_display" ) ) {
1060 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1062 else if ( key.equals( "overview_width" ) ) {
1063 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1066 else if ( key.equals( "overview_height" ) ) {
1067 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1068 setOvMaxHeight( i );
1070 else if ( key.equals( "overview_placement_type" ) ) {
1071 final String type_str = ( ( String ) st.nextElement() ).trim();
1072 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1073 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1075 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1076 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1078 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1079 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1081 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1082 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1085 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1086 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1087 + "] for [overview_placement_type]" );
1090 else if ( key.equals( "node_label_direction" ) ) {
1091 final String type_str = ( ( String ) st.nextElement() ).trim();
1092 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1093 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1095 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1096 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1099 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1100 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1101 + "] for [node_label_direction]" );
1104 else if ( key.equals( "branch_length_value_digits" ) ) {
1105 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1107 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1110 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1111 + "] for [branch_length_value_digits]" );
1114 else if ( key.equals( "confidence_value_digits" ) ) {
1115 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1117 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1120 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1121 + "] for [confidence_value_digits]" );
1124 else if ( key.equals( "allow_editing" ) ) {
1125 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1127 else if ( key.equals( "display_sequence_relations" ) ) {
1128 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1130 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1131 final boolean r = parseBoolean( ( String ) st.nextElement() );
1132 if ( r && isExtractPfamTaxonomyCodesInNhParsing() ) {
1134 .printWarningMessage( Constants.PRG_NAME,
1135 "attempt to extract taxonomies and replace underscores at the same time" );
1138 setReplaceUnderscoresInNhParsing( r );
1141 else if ( key.equals( "extract_taxonomy_codes_in_nh_parsing" ) ) {
1142 final boolean e = parseBoolean( ( String ) st.nextElement() );
1143 if ( e && isReplaceUnderscoresInNhParsing() ) {
1145 .printWarningMessage( Constants.PRG_NAME,
1146 "attempt to extract taxonomies and replace underscores at the same time" );
1149 setExtractPfamTaxonomyCodesInNhParsing( e );
1152 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1153 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1155 else if ( key.equals( "gui_background_color" ) ) {
1156 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1158 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1159 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1161 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1162 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1164 else if ( key.equals( "gui_button_text_color" ) ) {
1165 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1167 else if ( key.equals( "gui_button_background_color" ) ) {
1168 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1170 else if ( key.equals( "gui_menu_background_color" ) ) {
1171 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1173 else if ( key.equals( "gui_menu_text_color" ) ) {
1174 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1176 else if ( key.equals( "gui_button_border_color" ) ) {
1177 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1179 else if ( key.equals( "domain_structure_font_color" ) ) {
1180 _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
1182 else if ( key.equals( "domain_structure_base_color" ) ) {
1183 _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
1185 else if ( key.equals( "show_default_node_shapes" ) ) {
1186 setShowDefaultNodeShapes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1188 else if ( key.equals( "default_node_size" ) ) {
1189 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1190 setDefaultNodeShapeSize( i );
1192 else if ( key.equals( "default_node_fill" ) ) {
1193 final String fill_str = ( ( String ) st.nextElement() ).trim();
1194 if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.NONE.toString() ) ) {
1195 setDefaultNodeFill( NodeFill.NONE );
1197 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.GRADIENT.toString() ) ) {
1198 setDefaultNodeFill( NodeFill.GRADIENT );
1200 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.SOLID.toString() ) ) {
1201 setDefaultNodeFill( NodeFill.SOLID );
1204 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1205 + "] for [default_node_fill]" );
1208 else if ( key.equals( "default_node_shape" ) ) {
1209 final String shape_str = ( ( String ) st.nextElement() ).trim();
1210 if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.CIRCLE.toString() ) ) {
1211 setDefaultNodeShape( NodeShape.CIRCLE );
1213 else if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.RECTANGLE.toString() ) ) {
1214 setDefaultNodeShape( NodeShape.RECTANGLE );
1217 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1218 + "] for [default_node_shape]" );
1221 else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
1222 setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
1224 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1227 if ( key.equals( "use_real_br_lengths" ) || key.equals( "phylogram" ) ) {
1228 key_index = Configuration.display_as_phylogram;
1229 if ( key.equals( "use_real_br_lengths" ) ) {
1231 .printWarningMessage( Constants.PRG_NAME,
1232 "configuration key [use_real_br_lengths] is deprecated, use [phylogram] instead" );
1235 else if ( key.equals( "rollover" ) ) {
1236 key_index = Configuration.node_data_popup;
1238 else if ( key.equals( "color_according_to_species" ) ) {
1239 key_index = Configuration.color_according_to_species;
1241 else if ( key.equals( "show_node_names" ) ) {
1242 key_index = Configuration.show_node_names;
1244 else if ( key.equals( "show_taxonomy" ) || key.equals( "show_taxonomy_code" ) ) {
1245 key_index = Configuration.show_tax_code;
1246 if ( key.equals( "show_taxonomy" ) ) {
1248 .printWarningMessage( Constants.PRG_NAME,
1249 "configuration key [show_taxonomy] is deprecated, use [show_taxonomy_code] instead" );
1252 else if ( key.equals( "write_br_length_values" ) ) {
1253 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1254 "configuration key [write_br_length_values] is deprecated" );
1255 key_index = DEPRECATED;
1257 else if ( key.equals( "write_bootstrap_values" ) || key.equals( "write_confidence_values" ) ) {
1258 key_index = Configuration.write_confidence_values;
1259 if ( key.equals( "write_bootstrap_values" ) ) {
1261 .printWarningMessage( Constants.PRG_NAME,
1262 "configuration key [write_bootstrap_values] is deprecated, use [write_confidence_values] instead" );
1265 else if ( key.equals( "write_events" ) || key.equals( "write_dup_spec" ) ) {
1266 key_index = Configuration.write_events;
1267 if ( key.equals( "write_dup_spec" ) ) {
1269 .printWarningMessage( Constants.PRG_NAME,
1270 "configuration key [write_dup_spec] is deprecated, use [write_events] instead" );
1273 else if ( key.equals( "color_branches" ) ) {
1274 key_index = Configuration.color_branches;
1276 else if ( key.equals( "width_branches" ) ) {
1277 key_index = Configuration.width_branches;
1279 else if ( key.equals( "color_orthologous" ) ) {
1280 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1281 "configuration key [color_orthologous] is deprecated" );
1283 else if ( key.equals( "color_subtree_neighbors" ) ) {
1284 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1285 "configuration key [color_subtree_neighbors] is deprecated" );
1287 else if ( key.equals( "color_super_orthologous" ) ) {
1288 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1289 "configuration key [color_super_orthologous] is deprecated" );
1291 else if ( key.equals( "mark_nodes_with_box" ) ) {
1292 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1293 "configuration key [mark_nodes_with_box] is deprecated" );
1294 key_index = DEPRECATED;
1296 else if ( key.equals( "show_domain_architectures" ) ) {
1297 key_index = Configuration.show_domain_architectures;
1299 else if ( key.equals( "show_annotations" ) ) {
1300 key_index = Configuration.show_annotation;
1302 else if ( key.equals( "show_binary_characters" ) ) {
1303 key_index = Configuration.show_binary_characters;
1305 else if ( key.equals( "show_binary_character_counts" ) ) {
1306 key_index = Configuration.show_binary_character_counts;
1308 else if ( key.equals( "show_gene_names" ) ) {
1309 key_index = Configuration.show_gene_names;
1311 else if ( key.equals( "show_gene_symbols" ) ) {
1312 key_index = Configuration.show_gene_symbols;
1314 else if ( key.equals( "show_sequence_acc" ) ) {
1315 key_index = Configuration.show_sequence_acc;
1317 else if ( key.equals( "show_node_ids" ) ) {
1319 .printWarningMessage( Constants.PRG_NAME, "configuration key [show_node_ids] is deprecated" );
1320 key_index = DEPRECATED;
1322 else if ( key.equals( "display_internal_data" ) ) {
1323 key_index = Configuration.display_internal_data;
1325 else if ( key.equals( "dynamically_hide_data" ) ) {
1326 key_index = Configuration.dynamically_hide_data;
1328 else if ( key.equals( "show_taxonomy_names" ) ) {
1329 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1330 "configuration key [show_taxonomy_names] is deprecated" );
1331 key_index = DEPRECATED;
1333 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1334 key_index = Configuration.show_taxonomy_scientific_names;
1336 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1337 key_index = Configuration.show_taxonomy_common_names;
1339 else if ( key.equals( "show_taxonomy_images" ) ) {
1340 key_index = Configuration.show_taxonomy_images;
1342 else if ( key.equals( "color_according_to_annotation" ) ) {
1343 key_index = Configuration.color_according_to_annotation;
1345 else if ( key.equals( "show_vector_data" ) ) {
1346 key_index = Configuration.show_vector_data;
1348 else if ( key.equals( "show_properties" ) ) {
1349 key_index = Configuration.show_properties;
1351 else if ( key.equals( "show_relation_confidence" ) ) {
1352 key_index = Configuration.show_relation_confidence;
1354 else if ( key.equals( "show_custom_node_shapes" ) ) {
1355 key_index = Configuration.show_custom_node_shapes;
1357 // If we've found the key, set the values
1358 if ( key_index >= 0 ) {
1359 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1360 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1361 // otherwise, keep looking
1364 if ( key_index == DEPRECATED ) {
1367 else if ( key.equals( "click_to" ) ) {
1368 final String click_to_name = ( String ) st.nextElement();
1369 key_index = getClickToIndex( click_to_name );
1370 if ( key_index >= 0 ) {
1371 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1373 else if ( key_index == DEPRECATED ) {
1377 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1381 else if ( key.equals( "species_color" ) ) {
1382 getSpeciesColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1384 else if ( key.equals( "domain_color" ) ) {
1385 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1387 else if ( key.equals( "annotation_color" ) ) {
1388 getAnnotationColors()
1389 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1391 else if ( key.equals( "function_color" ) ) {
1392 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1393 "configuration key [function_color] is deprecated" );
1395 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1396 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1398 else if ( key.equals( WEB_LINK_KEY ) ) {
1399 if ( st.countTokens() == 3 ) {
1400 createWebLink( ( String ) st.nextElement(),
1401 ( String ) st.nextElement(),
1402 ( String ) st.nextElement() );
1405 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1406 "illegal format in configuration file for key [" + key + "]" );
1410 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1411 + "] in: " + config_filename );
1416 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1417 + config_filename );
1421 public void setMinConfidenceValue( final double min_confidence_value ) {
1422 _min_confidence_value = min_confidence_value;
1425 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
1426 _node_label_direction = node_label_direction;
1429 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short _number_of_digits_after_comma_for_branch_length_values ) {
1430 this._number_of_digits_after_comma_for_branch_length_values = _number_of_digits_after_comma_for_branch_length_values;
1433 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short _number_of_digits_after_comma_for_confidence_values ) {
1434 this._number_of_digits_after_comma_for_confidence_values = _number_of_digits_after_comma_for_confidence_values;
1437 private void setOvMaxHeight( final short ov_max_height ) {
1438 _ov_max_height = ov_max_height;
1441 private void setOvMaxWidth( final short ov_max_width ) {
1442 _ov_max_width = ov_max_width;
1445 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1446 _ov_placement = ov_placement;
1449 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
1450 _phylogeny_graphics_type = phylogeny_graphics_type;
1453 public void setPrintLineWidth( final float print_line_width ) {
1454 _print_line_width = print_line_width;
1457 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
1458 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
1461 public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
1462 _show_branch_length_values = show_branch_length_values;
1465 public void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
1466 _show_default_node_shapes = show_default_node_shapes;
1469 public void setShowDomainLabels( final boolean show_domain_labels ) {
1470 _show_domain_labels = show_domain_labels;
1473 private void setShowOverview( final boolean show_overview ) {
1474 _show_overview = show_overview;
1477 public void setShowScale( final boolean show_scale ) {
1478 _show_scale = show_scale;
1481 public void setTaxonomyColorize( final boolean b ) {
1482 display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
1485 public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
1486 _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
1489 public void setUseBranchesWidths( final boolean b ) {
1490 display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
1493 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1494 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1497 void setWebLinks( final SortedMap<String, WebLink> weblinks ) {
1498 _weblinks = weblinks;
1501 static String getDefaultFontFamilyName() {
1502 return DEFAULT_FONT_FAMILY;
1505 static enum TRIPLET {
1506 TRUE, FALSE, UNKNOWN
1510 NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN