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", "?" },
167 { "Node Events", "display", "?" }, { "Taxonomy Colorize", "display", "yes" },
168 { "Colorize Branches", "display", "no" }, { "Use Branch-Widths", "display", "no" },
169 { "Show Custom Nodes", "display", "yes" }, { "Domains", "nodisplay", "no" },
170 { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
171 { "Seq Name", "display", "yes" }, { "Seq Acc", "display", "no" },
172 { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
173 { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
174 { "Annotation Colorize", "nodisplay", "no" }, { "Seq Symbol", "display", "yes" },
175 { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
176 { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
177 { "Properties", "nodisplay", "no" } };
178 final static String clickto_options[][] = {
179 { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
180 { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
181 { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Blast", "display" },
182 { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" },
183 { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" },
184 { "Sort Descendants", "display" }, { "Return", "display" }, { "Select Node(s)", "display" } };
185 // This option is selected in the dropdown
186 int default_clickto = Configuration.display_node_data;
190 TreeColorSet tree_color_set;
194 TreeFontSet tree_font_set;
198 private static Hashtable<String, Color> _species_colors;
202 private static Hashtable<String, Color> _domain_colors;
206 private static Hashtable<String, Color> _annotation_colors;
207 boolean verbose = Constants.VERBOSE_DEFAULT;
208 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
209 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
210 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
211 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
212 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
213 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
214 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
215 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
216 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
217 private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
218 private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
219 private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
220 private String _label_for_get_ext_descendents_data = "";
221 private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
222 private int _frame_x_size;
223 private int _frame_y_size;
224 private static String DEFAULT_FONT_FAMILY = "";
226 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
227 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
228 DEFAULT_FONT_FAMILY = font_name;
232 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
233 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
237 public Configuration() {
238 this( null, false, false, false );
241 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
242 if ( ForesterUtil.isEmpty( cf ) ) {
243 config_filename = default_config_filename;
246 config_filename = cf;
248 setWebLinks( new TreeMap<String, WebLink>() );
249 setDisplayColors( new TreeMap<String, Color>() );
250 config_filename = config_filename.trim();
253 // If URL, open accordingly
255 u = new URL( config_filename );
257 final InputStreamReader isr = new InputStreamReader( u.openStream() );
258 final BufferedReader bf = new BufferedReader( isr );
261 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
262 + config_filename + "]" );
264 catch ( final Exception e ) {
265 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
266 + config_filename + "]: " + e.getLocalizedMessage() );
269 catch ( final Exception e ) {
270 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
271 + config_filename + "]" );
275 // Otherwise, open as a file
276 File f = new File( config_filename );
278 f = new File( config_filename + ".txt" );
280 if ( f.exists() && f.canRead() ) {
282 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
286 catch ( final Exception e ) {
288 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
289 + config_filename + "]: " + e );
295 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
296 + config_filename + "]" );
302 private void createWebLink( final String url_str, final String desc, final String source_identifier ) {
303 WebLink weblink = null;
306 weblink = new WebLink( new URL( url_str.trim() ), desc.trim(), source_identifier.trim() );
308 catch ( final MalformedURLException e ) {
309 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not create URL from [" + url_str + "]" );
312 if ( !ex && ( weblink != null ) ) {
313 getWebLinks().put( weblink.getSourceIdentifier().toLowerCase(), weblink );
317 boolean displaySequenceRelations() {
318 return _display_sequence_relations;
321 boolean doCheckOption( final int which ) {
322 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
323 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
326 boolean doDisplayClickToOption( final int which ) {
327 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
330 boolean doDisplayOption( final int which ) {
331 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
335 * Will attempt to use the phylogeny to determine whether to check
336 * this or not (e.g. phylogram)
339 boolean doGuessCheckOption( final int which ) {
340 return display_options[ which ][ 2 ].equals( "?" );
343 Map<String, Color> getAnnotationColors() {
344 if ( _annotation_colors == null ) {
345 _annotation_colors = new Hashtable<String, Color>();
347 return _annotation_colors;
350 public String getBaseFontFamilyName() {
351 return _base_font_family_name;
354 int getBaseFontSize() {
355 return _base_font_size;
358 CLADOGRAM_TYPE getCladogramType() {
359 return _cladogram_type;
362 private int getClickToIndex( final String name ) {
364 if ( name.equals( "edit_info" ) ) {
365 index = Configuration.display_node_data;
367 .printWarningMessage( Constants.PRG_NAME,
368 "configuration key [edit_info] is deprecated, use [display node data] instead" );
370 else if ( name.equals( "display_node_data" ) ) {
371 index = Configuration.display_node_data;
373 else if ( name.equals( "collapse_uncollapse" ) ) {
374 index = Configuration.collapse_uncollapse;
376 else if ( name.equals( "reroot" ) ) {
377 index = Configuration.reroot;
379 else if ( name.equals( "subtree" ) ) {
380 index = Configuration.subtree;
382 else if ( name.equals( "swap" ) ) {
383 index = Configuration.swap;
385 else if ( name.equals( "sort_descendants" ) ) {
386 index = Configuration.sort_descendents;
388 else if ( name.equals( "get_ext_descendents_data" ) ) {
389 index = Configuration.get_ext_desc_data;
391 else if ( name.equals( "display_sequences" ) ) {
393 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
396 else if ( name.equals( "open_seq_web" ) ) {
397 index = Configuration.open_seq_web;
399 else if ( name.equals( "open_tax_web" ) ) {
400 index = Configuration.open_tax_web;
402 else if ( name.equals( "blast" ) ) {
403 index = Configuration.blast;
405 else if ( name.equals( "cut_subtree" ) ) {
406 index = Configuration.cut_subtree;
408 else if ( name.equals( "copy_subtree" ) ) {
409 index = Configuration.copy_subtree;
411 else if ( name.equals( "paste_subtree" ) ) {
412 index = Configuration.paste_subtree;
414 else if ( name.equals( "delete" ) ) {
415 index = Configuration.delete_subtree_or_node;
417 else if ( name.equals( "add_new_node" ) ) {
418 index = Configuration.add_new_node;
420 else if ( name.equals( "edit_node_data" ) ) {
421 index = Configuration.edit_node_data;
423 else if ( name.equals( "select_nodes" ) ) {
424 index = Configuration.select_nodes;
426 else if ( name.equals( "display_node_popup" ) ) {
427 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
428 "configuration key [display_node_popup] is deprecated" );
431 else if ( name.equals( "custom_option" ) ) {
432 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
435 else if ( name.equals( "color_subtree" ) ) {
436 index = Configuration.color_subtree;
438 else if ( name.equals( "go_to_swiss_prot" ) ) {
439 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" );
445 int getClickToOptionsCount() {
446 return clickto_options.length;
449 String getClickToTitle( final int which ) {
450 return clickto_options[ which ][ 0 ];
453 public int getDefaultBootstrapSamples() {
454 return _default_bootstrap_samples;
457 public File getpathToLocalMafft() {
458 return _path_to_local_mafft;
461 public File getPathToLocalFastme() {
462 return _path_to_local_fastme;
465 public File getPathToLocalRaxml() {
466 return _path_to_local_raxml;
469 int getDefaultDisplayClicktoOption() {
470 return default_clickto;
473 public NodeFill getDefaultNodeFill() {
474 return _default_node_fill;
477 public NodeShape getDefaultNodeShape() {
478 return _default_node_shape;
481 public short getDefaultNodeShapeSize() {
482 return _default_node_shape_size;
485 SortedMap<String, Color> getDisplayColors() {
486 return _display_colors;
489 String getDisplayTitle( final int which ) {
490 return display_options[ which ][ 0 ];
493 Map<String, Color> getDomainColors() {
494 if ( _domain_colors == null ) {
495 _domain_colors = new Hashtable<String, Color>();
497 return _domain_colors;
500 public Color getDomainStructureBaseColor() {
501 return _domain_structure_base_color;
504 public Color getDomainStructureFontColor() {
505 return _domain_structure_font_color;
508 int getGraphicsExportX() {
509 return _graphics_export_x;
512 int getGraphicsExportY() {
513 return _graphics_export_y;
516 Color getGuiBackgroundColor() {
517 return _gui_background_color;
520 Color getGuiButtonBackgroundColor() {
521 return _gui_button_background_color;
524 Color getGuiButtonBorderColor() {
525 return _gui_button_border_color;
528 Color getGuiButtonTextColor() {
529 return _gui_button_text_color;
532 Color getGuiCheckboxAndButtonActiveColor() {
533 return _gui_checkbox_and_button_active_color;
536 Color getGuiCheckboxTextColor() {
537 return _gui_checkbox_text_color;
540 Color getGuiMenuBackgroundColor() {
541 return _gui_menu_background_color;
544 Color getGuiMenuTextColor() {
545 return _gui_menu_text_color;
548 double getMinConfidenceValue() {
549 return _min_confidence_value;
552 NODE_LABEL_DIRECTION getNodeLabelDirection() {
553 return _node_label_direction;
556 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
557 return _number_of_digits_after_comma_for_branch_length_values;
560 short getNumberOfDigitsAfterCommaForConfidenceValues() {
561 return _number_of_digits_after_comma_for_confidence_values;
564 short getOvMaxHeight() {
565 return _ov_max_height;
568 short getOvMaxWidth() {
569 return _ov_max_width;
572 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
573 return _ov_placement;
576 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
577 return _phylogeny_graphics_type;
580 float getPrintLineWidth() {
581 return _print_line_width;
584 Hashtable<String, Color> getSpeciesColors() {
585 if ( _species_colors == null ) {
586 _species_colors = new Hashtable<String, Color>();
588 return _species_colors;
591 TreeColorSet getTreeColorSet() {
595 TreeFontSet getTreeFontSet() {
599 WebLink getWebLink( final String source ) {
600 return getWebLinks().get( source );
603 Map<String, WebLink> getWebLinks() {
607 public boolean isAbbreviateScientificTaxonNames() {
608 return _abbreviate_scientific_names;
611 boolean isAntialiasScreen() {
612 return _antialias_screen;
615 public boolean isBackgroundColorGradient() {
616 return _background_color_gradient;
619 public boolean isColorLabelsSameAsParentBranch() {
620 return _color_labels_same_as_parent_branch;
624 * Convenience method.
626 * @return true if value in configuration file was 'yes'
628 boolean isDrawAsPhylogram() {
629 return doCheckOption( display_as_phylogram );
632 boolean isEditable() {
636 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
637 return _taxonomy_extraction;
640 boolean isHasWebLink( final String source ) {
641 return getWebLinks().containsKey( source );
645 * Only used by ArchaeoptryxE.
648 boolean isHideControlPanelAndMenubar() {
649 return _hide_controls_and_menus;
652 boolean isInternalNumberAreConfidenceForNhParsing() {
653 return _internal_number_are_confidence_for_nh_parsing;
656 boolean isReplaceUnderscoresInNhParsing() {
657 return _nh_parsing_replace_underscores;
660 boolean isShowBranchLengthValues() {
661 return _show_branch_length_values;
664 public boolean isShowDefaultNodeShapes() {
665 return _show_default_node_shapes;
668 public boolean isShowDomainLabels() {
669 return _show_domain_labels;
672 boolean isShowOverview() {
673 return _show_overview;
676 boolean isShowScale() {
680 public boolean isTaxonomyColorizeNodeShapes() {
681 return _taxonomy_colorize_node_shapes;
684 final boolean isUseNativeUI() {
685 if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) {
688 return _ui == UI.NATIVE;
692 * Only used by ArchaeoptryxE.
695 boolean isUseTabbedDisplay() {
696 return _use_tabbed_display;
699 boolean isValidatePhyloXmlAgainstSchema() {
700 return _validate_against_phyloxml_xsd_schema;
703 private boolean parseBoolean( final String str ) {
704 final String my_str = str.trim().toLowerCase();
705 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
708 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
712 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
717 private double parseDouble( final String str ) {
720 d = Double.parseDouble( str.trim() );
722 catch ( final Exception e ) {
723 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
729 private float parseFloat( final String str ) {
732 f = Float.parseFloat( str.trim() );
734 catch ( final Exception e ) {
735 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
741 private int parseInt( final String str ) {
744 i = Integer.parseInt( str.trim() );
746 catch ( final Exception e ) {
747 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
753 private short parseShort( final String str ) {
756 i = Short.parseShort( str.trim() );
758 catch ( final Exception e ) {
759 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
765 private void processFontFamily( final StringTokenizer st ) {
766 setBaseFontFamilyName( "" );
767 final String font_str = ( ( String ) st.nextElement() ).trim();
768 final String[] fonts = font_str.split( ",+" );
769 for( String font : fonts ) {
770 font = font.replace( '_', ' ' ).trim();
771 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
772 setBaseFontFamilyName( font );
778 public void putDisplayColors( final String key, final Color color ) {
779 getDisplayColors().put( key, color );
783 * read each line of config file, process non-comment lines
784 * @throws IOException
786 private void readConfig( final BufferedReader conf_in ) throws IOException {
789 line = conf_in.readLine();
790 if ( line != null ) {
792 // skip comments and blank lines
793 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
794 // convert runs of spaces to tabs
795 line = line.replaceAll( "\\s+", "\t" );
796 final StringTokenizer st = new StringTokenizer( line, "\t" );
800 } while ( line != null );
803 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
804 _abbreviate_scientific_names = abbreviate_scientific_names;
807 private void setAntialiasScreen( final boolean antialias_screen ) {
808 _antialias_screen = antialias_screen;
811 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
812 _background_color_gradient = background_color_gradient;
815 public void setBaseFontFamilyName( final String base_font_family_name ) {
816 _base_font_family_name = base_font_family_name;
819 public void setBaseFontSize( final int base_font_size ) {
820 _base_font_size = base_font_size;
823 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
824 _cladogram_type = cladogram_type;
827 public void setColorizeBranches( final boolean b ) {
828 display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
831 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
832 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
835 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
836 _default_bootstrap_samples = default_bootstrap_samples;
839 private void setPathToLocalMafft( final File path_to_local_mafft ) {
840 _path_to_local_mafft = path_to_local_mafft;
843 private void setPathToLocalFastme( final File path_to_local_fastme ) {
844 _path_to_local_fastme = path_to_local_fastme;
847 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
848 _path_to_local_raxml = path_to_local_raxml;
851 public File getPathToLocalClustalOmega() {
852 return _path_to_local_clustalo;
855 public void setPathToLocalClustalOmega( final File path_to_local_clustalo ) {
856 _path_to_local_clustalo = path_to_local_clustalo;
859 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
860 _default_node_fill = default_node_fill;
863 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
864 _default_node_shape = default_node_shape;
867 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
868 _default_node_shape_size = default_node_shape_size;
871 public void setDisplayAsPhylogram( final boolean b ) {
872 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
875 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
876 _display_colors = display_colors;
879 public void setDisplayConfidenceValues( final boolean b ) {
880 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
883 public void setDisplayInternalData( final boolean b ) {
884 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
887 public void setDisplayNodeNames( final boolean b ) {
888 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
891 public void setDisplaySequenceAcc( final boolean b ) {
892 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
895 public void setDisplaySequenceNames( final boolean b ) {
896 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
899 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
900 _display_sequence_relations = display_sequence_relations;
903 public void setDisplaySequenceSymbols( final boolean b ) {
904 display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no";
907 public void setDisplayTaxonomyCode( final boolean b ) {
908 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
911 public void setDisplayTaxonomyCommonNames( final boolean b ) {
912 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
915 public void setDisplayTaxonomyImages( final boolean b ) {
916 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
919 public void setDisplayTaxonomyScientificNames( final boolean b ) {
920 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
923 public void setDynamicallyHideData( final boolean b ) {
924 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
927 private void setEditable( final boolean editable ) {
928 _editable = editable;
931 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
932 _taxonomy_extraction = taxonomy_extraction;
935 private void setGraphicsExportX( final int graphics_export_x ) {
936 _graphics_export_x = graphics_export_x;
939 private void setGraphicsExportY( final int graphics_export_y ) {
940 _graphics_export_y = graphics_export_y;
943 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
944 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
948 * Set a key-value(s) tuple
950 private void setKeyValue( final StringTokenizer st ) {
951 final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
952 if ( !st.hasMoreElements() ) {
955 // Handle single value settings first:
956 if ( key.equals( "default_click_to" ) ) {
957 final String clickto_name = ( String ) st.nextElement();
958 default_clickto = getClickToIndex( clickto_name );
959 if ( default_clickto == -1 ) {
960 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
961 + "] for [default_click_to]" );
964 else if ( default_clickto == DEPRECATED ) {
968 else if ( key.equals( "native_ui" ) ) {
969 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
970 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
973 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
974 _ui = UI.CROSSPLATFORM;
976 else if ( my_str.equals( "?" ) ) {
980 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
985 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
986 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
988 else if ( key.equals( "antialias_screen" ) ) {
989 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
991 else if ( key.equals( "phylogeny_graphics_type" ) ) {
992 final String type_str = ( ( String ) st.nextElement() ).trim();
993 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
994 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
996 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
997 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
999 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
1000 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1002 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
1003 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1005 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
1006 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1008 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
1009 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1011 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
1012 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1014 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
1015 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1018 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1019 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1020 + "] for [phylogeny_graphics_type]" );
1023 else if ( key.equals( "min_confidence_value" ) ) {
1024 final String mcv_str = ( ( String ) st.nextElement() ).trim();
1025 final double d = parseDouble( mcv_str );
1026 setMinConfidenceValue( d );
1028 else if ( key.equals( "font_family" ) ) {
1029 processFontFamily( st );
1031 else if ( key.equals( "font_size" ) ) {
1032 final String size_str = ( ( String ) st.nextElement() ).trim();
1033 final int i = parseInt( size_str );
1035 setBaseFontSize( i );
1038 else if ( key.equals( "graphics_export_x" ) ) {
1039 final String str = ( ( String ) st.nextElement() ).trim();
1040 final int i = parseInt( str );
1042 setGraphicsExportX( i );
1045 else if ( key.equals( "graphics_export_y" ) ) {
1046 final String str = ( ( String ) st.nextElement() ).trim();
1047 final int i = parseInt( str );
1049 setGraphicsExportY( i );
1052 else if ( key.equals( "pdf_export_line_width" ) ) {
1053 final String str = ( ( String ) st.nextElement() ).trim();
1054 final float f = parseFloat( str );
1056 setPrintLineWidth( f );
1059 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1060 "value for [pdf_export_line_width] cannot be zero or negative" );
1063 else if ( key.equals( "window_initial_size_x" ) ) {
1064 final String str = ( ( String ) st.nextElement() ).trim();
1065 final int i = parseInt( str );
1070 else if ( key.equals( "window_initial_size_y" ) ) {
1071 final String str = ( ( String ) st.nextElement() ).trim();
1072 final int i = parseInt( str );
1077 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1078 final String str = ( ( String ) st.nextElement() ).trim();
1079 final int i = parseInt( str );
1081 setDefaultBootstrapSamples( i );
1085 .printWarningMessage( Constants.PRG_NAME,
1086 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1089 else if ( key.equals( "clustalo_local" ) ) {
1090 final String str = ( ( String ) st.nextElement() ).trim();
1091 if ( !ForesterUtil.isEmpty( str ) ) {
1092 setPathToLocalClustalOmega( new File( str ) );
1095 else if ( key.equals( "mafft_local" ) ) {
1096 final String str = ( ( String ) st.nextElement() ).trim();
1097 if ( !ForesterUtil.isEmpty( str ) ) {
1098 setPathToLocalMafft( new File( str ) );
1101 else if ( key.equals( "fastme_local" ) ) {
1102 final String str = ( ( String ) st.nextElement() ).trim();
1103 if ( !ForesterUtil.isEmpty( str ) ) {
1104 setPathToLocalFastme( new File( str ) );
1107 else if ( key.equals( "raxml_local" ) ) {
1108 final String str = ( ( String ) st.nextElement() ).trim();
1109 if ( !ForesterUtil.isEmpty( str ) ) {
1110 setPathToLocalRaxml( new File( str ) );
1113 else if ( key.equals( "show_scale" ) ) {
1114 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1116 else if ( key.equals( "show_overview" ) ) {
1117 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1119 else if ( key.equals( "show_branch_length_values" ) ) {
1120 setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
1122 else if ( key.equals( "background_gradient" ) ) {
1123 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1125 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1126 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1128 else if ( key.equals( "show_domain_labels" ) ) {
1129 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1131 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1132 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1134 else if ( key.equals( "cladogram_type" ) ) {
1135 final String type_str = ( ( String ) st.nextElement() ).trim();
1136 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1137 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1139 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1140 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1142 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1143 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1146 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1147 + "] for [cladogram_type]" );
1150 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1152 .printWarningMessage( Constants.PRG_NAME,
1153 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1155 else if ( key.equals( "hide_controls_and_menus" ) ) {
1156 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1158 else if ( key.equals( "use_tabbed_display" ) ) {
1159 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1161 else if ( key.equals( "overview_width" ) ) {
1162 final short i = parseShort( ( ( String ) st.nextElement() ) );
1165 else if ( key.equals( "overview_height" ) ) {
1166 final short i = parseShort( ( ( String ) st.nextElement() ) );
1167 setOvMaxHeight( i );
1169 else if ( key.equals( "overview_placement_type" ) ) {
1170 final String type_str = ( ( String ) st.nextElement() ).trim();
1171 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1172 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1174 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1175 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1177 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1178 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1180 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1181 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1184 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1185 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1186 + "] for [overview_placement_type]" );
1189 else if ( key.equals( "node_label_direction" ) ) {
1190 final String type_str = ( ( String ) st.nextElement() ).trim();
1191 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1192 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1194 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1195 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1198 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1199 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1200 + "] for [node_label_direction]" );
1203 else if ( key.equals( "branch_length_value_digits" ) ) {
1204 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1206 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1209 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1210 + "] for [branch_length_value_digits]" );
1213 else if ( key.equals( "confidence_value_digits" ) ) {
1214 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1216 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1219 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1220 + "] for [confidence_value_digits]" );
1223 else if ( key.equals( "allow_editing" ) ) {
1224 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1226 else if ( key.equals( "display_sequence_relations" ) ) {
1227 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1229 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1230 final boolean r = parseBoolean( ( String ) st.nextElement() );
1231 if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
1233 .printWarningMessage( Constants.PRG_NAME,
1234 "attempt to extract taxonomies and replace underscores at the same time" );
1237 setReplaceUnderscoresInNhParsing( r );
1240 else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
1241 final String s = ( String ) st.nextElement();
1242 if ( s.equalsIgnoreCase( "no" ) ) {
1243 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1245 else if ( s.equalsIgnoreCase( "yes" ) ) {
1246 setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES );
1248 else if ( s.equalsIgnoreCase( "pfam" ) ) {
1249 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
1252 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1253 "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + s );
1255 if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
1257 .printWarningMessage( Constants.PRG_NAME,
1258 "attempt to extract taxonomies and replace underscores at the same time" );
1261 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1262 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1264 else if ( key.equals( "gui_background_color" ) ) {
1265 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1267 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1268 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1270 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1271 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1273 else if ( key.equals( "gui_button_text_color" ) ) {
1274 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1276 else if ( key.equals( "gui_button_background_color" ) ) {
1277 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1279 else if ( key.equals( "gui_menu_background_color" ) ) {
1280 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1282 else if ( key.equals( "gui_menu_text_color" ) ) {
1283 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1285 else if ( key.equals( "gui_button_border_color" ) ) {
1286 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1288 else if ( key.equals( "domain_structure_font_color" ) ) {
1289 _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
1291 else if ( key.equals( "domain_structure_base_color" ) ) {
1292 _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
1294 else if ( key.equals( "show_default_node_shapes" ) ) {
1295 setShowDefaultNodeShapes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1297 else if ( key.equals( "default_node_size" ) ) {
1298 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1299 setDefaultNodeShapeSize( i );
1301 else if ( key.equals( "default_node_fill" ) ) {
1302 final String fill_str = ( ( String ) st.nextElement() ).trim();
1303 if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.NONE.toString() ) ) {
1304 setDefaultNodeFill( NodeFill.NONE );
1306 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.GRADIENT.toString() ) ) {
1307 setDefaultNodeFill( NodeFill.GRADIENT );
1309 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.SOLID.toString() ) ) {
1310 setDefaultNodeFill( NodeFill.SOLID );
1313 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1314 + "] for [default_node_fill]" );
1317 else if ( key.equals( "default_node_shape" ) ) {
1318 final String shape_str = ( ( String ) st.nextElement() ).trim();
1319 if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.CIRCLE.toString() ) ) {
1320 setDefaultNodeShape( NodeShape.CIRCLE );
1322 else if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.RECTANGLE.toString() ) ) {
1323 setDefaultNodeShape( NodeShape.RECTANGLE );
1326 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1327 + "] for [default_node_shape]" );
1330 else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
1331 setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
1333 else if ( key.equals( "ext_descendents_data_to_return" ) ) {
1334 final String s = ( ( String ) st.nextElement() ).trim();
1335 if ( s.equalsIgnoreCase( "node_name" ) ) {
1336 setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
1338 else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
1339 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
1341 else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
1342 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
1344 else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
1345 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
1347 else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
1348 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
1350 else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
1351 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME );
1353 else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
1354 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
1356 else if ( s.equalsIgnoreCase( "user_selected" ) ) {
1357 setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
1360 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1361 + "] for [ext_descendents_data_to_return]" );
1364 else if ( key.equals( "label_for_get_ext_descendents_data" ) ) {
1365 final String s = ( ( String ) st.nextElement() ).trim();
1366 if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) {
1367 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s
1368 + "] for [label_for_get_ext_descendents_data]" );
1371 setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
1374 else if ( key.equals( "ext_descendents_data_to_return_on" ) ) {
1375 final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
1376 if ( s.equals( "console" ) ) {
1377 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
1379 else if ( s.equals( "window" ) ) {
1380 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
1382 else if ( s.equals( "buffer_only" ) ) {
1383 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
1386 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1387 + "] for [ext_descendents_data_to_return_on]" );
1390 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1393 if ( key.equals( "use_real_br_lengths" ) || key.equals( "phylogram" ) ) {
1394 key_index = Configuration.display_as_phylogram;
1395 if ( key.equals( "use_real_br_lengths" ) ) {
1397 .printWarningMessage( Constants.PRG_NAME,
1398 "configuration key [use_real_br_lengths] is deprecated, use [phylogram] instead" );
1401 else if ( key.equals( "rollover" ) ) {
1402 key_index = Configuration.node_data_popup;
1404 else if ( key.equals( "color_according_to_species" ) ) {
1405 key_index = Configuration.color_according_to_species;
1407 else if ( key.equals( "show_node_names" ) ) {
1408 key_index = Configuration.show_node_names;
1410 else if ( key.equals( "show_taxonomy" ) || key.equals( "show_taxonomy_code" ) ) {
1411 key_index = Configuration.show_tax_code;
1412 if ( key.equals( "show_taxonomy" ) ) {
1414 .printWarningMessage( Constants.PRG_NAME,
1415 "configuration key [show_taxonomy] is deprecated, use [show_taxonomy_code] instead" );
1418 else if ( key.equals( "write_br_length_values" ) ) {
1419 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1420 "configuration key [write_br_length_values] is deprecated" );
1421 key_index = DEPRECATED;
1423 else if ( key.equals( "write_bootstrap_values" ) || key.equals( "write_confidence_values" ) ) {
1424 key_index = Configuration.write_confidence_values;
1425 if ( key.equals( "write_bootstrap_values" ) ) {
1427 .printWarningMessage( Constants.PRG_NAME,
1428 "configuration key [write_bootstrap_values] is deprecated, use [write_confidence_values] instead" );
1431 else if ( key.equals( "write_events" ) || key.equals( "write_dup_spec" ) ) {
1432 key_index = Configuration.write_events;
1433 if ( key.equals( "write_dup_spec" ) ) {
1435 .printWarningMessage( Constants.PRG_NAME,
1436 "configuration key [write_dup_spec] is deprecated, use [write_events] instead" );
1439 else if ( key.equals( "color_branches" ) ) {
1440 key_index = Configuration.color_branches;
1442 else if ( key.equals( "width_branches" ) ) {
1443 key_index = Configuration.width_branches;
1445 else if ( key.equals( "color_orthologous" ) ) {
1446 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1447 "configuration key [color_orthologous] is deprecated" );
1449 else if ( key.equals( "color_subtree_neighbors" ) ) {
1450 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1451 "configuration key [color_subtree_neighbors] is deprecated" );
1453 else if ( key.equals( "color_super_orthologous" ) ) {
1454 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1455 "configuration key [color_super_orthologous] is deprecated" );
1457 else if ( key.equals( "mark_nodes_with_box" ) ) {
1458 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1459 "configuration key [mark_nodes_with_box] is deprecated" );
1460 key_index = DEPRECATED;
1462 else if ( key.equals( "show_domain_architectures" ) ) {
1463 key_index = Configuration.show_domain_architectures;
1465 else if ( key.equals( "show_annotations" ) ) {
1466 key_index = Configuration.show_annotation;
1468 else if ( key.equals( "show_binary_characters" ) ) {
1469 key_index = Configuration.show_binary_characters;
1471 else if ( key.equals( "show_binary_character_counts" ) ) {
1472 key_index = Configuration.show_binary_character_counts;
1474 else if ( key.equals( "show_gene_names" ) ) {
1475 key_index = Configuration.show_gene_names;
1477 else if ( key.equals( "show_gene_symbols" ) ) {
1478 key_index = Configuration.show_gene_symbols;
1480 else if ( key.equals( "show_sequence_acc" ) ) {
1481 key_index = Configuration.show_sequence_acc;
1483 else if ( key.equals( "show_node_ids" ) ) {
1485 .printWarningMessage( Constants.PRG_NAME, "configuration key [show_node_ids] is deprecated" );
1486 key_index = DEPRECATED;
1488 else if ( key.equals( "display_internal_data" ) ) {
1489 key_index = Configuration.display_internal_data;
1491 else if ( key.equals( "dynamically_hide_data" ) ) {
1492 key_index = Configuration.dynamically_hide_data;
1494 else if ( key.equals( "show_taxonomy_names" ) ) {
1495 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1496 "configuration key [show_taxonomy_names] is deprecated" );
1497 key_index = DEPRECATED;
1499 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1500 key_index = Configuration.show_taxonomy_scientific_names;
1502 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1503 key_index = Configuration.show_taxonomy_common_names;
1505 else if ( key.equals( "show_taxonomy_images" ) ) {
1506 key_index = Configuration.show_taxonomy_images;
1508 else if ( key.equals( "color_according_to_annotation" ) ) {
1509 key_index = Configuration.color_according_to_annotation;
1511 else if ( key.equals( "show_vector_data" ) ) {
1512 key_index = Configuration.show_vector_data;
1514 else if ( key.equals( "show_properties" ) ) {
1515 key_index = Configuration.show_properties;
1517 else if ( key.equals( "show_relation_confidence" ) ) {
1518 key_index = Configuration.show_relation_confidence;
1520 else if ( key.equals( "show_custom_node_shapes" ) ) {
1521 key_index = Configuration.show_custom_node_shapes;
1523 // If we've found the key, set the values
1524 if ( key_index >= 0 ) {
1525 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1526 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1527 // otherwise, keep looking
1530 if ( key_index == DEPRECATED ) {
1533 else if ( key.equals( "click_to" ) ) {
1534 final String click_to_name = ( String ) st.nextElement();
1535 key_index = getClickToIndex( click_to_name );
1536 if ( key_index >= 0 ) {
1537 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1539 else if ( key_index == DEPRECATED ) {
1543 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1547 else if ( key.equals( "species_color" ) ) {
1548 getSpeciesColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1550 else if ( key.equals( "domain_color" ) ) {
1551 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1553 else if ( key.equals( "annotation_color" ) ) {
1554 getAnnotationColors()
1555 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1557 else if ( key.equals( "function_color" ) ) {
1558 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1559 "configuration key [function_color] is deprecated" );
1561 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1562 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1564 else if ( key.equals( WEB_LINK_KEY ) ) {
1565 if ( st.countTokens() == 3 ) {
1566 createWebLink( ( String ) st.nextElement(),
1567 ( String ) st.nextElement(),
1568 ( String ) st.nextElement() );
1571 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1572 "illegal format in configuration file for key [" + key + "]" );
1576 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1577 + "] in: " + config_filename );
1582 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1583 + config_filename );
1587 private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
1588 _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
1591 public String getLabelForGetExtDescendentsData() {
1592 return _label_for_get_ext_descendents_data;
1595 public void setMinConfidenceValue( final double min_confidence_value ) {
1596 _min_confidence_value = min_confidence_value;
1599 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
1600 _node_label_direction = node_label_direction;
1603 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
1604 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
1607 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
1608 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
1611 private void setOvMaxHeight( final short ov_max_height ) {
1612 _ov_max_height = ov_max_height;
1615 private void setOvMaxWidth( final short ov_max_width ) {
1616 _ov_max_width = ov_max_width;
1619 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1620 _ov_placement = ov_placement;
1623 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
1624 _phylogeny_graphics_type = phylogeny_graphics_type;
1627 public void setPrintLineWidth( final float print_line_width ) {
1628 _print_line_width = print_line_width;
1631 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
1632 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
1635 public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
1636 _show_branch_length_values = show_branch_length_values;
1639 public void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
1640 _show_default_node_shapes = show_default_node_shapes;
1643 public void setShowDomainLabels( final boolean show_domain_labels ) {
1644 _show_domain_labels = show_domain_labels;
1647 private void setShowOverview( final boolean show_overview ) {
1648 _show_overview = show_overview;
1651 public void setShowScale( final boolean show_scale ) {
1652 _show_scale = show_scale;
1655 public void setTaxonomyColorize( final boolean b ) {
1656 display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
1659 public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
1660 _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
1663 public void setUseBranchesWidths( final boolean b ) {
1664 display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
1667 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1668 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1671 void setWebLinks( final SortedMap<String, WebLink> weblinks ) {
1672 _weblinks = weblinks;
1675 static String getDefaultFontFamilyName() {
1676 return DEFAULT_FONT_FAMILY;
1679 static enum TRIPLET {
1680 TRUE, FALSE, UNKNOWN
1684 NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN
1687 public NODE_DATA getExtDescNodeDataToReturn() {
1688 return _ext_desc_data_to_return;
1691 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
1692 _ext_desc_data_to_return = ext_desc_data_to_return;
1695 public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
1696 return _ext_node_data_return_on;
1699 private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
1700 _ext_node_data_return_on = ext_node_data_return_on;
1703 public int getFrameXSize() {
1704 return _frame_x_size;
1707 public int getFrameYSize() {
1708 return _frame_y_size;
1711 public void setFrameXSize( final int frame_x_size ) {
1712 _frame_x_size = frame_x_size;
1715 public void setFrameYSize( final int frame_y_size ) {
1716 _frame_y_size = frame_y_size;