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 File _mafft = null;
66 private File _clustalo = null;
67 private File _fastme = null;
68 private SortedMap<String, WebLink> _weblinks = null;
69 private SortedMap<String, Color> _display_colors = null;
70 private boolean _antialias_screen = true;
71 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
72 private String _base_font_family_name = "";
73 private int _base_font_size = -1;
74 private int _graphics_export_x = -1;
75 private int _graphics_export_y = -1;
76 private short _ov_max_width = 80;
77 private short _ov_max_height = 80;
78 private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
79 private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
80 private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
81 private boolean _show_scale = false;
82 private boolean _show_branch_length_values = false;
83 private boolean _show_overview = true;
84 private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
85 private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
86 private boolean _editable = true;
87 private boolean _nh_parsing_replace_underscores = false;
88 private boolean _nh_parsing_extract_pfam_taxonomy_codes = false;
89 private boolean _internal_number_are_confidence_for_nh_parsing = false;
90 private boolean _display_sequence_relations = false;
91 private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
92 private boolean _background_color_gradient = false;
93 private boolean _show_domain_labels = true;
94 private boolean _abbreviate_scientific_names = false;
95 private boolean _color_labels_same_as_parent_branch = false;
96 private int _default_bootstrap_samples = -1;
97 private boolean _show_default_node_shapes = false;
98 private NodeShape _default_node_shape = NodeShape.CIRCLE;
99 private NodeFill _default_node_fill = NodeFill.GRADIENT;
100 private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
101 private boolean _taxonomy_colorize_node_shapes = false;
102 final static int display_as_phylogram = 0;
103 final static int show_node_names = 1;
104 final static int show_tax_code = 2;
105 final static int show_annotation = 3;
106 final static int write_confidence_values = 4;
107 final static int write_events = 5;
108 final static int color_according_to_species = 6;
109 final static int color_branches = 7;
110 final static int width_branches = 8;
111 final static int show_custom_node_shapes = 9;
112 final static int show_domain_architectures = 10;
113 final static int show_binary_characters = 11;
114 final static int show_binary_character_counts = 12;
115 final static int show_gene_names = 13;
116 final static int show_sequence_acc = 14;
117 final static int display_internal_data = 15;
118 final static int dynamically_hide_data = 16;
119 final static int show_taxonomy_scientific_names = 17;
120 final static int show_taxonomy_common_names = 18;
121 final static int color_according_to_annotation = 19;
122 final static int show_gene_symbols = 20;
123 final static int node_data_popup = 21;
124 final static int show_relation_confidence = 22;
125 final static int show_vector_data = 23;
126 final static int show_taxonomy_images = 24;
127 final static int show_properties = 25;
128 // ------------------
130 // ------------------
131 final static int display_node_data = 0;
132 final static int collapse_uncollapse = 1;
133 final static int reroot = 2;
134 final static int subtree = 3;
135 final static int swap = 4;
136 final static int color_subtree = 5;
137 final static int open_seq_web = 6;
138 final static int open_tax_web = 7;
139 final static int blast = 8;
140 final static int cut_subtree = 9;
141 final static int copy_subtree = 10;
142 final static int paste_subtree = 11;
143 final static int delete_subtree_or_node = 12;
144 final static int add_new_node = 13;
145 final static int edit_node_data = 14;
146 final static int sort_descendents = 15;
147 // ---------------------------
148 // Display options for trees
149 // ---------------------------
150 // ---------------------------------
151 // Pertaining to the config itself
152 // ---------------------------------
153 // Full path to config (may be URL)
154 String config_filename;
155 String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
156 final static String display_options[][] = {
157 { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
158 { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, { "Event", "display", "?" },
159 { "Taxonomy Colorize", "display", "no" }, { "Colorize Branches", "display", "no" },
160 { "Use Branch-Widths", "display", "no" }, { "Show Custom Nodes", "display", "yes" },
161 { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" },
162 { "Binary Char Counts", "nodisplay", "no" }, { "Prot/Gene Name", "display", "yes" },
163 { "Prot/Gene Acc", "display", "no" }, { "Show Internal Data", "display", "yes" },
164 { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" },
165 { "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" },
166 { "Prot/Gene Symbol", "display", "yes" }, { "Rollover", "display", "yes" },
167 { "Relation Confidence", "display", "no" }, { "Vector Data", "display", "no" },
