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 boolean _show_default_node_shapes = false;
94 private NodeShape _default_node_shape = NodeShape.CIRCLE;
95 private NodeFill _default_node_fill = NodeFill.GRADIENT;
96 private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
97 private boolean _taxonomy_colorize_node_shapes = false;
98 private int _default_bootstrap_samples = -1;
99 private File _path_to_local_mafft = null;
100 private File _path_to_local_fastme = null;
101 private File _path_to_local_raxml = null;
102 private File _path_to_local_clustalo = null;
103 final static int display_as_phylogram = 0;
104 final static int show_node_names = 1;
105 final static int show_tax_code = 2;
106 final static int show_annotation = 3;
107 final static int write_confidence_values = 4;
108 final static int write_events = 5;
109 final static int color_according_to_species = 6;
110 final static int color_branches = 7;
111 final static int width_branches = 8;
112 final static int show_custom_node_shapes = 9;
113 final static int show_domain_architectures = 10;
114 final static int show_binary_characters = 11;
115 final static int show_binary_character_counts = 12;
116 final static int show_gene_names = 13;
117 final static int show_sequence_acc = 14;
118 final static int display_internal_data = 15;
119 final static int dynamically_hide_data = 16;
120 final static int show_taxonomy_scientific_names = 17;
121 final static int show_taxonomy_common_names = 18;
122 final static int color_according_to_annotation = 19;
123 final static int show_gene_symbols = 20;
124 final static int node_data_popup = 21;
125 final static int show_relation_confidence = 22;
126 final static int show_vector_data = 23;
127 final static int show_taxonomy_images = 24;
128 final static int show_properties = 25;
129 // ------------------
131 // ------------------
132 final static int display_node_data = 0;
133 final static int collapse_uncollapse = 1;
134 final static int reroot = 2;
135 final static int subtree = 3;
136 final static int swap = 4;
137 final static int color_subtree = 5;
138 final static int open_seq_web = 6;
139 final static int open_tax_web = 7;
140 final static int blast = 8;
141 final static int cut_subtree = 9;
142 final static int copy_subtree = 10;
143 final static int paste_subtree = 11;
144 final static int delete_subtree_or_node = 12;
145 final static int add_new_node = 13;
146 final static int edit_node_data = 14;
147 final static int sort_descendents = 15;
148 // ---------------------------
149 // Display options for trees
150 // ---------------------------
151 // ---------------------------------
152 // Pertaining to the config itself
153 // ---------------------------------
154 // Full path to config (may be URL)
155 String config_filename;
156 String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
157 final static String display_options[][] = {
158 { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
159 { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, { "Event", "display", "?" },
160 { "Taxonomy Colorize", "display", "no" }, { "Colorize Branches", "display", "no" },
161 { "Use Branch-Widths", "display", "no" }, { "Show Custom Nodes", "display", "yes" },
162 { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" },
163 { "Binary Char Counts", "nodisplay", "no" }, { "Prot/Gene Name", "display", "yes" },
164 { "Prot/Gene Acc", "display", "no" }, { "Show Internal Data", "display", "yes" },
165 { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" },
166 { "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" },
167 { "Prot/Gene Symbol", "display", "yes" }, { "Rollover", "display", "yes" },
168 { "Relation Confidence", "display", "no" }, { "Vector Data", "display", "no" },
169 { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" } };
170 final static String clickto_options[][] = {
171 { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
172 { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
173 { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Blast", "display" },
174 { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" },
175 { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" },
176 { "Sort Descendants", "display" } };
177 // This option is selected in the dropdown
178 int default_clickto = Configuration.display_node_data;
182 TreeColorSet tree_color_set;
186 TreeFontSet tree_font_set;
190 private static Hashtable<String, Color> _species_colors;
194 private static Hashtable<String, Color> _domain_colors;
198 private static Hashtable<String, Color> _annotation_colors;
199 boolean verbose = Constants.VERBOSE_DEFAULT;
200 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
201 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
202 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
203 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
204 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
205 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
206 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
207 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
208 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
209 private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
210 private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
211 private static String DEFAULT_FONT_FAMILY = "";
213 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
214 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
215 DEFAULT_FONT_FAMILY = font_name;
219 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
220 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
224 public Configuration() {
225 this( null, false, false, false );
228 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
229 if ( ForesterUtil.isEmpty( cf ) ) {
230 config_filename = default_config_filename;
233 config_filename = cf;
235 setWebLinks( new TreeMap<String, WebLink>() );
236 setDisplayColors( new TreeMap<String, Color>() );
237 config_filename = config_filename.trim();
240 // If URL, open accordingly
242 u = new URL( config_filename );
244 final InputStreamReader isr = new InputStreamReader( u.openStream() );
245 final BufferedReader bf = new BufferedReader( isr );
248 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
249 + config_filename + "]" );
251 catch ( final Exception e ) {
252 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
253 + config_filename + "]: " + e.getLocalizedMessage() );
256 catch ( final Exception e ) {
257 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
258 + config_filename + "]" );
262 // Otherwise, open as a file
263 File f = new File( config_filename );
265 f = new File( config_filename + ".txt" );
267 if ( f.exists() && f.canRead() ) {
269 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
273 catch ( final Exception e ) {
275 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
276 + config_filename + "]: " + e );
282 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
283 + config_filename + "]" );
289 private void createWebLink( final String url_str, final String desc, final String source_identifier ) {
290 WebLink weblink = null;
293 weblink = new WebLink( new URL( url_str.trim() ), desc.trim(), source_identifier.trim() );
295 catch ( final MalformedURLException e ) {
296 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not create URL from [" + url_str + "]" );
299 if ( !ex && ( weblink != null ) ) {
300 getWebLinks().put( weblink.getSourceIdentifier().toLowerCase(), weblink );
304 boolean displaySequenceRelations() {
305 return _display_sequence_relations;
308 boolean doCheckOption( final int which ) {
309 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
310 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
313 boolean doDisplayClickToOption( final int which ) {
314 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
317 boolean doDisplayOption( final int which ) {
318 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
322 * Will attempt to use the phylogeny to determine whether to check
323 * this or not (e.g. phylogram)
326 boolean doGuessCheckOption( final int which ) {
327 return display_options[ which ][ 2 ].equals( "?" );
330 Map<String, Color> getAnnotationColors() {
331 if ( _annotation_colors == null ) {
332 _annotation_colors = new Hashtable<String, Color>();
334 return _annotation_colors;
337 public String getBaseFontFamilyName() {
338 return _base_font_family_name;
341 int getBaseFontSize() {
342 return _base_font_size;
345 CLADOGRAM_TYPE getCladogramType() {
346 return _cladogram_type;
349 private int getClickToIndex( final String name ) {
351 if ( name.equals( "edit_info" ) ) {
352 index = Configuration.display_node_data;
354 .printWarningMessage( Constants.PRG_NAME,
355 "configuration key [edit_info] is deprecated, use [display node data] instead" );
357 else if ( name.equals( "display_node_data" ) ) {
358 index = Configuration.display_node_data;
360 else if ( name.equals( "collapse_uncollapse" ) ) {
361 index = Configuration.collapse_uncollapse;
363 else if ( name.equals( "reroot" ) ) {
364 index = Configuration.reroot;
366 else if ( name.equals( "subtree" ) ) {
367 index = Configuration.subtree;
369 else if ( name.equals( "swap" ) ) {
370 index = Configuration.swap;
372 else if ( name.equals( "sort_descendants" ) ) {
373 index = Configuration.sort_descendents;
375 else if ( name.equals( "display_sequences" ) ) {
377 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
380 else if ( name.equals( "open_seq_web" ) ) {
381 index = Configuration.open_seq_web;
383 else if ( name.equals( "open_tax_web" ) ) {
384 index = Configuration.open_tax_web;
386 else if ( name.equals( "blast" ) ) {
387 index = Configuration.blast;
389 else if ( name.equals( "cut_subtree" ) ) {
390 index = Configuration.cut_subtree;
392 else if ( name.equals( "copy_subtree" ) ) {
393 index = Configuration.copy_subtree;
395 else if ( name.equals( "paste_subtree" ) ) {
396 index = Configuration.paste_subtree;
398 else if ( name.equals( "delete" ) ) {
399 index = Configuration.delete_subtree_or_node;
401 else if ( name.equals( "add_new_node" ) ) {
402 index = Configuration.add_new_node;
404 else if ( name.equals( "edit_node_data" ) ) {
405 index = Configuration.edit_node_data;
407 else if ( name.equals( "display_node_popup" ) ) {
408 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
409 "configuration key [display_node_popup] is deprecated" );
412 else if ( name.equals( "custom_option" ) ) {
413 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
416 else if ( name.equals( "color_subtree" ) ) {
417 index = Configuration.color_subtree;
419 else if ( name.equals( "go_to_swiss_prot" ) ) {
420 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" );
426 int getClickToOptionsCount() {
427 return clickto_options.length;
430 String getClickToTitle( final int which ) {
431 return clickto_options[ which ][ 0 ];
434 public int getDefaultBootstrapSamples() {
435 return _default_bootstrap_samples;
438 public File getpathToLocalMafft() {
439 return _path_to_local_mafft;
442 public File getPathToLocalFastme() {
443 return _path_to_local_fastme;
446 public File getPathToLocalRaxml() {
447 return _path_to_local_raxml;
450 int getDefaultDisplayClicktoOption() {
451 return default_clickto;
454 public NodeFill getDefaultNodeFill() {
455 return _default_node_fill;
458 public NodeShape getDefaultNodeShape() {
459 return _default_node_shape;
462 public short getDefaultNodeShapeSize() {
463 return _default_node_shape_size;
466 SortedMap<String, Color> getDisplayColors() {
467 return _display_colors;
470 String getDisplayTitle( final int which ) {
471 return display_options[ which ][ 0 ];
474 Map<String, Color> getDomainColors() {
475 if ( _domain_colors == null ) {
476 _domain_colors = new Hashtable<String, Color>();
478 return _domain_colors;
481 public Color getDomainStructureBaseColor() {
482 return _domain_structure_base_color;
485 public Color getDomainStructureFontColor() {
486 return _domain_structure_font_color;
489 int getGraphicsExportX() {
490 return _graphics_export_x;
493 int getGraphicsExportY() {
494 return _graphics_export_y;
497 Color getGuiBackgroundColor() {
498 return _gui_background_color;
501 Color getGuiButtonBackgroundColor() {
502 return _gui_button_background_color;
505 Color getGuiButtonBorderColor() {
506 return _gui_button_border_color;
509 Color getGuiButtonTextColor() {
510 return _gui_button_text_color;
513 Color getGuiCheckboxAndButtonActiveColor() {
514 return _gui_checkbox_and_button_active_color;
517 Color getGuiCheckboxTextColor() {
518 return _gui_checkbox_text_color;
521 Color getGuiMenuBackgroundColor() {
522 return _gui_menu_background_color;
525 Color getGuiMenuTextColor() {
526 return _gui_menu_text_color;
529 double getMinConfidenceValue() {
530 return _min_confidence_value;
533 NODE_LABEL_DIRECTION getNodeLabelDirection() {
534 return _node_label_direction;
537 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
538 return _number_of_digits_after_comma_for_branch_length_values;
541 short getNumberOfDigitsAfterCommaForConfidenceValues() {
542 return _number_of_digits_after_comma_for_confidence_values;
545 short getOvMaxHeight() {
546 return _ov_max_height;
549 short getOvMaxWidth() {
550 return _ov_max_width;
553 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
554 return _ov_placement;
557 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
558 return _phylogeny_graphics_type;
561 float getPrintLineWidth() {
562 return _print_line_width;
565 Hashtable<String, Color> getSpeciesColors() {
566 if ( _species_colors == null ) {
567 _species_colors = new Hashtable<String, Color>();
569 return _species_colors;
572 TreeColorSet getTreeColorSet() {
576 TreeFontSet getTreeFontSet() {
580 WebLink getWebLink( final String source ) {
581 return getWebLinks().get( source );
584 Map<String, WebLink> getWebLinks() {
588 public boolean isAbbreviateScientificTaxonNames() {
589 return _abbreviate_scientific_names;
592 boolean isAntialiasScreen() {
593 return _antialias_screen;
596 public boolean isBackgroundColorGradient() {
597 return _background_color_gradient;
600 public boolean isColorLabelsSameAsParentBranch() {
601 return _color_labels_same_as_parent_branch;
605 * Convenience method.
607 * @return true if value in configuration file was 'yes'
609 boolean isDrawAsPhylogram() {
610 return doCheckOption( display_as_phylogram );
613 boolean isEditable() {
617 boolean isExtractPfamTaxonomyCodesInNhParsing() {
618 return _nh_parsing_extract_pfam_taxonomy_codes;
621 boolean isHasWebLink( final String source ) {
622 return getWebLinks().containsKey( source );
626 * Only used by ArchaeoptryxE.
629 boolean isHideControlPanelAndMenubar() {
630 return _hide_controls_and_menus;
633 boolean isInternalNumberAreConfidenceForNhParsing() {
634 return _internal_number_are_confidence_for_nh_parsing;
637 boolean isReplaceUnderscoresInNhParsing() {
638 return _nh_parsing_replace_underscores;
641 boolean isShowBranchLengthValues() {
642 return _show_branch_length_values;
645 public boolean isShowDefaultNodeShapes() {
646 return _show_default_node_shapes;
649 public boolean isShowDomainLabels() {
650 return _show_domain_labels;
653 boolean isShowOverview() {
654 return _show_overview;
657 boolean isShowScale() {
661 public boolean isTaxonomyColorizeNodeShapes() {
662 return _taxonomy_colorize_node_shapes;
665 final boolean isUseNativeUI() {
666 if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) {
669 return _ui == UI.NATIVE;
673 * Only used by ArchaeoptryxE.
676 boolean isUseTabbedDisplay() {
677 return _use_tabbed_display;
680 boolean isValidatePhyloXmlAgainstSchema() {
681 return _validate_against_phyloxml_xsd_schema;
684 private boolean parseBoolean( final String str ) {
685 final String my_str = str.trim().toLowerCase();
686 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
689 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
693 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
698 private double parseDouble( final String str ) {
701 d = Double.parseDouble( str );
703 catch ( final Exception e ) {
704 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
710 private float parseFloat( final String str ) {
713 f = Float.parseFloat( str );
715 catch ( final Exception e ) {
716 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
722 private int parseInt( final String str ) {
725 i = Integer.parseInt( str );
727 catch ( final Exception e ) {
728 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
734 private short parseShort( final String str ) {
737 i = Short.parseShort( str );
739 catch ( final Exception e ) {
740 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
746 private void processFontFamily( final StringTokenizer st ) {
747 setBaseFontFamilyName( "" );
748 final String font_str = ( ( String ) st.nextElement() ).trim();
749 final String[] fonts = font_str.split( ",+" );
750 for( String font : fonts ) {
751 font = font.replace( '_', ' ' ).trim();
752 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
753 setBaseFontFamilyName( font );
759 public void putDisplayColors( final String key, final Color color ) {
760 getDisplayColors().put( key, color );
764 * read each line of config file, process non-comment lines
765 * @throws IOException
767 private void readConfig( final BufferedReader conf_in ) throws IOException {
770 line = conf_in.readLine();
771 if ( line != null ) {
773 // skip comments and blank lines
774 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
775 // convert runs of spaces to tabs
776 line = line.replaceAll( "\\s+", "\t" );
777 final StringTokenizer st = new StringTokenizer( line, "\t" );
781 } while ( line != null );
784 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
785 _abbreviate_scientific_names = abbreviate_scientific_names;
788 private void setAntialiasScreen( final boolean antialias_screen ) {
789 _antialias_screen = antialias_screen;
792 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
793 _background_color_gradient = background_color_gradient;
796 public void setBaseFontFamilyName( final String base_font_family_name ) {
797 _base_font_family_name = base_font_family_name;
800 public void setBaseFontSize( final int base_font_size ) {
801 _base_font_size = base_font_size;
804 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
805 _cladogram_type = cladogram_type;
808 public void setColorizeBranches( final boolean b ) {
809 display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
812 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
813 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
816 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
817 _default_bootstrap_samples = default_bootstrap_samples;
820 private void setPathToLocalMafft( final File path_to_local_mafft ) {
821 _path_to_local_mafft = path_to_local_mafft;
824 private void setPathToLocalFastme( final File path_to_local_fastme ) {
825 _path_to_local_fastme = path_to_local_fastme;
828 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
829 _path_to_local_raxml = path_to_local_raxml;
832 public File getPathToLocalClustalOmega() {
833 return _path_to_local_clustalo;
836 public void setPathToLocalClustalOmega( final File path_to_local_clustalo ) {
837 _path_to_local_clustalo = path_to_local_clustalo;
840 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
841 _default_node_fill = default_node_fill;
844 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
845 _default_node_shape = default_node_shape;
848 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
849 _default_node_shape_size = default_node_shape_size;
852 public void setDisplayAsPhylogram( final boolean b ) {
853 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
856 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
857 _display_colors = display_colors;
860 public void setDisplayConfidenceValues( final boolean b ) {
861 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
864 public void setDisplayInternalData( final boolean b ) {
865 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
868 public void setDisplayNodeNames( final boolean b ) {
869 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
872 public void setDisplaySequenceAcc( final boolean b ) {
873 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
876 public void setDisplaySequenceNames( final boolean b ) {
877 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
880 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
881 _display_sequence_relations = display_sequence_relations;
884 public void setDisplaySequenceSymbols( final boolean b ) {
885 display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no";
888 public void setDisplayTaxonomyCode( final boolean b ) {
889 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
892 public void setDisplayTaxonomyCommonNames( final boolean b ) {
893 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
896 public void setDisplayTaxonomyImages( final boolean b ) {
897 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
900 public void setDisplayTaxonomyScientificNames( final boolean b ) {
901 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
904 public void setDynamicallyHideData( final boolean b ) {
905 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
908 private void setEditable( final boolean editable ) {
909 _editable = editable;
912 public void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) {
913 _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes;
916 private void setGraphicsExportX( final int graphics_export_x ) {
917 _graphics_export_x = graphics_export_x;
920 private void setGraphicsExportY( final int graphics_export_y ) {
921 _graphics_export_y = graphics_export_y;
924 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
925 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
929 * Set a key-value(s) tuple
931 private void setKeyValue( final StringTokenizer st ) {
932 String key = ( String ) st.nextElement();
933 key = key.replace( ':', ' ' );
935 key = key.toLowerCase();
936 // Handle single value settings first:
937 if ( key.equals( "default_click_to" ) ) {
938 final String clickto_name = ( String ) st.nextElement();
939 default_clickto = getClickToIndex( clickto_name );
940 if ( default_clickto == -1 ) {
941 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
942 + "] for [default_click_to]" );
945 else if ( default_clickto == DEPRECATED ) {
949 else if ( key.equals( "native_ui" ) ) {
950 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
951 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
954 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
955 _ui = UI.CROSSPLATFORM;
957 else if ( my_str.equals( "?" ) ) {
961 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
966 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
967 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
969 else if ( key.equals( "antialias_screen" ) ) {
970 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
972 else if ( key.equals( "phylogeny_graphics_type" ) ) {
973 final String type_str = ( ( String ) st.nextElement() ).trim();
974 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
975 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
977 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
978 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
980 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
981 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
983 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
984 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
986 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
987 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
989 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
990 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
992 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
993 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
995 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
996 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
999 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1000 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1001 + "] for [phylogeny_graphics_type]" );
1004 else if ( key.equals( "min_confidence_value" ) ) {
1005 final String mcv_str = ( ( String ) st.nextElement() ).trim();
1006 final double d = parseDouble( mcv_str );
1007 setMinConfidenceValue( d );
1009 else if ( key.equals( "font_family" ) ) {
1010 processFontFamily( st );
1012 else if ( key.equals( "font_size" ) ) {
1013 final String size_str = ( ( String ) st.nextElement() ).trim();
1014 final int i = parseInt( size_str );
1015 setBaseFontSize( i );
1017 else if ( key.equals( "graphics_export_x" ) ) {
1018 final String str = ( ( String ) st.nextElement() ).trim();
1019 final int i = parseInt( str );
1020 setGraphicsExportX( i );
1022 else if ( key.equals( "graphics_export_y" ) ) {
1023 final String str = ( ( String ) st.nextElement() ).trim();
1024 final int i = parseInt( str );
1025 setGraphicsExportY( i );
1027 else if ( key.equals( "pdf_export_line_width" ) ) {
1028 final String str = ( ( String ) st.nextElement() ).trim();
1029 final float f = parseFloat( str );
1031 setPrintLineWidth( f );
1034 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1035 "value for [pdf_export_line_width] cannot be zero or negative" );
1038 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1039 final String str = ( ( String ) st.nextElement() ).trim();
1040 final int i = parseInt( str );
1042 setDefaultBootstrapSamples( i );
1046 .printWarningMessage( Constants.PRG_NAME,
1047 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1050 else if ( key.equals( "clustalo_local" ) ) {
1051 final String str = ( ( String ) st.nextElement() ).trim();
1052 if ( !ForesterUtil.isEmpty( str ) ) {
1053 setPathToLocalClustalOmega( new File( str ) );
1056 else if ( key.equals( "mafft_local" ) ) {
1057 final String str = ( ( String ) st.nextElement() ).trim();
1058 if ( !ForesterUtil.isEmpty( str ) ) {
1059 setPathToLocalMafft( new File( str ) );
1062 else if ( key.equals( "fastme_local" ) ) {
1063 final String str = ( ( String ) st.nextElement() ).trim();
1064 if ( !ForesterUtil.isEmpty( str ) ) {
1065 setPathToLocalFastme( new File( str ) );
1068 else if ( key.equals( "raxml_local" ) ) {
1069 final String str = ( ( String ) st.nextElement() ).trim();
1070 if ( !ForesterUtil.isEmpty( str ) ) {
1071 setPathToLocalRaxml( new File( str ) );
1074 else if ( key.equals( "show_scale" ) ) {
1075 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1077 else if ( key.equals( "show_overview" ) ) {
1078 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1080 else if ( key.equals( "show_branch_length_values" ) ) {
1081 setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
1083 else if ( key.equals( "background_gradient" ) ) {
1084 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1086 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1087 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1089 else if ( key.equals( "show_domain_labels" ) ) {
1090 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1092 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1093 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1095 else if ( key.equals( "cladogram_type" ) ) {
1096 final String type_str = ( ( String ) st.nextElement() ).trim();
1097 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1098 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1100 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1101 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1103 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1104 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1107 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1108 + "] for [cladogram_type]" );
1111 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1113 .printWarningMessage( Constants.PRG_NAME,
1114 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1116 else if ( key.equals( "hide_controls_and_menus" ) ) {
1117 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1119 else if ( key.equals( "use_tabbed_display" ) ) {
1120 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1122 else if ( key.equals( "overview_width" ) ) {
1123 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1126 else if ( key.equals( "overview_height" ) ) {
1127 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1128 setOvMaxHeight( i );
1130 else if ( key.equals( "overview_placement_type" ) ) {
1131 final String type_str = ( ( String ) st.nextElement() ).trim();
1132 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1133 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1135 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1136 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1138 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1139 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1141 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1142 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1145 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1146 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1147 + "] for [overview_placement_type]" );
1150 else if ( key.equals( "node_label_direction" ) ) {
1151 final String type_str = ( ( String ) st.nextElement() ).trim();
1152 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1153 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1155 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1156 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1159 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1160 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1161 + "] for [node_label_direction]" );
1164 else if ( key.equals( "branch_length_value_digits" ) ) {
1165 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1167 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1170 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1171 + "] for [branch_length_value_digits]" );
1174 else if ( key.equals( "confidence_value_digits" ) ) {
1175 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1177 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1180 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1181 + "] for [confidence_value_digits]" );
1184 else if ( key.equals( "allow_editing" ) ) {
1185 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1187 else if ( key.equals( "display_sequence_relations" ) ) {
1188 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1190 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1191 final boolean r = parseBoolean( ( String ) st.nextElement() );
1192 if ( r && isExtractPfamTaxonomyCodesInNhParsing() ) {
1194 .printWarningMessage( Constants.PRG_NAME,
1195 "attempt to extract taxonomies and replace underscores at the same time" );
1198 setReplaceUnderscoresInNhParsing( r );
1201 else if ( key.equals( "extract_taxonomy_codes_in_nh_parsing" ) ) {
1202 final boolean e = parseBoolean( ( String ) st.nextElement() );
1203 if ( e && isReplaceUnderscoresInNhParsing() ) {
1205 .printWarningMessage( Constants.PRG_NAME,
1206 "attempt to extract taxonomies and replace underscores at the same time" );
1209 setExtractPfamTaxonomyCodesInNhParsing( e );
1212 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1213 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1215 else if ( key.equals( "gui_background_color" ) ) {
1216 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1218 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1219 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1221 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1222 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1224 else if ( key.equals( "gui_button_text_color" ) ) {
1225 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1227 else if ( key.equals( "gui_button_background_color" ) ) {
1228 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1230 else if ( key.equals( "gui_menu_background_color" ) ) {
1231 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1233 else if ( key.equals( "gui_menu_text_color" ) ) {
1234 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1236 else if ( key.equals( "gui_button_border_color" ) ) {
1237 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1239 else if ( key.equals( "domain_structure_font_color" ) ) {
1240 _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
1242 else if ( key.equals( "domain_structure_base_color" ) ) {
1243 _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
1245 else if ( key.equals( "show_default_node_shapes" ) ) {
1246 setShowDefaultNodeShapes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1248 else if ( key.equals( "default_node_size" ) ) {
1249 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1250 setDefaultNodeShapeSize( i );
1252 else if ( key.equals( "default_node_fill" ) ) {
1253 final String fill_str = ( ( String ) st.nextElement() ).trim();
1254 if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.NONE.toString() ) ) {
1255 setDefaultNodeFill( NodeFill.NONE );
1257 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.GRADIENT.toString() ) ) {
1258 setDefaultNodeFill( NodeFill.GRADIENT );
1260 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.SOLID.toString() ) ) {
1261 setDefaultNodeFill( NodeFill.SOLID );
1264 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1265 + "] for [default_node_fill]" );
1268 else if ( key.equals( "default_node_shape" ) ) {
1269 final String shape_str = ( ( String ) st.nextElement() ).trim();
1270 if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.CIRCLE.toString() ) ) {
1271 setDefaultNodeShape( NodeShape.CIRCLE );
1273 else if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.RECTANGLE.toString() ) ) {
1274 setDefaultNodeShape( NodeShape.RECTANGLE );
1277 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1278 + "] for [default_node_shape]" );
1281 else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
1282 setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
1284 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1287 if ( key.equals( "use_real_br_lengths" ) || key.equals( "phylogram" ) ) {
1288 key_index = Configuration.display_as_phylogram;
1289 if ( key.equals( "use_real_br_lengths" ) ) {
1291 .printWarningMessage( Constants.PRG_NAME,
1292 "configuration key [use_real_br_lengths] is deprecated, use [phylogram] instead" );
1295 else if ( key.equals( "rollover" ) ) {
1296 key_index = Configuration.node_data_popup;
1298 else if ( key.equals( "color_according_to_species" ) ) {
1299 key_index = Configuration.color_according_to_species;
1301 else if ( key.equals( "show_node_names" ) ) {
1302 key_index = Configuration.show_node_names;
1304 else if ( key.equals( "show_taxonomy" ) || key.equals( "show_taxonomy_code" ) ) {
1305 key_index = Configuration.show_tax_code;
1306 if ( key.equals( "show_taxonomy" ) ) {
1308 .printWarningMessage( Constants.PRG_NAME,
1309 "configuration key [show_taxonomy] is deprecated, use [show_taxonomy_code] instead" );
1312 else if ( key.equals( "write_br_length_values" ) ) {
1313 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1314 "configuration key [write_br_length_values] is deprecated" );
1315 key_index = DEPRECATED;
1317 else if ( key.equals( "write_bootstrap_values" ) || key.equals( "write_confidence_values" ) ) {
1318 key_index = Configuration.write_confidence_values;
1319 if ( key.equals( "write_bootstrap_values" ) ) {
1321 .printWarningMessage( Constants.PRG_NAME,
1322 "configuration key [write_bootstrap_values] is deprecated, use [write_confidence_values] instead" );
1325 else if ( key.equals( "write_events" ) || key.equals( "write_dup_spec" ) ) {
1326 key_index = Configuration.write_events;
1327 if ( key.equals( "write_dup_spec" ) ) {
1329 .printWarningMessage( Constants.PRG_NAME,
1330 "configuration key [write_dup_spec] is deprecated, use [write_events] instead" );
1333 else if ( key.equals( "color_branches" ) ) {
1334 key_index = Configuration.color_branches;
1336 else if ( key.equals( "width_branches" ) ) {
1337 key_index = Configuration.width_branches;
1339 else if ( key.equals( "color_orthologous" ) ) {
1340 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1341 "configuration key [color_orthologous] is deprecated" );
1343 else if ( key.equals( "color_subtree_neighbors" ) ) {
1344 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1345 "configuration key [color_subtree_neighbors] is deprecated" );
1347 else if ( key.equals( "color_super_orthologous" ) ) {
1348 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1349 "configuration key [color_super_orthologous] is deprecated" );
1351 else if ( key.equals( "mark_nodes_with_box" ) ) {
1352 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1353 "configuration key [mark_nodes_with_box] is deprecated" );
1354 key_index = DEPRECATED;
1356 else if ( key.equals( "show_domain_architectures" ) ) {
1357 key_index = Configuration.show_domain_architectures;
1359 else if ( key.equals( "show_annotations" ) ) {
1360 key_index = Configuration.show_annotation;
1362 else if ( key.equals( "show_binary_characters" ) ) {
1363 key_index = Configuration.show_binary_characters;
1365 else if ( key.equals( "show_binary_character_counts" ) ) {
1366 key_index = Configuration.show_binary_character_counts;
1368 else if ( key.equals( "show_gene_names" ) ) {
1369 key_index = Configuration.show_gene_names;
1371 else if ( key.equals( "show_gene_symbols" ) ) {
1372 key_index = Configuration.show_gene_symbols;
1374 else if ( key.equals( "show_sequence_acc" ) ) {
1375 key_index = Configuration.show_sequence_acc;
1377 else if ( key.equals( "show_node_ids" ) ) {
1379 .printWarningMessage( Constants.PRG_NAME, "configuration key [show_node_ids] is deprecated" );
1380 key_index = DEPRECATED;
1382 else if ( key.equals( "display_internal_data" ) ) {
1383 key_index = Configuration.display_internal_data;
1385 else if ( key.equals( "dynamically_hide_data" ) ) {
1386 key_index = Configuration.dynamically_hide_data;
1388 else if ( key.equals( "show_taxonomy_names" ) ) {
1389 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1390 "configuration key [show_taxonomy_names] is deprecated" );
1391 key_index = DEPRECATED;
1393 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1394 key_index = Configuration.show_taxonomy_scientific_names;
1396 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1397 key_index = Configuration.show_taxonomy_common_names;
1399 else if ( key.equals( "show_taxonomy_images" ) ) {
1400 key_index = Configuration.show_taxonomy_images;
1402 else if ( key.equals( "color_according_to_annotation" ) ) {
1403 key_index = Configuration.color_according_to_annotation;
1405 else if ( key.equals( "show_vector_data" ) ) {
1406 key_index = Configuration.show_vector_data;
1408 else if ( key.equals( "show_properties" ) ) {
1409 key_index = Configuration.show_properties;
1411 else if ( key.equals( "show_relation_confidence" ) ) {
1412 key_index = Configuration.show_relation_confidence;
1414 else if ( key.equals( "show_custom_node_shapes" ) ) {
1415 key_index = Configuration.show_custom_node_shapes;
1417 // If we've found the key, set the values
1418 if ( key_index >= 0 ) {
1419 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1420 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1421 // otherwise, keep looking
1424 if ( key_index == DEPRECATED ) {
1427 else if ( key.equals( "click_to" ) ) {
1428 final String click_to_name = ( String ) st.nextElement();
1429 key_index = getClickToIndex( click_to_name );
1430 if ( key_index >= 0 ) {
1431 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1433 else if ( key_index == DEPRECATED ) {
1437 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1441 else if ( key.equals( "species_color" ) ) {
1442 getSpeciesColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1444 else if ( key.equals( "domain_color" ) ) {
1445 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1447 else if ( key.equals( "annotation_color" ) ) {
1448 getAnnotationColors()
1449 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1451 else if ( key.equals( "function_color" ) ) {
1452 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1453 "configuration key [function_color] is deprecated" );
1455 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1456 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1458 else if ( key.equals( WEB_LINK_KEY ) ) {
1459 if ( st.countTokens() == 3 ) {
1460 createWebLink( ( String ) st.nextElement(),
1461 ( String ) st.nextElement(),
1462 ( String ) st.nextElement() );
1465 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1466 "illegal format in configuration file for key [" + key + "]" );
1470 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1471 + "] in: " + config_filename );
1476 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1477 + config_filename );
1481 public void setMinConfidenceValue( final double min_confidence_value ) {
1482 _min_confidence_value = min_confidence_value;
1485 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
1486 _node_label_direction = node_label_direction;
1489 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short _number_of_digits_after_comma_for_branch_length_values ) {
1490 this._number_of_digits_after_comma_for_branch_length_values = _number_of_digits_after_comma_for_branch_length_values;
1493 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short _number_of_digits_after_comma_for_confidence_values ) {
1494 this._number_of_digits_after_comma_for_confidence_values = _number_of_digits_after_comma_for_confidence_values;
1497 private void setOvMaxHeight( final short ov_max_height ) {
1498 _ov_max_height = ov_max_height;
1501 private void setOvMaxWidth( final short ov_max_width ) {
1502 _ov_max_width = ov_max_width;
1505 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1506 _ov_placement = ov_placement;
1509 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
1510 _phylogeny_graphics_type = phylogeny_graphics_type;
1513 public void setPrintLineWidth( final float print_line_width ) {
1514 _print_line_width = print_line_width;
1517 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
1518 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
1521 public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
1522 _show_branch_length_values = show_branch_length_values;
1525 public void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
1526 _show_default_node_shapes = show_default_node_shapes;
1529 public void setShowDomainLabels( final boolean show_domain_labels ) {
1530 _show_domain_labels = show_domain_labels;
1533 private void setShowOverview( final boolean show_overview ) {
1534 _show_overview = show_overview;
1537 public void setShowScale( final boolean show_scale ) {
1538 _show_scale = show_scale;
1541 public void setTaxonomyColorize( final boolean b ) {
1542 display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
1545 public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
1546 _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
1549 public void setUseBranchesWidths( final boolean b ) {
1550 display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
1553 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1554 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1557 void setWebLinks( final SortedMap<String, WebLink> weblinks ) {
1558 _weblinks = weblinks;
1561 static String getDefaultFontFamilyName() {
1562 return DEFAULT_FONT_FAMILY;
1565 static enum TRIPLET {
1566 TRUE, FALSE, UNKNOWN
1570 NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN