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: https://sites.google.com/site/cmzmasek/home/software/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.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
51 import org.forester.phylogeny.data.NodeData.NODE_DATA;
52 import org.forester.phylogeny.data.NodeVisualization;
53 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
54 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
55 import org.forester.util.ForesterUtil;
57 public final class Configuration {
59 public enum EXT_NODE_DATA_RETURN_ON {
60 CONSOLE, WINODW, BUFFER_ONLY;
62 static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
63 private static final String WEB_LINK_KEY = "web_link";
64 private static final String DISPLAY_COLOR_KEY = "display_color";
65 private static final int DEPRECATED = -2;
66 private UI _ui = UI.UNKNOWN;
67 private boolean _use_tabbed_display = false;
68 private boolean _hide_controls_and_menus = false;
69 private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
70 private SortedMap<String, WebLink> _weblinks = null;
71 private SortedMap<String, Color> _display_colors = null;
72 private boolean _antialias_screen = true;
73 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
74 private String _base_font_family_name = "";
75 private int _base_font_size = -1;
76 private int _graphics_export_x = -1;
77 private int _graphics_export_y = -1;
78 private short _ov_max_width = 80;
79 private short _ov_max_height = 80;
80 private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
81 private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
82 private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
83 private boolean _show_scale = false;
84 private boolean _show_branch_length_values = false;
85 private boolean _show_overview = true;
86 private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
87 private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
88 private boolean _editable = true;
89 private boolean _nh_parsing_replace_underscores = false;
90 private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
91 private boolean _internal_number_are_confidence_for_nh_parsing = false;
92 private boolean _display_sequence_relations = false;
93 private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
94 private boolean _background_color_gradient = false;
95 private boolean _show_domain_labels = true;
96 private boolean _abbreviate_scientific_names = false;
97 private boolean _color_labels_same_as_parent_branch = false;
98 private boolean _show_default_node_shapes = false;
99 private NodeShape _default_node_shape = NodeShape.CIRCLE;
100 private NodeFill _default_node_fill = NodeFill.GRADIENT;
101 private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
102 private boolean _taxonomy_colorize_node_shapes = false;
103 private int _default_bootstrap_samples = -1;
104 private File _path_to_local_mafft = null;
105 private File _path_to_local_fastme = null;
106 private File _path_to_local_raxml = null;
107 private File _path_to_local_clustalo = null;
108 final static int display_as_phylogram = 0;
109 final static int show_node_names = 1;
110 final static int show_tax_code = 2;
111 final static int show_annotation = 3;
112 final static int write_confidence_values = 4;
113 final static int write_events = 5;
114 final static int color_according_to_species = 6;
115 final static int color_branches = 7;
116 final static int width_branches = 8;
117 final static int show_custom_node_shapes = 9;
118 final static int show_domain_architectures = 10;
119 final static int show_binary_characters = 11;
120 final static int show_binary_character_counts = 12;
121 final static int show_gene_names = 13;
122 final static int show_sequence_acc = 14;
123 final static int display_internal_data = 15;
124 final static int dynamically_hide_data = 16;
125 final static int show_taxonomy_scientific_names = 17;
126 final static int show_taxonomy_common_names = 18;
127 final static int color_according_to_annotation = 19;
128 final static int show_gene_symbols = 20;
129 final static int node_data_popup = 21;
130 final static int show_relation_confidence = 22;
131 final static int show_vector_data = 23;
132 final static int show_taxonomy_images = 24;
133 final static int show_properties = 25;
134 // ------------------
136 // ------------------
137 final static int display_node_data = 0;
138 final static int collapse_uncollapse = 1;
139 final static int reroot = 2;
140 final static int subtree = 3;
141 final static int swap = 4;
142 final static int color_subtree = 5;
143 final static int open_seq_web = 6;
144 final static int open_tax_web = 7;
145 final static int blast = 8;
146 final static int cut_subtree = 9;
147 final static int copy_subtree = 10;
148 final static int paste_subtree = 11;
149 final static int delete_subtree_or_node = 12;
150 final static int add_new_node = 13;
151 final static int edit_node_data = 14;
152 final static int sort_descendents = 15;
153 final static int get_ext_desc_data = 16;
154 final static int select_nodes = 17;
155 // ---------------------------
156 // Display options for trees
157 // ---------------------------
158 // ---------------------------------
159 // Pertaining to the config itself
160 // ---------------------------------
161 // Full path to config (may be URL)
162 String config_filename;
163 String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
164 final static String display_options[][] = {
165 { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
166 { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, { "Node Events", "display", "?" },
167 { "Taxonomy Colorize", "display", "yes" }, { "Colorize Branches", "display", "no" },
168 { "Use Branch-Widths", "display", "no" }, { "Show Custom Nodes", "display", "yes" },
169 { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" },
170 { "Binary Char Counts", "nodisplay", "no" }, { "Seq Name", "display", "yes" },
171 { "Seq Acc", "display", "no" }, { "Show Internal Data", "display", "yes" },
172 { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" },
173 { "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" },
174 { "Seq Symbol", "display", "yes" }, { "Rollover", "display", "yes" },
175 { "Relation Confidence", "nodisplay", "no" }, { "Vector Data", "nodisplay", "no" },
176 { "Taxonomy Images", "display", "no" }, { "Properties", "nodisplay", "no" } };
177 final static String clickto_options[][] = {
178 { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
179 { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
180 { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Blast", "display" },
181 { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" },
182 { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" },
183 { "Sort Descendants", "display" }, { "Return", "display" }, { "Select Node(s)", "display" } };
184 // This option is selected in the dropdown
185 int default_clickto = Configuration.display_node_data;
189 TreeColorSet tree_color_set;
193 TreeFontSet tree_font_set;
197 private static Hashtable<String, Color> _species_colors;
201 private static Hashtable<String, Color> _domain_colors;
205 private static Hashtable<String, Color> _annotation_colors;
206 boolean verbose = Constants.VERBOSE_DEFAULT;
207 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
208 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
209 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
210 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
211 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
212 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
213 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
214 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
215 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
216 private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
217 private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
218 private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
219 private String _label_for_get_ext_descendents_data = "";
220 private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
221 private int _frame_x_size;
222 private int _frame_y_size;
223 private static String DEFAULT_FONT_FAMILY = "";
225 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
226 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
227 DEFAULT_FONT_FAMILY = font_name;
231 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
232 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
236 public Configuration() {
237 this( null, false, false, false );
240 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
241 if ( ForesterUtil.isEmpty( cf ) ) {
242 config_filename = default_config_filename;
245 config_filename = cf;
247 setWebLinks( new TreeMap<String, WebLink>() );
248 setDisplayColors( new TreeMap<String, Color>() );
249 config_filename = config_filename.trim();
252 // If URL, open accordingly
254 u = new URL( config_filename );
256 final InputStreamReader isr = new InputStreamReader( u.openStream() );
257 final BufferedReader bf = new BufferedReader( isr );
260 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
261 + config_filename + "]" );
263 catch ( final Exception e ) {
264 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
265 + config_filename + "]: " + e.getLocalizedMessage() );
268 catch ( final Exception e ) {
269 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
270 + config_filename + "]" );
274 // Otherwise, open as a file
275 File f = new File( config_filename );
277 f = new File( config_filename + ".txt" );
279 if ( f.exists() && f.canRead() ) {
281 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
285 catch ( final Exception e ) {
287 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
288 + config_filename + "]: " + e );
294 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
295 + config_filename + "]" );
301 private void createWebLink( final String url_str, final String desc, final String source_identifier ) {
302 WebLink weblink = null;
305 weblink = new WebLink( new URL( url_str.trim() ), desc.trim(), source_identifier.trim() );
307 catch ( final MalformedURLException e ) {
308 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not create URL from [" + url_str + "]" );
311 if ( !ex && ( weblink != null ) ) {
312 getWebLinks().put( weblink.getSourceIdentifier().toLowerCase(), weblink );
316 boolean displaySequenceRelations() {
317 return _display_sequence_relations;
320 boolean doCheckOption( final int which ) {
321 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
322 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
325 boolean doDisplayClickToOption( final int which ) {
326 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
329 boolean doDisplayOption( final int which ) {
330 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
334 * Will attempt to use the phylogeny to determine whether to check
335 * this or not (e.g. phylogram)
338 boolean doGuessCheckOption( final int which ) {
339 return display_options[ which ][ 2 ].equals( "?" );
342 Map<String, Color> getAnnotationColors() {
343 if ( _annotation_colors == null ) {
344 _annotation_colors = new Hashtable<String, Color>();
346 return _annotation_colors;
349 public String getBaseFontFamilyName() {
350 return _base_font_family_name;
353 int getBaseFontSize() {
354 return _base_font_size;
357 CLADOGRAM_TYPE getCladogramType() {
358 return _cladogram_type;
361 private int getClickToIndex( final String name ) {
363 if ( name.equals( "edit_info" ) ) {
364 index = Configuration.display_node_data;
366 .printWarningMessage( Constants.PRG_NAME,
367 "configuration key [edit_info] is deprecated, use [display node data] instead" );
369 else if ( name.equals( "display_node_data" ) ) {
370 index = Configuration.display_node_data;
372 else if ( name.equals( "collapse_uncollapse" ) ) {
373 index = Configuration.collapse_uncollapse;
375 else if ( name.equals( "reroot" ) ) {
376 index = Configuration.reroot;
378 else if ( name.equals( "subtree" ) ) {
379 index = Configuration.subtree;
381 else if ( name.equals( "swap" ) ) {
382 index = Configuration.swap;
384 else if ( name.equals( "sort_descendants" ) ) {
385 index = Configuration.sort_descendents;
387 else if ( name.equals( "get_ext_descendents_data" ) ) {
388 index = Configuration.get_ext_desc_data;
390 else if ( name.equals( "display_sequences" ) ) {
392 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
395 else if ( name.equals( "open_seq_web" ) ) {
396 index = Configuration.open_seq_web;
398 else if ( name.equals( "open_tax_web" ) ) {
399 index = Configuration.open_tax_web;
401 else if ( name.equals( "blast" ) ) {
402 index = Configuration.blast;
404 else if ( name.equals( "cut_subtree" ) ) {
405 index = Configuration.cut_subtree;
407 else if ( name.equals( "copy_subtree" ) ) {
408 index = Configuration.copy_subtree;
410 else if ( name.equals( "paste_subtree" ) ) {
411 index = Configuration.paste_subtree;
413 else if ( name.equals( "delete" ) ) {
414 index = Configuration.delete_subtree_or_node;
416 else if ( name.equals( "add_new_node" ) ) {
417 index = Configuration.add_new_node;
419 else if ( name.equals( "edit_node_data" ) ) {
420 index = Configuration.edit_node_data;
422 else if ( name.equals( "select_nodes" ) ) {
423 index = Configuration.select_nodes;
425 else if ( name.equals( "display_node_popup" ) ) {
426 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
427 "configuration key [display_node_popup] is deprecated" );
430 else if ( name.equals( "custom_option" ) ) {
431 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
434 else if ( name.equals( "color_subtree" ) ) {
435 index = Configuration.color_subtree;
437 else if ( name.equals( "go_to_swiss_prot" ) ) {
438 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" );
444 int getClickToOptionsCount() {
445 return clickto_options.length;
448 String getClickToTitle( final int which ) {
449 return clickto_options[ which ][ 0 ];
452 public int getDefaultBootstrapSamples() {
453 return _default_bootstrap_samples;
456 public File getpathToLocalMafft() {
457 return _path_to_local_mafft;
460 public File getPathToLocalFastme() {
461 return _path_to_local_fastme;
464 public File getPathToLocalRaxml() {
465 return _path_to_local_raxml;
468 int getDefaultDisplayClicktoOption() {
469 return default_clickto;
472 public NodeFill getDefaultNodeFill() {
473 return _default_node_fill;
476 public NodeShape getDefaultNodeShape() {
477 return _default_node_shape;
480 public short getDefaultNodeShapeSize() {
481 return _default_node_shape_size;
484 SortedMap<String, Color> getDisplayColors() {
485 return _display_colors;
488 String getDisplayTitle( final int which ) {
489 return display_options[ which ][ 0 ];
492 Map<String, Color> getDomainColors() {
493 if ( _domain_colors == null ) {
494 _domain_colors = new Hashtable<String, Color>();
496 return _domain_colors;
499 public Color getDomainStructureBaseColor() {
500 return _domain_structure_base_color;
503 public Color getDomainStructureFontColor() {
504 return _domain_structure_font_color;
507 int getGraphicsExportX() {
508 return _graphics_export_x;
511 int getGraphicsExportY() {
512 return _graphics_export_y;
515 Color getGuiBackgroundColor() {
516 return _gui_background_color;
519 Color getGuiButtonBackgroundColor() {
520 return _gui_button_background_color;
523 Color getGuiButtonBorderColor() {
524 return _gui_button_border_color;
527 Color getGuiButtonTextColor() {
528 return _gui_button_text_color;
531 Color getGuiCheckboxAndButtonActiveColor() {
532 return _gui_checkbox_and_button_active_color;
535 Color getGuiCheckboxTextColor() {
536 return _gui_checkbox_text_color;
539 Color getGuiMenuBackgroundColor() {
540 return _gui_menu_background_color;
543 Color getGuiMenuTextColor() {
544 return _gui_menu_text_color;
547 double getMinConfidenceValue() {
548 return _min_confidence_value;
551 NODE_LABEL_DIRECTION getNodeLabelDirection() {
552 return _node_label_direction;
555 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
556 return _number_of_digits_after_comma_for_branch_length_values;
559 short getNumberOfDigitsAfterCommaForConfidenceValues() {
560 return _number_of_digits_after_comma_for_confidence_values;
563 short getOvMaxHeight() {
564 return _ov_max_height;
567 short getOvMaxWidth() {
568 return _ov_max_width;
571 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
572 return _ov_placement;
575 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
576 return _phylogeny_graphics_type;
579 float getPrintLineWidth() {
580 return _print_line_width;
583 Hashtable<String, Color> getSpeciesColors() {
584 if ( _species_colors == null ) {
585 _species_colors = new Hashtable<String, Color>();
587 return _species_colors;
590 TreeColorSet getTreeColorSet() {
594 TreeFontSet getTreeFontSet() {
598 WebLink getWebLink( final String source ) {
599 return getWebLinks().get( source );
602 Map<String, WebLink> getWebLinks() {
606 public boolean isAbbreviateScientificTaxonNames() {
607 return _abbreviate_scientific_names;
610 boolean isAntialiasScreen() {
611 return _antialias_screen;
614 public boolean isBackgroundColorGradient() {
615 return _background_color_gradient;
618 public boolean isColorLabelsSameAsParentBranch() {
619 return _color_labels_same_as_parent_branch;
623 * Convenience method.
625 * @return true if value in configuration file was 'yes'
627 boolean isDrawAsPhylogram() {
628 return doCheckOption( display_as_phylogram );
631 boolean isEditable() {
635 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
636 return _taxonomy_extraction;
639 boolean isHasWebLink( final String source ) {
640 return getWebLinks().containsKey( source );
644 * Only used by ArchaeoptryxE.
647 boolean isHideControlPanelAndMenubar() {
648 return _hide_controls_and_menus;
651 boolean isInternalNumberAreConfidenceForNhParsing() {
652 return _internal_number_are_confidence_for_nh_parsing;
655 boolean isReplaceUnderscoresInNhParsing() {
656 return _nh_parsing_replace_underscores;
659 boolean isShowBranchLengthValues() {
660 return _show_branch_length_values;
663 public boolean isShowDefaultNodeShapes() {
664 return _show_default_node_shapes;
667 public boolean isShowDomainLabels() {
668 return _show_domain_labels;
671 boolean isShowOverview() {
672 return _show_overview;
675 boolean isShowScale() {
679 public boolean isTaxonomyColorizeNodeShapes() {
680 return _taxonomy_colorize_node_shapes;
683 final boolean isUseNativeUI() {
684 if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) {
687 return _ui == UI.NATIVE;
691 * Only used by ArchaeoptryxE.
694 boolean isUseTabbedDisplay() {
695 return _use_tabbed_display;
698 boolean isValidatePhyloXmlAgainstSchema() {
699 return _validate_against_phyloxml_xsd_schema;
702 private boolean parseBoolean( final String str ) {
703 final String my_str = str.trim().toLowerCase();
704 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
707 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
711 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
716 private double parseDouble( final String str ) {
719 d = Double.parseDouble( str.trim() );
721 catch ( final Exception e ) {
722 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
728 private float parseFloat( final String str ) {
731 f = Float.parseFloat( str.trim() );
733 catch ( final Exception e ) {
734 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
740 private int parseInt( final String str ) {
743 i = Integer.parseInt( str.trim() );
745 catch ( final Exception e ) {
746 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
752 private short parseShort( final String str ) {
755 i = Short.parseShort( str.trim() );
757 catch ( final Exception e ) {
758 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
764 private void processFontFamily( final StringTokenizer st ) {
765 setBaseFontFamilyName( "" );
766 final String font_str = ( ( String ) st.nextElement() ).trim();
767 final String[] fonts = font_str.split( ",+" );
768 for( String font : fonts ) {
769 font = font.replace( '_', ' ' ).trim();
770 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
771 setBaseFontFamilyName( font );
777 public void putDisplayColors( final String key, final Color color ) {
778 getDisplayColors().put( key, color );
782 * read each line of config file, process non-comment lines
783 * @throws IOException
785 private void readConfig( final BufferedReader conf_in ) throws IOException {
788 line = conf_in.readLine();
789 if ( line != null ) {
791 // skip comments and blank lines
792 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
793 // convert runs of spaces to tabs
794 line = line.replaceAll( "\\s+", "\t" );
795 final StringTokenizer st = new StringTokenizer( line, "\t" );
799 } while ( line != null );
802 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
803 _abbreviate_scientific_names = abbreviate_scientific_names;
806 private void setAntialiasScreen( final boolean antialias_screen ) {
807 _antialias_screen = antialias_screen;
810 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
811 _background_color_gradient = background_color_gradient;
814 public void setBaseFontFamilyName( final String base_font_family_name ) {
815 _base_font_family_name = base_font_family_name;
818 public void setBaseFontSize( final int base_font_size ) {
819 _base_font_size = base_font_size;
822 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
823 _cladogram_type = cladogram_type;
826 public void setColorizeBranches( final boolean b ) {
827 display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
830 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
831 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
834 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
835 _default_bootstrap_samples = default_bootstrap_samples;
838 private void setPathToLocalMafft( final File path_to_local_mafft ) {
839 _path_to_local_mafft = path_to_local_mafft;
842 private void setPathToLocalFastme( final File path_to_local_fastme ) {
843 _path_to_local_fastme = path_to_local_fastme;
846 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
847 _path_to_local_raxml = path_to_local_raxml;
850 public File getPathToLocalClustalOmega() {
851 return _path_to_local_clustalo;
854 public void setPathToLocalClustalOmega( final File path_to_local_clustalo ) {
855 _path_to_local_clustalo = path_to_local_clustalo;
858 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
859 _default_node_fill = default_node_fill;
862 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
863 _default_node_shape = default_node_shape;
866 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
867 _default_node_shape_size = default_node_shape_size;
870 public void setDisplayAsPhylogram( final boolean b ) {
871 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
874 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
875 _display_colors = display_colors;
878 public void setDisplayConfidenceValues( final boolean b ) {
879 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
882 public void setDisplayInternalData( final boolean b ) {
883 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
886 public void setDisplayNodeNames( final boolean b ) {
887 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
890 public void setDisplaySequenceAcc( final boolean b ) {
891 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
894 public void setDisplaySequenceNames( final boolean b ) {
895 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
898 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
899 _display_sequence_relations = display_sequence_relations;
902 public void setDisplaySequenceSymbols( final boolean b ) {
903 display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no";
906 public void setDisplayTaxonomyCode( final boolean b ) {
907 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
910 public void setDisplayTaxonomyCommonNames( final boolean b ) {
911 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
914 public void setDisplayTaxonomyImages( final boolean b ) {
915 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
918 public void setDisplayTaxonomyScientificNames( final boolean b ) {
919 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
922 public void setDynamicallyHideData( final boolean b ) {
923 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
926 private void setEditable( final boolean editable ) {
927 _editable = editable;
930 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
931 _taxonomy_extraction = taxonomy_extraction;
934 private void setGraphicsExportX( final int graphics_export_x ) {
935 _graphics_export_x = graphics_export_x;
938 private void setGraphicsExportY( final int graphics_export_y ) {
939 _graphics_export_y = graphics_export_y;
942 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
943 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
947 * Set a key-value(s) tuple
949 private void setKeyValue( final StringTokenizer st ) {
950 final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
951 if ( !st.hasMoreElements() ) {
954 // Handle single value settings first:
955 if ( key.equals( "default_click_to" ) ) {
956 final String clickto_name = ( String ) st.nextElement();
957 default_clickto = getClickToIndex( clickto_name );
958 if ( default_clickto == -1 ) {
959 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
960 + "] for [default_click_to]" );
963 else if ( default_clickto == DEPRECATED ) {
967 else if ( key.equals( "native_ui" ) ) {
968 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
969 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
972 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
973 _ui = UI.CROSSPLATFORM;
975 else if ( my_str.equals( "?" ) ) {
979 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
984 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
985 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
987 else if ( key.equals( "antialias_screen" ) ) {
988 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
990 else if ( key.equals( "phylogeny_graphics_type" ) ) {
991 final String type_str = ( ( String ) st.nextElement() ).trim();
992 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
993 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
995 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
996 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
998 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
999 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1001 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
1002 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1004 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
1005 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1007 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
1008 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1010 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
1011 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1013 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
1014 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1017 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1018 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1019 + "] for [phylogeny_graphics_type]" );
1022 else if ( key.equals( "min_confidence_value" ) ) {
1023 final String mcv_str = ( ( String ) st.nextElement() ).trim();
1024 final double d = parseDouble( mcv_str );
1025 setMinConfidenceValue( d );
1027 else if ( key.equals( "font_family" ) ) {
1028 processFontFamily( st );
1030 else if ( key.equals( "font_size" ) ) {
1031 final String size_str = ( ( String ) st.nextElement() ).trim();
1032 final int i = parseInt( size_str );
1034 setBaseFontSize( i );
1037 else if ( key.equals( "graphics_export_x" ) ) {
1038 final String str = ( ( String ) st.nextElement() ).trim();
1039 final int i = parseInt( str );
1041 setGraphicsExportX( i );
1044 else if ( key.equals( "graphics_export_y" ) ) {
1045 final String str = ( ( String ) st.nextElement() ).trim();
1046 final int i = parseInt( str );
1048 setGraphicsExportY( i );
1051 else if ( key.equals( "pdf_export_line_width" ) ) {
1052 final String str = ( ( String ) st.nextElement() ).trim();
1053 final float f = parseFloat( str );
1055 setPrintLineWidth( f );
1058 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1059 "value for [pdf_export_line_width] cannot be zero or negative" );
1062 else if ( key.equals( "window_initial_size_x" ) ) {
1063 final String str = ( ( String ) st.nextElement() ).trim();
1064 final int i = parseInt( str );
1069 else if ( key.equals( "window_initial_size_y" ) ) {
1070 final String str = ( ( String ) st.nextElement() ).trim();
1071 final int i = parseInt( str );
1076 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1077 final String str = ( ( String ) st.nextElement() ).trim();
1078 final int i = parseInt( str );
1080 setDefaultBootstrapSamples( i );
1084 .printWarningMessage( Constants.PRG_NAME,
1085 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1088 else if ( key.equals( "clustalo_local" ) ) {
1089 final String str = ( ( String ) st.nextElement() ).trim();
1090 if ( !ForesterUtil.isEmpty( str ) ) {
1091 setPathToLocalClustalOmega( new File( str ) );
1094 else if ( key.equals( "mafft_local" ) ) {
1095 final String str = ( ( String ) st.nextElement() ).trim();
1096 if ( !ForesterUtil.isEmpty( str ) ) {
1097 setPathToLocalMafft( new File( str ) );
1100 else if ( key.equals( "fastme_local" ) ) {
1101 final String str = ( ( String ) st.nextElement() ).trim();
1102 if ( !ForesterUtil.isEmpty( str ) ) {
1103 setPathToLocalFastme( new File( str ) );
1106 else if ( key.equals( "raxml_local" ) ) {
1107 final String str = ( ( String ) st.nextElement() ).trim();
1108 if ( !ForesterUtil.isEmpty( str ) ) {
1109 setPathToLocalRaxml( new File( str ) );
1112 else if ( key.equals( "show_scale" ) ) {
1113 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1115 else if ( key.equals( "show_overview" ) ) {
1116 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1118 else if ( key.equals( "show_branch_length_values" ) ) {
1119 setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
1121 else if ( key.equals( "background_gradient" ) ) {
1122 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1124 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1125 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1127 else if ( key.equals( "show_domain_labels" ) ) {
1128 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1130 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1131 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1133 else if ( key.equals( "cladogram_type" ) ) {
1134 final String type_str = ( ( String ) st.nextElement() ).trim();
1135 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1136 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1138 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1139 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1141 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1142 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1145 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1146 + "] for [cladogram_type]" );
1149 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1151 .printWarningMessage( Constants.PRG_NAME,
1152 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1154 else if ( key.equals( "hide_controls_and_menus" ) ) {
1155 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1157 else if ( key.equals( "use_tabbed_display" ) ) {
1158 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1160 else if ( key.equals( "overview_width" ) ) {
1161 final short i = parseShort( ( ( String ) st.nextElement() ) );
1164 else if ( key.equals( "overview_height" ) ) {
1165 final short i = parseShort( ( ( String ) st.nextElement() ) );
1166 setOvMaxHeight( i );
1168 else if ( key.equals( "overview_placement_type" ) ) {
1169 final String type_str = ( ( String ) st.nextElement() ).trim();
1170 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1171 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1173 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1174 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1176 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1177 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1179 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1180 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1183 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1184 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1185 + "] for [overview_placement_type]" );
1188 else if ( key.equals( "node_label_direction" ) ) {
1189 final String type_str = ( ( String ) st.nextElement() ).trim();
1190 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1191 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1193 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1194 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1197 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1198 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1199 + "] for [node_label_direction]" );
1202 else if ( key.equals( "branch_length_value_digits" ) ) {
1203 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1205 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1208 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1209 + "] for [branch_length_value_digits]" );
1212 else if ( key.equals( "confidence_value_digits" ) ) {
1213 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1215 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1218 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1219 + "] for [confidence_value_digits]" );
1222 else if ( key.equals( "allow_editing" ) ) {
1223 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1225 else if ( key.equals( "display_sequence_relations" ) ) {
1226 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1228 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1229 final boolean r = parseBoolean( ( String ) st.nextElement() );
1230 if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
1232 .printWarningMessage( Constants.PRG_NAME,
1233 "attempt to extract taxonomies and replace underscores at the same time" );
1236 setReplaceUnderscoresInNhParsing( r );
1239 else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
1240 final String s = ( String ) st.nextElement();
1241 if ( s.equalsIgnoreCase( "no" ) ) {
1242 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1244 else if ( s.equalsIgnoreCase( "yes" ) ) {
1245 setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES );
1247 else if ( s.equalsIgnoreCase( "pfam" ) ) {
1248 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
1251 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1252 "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + s );
1254 if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
1256 .printWarningMessage( Constants.PRG_NAME,
1257 "attempt to extract taxonomies and replace underscores at the same time" );
1260 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1261 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1263 else if ( key.equals( "gui_background_color" ) ) {
1264 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1266 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1267 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1269 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1270 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1272 else if ( key.equals( "gui_button_text_color" ) ) {
1273 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1275 else if ( key.equals( "gui_button_background_color" ) ) {
1276 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1278 else if ( key.equals( "gui_menu_background_color" ) ) {
1279 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1281 else if ( key.equals( "gui_menu_text_color" ) ) {
1282 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1284 else if ( key.equals( "gui_button_border_color" ) ) {
1285 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1287 else if ( key.equals( "domain_structure_font_color" ) ) {
1288 _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
1290 else if ( key.equals( "domain_structure_base_color" ) ) {
1291 _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
1293 else if ( key.equals( "show_default_node_shapes" ) ) {
1294 setShowDefaultNodeShapes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1296 else if ( key.equals( "default_node_size" ) ) {
1297 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1298 setDefaultNodeShapeSize( i );
1300 else if ( key.equals( "default_node_fill" ) ) {
1301 final String fill_str = ( ( String ) st.nextElement() ).trim();
1302 if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.NONE.toString() ) ) {
1303 setDefaultNodeFill( NodeFill.NONE );
1305 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.GRADIENT.toString() ) ) {
1306 setDefaultNodeFill( NodeFill.GRADIENT );
1308 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.SOLID.toString() ) ) {
1309 setDefaultNodeFill( NodeFill.SOLID );
1312 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1313 + "] for [default_node_fill]" );
1316 else if ( key.equals( "default_node_shape" ) ) {
1317 final String shape_str = ( ( String ) st.nextElement() ).trim();
1318 if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.CIRCLE.toString() ) ) {
1319 setDefaultNodeShape( NodeShape.CIRCLE );
1321 else if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.RECTANGLE.toString() ) ) {
1322 setDefaultNodeShape( NodeShape.RECTANGLE );
1325 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1326 + "] for [default_node_shape]" );
1329 else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
1330 setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
1332 else if ( key.equals( "ext_descendents_data_to_return" ) ) {
1333 final String s = ( ( String ) st.nextElement() ).trim();
1334 if ( s.equalsIgnoreCase( "node_name" ) ) {
1335 setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
1337 else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
1338 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
1340 else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
1341 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
1343 else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
1344 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
1346 else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
1347 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
1349 else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
1350 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME );
1352 else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
1353 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
1355 else if ( s.equalsIgnoreCase( "user_selected" ) ) {
1356 setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
1359 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1360 + "] for [ext_descendents_data_to_return]" );
1363 else if ( key.equals( "label_for_get_ext_descendents_data" ) ) {
1364 final String s = ( ( String ) st.nextElement() ).trim();
1365 if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) {
1366 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s
1367 + "] for [label_for_get_ext_descendents_data]" );
1370 setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
1373 else if ( key.equals( "ext_descendents_data_to_return_on" ) ) {
1374 final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
1375 if ( s.equals( "console" ) ) {
1376 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
1378 else if ( s.equals( "window" ) ) {
1379 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
1381 else if ( s.equals( "buffer_only" ) ) {
1382 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
1385 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1386 + "] for [ext_descendents_data_to_return_on]" );
1389 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1392 if ( key.equals( "use_real_br_lengths" ) || key.equals( "phylogram" ) ) {
1393 key_index = Configuration.display_as_phylogram;
1394 if ( key.equals( "use_real_br_lengths" ) ) {
1396 .printWarningMessage( Constants.PRG_NAME,
1397 "configuration key [use_real_br_lengths] is deprecated, use [phylogram] instead" );
1400 else if ( key.equals( "rollover" ) ) {
1401 key_index = Configuration.node_data_popup;
1403 else if ( key.equals( "color_according_to_species" ) ) {
1404 key_index = Configuration.color_according_to_species;
1406 else if ( key.equals( "show_node_names" ) ) {
1407 key_index = Configuration.show_node_names;
1409 else if ( key.equals( "show_taxonomy" ) || key.equals( "show_taxonomy_code" ) ) {
1410 key_index = Configuration.show_tax_code;
1411 if ( key.equals( "show_taxonomy" ) ) {
1413 .printWarningMessage( Constants.PRG_NAME,
1414 "configuration key [show_taxonomy] is deprecated, use [show_taxonomy_code] instead" );
1417 else if ( key.equals( "write_br_length_values" ) ) {
1418 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1419 "configuration key [write_br_length_values] is deprecated" );
1420 key_index = DEPRECATED;
1422 else if ( key.equals( "write_bootstrap_values" ) || key.equals( "write_confidence_values" ) ) {
1423 key_index = Configuration.write_confidence_values;
1424 if ( key.equals( "write_bootstrap_values" ) ) {
1426 .printWarningMessage( Constants.PRG_NAME,
1427 "configuration key [write_bootstrap_values] is deprecated, use [write_confidence_values] instead" );
1430 else if ( key.equals( "write_events" ) || key.equals( "write_dup_spec" ) ) {
1431 key_index = Configuration.write_events;
1432 if ( key.equals( "write_dup_spec" ) ) {
1434 .printWarningMessage( Constants.PRG_NAME,
1435 "configuration key [write_dup_spec] is deprecated, use [write_events] instead" );
1438 else if ( key.equals( "color_branches" ) ) {
1439 key_index = Configuration.color_branches;
1441 else if ( key.equals( "width_branches" ) ) {
1442 key_index = Configuration.width_branches;
1444 else if ( key.equals( "color_orthologous" ) ) {
1445 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1446 "configuration key [color_orthologous] is deprecated" );
1448 else if ( key.equals( "color_subtree_neighbors" ) ) {
1449 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1450 "configuration key [color_subtree_neighbors] is deprecated" );
1452 else if ( key.equals( "color_super_orthologous" ) ) {
1453 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1454 "configuration key [color_super_orthologous] is deprecated" );
1456 else if ( key.equals( "mark_nodes_with_box" ) ) {
1457 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1458 "configuration key [mark_nodes_with_box] is deprecated" );
1459 key_index = DEPRECATED;
1461 else if ( key.equals( "show_domain_architectures" ) ) {
1462 key_index = Configuration.show_domain_architectures;
1464 else if ( key.equals( "show_annotations" ) ) {
1465 key_index = Configuration.show_annotation;
1467 else if ( key.equals( "show_binary_characters" ) ) {
1468 key_index = Configuration.show_binary_characters;
1470 else if ( key.equals( "show_binary_character_counts" ) ) {
1471 key_index = Configuration.show_binary_character_counts;
1473 else if ( key.equals( "show_gene_names" ) ) {
1474 key_index = Configuration.show_gene_names;
1476 else if ( key.equals( "show_gene_symbols" ) ) {
1477 key_index = Configuration.show_gene_symbols;
1479 else if ( key.equals( "show_sequence_acc" ) ) {
1480 key_index = Configuration.show_sequence_acc;
1482 else if ( key.equals( "show_node_ids" ) ) {
1484 .printWarningMessage( Constants.PRG_NAME, "configuration key [show_node_ids] is deprecated" );
1485 key_index = DEPRECATED;
1487 else if ( key.equals( "display_internal_data" ) ) {
1488 key_index = Configuration.display_internal_data;
1490 else if ( key.equals( "dynamically_hide_data" ) ) {
1491 key_index = Configuration.dynamically_hide_data;
1493 else if ( key.equals( "show_taxonomy_names" ) ) {
1494 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1495 "configuration key [show_taxonomy_names] is deprecated" );
1496 key_index = DEPRECATED;
1498 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1499 key_index = Configuration.show_taxonomy_scientific_names;
1501 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1502 key_index = Configuration.show_taxonomy_common_names;
1504 else if ( key.equals( "show_taxonomy_images" ) ) {
1505 key_index = Configuration.show_taxonomy_images;
1507 else if ( key.equals( "color_according_to_annotation" ) ) {
1508 key_index = Configuration.color_according_to_annotation;
1510 else if ( key.equals( "show_vector_data" ) ) {
1511 key_index = Configuration.show_vector_data;
1513 else if ( key.equals( "show_properties" ) ) {
1514 key_index = Configuration.show_properties;
1516 else if ( key.equals( "show_relation_confidence" ) ) {
1517 key_index = Configuration.show_relation_confidence;
1519 else if ( key.equals( "show_custom_node_shapes" ) ) {
1520 key_index = Configuration.show_custom_node_shapes;
1522 // If we've found the key, set the values
1523 if ( key_index >= 0 ) {
1524 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1525 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1526 // otherwise, keep looking
1529 if ( key_index == DEPRECATED ) {
1532 else if ( key.equals( "click_to" ) ) {
1533 final String click_to_name = ( String ) st.nextElement();
1534 key_index = getClickToIndex( click_to_name );
1535 if ( key_index >= 0 ) {
1536 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1538 else if ( key_index == DEPRECATED ) {
1542 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1546 else if ( key.equals( "species_color" ) ) {
1547 getSpeciesColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1549 else if ( key.equals( "domain_color" ) ) {
1550 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1552 else if ( key.equals( "annotation_color" ) ) {
1553 getAnnotationColors()
1554 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1556 else if ( key.equals( "function_color" ) ) {
1557 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1558 "configuration key [function_color] is deprecated" );
1560 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1561 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1563 else if ( key.equals( WEB_LINK_KEY ) ) {
1564 if ( st.countTokens() == 3 ) {
1565 createWebLink( ( String ) st.nextElement(),
1566 ( String ) st.nextElement(),
1567 ( String ) st.nextElement() );
1570 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1571 "illegal format in configuration file for key [" + key + "]" );
1575 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1576 + "] in: " + config_filename );
1581 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1582 + config_filename );
1586 private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
1587 _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
1590 public String getLabelForGetExtDescendentsData() {
1591 return _label_for_get_ext_descendents_data;
1594 public void setMinConfidenceValue( final double min_confidence_value ) {
1595 _min_confidence_value = min_confidence_value;
1598 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
1599 _node_label_direction = node_label_direction;
1602 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
1603 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
1606 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
1607 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
1610 private void setOvMaxHeight( final short ov_max_height ) {
1611 _ov_max_height = ov_max_height;
1614 private void setOvMaxWidth( final short ov_max_width ) {
1615 _ov_max_width = ov_max_width;
1618 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1619 _ov_placement = ov_placement;
1622 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
1623 _phylogeny_graphics_type = phylogeny_graphics_type;
1626 public void setPrintLineWidth( final float print_line_width ) {
1627 _print_line_width = print_line_width;
1630 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
1631 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
1634 public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
1635 _show_branch_length_values = show_branch_length_values;
1638 public void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
1639 _show_default_node_shapes = show_default_node_shapes;
1642 public void setShowDomainLabels( final boolean show_domain_labels ) {
1643 _show_domain_labels = show_domain_labels;
1646 private void setShowOverview( final boolean show_overview ) {
1647 _show_overview = show_overview;
1650 public void setShowScale( final boolean show_scale ) {
1651 _show_scale = show_scale;
1654 public void setTaxonomyColorize( final boolean b ) {
1655 display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
1658 public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
1659 _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
1662 public void setUseBranchesWidths( final boolean b ) {
1663 display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
1666 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1667 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1670 void setWebLinks( final SortedMap<String, WebLink> weblinks ) {
1671 _weblinks = weblinks;
1674 static String getDefaultFontFamilyName() {
1675 return DEFAULT_FONT_FAMILY;
1678 static enum TRIPLET {
1679 TRUE, FALSE, UNKNOWN
1683 NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN
1686 public NODE_DATA getExtDescNodeDataToReturn() {
1687 return _ext_desc_data_to_return;
1690 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
1691 _ext_desc_data_to_return = ext_desc_data_to_return;
1694 public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
1695 return _ext_node_data_return_on;
1698 private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
1699 _ext_node_data_return_on = ext_node_data_return_on;
1702 public int getFrameXSize() {
1703 return _frame_x_size;
1706 public int getFrameYSize() {
1707 return _frame_y_size;
1710 public void setFrameXSize( final int frame_x_size ) {
1711 _frame_x_size = frame_x_size;
1714 public void setFrameYSize( final int frame_y_size ) {
1715 _frame_y_size = frame_y_size;