168 { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" } };
169 final static String clickto_options[][] = {
170 { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
171 { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
172 { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Blast", "display" },
173 { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" },
174 { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" },
175 { "Sort Descendants", "display" } };
176 // This option is selected in the dropdown
177 int default_clickto = Configuration.display_node_data;
181 TreeColorSet tree_color_set;
185 TreeFontSet tree_font_set;
189 private static Hashtable<String, Color> _species_colors;
193 private static Hashtable<String, Color> _domain_colors;
197 private static Hashtable<String, Color> _annotation_colors;
198 boolean verbose = Constants.VERBOSE_DEFAULT;
199 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
200 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
201 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
202 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
203 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
204 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
205 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
206 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
207 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
208 private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
209 private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
210 private static String DEFAULT_FONT_FAMILY = "";
212 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
213 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
214 DEFAULT_FONT_FAMILY = font_name;
218 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
219 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
223 public Configuration() {
224 this( null, false, false, false );
227 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
228 if ( ForesterUtil.isEmpty( cf ) ) {
229 config_filename = default_config_filename;
232 config_filename = cf;
234 setWebLinks( new TreeMap<String, WebLink>() );
235 setDisplayColors( new TreeMap<String, Color>() );
236 config_filename = config_filename.trim();
239 // If URL, open accordingly
241 u = new URL( config_filename );
243 final InputStreamReader isr = new InputStreamReader( u.openStream() );
244 final BufferedReader bf = new BufferedReader( isr );
247 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
248 + config_filename + "]" );
250 catch ( final Exception e ) {
251 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
252 + config_filename + "]: " + e.getLocalizedMessage() );
255 catch ( final Exception e ) {
256 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
257 + config_filename + "]" );
261 // Otherwise, open as a file
262 File f = new File( config_filename );
264 f = new File( config_filename + ".txt" );
266 if ( f.exists() && f.canRead() ) {
268 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
272 catch ( final Exception e ) {
274 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
275 + config_filename + "]: " + e );
281 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
282 + config_filename + "]" );
288 private void createWebLink( final String url_str, final String desc, final String source_identifier ) {
289 WebLink weblink = null;
292 weblink = new WebLink( new URL( url_str.trim() ), desc.trim(), source_identifier.trim() );
294 catch ( final MalformedURLException e ) {
295 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not create URL from [" + url_str + "]" );
298 if ( !ex && ( weblink != null ) ) {
299 getWebLinks().put( weblink.getSourceIdentifier().toLowerCase(), weblink );
303 boolean displaySequenceRelations() {
304 return _display_sequence_relations;
307 boolean doCheckOption( final int which ) {
308 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
309 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
312 boolean doDisplayClickToOption( final int which ) {
313 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
316 boolean doDisplayOption( final int which ) {
317 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
321 * Will attempt to use the phylogeny to determine whether to check
322 * this or not (e.g. phylogram)
325 boolean doGuessCheckOption( final int which ) {
326 return display_options[ which ][ 2 ].equals( "?" );
329 Map<String, Color> getAnnotationColors() {
330 if ( _annotation_colors == null ) {
331 _annotation_colors = new Hashtable<String, Color>();
333 return _annotation_colors;
336 public String getBaseFontFamilyName() {
337 return _base_font_family_name;
340 int getBaseFontSize() {
341 return _base_font_size;
344 CLADOGRAM_TYPE getCladogramType() {
345 return _cladogram_type;
348 private int getClickToIndex( final String name ) {
350 if ( name.equals( "edit_info" ) ) {
351 index = Configuration.display_node_data;
353 .printWarningMessage( Constants.PRG_NAME,
354 "configuration key [edit_info] is deprecated, use [display node data] instead" );
356 else if ( name.equals( "display_node_data" ) ) {
357 index = Configuration.display_node_data;
359 else if ( name.equals( "collapse_uncollapse" ) ) {
360 index = Configuration.collapse_uncollapse;
362 else if ( name.equals( "reroot" ) ) {
363 index = Configuration.reroot;
365 else if ( name.equals( "subtree" ) ) {
366 index = Configuration.subtree;
368 else if ( name.equals( "swap" ) ) {
369 index = Configuration.swap;
371 else if ( name.equals( "sort_descendants" ) ) {
372 index = Configuration.sort_descendents;
374 else if ( name.equals( "display_sequences" ) ) {
376 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
379 else if ( name.equals( "open_seq_web" ) ) {
380 index = Configuration.open_seq_web;
382 else if ( name.equals( "open_tax_web" ) ) {
383 index = Configuration.open_tax_web;
385 else if ( name.equals( "blast" ) ) {
386 index = Configuration.blast;
388 else if ( name.equals( "cut_subtree" ) ) {
389 index = Configuration.cut_subtree;
391 else if ( name.equals( "copy_subtree" ) ) {
392 index = Configuration.copy_subtree;
394 else if ( name.equals( "paste_subtree" ) ) {
395 index = Configuration.paste_subtree;
397 else if ( name.equals( "delete" ) ) {
398 index = Configuration.delete_subtree_or_node;
400 else if ( name.equals( "add_new_node" ) ) {
401 index = Configuration.add_new_node;
403 else if ( name.equals( "edit_node_data" ) ) {
404 index = Configuration.edit_node_data;
406 else if ( name.equals( "display_node_popup" ) ) {
407 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
408 "configuration key [display_node_popup] is deprecated" );
411 else if ( name.equals( "custom_option" ) ) {
412 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
415 else if ( name.equals( "color_subtree" ) ) {
416 index = Configuration.color_subtree;
418 else if ( name.equals( "go_to_swiss_prot" ) ) {
419 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" );
425 int getClickToOptionsCount() {
426 return clickto_options.length;
429 String getClickToTitle( final int which ) {
430 return clickto_options[ which ][ 0 ];
433 public int getDefaultBootstrapSamples() {
434 return _default_bootstrap_samples;
437 int getDefaultDisplayClicktoOption() {
438 return default_clickto;
441 public NodeFill getDefaultNodeFill() {
442 return _default_node_fill;
445 public NodeShape getDefaultNodeShape() {
446 return _default_node_shape;
449 public short getDefaultNodeShapeSize() {
450 return _default_node_shape_size;
453 SortedMap<String, Color> getDisplayColors() {
454 return _display_colors;
457 String getDisplayTitle( final int which ) {
458 return display_options[ which ][ 0 ];
461 Map<String, Color> getDomainColors() {
462 if ( _domain_colors == null ) {
463 _domain_colors = new Hashtable<String, Color>();
465 return _domain_colors;
468 public Color getDomainStructureBaseColor() {
469 return _domain_structure_base_color;
472 public Color getDomainStructureFontColor() {
473 return _domain_structure_font_color;
476 int getGraphicsExportX() {
477 return _graphics_export_x;
480 int getGraphicsExportY() {
481 return _graphics_export_y;
484 Color getGuiBackgroundColor() {
485 return _gui_background_color;
488 Color getGuiButtonBackgroundColor() {
489 return _gui_button_background_color;
492 Color getGuiButtonBorderColor() {
493 return _gui_button_border_color;
496 Color getGuiButtonTextColor() {
497 return _gui_button_text_color;
500 Color getGuiCheckboxAndButtonActiveColor() {
501 return _gui_checkbox_and_button_active_color;
504 Color getGuiCheckboxTextColor() {
505 return _gui_checkbox_text_color;
508 Color getGuiMenuBackgroundColor() {
509 return _gui_menu_background_color;
512 Color getGuiMenuTextColor() {
513 return _gui_menu_text_color;
516 double getMinConfidenceValue() {
517 return _min_confidence_value;
520 NODE_LABEL_DIRECTION getNodeLabelDirection() {
521 return _node_label_direction;
524 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
525 return _number_of_digits_after_comma_for_branch_length_values;
528 short getNumberOfDigitsAfterCommaForConfidenceValues() {
529 return _number_of_digits_after_comma_for_confidence_values;
532 short getOvMaxHeight() {
533 return _ov_max_height;
536 short getOvMaxWidth() {
537 return _ov_max_width;
540 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
541 return _ov_placement;
544 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
545 return _phylogeny_graphics_type;
548 float getPrintLineWidth() {
549 return _print_line_width;
552 Hashtable<String, Color> getSpeciesColors() {
553 if ( _species_colors == null ) {
554 _species_colors = new Hashtable<String, Color>();
556 return _species_colors;
559 TreeColorSet getTreeColorSet() {
563 TreeFontSet getTreeFontSet() {
567 WebLink getWebLink( final String source ) {
568 return getWebLinks().get( source );
571 Map<String, WebLink> getWebLinks() {
575 public boolean isAbbreviateScientificTaxonNames() {
576 return _abbreviate_scientific_names;
579 boolean isAntialiasScreen() {
580 return _antialias_screen;
583 public boolean isBackgroundColorGradient() {
584 return _background_color_gradient;
587 public boolean isColorLabelsSameAsParentBranch() {
588 return _color_labels_same_as_parent_branch;
592 * Convenience method.
594 * @return true if value in configuration file was 'yes'
596 boolean isDrawAsPhylogram() {
597 return doCheckOption( display_as_phylogram );
600 boolean isEditable() {
604 boolean isExtractPfamTaxonomyCodesInNhParsing() {
605 return _nh_parsing_extract_pfam_taxonomy_codes;
608 boolean isHasWebLink( final String source ) {
609 return getWebLinks().containsKey( source );
613 * Only used by ArchaeoptryxE.
616 boolean isHideControlPanelAndMenubar() {
617 return _hide_controls_and_menus;
620 boolean isInternalNumberAreConfidenceForNhParsing() {
621 return _internal_number_are_confidence_for_nh_parsing;
624 boolean isReplaceUnderscoresInNhParsing() {
625 return _nh_parsing_replace_underscores;
628 boolean isShowBranchLengthValues() {
629 return _show_branch_length_values;
632 public boolean isShowDefaultNodeShapes() {
633 return _show_default_node_shapes;
636 public boolean isShowDomainLabels() {
637 return _show_domain_labels;
640 boolean isShowOverview() {
641 return _show_overview;
644 boolean isShowScale() {
648 public boolean isTaxonomyColorizeNodeShapes() {
649 return _taxonomy_colorize_node_shapes;
652 final boolean isUseNativeUI() {
653 if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) {
656 return _ui == UI.NATIVE;
660 * Only used by ArchaeoptryxE.
663 boolean isUseTabbedDisplay() {
664 return _use_tabbed_display;
667 boolean isValidatePhyloXmlAgainstSchema() {
668 return _validate_against_phyloxml_xsd_schema;
671 private boolean parseBoolean( final String str ) {
672 final String my_str = str.trim().toLowerCase();
673 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
676 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
680 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
685 private double parseDouble( final String str ) {
688 d = Double.parseDouble( str );
690 catch ( final Exception e ) {
691 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
697 private float parseFloat( final String str ) {
700 f = Float.parseFloat( str );
702 catch ( final Exception e ) {
703 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
709 private int parseInt( final String str ) {
712 i = Integer.parseInt( str );
714 catch ( final Exception e ) {
715 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
721 private short parseShort( final String str ) {
724 i = Short.parseShort( str );
726 catch ( final Exception e ) {
727 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
733 private void processFontFamily( final StringTokenizer st ) {
734 setBaseFontFamilyName( "" );
735 final String font_str = ( ( String ) st.nextElement() ).trim();
736 final String[] fonts = font_str.split( ",+" );
737 for( String font : fonts ) {
738 font = font.replace( '_', ' ' ).trim();
739 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
740 setBaseFontFamilyName( font );
746 public void putDisplayColors( final String key, final Color color ) {
747 getDisplayColors().put( key, color );
751 * read each line of config file, process non-comment lines
752 * @throws IOException
754 private void readConfig( final BufferedReader conf_in ) throws IOException {
757 line = conf_in.readLine();
758 if ( line != null ) {
760 // skip comments and blank lines
761 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
762 // convert runs of spaces to tabs
763 line = line.replaceAll( "\\s+", "\t" );
764 final StringTokenizer st = new StringTokenizer( line, "\t" );
768 } while ( line != null );
771 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
772 _abbreviate_scientific_names = abbreviate_scientific_names;
775 private void setAntialiasScreen( final boolean antialias_screen ) {
776 _antialias_screen = antialias_screen;
779 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
780 _background_color_gradient = background_color_gradient;
783 public void setBaseFontFamilyName( final String base_font_family_name ) {
784 _base_font_family_name = base_font_family_name;
787 public void setBaseFontSize( final int base_font_size ) {
788 _base_font_size = base_font_size;
791 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
792 _cladogram_type = cladogram_type;
795 public void setColorizeBranches( final boolean b ) {
796 display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
799 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
800 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
803 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
804 _default_bootstrap_samples = default_bootstrap_samples;
807 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
808 _default_node_fill = default_node_fill;
811 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
812 _default_node_shape = default_node_shape;
815 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
816 _default_node_shape_size = default_node_shape_size;
819 public void setDisplayAsPhylogram( final boolean b ) {
820 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
823 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
824 _display_colors = display_colors;
827 public void setDisplayConfidenceValues( final boolean b ) {
828 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
831 public void setDisplayInternalData( final boolean b ) {
832 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
835 public void setDisplayNodeNames( final boolean b ) {
836 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
839 public void setDisplaySequenceAcc( final boolean b ) {
840 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
843 public void setDisplaySequenceNames( final boolean b ) {
844 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
847 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
848 _display_sequence_relations = display_sequence_relations;
851 public void setDisplaySequenceSymbols( final boolean b ) {
852 display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no";
855 public void setDisplayTaxonomyCode( final boolean b ) {
856 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
859 public void setDisplayTaxonomyCommonNames( final boolean b ) {
860 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
863 public void setDisplayTaxonomyImages( final boolean b ) {
864 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
867 public void setDisplayTaxonomyScientificNames( final boolean b ) {
868 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
871 public void setDynamicallyHideData( final boolean b ) {
872 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
875 private void setEditable( final boolean editable ) {
876 _editable = editable;
879 public void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) {
880 _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes;
883 private void setGraphicsExportX( final int graphics_export_x ) {
884 _graphics_export_x = graphics_export_x;
887 private void setGraphicsExportY( final int graphics_export_y ) {
888 _graphics_export_y = graphics_export_y;
891 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
892 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
896 * Set a key-value(s) tuple
898 private void setKeyValue( final StringTokenizer st ) {
899 String key = ( String ) st.nextElement();
900 key = key.replace( ':', ' ' );
902 key = key.toLowerCase();
903 // Handle single value settings first:
904 if ( key.equals( "default_click_to" ) ) {
905 final String clickto_name = ( String ) st.nextElement();
906 default_clickto = getClickToIndex( clickto_name );
907 if ( default_clickto == -1 ) {
908 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
909 + "] for [default_click_to]" );
912 else if ( default_clickto == DEPRECATED ) {
916 else if ( key.equals( "native_ui" ) ) {
917 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
918 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
921 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
922 _ui = UI.CROSSPLATFORM;
924 else if ( my_str.equals( "?" ) ) {
928 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
933 else if ( key.equals( "path_to_mafft" ) ) {
934 setPathToMafft( new File( ( String ) st.nextElement() ) );
936 else if ( key.equals( "path_to_clustalo" ) ) {
937 setPathToClustalOmega( new File( ( String ) st.nextElement() ) );
939 else if ( key.equals( "path_to_fastme" ) ) {
940 setPathToFastME( new File( ( String ) st.nextElement() ) );
942 else if ( key.equals( "path_to_mafft" ) ) {
943 setPathToMafft( new File( ( String ) st.nextElement() ) );
945 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
946 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
948 else if ( key.equals( "antialias_screen" ) ) {
949 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
951 else if ( key.equals( "phylogeny_graphics_type" ) ) {
952 final String type_str = ( ( String ) st.nextElement() ).trim();
953 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
954 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
956 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
957 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
959 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
960 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
962 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
963 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
965 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
966 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
968 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
969 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
971 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
972 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
974 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
975 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
978 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
979 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
980 + "] for [phylogeny_graphics_type]" );
983 else if ( key.equals( "min_confidence_value" ) ) {
984 final String mcv_str = ( ( String ) st.nextElement() ).trim();
985 final double d = parseDouble( mcv_str );
986 setMinConfidenceValue( d );
988 else if ( key.equals( "font_family" ) ) {
989 processFontFamily( st );
991 else if ( key.equals( "font_size" ) ) {
992 final String size_str = ( ( String ) st.nextElement() ).trim();
993 final int i = parseInt( size_str );
994 setBaseFontSize( i );
996 else if ( key.equals( "graphics_export_x" ) ) {
997 final String str = ( ( String ) st.nextElement() ).trim();
998 final int i = parseInt( str );
999 setGraphicsExportX( i );
1001 else if ( key.equals( "graphics_export_y" ) ) {
1002 final String str = ( ( String ) st.nextElement() ).trim();
1003 final int i = parseInt( str );
1004 setGraphicsExportY( i );
1006 else if ( key.equals( "pdf_export_line_width" ) ) {
1007 final String str = ( ( String ) st.nextElement() ).trim();
1008 final float f = parseFloat( str );
1010 setPrintLineWidth( f );
1013 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1014 "value for [pdf_export_line_width] cannot be zero or negative" );
1017 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1018 final String str = ( ( String ) st.nextElement() ).trim();
1019 final int i = parseInt( str );
1021 setDefaultBootstrapSamples( i );
1025 .printWarningMessage( Constants.PRG_NAME,
1026 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1029 else if ( key.equals( "show_scale" ) ) {
1030 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1032 else if ( key.equals( "show_overview" ) ) {
1033 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1035 else if ( key.equals( "show_branch_length_values" ) ) {
1036 setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
1038 else if ( key.equals( "background_gradient" ) ) {
1039 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1041 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1042 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1044 else if ( key.equals( "show_domain_labels" ) ) {
1045 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1047 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1048 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1050 else if ( key.equals( "cladogram_type" ) ) {
1051 final String type_str = ( ( String ) st.nextElement() ).trim();
1052 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1053 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1055 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1056 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1058 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1059 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1062 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1063 + "] for [cladogram_type]" );
1066 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1068 .printWarningMessage( Constants.PRG_NAME,
1069 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1071 else if ( key.equals( "hide_controls_and_menus" ) ) {
1072 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1074 else if ( key.equals( "use_tabbed_display" ) ) {
1075 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1077 else if ( key.equals( "overview_width" ) ) {
1078 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1081 else if ( key.equals( "overview_height" ) ) {
1082 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1083 setOvMaxHeight( i );
1085 else if ( key.equals( "overview_placement_type" ) ) {
1086 final String type_str = ( ( String ) st.nextElement() ).trim();
1087 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1088 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1090 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1091 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1093 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1094 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1096 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1097 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1100 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1101 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1102 + "] for [overview_placement_type]" );
1105 else if ( key.equals( "node_label_direction" ) ) {
1106 final String type_str = ( ( String ) st.nextElement() ).trim();
1107 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1108 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1110 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1111 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1114 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1115 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1116 + "] for [node_label_direction]" );
1119 else if ( key.equals( "branch_length_value_digits" ) ) {
1120 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1122 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1125 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1126 + "] for [branch_length_value_digits]" );
1129 else if ( key.equals( "confidence_value_digits" ) ) {
1130 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1132 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1135 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1136 + "] for [confidence_value_digits]" );
1139 else if ( key.equals( "allow_editing" ) ) {
1140 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1142 else if ( key.equals( "display_sequence_relations" ) ) {
1143 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1145 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1146 final boolean r = parseBoolean( ( String ) st.nextElement() );
1147 if ( r && isExtractPfamTaxonomyCodesInNhParsing() ) {
1149 .printWarningMessage( Constants.PRG_NAME,
1150 "attempt to extract taxonomies and replace underscores at the same time" );
1153 setReplaceUnderscoresInNhParsing( r );
1156 else if ( key.equals( "extract_taxonomy_codes_in_nh_parsing" ) ) {
1157 final boolean e = parseBoolean( ( String ) st.nextElement() );
1158 if ( e && isReplaceUnderscoresInNhParsing() ) {
1160 .printWarningMessage( Constants.PRG_NAME,
1161 "attempt to extract taxonomies and replace underscores at the same time" );
1164 setExtractPfamTaxonomyCodesInNhParsing( e );
1167 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1168 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1170 else if ( key.equals( "gui_background_color" ) ) {
1171 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1173 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1174 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1176 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1177 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1179 else if ( key.equals( "gui_button_text_color" ) ) {
1180 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1182 else if ( key.equals( "gui_button_background_color" ) ) {
1183 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1185 else if ( key.equals( "gui_menu_background_color" ) ) {
1186 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1188 else if ( key.equals( "gui_menu_text_color" ) ) {
1189 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1191 else if ( key.equals( "gui_button_border_color" ) ) {
1192 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1194 else if ( key.equals( "domain_structure_font_color" ) ) {
1195 _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
1197 else if ( key.equals( "domain_structure_base_color" ) ) {
1198 _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
1200 else if ( key.equals( "show_default_node_shapes" ) ) {
1201 setShowDefaultNodeShapes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1203 else if ( key.equals( "default_node_size" ) ) {
1204 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1205 setDefaultNodeShapeSize( i );
1207 else if ( key.equals( "default_node_fill" ) ) {
1208 final String fill_str = ( ( String ) st.nextElement() ).trim();
1209 if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.NONE.toString() ) ) {
1210 setDefaultNodeFill( NodeFill.NONE );
1212 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.GRADIENT.toString() ) ) {
1213 setDefaultNodeFill( NodeFill.GRADIENT );
1215 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.SOLID.toString() ) ) {
1216 setDefaultNodeFill( NodeFill.SOLID );
1219 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1220 + "] for [default_node_fill]" );
1223 else if ( key.equals( "default_node_shape" ) ) {
1224 final String shape_str = ( ( String ) st.nextElement() ).trim();
1225 if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.CIRCLE.toString() ) ) {
1226 setDefaultNodeShape( NodeShape.CIRCLE );
1228 else if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.RECTANGLE.toString() ) ) {
1229 setDefaultNodeShape( NodeShape.RECTANGLE );
1232 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1233 + "] for [default_node_shape]" );
1236 else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
1237 setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
1239 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1242 if ( key.equals( "use_real_br_lengths" ) || key.equals( "phylogram" ) ) {
1243 key_index = Configuration.display_as_phylogram;
1244 if ( key.equals( "use_real_br_lengths" ) ) {
1246 .printWarningMessage( Constants.PRG_NAME,
1247 "configuration key [use_real_br_lengths] is deprecated, use [phylogram] instead" );
1250 else if ( key.equals( "rollover" ) ) {
1251 key_index = Configuration.node_data_popup;
1253 else if ( key.equals( "color_according_to_species" ) ) {
1254 key_index = Configuration.color_according_to_species;
1256 else if ( key.equals( "show_node_names" ) ) {
1257 key_index = Configuration.show_node_names;
1259 else if ( key.equals( "show_taxonomy" ) || key.equals( "show_taxonomy_code" ) ) {
1260 key_index = Configuration.show_tax_code;
1261 if ( key.equals( "show_taxonomy" ) ) {
1263 .printWarningMessage( Constants.PRG_NAME,
1264 "configuration key [show_taxonomy] is deprecated, use [show_taxonomy_code] instead" );
1267 else if ( key.equals( "write_br_length_values" ) ) {
1268 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1269 "configuration key [write_br_length_values] is deprecated" );
1270 key_index = DEPRECATED;
1272 else if ( key.equals( "write_bootstrap_values" ) || key.equals( "write_confidence_values" ) ) {
1273 key_index = Configuration.write_confidence_values;
1274 if ( key.equals( "write_bootstrap_values" ) ) {
1276 .printWarningMessage( Constants.PRG_NAME,
1277 "configuration key [write_bootstrap_values] is deprecated, use [write_confidence_values] instead" );
1280 else if ( key.equals( "write_events" ) || key.equals( "write_dup_spec" ) ) {
1281 key_index = Configuration.write_events;
1282 if ( key.equals( "write_dup_spec" ) ) {
1284 .printWarningMessage( Constants.PRG_NAME,
1285 "configuration key [write_dup_spec] is deprecated, use [write_events] instead" );
1288 else if ( key.equals( "color_branches" ) ) {
1289 key_index = Configuration.color_branches;
1291 else if ( key.equals( "width_branches" ) ) {
1292 key_index = Configuration.width_branches;
1294 else if ( key.equals( "color_orthologous" ) ) {
1295 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1296 "configuration key [color_orthologous] is deprecated" );
1298 else if ( key.equals( "color_subtree_neighbors" ) ) {
1299 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1300 "configuration key [color_subtree_neighbors] is deprecated" );
1302 else if ( key.equals( "color_super_orthologous" ) ) {
1303 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1304 "configuration key [color_super_orthologous] is deprecated" );
1306 else if ( key.equals( "mark_nodes_with_box" ) ) {
1307 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1308 "configuration key [mark_nodes_with_box] is deprecated" );
1309 key_index = DEPRECATED;
1311 else if ( key.equals( "show_domain_architectures" ) ) {
1312 key_index = Configuration.show_domain_architectures;
1314 else if ( key.equals( "show_annotations" ) ) {
1315 key_index = Configuration.show_annotation;
1317 else if ( key.equals( "show_binary_characters" ) ) {
1318 key_index = Configuration.show_binary_characters;
1320 else if ( key.equals( "show_binary_character_counts" ) ) {
1321 key_index = Configuration.show_binary_character_counts;
1323 else if ( key.equals( "show_gene_names" ) ) {
1324 key_index = Configuration.show_gene_names;
1326 else if ( key.equals( "show_gene_symbols" ) ) {
1327 key_index = Configuration.show_gene_symbols;
1329 else if ( key.equals( "show_sequence_acc" ) ) {
1330 key_index = Configuration.show_sequence_acc;
1332 else if ( key.equals( "show_node_ids" ) ) {
1334 .printWarningMessage( Constants.PRG_NAME, "configuration key [show_node_ids] is deprecated" );
1335 key_index = DEPRECATED;
1337 else if ( key.equals( "display_internal_data" ) ) {
1338 key_index = Configuration.display_internal_data;
1340 else if ( key.equals( "dynamically_hide_data" ) ) {
1341 key_index = Configuration.dynamically_hide_data;
1343 else if ( key.equals( "show_taxonomy_names" ) ) {
1344 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1345 "configuration key [show_taxonomy_names] is deprecated" );
1346 key_index = DEPRECATED;
1348 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1349 key_index = Configuration.show_taxonomy_scientific_names;
1351 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1352 key_index = Configuration.show_taxonomy_common_names;
1354 else if ( key.equals( "show_taxonomy_images" ) ) {
1355 key_index = Configuration.show_taxonomy_images;
1357 else if ( key.equals( "color_according_to_annotation" ) ) {
1358 key_index = Configuration.color_according_to_annotation;
1360 else if ( key.equals( "show_vector_data" ) ) {
1361 key_index = Configuration.show_vector_data;
1363 else if ( key.equals( "show_properties" ) ) {
1364 key_index = Configuration.show_properties;
1366 else if ( key.equals( "show_relation_confidence" ) ) {
1367 key_index = Configuration.show_relation_confidence;
1369 else if ( key.equals( "show_custom_node_shapes" ) ) {
1370 key_index = Configuration.show_custom_node_shapes;
1372 // If we've found the key, set the values
1373 if ( key_index >= 0 ) {
1374 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1375 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1376 // otherwise, keep looking
1379 if ( key_index == DEPRECATED ) {
1382 else if ( key.equals( "click_to" ) ) {
1383 final String click_to_name = ( String ) st.nextElement();
1384 key_index = getClickToIndex( click_to_name );
1385 if ( key_index >= 0 ) {
1386 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1388 else if ( key_index == DEPRECATED ) {
1392 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1396 else if ( key.equals( "species_color" ) ) {
1397 getSpeciesColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1399 else if ( key.equals( "domain_color" ) ) {
1400 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1402 else if ( key.equals( "annotation_color" ) ) {
1403 getAnnotationColors()
1404 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1406 else if ( key.equals( "function_color" ) ) {
1407 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1408 "configuration key [function_color] is deprecated" );
1410 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1411 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1413 else if ( key.equals( WEB_LINK_KEY ) ) {
1414 if ( st.countTokens() == 3 ) {
1415 createWebLink( ( String ) st.nextElement(),
1416 ( String ) st.nextElement(),
1417 ( String ) st.nextElement() );
1420 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1421 "illegal format in configuration file for key [" + key + "]" );
1425 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1426 + "] in: " + config_filename );
1431 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1432 + config_filename );
1436 public void setMinConfidenceValue( final double min_confidence_value ) {
1437 _min_confidence_value = min_confidence_value;
1440 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
1441 _node_label_direction = node_label_direction;
1444 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short _number_of_digits_after_comma_for_branch_length_values ) {
1445 this._number_of_digits_after_comma_for_branch_length_values = _number_of_digits_after_comma_for_branch_length_values;
1448 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short _number_of_digits_after_comma_for_confidence_values ) {
1449 this._number_of_digits_after_comma_for_confidence_values = _number_of_digits_after_comma_for_confidence_values;
1452 private void setOvMaxHeight( final short ov_max_height ) {
1453 _ov_max_height = ov_max_height;
1456 private void setOvMaxWidth( final short ov_max_width ) {
1457 _ov_max_width = ov_max_width;
1460 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1461 _ov_placement = ov_placement;
1464 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
1465 _phylogeny_graphics_type = phylogeny_graphics_type;
1468 public void setPrintLineWidth( final float print_line_width ) {
1469 _print_line_width = print_line_width;
1472 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
1473 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
1476 public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
1477 _show_branch_length_values = show_branch_length_values;
1480 public void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
1481 _show_default_node_shapes = show_default_node_shapes;
1484 public void setShowDomainLabels( final boolean show_domain_labels ) {
1485 _show_domain_labels = show_domain_labels;
1488 private void setShowOverview( final boolean show_overview ) {
1489 _show_overview = show_overview;
1492 public void setShowScale( final boolean show_scale ) {
1493 _show_scale = show_scale;
1496 public void setTaxonomyColorize( final boolean b ) {
1497 display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
1500 public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
1501 _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
1504 public void setUseBranchesWidths( final boolean b ) {
1505 display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
1508 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1509 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1512 void setWebLinks( final SortedMap<String, WebLink> weblinks ) {
1513 _weblinks = weblinks;
1516 static String getDefaultFontFamilyName() {
1517 return DEFAULT_FONT_FAMILY;
1520 public File getPathToMafft() {
1524 public File getPathToClustalOmega() {
1528 public File getPathToFastME() {
1532 public void setPathToMafft( final File mafft ) {
1536 public void setPathToClustalOmega( final File clustalo ) {
1537 _clustalo = clustalo;
1540 public void setPathToFastME( final File fastme ) {
1544 static enum TRIPLET {
1545 TRUE, FALSE, UNKNOWN
1549 NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN