2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
7 // Copyright (C) 2000-2001 Washington University School of Medicine
8 // and Howard Hughes Medical Institute
9 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
10 // All rights reserved
12 // This library is free software; you can redistribute it and/or
13 // modify it under the terms of the GNU Lesser General Public
14 // License as published by the Free Software Foundation; either
15 // version 2.1 of the License, or (at your option) any later version.
17 // This library is distributed in the hope that it will be useful,
18 // but WITHOUT ANY WARRANTY; without even the implied warranty of
19 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20 // Lesser General Public License for more details.
22 // You should have received a copy of the GNU Lesser General Public
23 // License along with this library; if not, write to the Free Software
24 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
26 // Contact: phylosoft @ gmail . com
27 // WWW: www.phylosoft.org/forester
29 package org.forester.archaeopteryx;
31 import java.awt.Color;
32 import java.io.BufferedReader;
34 import java.io.FileReader;
35 import java.io.IOException;
36 import java.io.InputStreamReader;
37 import java.net.MalformedURLException;
39 import java.util.Arrays;
40 import java.util.Hashtable;
42 import java.util.SortedMap;
43 import java.util.StringTokenizer;
44 import java.util.TreeMap;
46 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
47 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
48 import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE;
49 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
50 import org.forester.phylogeny.data.NodeData.NODE_DATA;
51 import org.forester.phylogeny.data.NodeVisualization;
52 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
53 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
54 import org.forester.util.ForesterUtil;
56 public final class Configuration {
58 public enum EXT_NODE_DATA_RETURN_ON {
61 static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
62 private static final String WEB_LINK_KEY = "web_link";
63 private static final String DISPLAY_COLOR_KEY = "display_color";
64 private static final int DEPRECATED = -2;
65 private UI _ui = UI.UNKNOWN;
66 private boolean _use_tabbed_display = false;
67 private boolean _hide_controls_and_menus = false;
68 private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
69 private SortedMap<String, WebLink> _weblinks = null;
70 private SortedMap<String, Color> _display_colors = null;
71 private boolean _antialias_screen = true;
72 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
73 private String _base_font_family_name = "";
74 private int _base_font_size = -1;
75 private int _graphics_export_x = -1;
76 private int _graphics_export_y = -1;
77 private short _ov_max_width = 80;
78 private short _ov_max_height = 80;
79 private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
80 private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
81 private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
82 private boolean _show_scale = false;
83 private boolean _show_branch_length_values = false;
84 private boolean _show_overview = true;
85 private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
86 private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
87 private boolean _editable = true;
88 private boolean _nh_parsing_replace_underscores = false;
89 private boolean _nh_parsing_extract_pfam_taxonomy_codes = false;
90 private boolean _internal_number_are_confidence_for_nh_parsing = false;
91 private boolean _display_sequence_relations = false;
92 private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
93 private boolean _background_color_gradient = false;
94 private boolean _show_domain_labels = true;
95 private boolean _abbreviate_scientific_names = false;
96 private boolean _color_labels_same_as_parent_branch = false;
97 private boolean _show_default_node_shapes = false;
98 private NodeShape _default_node_shape = NodeShape.CIRCLE;
99 private NodeFill _default_node_fill = NodeFill.GRADIENT;
100 private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
101 private boolean _taxonomy_colorize_node_shapes = false;
102 private int _default_bootstrap_samples = -1;
103 private File _path_to_local_mafft = null;
104 private File _path_to_local_fastme = null;
105 private File _path_to_local_raxml = null;
106 private File _path_to_local_clustalo = null;
107 final static int display_as_phylogram = 0;
108 final static int show_node_names = 1;
109 final static int show_tax_code = 2;
110 final static int show_annotation = 3;
111 final static int write_confidence_values = 4;
112 final static int write_events = 5;
113 final static int color_according_to_species = 6;
114 final static int color_branches = 7;
115 final static int width_branches = 8;
116 final static int show_custom_node_shapes = 9;
117 final static int show_domain_architectures = 10;
118 final static int show_binary_characters = 11;
119 final static int show_binary_character_counts = 12;
120 final static int show_gene_names = 13;
121 final static int show_sequence_acc = 14;
122 final static int display_internal_data = 15;
123 final static int dynamically_hide_data = 16;
124 final static int show_taxonomy_scientific_names = 17;
125 final static int show_taxonomy_common_names = 18;
126 final static int color_according_to_annotation = 19;
127 final static int show_gene_symbols = 20;
128 final static int node_data_popup = 21;
129 final static int show_relation_confidence = 22;
130 final static int show_vector_data = 23;
131 final static int show_taxonomy_images = 24;
132 final static int show_properties = 25;
133 // ------------------
135 // ------------------
136 final static int display_node_data = 0;
137 final static int collapse_uncollapse = 1;
138 final static int reroot = 2;
139 final static int subtree = 3;
140 final static int swap = 4;
141 final static int color_subtree = 5;
142 final static int open_seq_web = 6;
143 final static int open_tax_web = 7;
144 final static int blast = 8;
145 final static int cut_subtree = 9;
146 final static int copy_subtree = 10;
147 final static int paste_subtree = 11;
148 final static int delete_subtree_or_node = 12;
149 final static int add_new_node = 13;
150 final static int edit_node_data = 14;
151 final static int sort_descendents = 15;
152 final static int get_ext_desc_data = 16;
153 // ---------------------------
154 // Display options for trees
155 // ---------------------------
156 // ---------------------------------
157 // Pertaining to the config itself
158 // ---------------------------------
159 // Full path to config (may be URL)
160 String config_filename;
161 String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
162 final static String display_options[][] = {
163 { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
164 { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, { "Event", "display", "?" },
165 { "Taxonomy Colorize", "display", "no" }, { "Colorize Branches", "display", "no" },
166 { "Use Branch-Widths", "display", "no" }, { "Show Custom Nodes", "display", "yes" },
167 { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" },
168 { "Binary Char Counts", "nodisplay", "no" }, { "Prot/Gene Name", "display", "yes" },
169 { "Prot/Gene Acc", "display", "no" }, { "Show Internal Data", "display", "yes" },
170 { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" },
171 { "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" },
172 { "Prot/Gene Symbol", "display", "yes" }, { "Rollover", "display", "yes" },
173 { "Relation Confidence", "display", "no" }, { "Vector Data", "display", "no" },
174 { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" } };
175 final static String clickto_options[][] = {
176 { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
177 { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
178 { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Blast", "display" },
179 { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" },
180 { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" },
181 { "Sort Descendants", "display" }, { "Return", "display" } };
182 // This option is selected in the dropdown
183 int default_clickto = Configuration.display_node_data;
187 TreeColorSet tree_color_set;
191 TreeFontSet tree_font_set;
195 private static Hashtable<String, Color> _species_colors;
199 private static Hashtable<String, Color> _domain_colors;
203 private static Hashtable<String, Color> _annotation_colors;
204 boolean verbose = Constants.VERBOSE_DEFAULT;
205 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
206 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
207 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
208 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
209 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
210 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
211 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
212 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
213 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
214 private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
215 private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
216 private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
217 private String _label_for_get_ext_descendents_data = "";
218 private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
219 private static String DEFAULT_FONT_FAMILY = "";
221 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
222 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
223 DEFAULT_FONT_FAMILY = font_name;
227 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
228 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
232 public Configuration() {
233 this( null, false, false, false );
236 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
237 if ( ForesterUtil.isEmpty( cf ) ) {
238 config_filename = default_config_filename;
241 config_filename = cf;
243 setWebLinks( new TreeMap<String, WebLink>() );
244 setDisplayColors( new TreeMap<String, Color>() );
245 config_filename = config_filename.trim();
248 // If URL, open accordingly
250 u = new URL( config_filename );
252 final InputStreamReader isr = new InputStreamReader( u.openStream() );
253 final BufferedReader bf = new BufferedReader( isr );
256 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
257 + config_filename + "]" );
259 catch ( final Exception e ) {
260 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
261 + config_filename + "]: " + e.getLocalizedMessage() );
264 catch ( final Exception e ) {
265 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
266 + config_filename + "]" );
270 // Otherwise, open as a file
271 File f = new File( config_filename );
273 f = new File( config_filename + ".txt" );
275 if ( f.exists() && f.canRead() ) {
277 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
281 catch ( final Exception e ) {
283 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
284 + config_filename + "]: " + e );
290 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
291 + config_filename + "]" );
297 private void createWebLink( final String url_str, final String desc, final String source_identifier ) {
298 WebLink weblink = null;
301 weblink = new WebLink( new URL( url_str.trim() ), desc.trim(), source_identifier.trim() );
303 catch ( final MalformedURLException e ) {
304 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not create URL from [" + url_str + "]" );
307 if ( !ex && ( weblink != null ) ) {
308 getWebLinks().put( weblink.getSourceIdentifier().toLowerCase(), weblink );
312 boolean displaySequenceRelations() {
313 return _display_sequence_relations;
316 boolean doCheckOption( final int which ) {
317 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
318 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
321 boolean doDisplayClickToOption( final int which ) {
322 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
325 boolean doDisplayOption( final int which ) {
326 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
330 * Will attempt to use the phylogeny to determine whether to check
331 * this or not (e.g. phylogram)
334 boolean doGuessCheckOption( final int which ) {
335 return display_options[ which ][ 2 ].equals( "?" );
338 Map<String, Color> getAnnotationColors() {
339 if ( _annotation_colors == null ) {
340 _annotation_colors = new Hashtable<String, Color>();
342 return _annotation_colors;
345 public String getBaseFontFamilyName() {
346 return _base_font_family_name;
349 int getBaseFontSize() {
350 return _base_font_size;
353 CLADOGRAM_TYPE getCladogramType() {
354 return _cladogram_type;
357 private int getClickToIndex( final String name ) {
359 if ( name.equals( "edit_info" ) ) {
360 index = Configuration.display_node_data;
362 .printWarningMessage( Constants.PRG_NAME,
363 "configuration key [edit_info] is deprecated, use [display node data] instead" );
365 else if ( name.equals( "display_node_data" ) ) {
366 index = Configuration.display_node_data;
368 else if ( name.equals( "collapse_uncollapse" ) ) {
369 index = Configuration.collapse_uncollapse;
371 else if ( name.equals( "reroot" ) ) {
372 index = Configuration.reroot;
374 else if ( name.equals( "subtree" ) ) {
375 index = Configuration.subtree;
377 else if ( name.equals( "swap" ) ) {
378 index = Configuration.swap;
380 else if ( name.equals( "sort_descendants" ) ) {
381 index = Configuration.sort_descendents;
383 else if ( name.equals( "get_ext_descendents_data" ) ) {
384 index = Configuration.get_ext_desc_data;
386 else if ( name.equals( "display_sequences" ) ) {
388 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
391 else if ( name.equals( "open_seq_web" ) ) {
392 index = Configuration.open_seq_web;
394 else if ( name.equals( "open_tax_web" ) ) {
395 index = Configuration.open_tax_web;
397 else if ( name.equals( "blast" ) ) {
398 index = Configuration.blast;
400 else if ( name.equals( "cut_subtree" ) ) {
401 index = Configuration.cut_subtree;
403 else if ( name.equals( "copy_subtree" ) ) {
404 index = Configuration.copy_subtree;
406 else if ( name.equals( "paste_subtree" ) ) {
407 index = Configuration.paste_subtree;
409 else if ( name.equals( "delete" ) ) {
410 index = Configuration.delete_subtree_or_node;
412 else if ( name.equals( "add_new_node" ) ) {
413 index = Configuration.add_new_node;
415 else if ( name.equals( "edit_node_data" ) ) {
416 index = Configuration.edit_node_data;
418 else if ( name.equals( "display_node_popup" ) ) {
419 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
420 "configuration key [display_node_popup] is deprecated" );
423 else if ( name.equals( "custom_option" ) ) {
424 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
427 else if ( name.equals( "color_subtree" ) ) {
428 index = Configuration.color_subtree;
430 else if ( name.equals( "go_to_swiss_prot" ) ) {
431 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" );
437 int getClickToOptionsCount() {
438 return clickto_options.length;
441 String getClickToTitle( final int which ) {
442 return clickto_options[ which ][ 0 ];
445 public int getDefaultBootstrapSamples() {
446 return _default_bootstrap_samples;
449 public File getpathToLocalMafft() {
450 return _path_to_local_mafft;
453 public File getPathToLocalFastme() {
454 return _path_to_local_fastme;
457 public File getPathToLocalRaxml() {
458 return _path_to_local_raxml;
461 int getDefaultDisplayClicktoOption() {
462 return default_clickto;
465 public NodeFill getDefaultNodeFill() {
466 return _default_node_fill;
469 public NodeShape getDefaultNodeShape() {
470 return _default_node_shape;
473 public short getDefaultNodeShapeSize() {
474 return _default_node_shape_size;
477 SortedMap<String, Color> getDisplayColors() {
478 return _display_colors;
481 String getDisplayTitle( final int which ) {
482 return display_options[ which ][ 0 ];
485 Map<String, Color> getDomainColors() {
486 if ( _domain_colors == null ) {
487 _domain_colors = new Hashtable<String, Color>();
489 return _domain_colors;
492 public Color getDomainStructureBaseColor() {
493 return _domain_structure_base_color;
496 public Color getDomainStructureFontColor() {
497 return _domain_structure_font_color;
500 int getGraphicsExportX() {
501 return _graphics_export_x;
504 int getGraphicsExportY() {
505 return _graphics_export_y;
508 Color getGuiBackgroundColor() {
509 return _gui_background_color;
512 Color getGuiButtonBackgroundColor() {
513 return _gui_button_background_color;
516 Color getGuiButtonBorderColor() {
517 return _gui_button_border_color;
520 Color getGuiButtonTextColor() {
521 return _gui_button_text_color;
524 Color getGuiCheckboxAndButtonActiveColor() {
525 return _gui_checkbox_and_button_active_color;
528 Color getGuiCheckboxTextColor() {
529 return _gui_checkbox_text_color;
532 Color getGuiMenuBackgroundColor() {
533 return _gui_menu_background_color;
536 Color getGuiMenuTextColor() {
537 return _gui_menu_text_color;
540 double getMinConfidenceValue() {
541 return _min_confidence_value;
544 NODE_LABEL_DIRECTION getNodeLabelDirection() {
545 return _node_label_direction;
548 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
549 return _number_of_digits_after_comma_for_branch_length_values;
552 short getNumberOfDigitsAfterCommaForConfidenceValues() {
553 return _number_of_digits_after_comma_for_confidence_values;
556 short getOvMaxHeight() {
557 return _ov_max_height;
560 short getOvMaxWidth() {
561 return _ov_max_width;
564 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
565 return _ov_placement;
568 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
569 return _phylogeny_graphics_type;
572 float getPrintLineWidth() {
573 return _print_line_width;
576 Hashtable<String, Color> getSpeciesColors() {
577 if ( _species_colors == null ) {
578 _species_colors = new Hashtable<String, Color>();
580 return _species_colors;
583 TreeColorSet getTreeColorSet() {
587 TreeFontSet getTreeFontSet() {
591 WebLink getWebLink( final String source ) {
592 return getWebLinks().get( source );
595 Map<String, WebLink> getWebLinks() {
599 public boolean isAbbreviateScientificTaxonNames() {
600 return _abbreviate_scientific_names;
603 boolean isAntialiasScreen() {
604 return _antialias_screen;
607 public boolean isBackgroundColorGradient() {
608 return _background_color_gradient;
611 public boolean isColorLabelsSameAsParentBranch() {
612 return _color_labels_same_as_parent_branch;
616 * Convenience method.
618 * @return true if value in configuration file was 'yes'
620 boolean isDrawAsPhylogram() {
621 return doCheckOption( display_as_phylogram );
624 boolean isEditable() {
628 boolean isExtractPfamTaxonomyCodesInNhParsing() {
629 return _nh_parsing_extract_pfam_taxonomy_codes;
632 boolean isHasWebLink( final String source ) {
633 return getWebLinks().containsKey( source );
637 * Only used by ArchaeoptryxE.
640 boolean isHideControlPanelAndMenubar() {
641 return _hide_controls_and_menus;
644 boolean isInternalNumberAreConfidenceForNhParsing() {
645 return _internal_number_are_confidence_for_nh_parsing;
648 boolean isReplaceUnderscoresInNhParsing() {
649 return _nh_parsing_replace_underscores;
652 boolean isShowBranchLengthValues() {
653 return _show_branch_length_values;
656 public boolean isShowDefaultNodeShapes() {
657 return _show_default_node_shapes;
660 public boolean isShowDomainLabels() {
661 return _show_domain_labels;
664 boolean isShowOverview() {
665 return _show_overview;
668 boolean isShowScale() {
672 public boolean isTaxonomyColorizeNodeShapes() {
673 return _taxonomy_colorize_node_shapes;
676 final boolean isUseNativeUI() {
677 if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) {
680 return _ui == UI.NATIVE;
684 * Only used by ArchaeoptryxE.
687 boolean isUseTabbedDisplay() {
688 return _use_tabbed_display;
691 boolean isValidatePhyloXmlAgainstSchema() {
692 return _validate_against_phyloxml_xsd_schema;
695 private boolean parseBoolean( final String str ) {
696 final String my_str = str.trim().toLowerCase();
697 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
700 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
704 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
709 private double parseDouble( final String str ) {
712 d = Double.parseDouble( str.trim() );
714 catch ( final Exception e ) {
715 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
721 private float parseFloat( final String str ) {
724 f = Float.parseFloat( str.trim() );
726 catch ( final Exception e ) {
727 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
733 private int parseInt( final String str ) {
736 i = Integer.parseInt( str.trim() );
738 catch ( final Exception e ) {
739 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
745 private short parseShort( final String str ) {
748 i = Short.parseShort( str.trim() );
750 catch ( final Exception e ) {
751 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
757 private void processFontFamily( final StringTokenizer st ) {
758 setBaseFontFamilyName( "" );
759 final String font_str = ( ( String ) st.nextElement() ).trim();
760 final String[] fonts = font_str.split( ",+" );
761 for( String font : fonts ) {
762 font = font.replace( '_', ' ' ).trim();
763 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
764 setBaseFontFamilyName( font );
770 public void putDisplayColors( final String key, final Color color ) {
771 getDisplayColors().put( key, color );
775 * read each line of config file, process non-comment lines
776 * @throws IOException
778 private void readConfig( final BufferedReader conf_in ) throws IOException {
781 line = conf_in.readLine();
782 if ( line != null ) {
784 // skip comments and blank lines
785 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
786 // convert runs of spaces to tabs
787 line = line.replaceAll( "\\s+", "\t" );
788 final StringTokenizer st = new StringTokenizer( line, "\t" );
792 } while ( line != null );
795 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
796 _abbreviate_scientific_names = abbreviate_scientific_names;
799 private void setAntialiasScreen( final boolean antialias_screen ) {
800 _antialias_screen = antialias_screen;
803 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
804 _background_color_gradient = background_color_gradient;
807 public void setBaseFontFamilyName( final String base_font_family_name ) {
808 _base_font_family_name = base_font_family_name;
811 public void setBaseFontSize( final int base_font_size ) {
812 _base_font_size = base_font_size;
815 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
816 _cladogram_type = cladogram_type;
819 public void setColorizeBranches( final boolean b ) {
820 display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
823 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
824 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
827 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
828 _default_bootstrap_samples = default_bootstrap_samples;
831 private void setPathToLocalMafft( final File path_to_local_mafft ) {
832 _path_to_local_mafft = path_to_local_mafft;
835 private void setPathToLocalFastme( final File path_to_local_fastme ) {
836 _path_to_local_fastme = path_to_local_fastme;
839 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
840 _path_to_local_raxml = path_to_local_raxml;
843 public File getPathToLocalClustalOmega() {
844 return _path_to_local_clustalo;
847 public void setPathToLocalClustalOmega( final File path_to_local_clustalo ) {
848 _path_to_local_clustalo = path_to_local_clustalo;
851 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
852 _default_node_fill = default_node_fill;
855 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
856 _default_node_shape = default_node_shape;
859 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
860 _default_node_shape_size = default_node_shape_size;
863 public void setDisplayAsPhylogram( final boolean b ) {
864 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
867 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
868 _display_colors = display_colors;
871 public void setDisplayConfidenceValues( final boolean b ) {
872 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
875 public void setDisplayInternalData( final boolean b ) {
876 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
879 public void setDisplayNodeNames( final boolean b ) {
880 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
883 public void setDisplaySequenceAcc( final boolean b ) {
884 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
887 public void setDisplaySequenceNames( final boolean b ) {
888 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
891 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
892 _display_sequence_relations = display_sequence_relations;
895 public void setDisplaySequenceSymbols( final boolean b ) {
896 display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no";
899 public void setDisplayTaxonomyCode( final boolean b ) {
900 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
903 public void setDisplayTaxonomyCommonNames( final boolean b ) {
904 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
907 public void setDisplayTaxonomyImages( final boolean b ) {
908 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
911 public void setDisplayTaxonomyScientificNames( final boolean b ) {
912 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
915 public void setDynamicallyHideData( final boolean b ) {
916 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
919 private void setEditable( final boolean editable ) {
920 _editable = editable;
923 public void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) {
924 _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes;
927 private void setGraphicsExportX( final int graphics_export_x ) {
928 _graphics_export_x = graphics_export_x;
931 private void setGraphicsExportY( final int graphics_export_y ) {
932 _graphics_export_y = graphics_export_y;
935 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
936 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
940 * Set a key-value(s) tuple
942 private void setKeyValue( final StringTokenizer st ) {
943 final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
944 if ( !st.hasMoreElements() ) {
947 // Handle single value settings first:
948 if ( key.equals( "default_click_to" ) ) {
949 final String clickto_name = ( String ) st.nextElement();
950 default_clickto = getClickToIndex( clickto_name );
951 if ( default_clickto == -1 ) {
952 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
953 + "] for [default_click_to]" );
956 else if ( default_clickto == DEPRECATED ) {
960 else if ( key.equals( "native_ui" ) ) {
961 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
962 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
965 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
966 _ui = UI.CROSSPLATFORM;
968 else if ( my_str.equals( "?" ) ) {
972 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
977 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
978 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
980 else if ( key.equals( "antialias_screen" ) ) {
981 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
983 else if ( key.equals( "phylogeny_graphics_type" ) ) {
984 final String type_str = ( ( String ) st.nextElement() ).trim();
985 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
986 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
988 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
989 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
991 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
992 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
994 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
995 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
997 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
998 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1000 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
1001 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1003 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
1004 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1006 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
1007 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1010 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1011 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1012 + "] for [phylogeny_graphics_type]" );
1015 else if ( key.equals( "min_confidence_value" ) ) {
1016 final String mcv_str = ( ( String ) st.nextElement() ).trim();
1017 final double d = parseDouble( mcv_str );
1018 setMinConfidenceValue( d );
1020 else if ( key.equals( "font_family" ) ) {
1021 processFontFamily( st );
1023 else if ( key.equals( "font_size" ) ) {
1024 final String size_str = ( ( String ) st.nextElement() ).trim();
1025 final int i = parseInt( size_str );
1026 setBaseFontSize( i );
1028 else if ( key.equals( "graphics_export_x" ) ) {
1029 final String str = ( ( String ) st.nextElement() ).trim();
1030 final int i = parseInt( str );
1031 setGraphicsExportX( i );
1033 else if ( key.equals( "graphics_export_y" ) ) {
1034 final String str = ( ( String ) st.nextElement() ).trim();
1035 final int i = parseInt( str );
1036 setGraphicsExportY( i );
1038 else if ( key.equals( "pdf_export_line_width" ) ) {
1039 final String str = ( ( String ) st.nextElement() ).trim();
1040 final float f = parseFloat( str );
1042 setPrintLineWidth( f );
1045 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1046 "value for [pdf_export_line_width] cannot be zero or negative" );
1049 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1050 final String str = ( ( String ) st.nextElement() ).trim();
1051 final int i = parseInt( str );
1053 setDefaultBootstrapSamples( i );
1057 .printWarningMessage( Constants.PRG_NAME,
1058 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1061 else if ( key.equals( "clustalo_local" ) ) {
1062 final String str = ( ( String ) st.nextElement() ).trim();
1063 if ( !ForesterUtil.isEmpty( str ) ) {
1064 setPathToLocalClustalOmega( new File( str ) );
1067 else if ( key.equals( "mafft_local" ) ) {
1068 final String str = ( ( String ) st.nextElement() ).trim();
1069 if ( !ForesterUtil.isEmpty( str ) ) {
1070 setPathToLocalMafft( new File( str ) );
1073 else if ( key.equals( "fastme_local" ) ) {
1074 final String str = ( ( String ) st.nextElement() ).trim();
1075 if ( !ForesterUtil.isEmpty( str ) ) {
1076 setPathToLocalFastme( new File( str ) );
1079 else if ( key.equals( "raxml_local" ) ) {
1080 final String str = ( ( String ) st.nextElement() ).trim();
1081 if ( !ForesterUtil.isEmpty( str ) ) {
1082 setPathToLocalRaxml( new File( str ) );
1085 else if ( key.equals( "show_scale" ) ) {
1086 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1088 else if ( key.equals( "show_overview" ) ) {
1089 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1091 else if ( key.equals( "show_branch_length_values" ) ) {
1092 setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
1094 else if ( key.equals( "background_gradient" ) ) {
1095 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1097 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1098 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1100 else if ( key.equals( "show_domain_labels" ) ) {
1101 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1103 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1104 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1106 else if ( key.equals( "cladogram_type" ) ) {
1107 final String type_str = ( ( String ) st.nextElement() ).trim();
1108 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1109 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1111 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1112 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1114 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1115 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1118 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1119 + "] for [cladogram_type]" );
1122 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1124 .printWarningMessage( Constants.PRG_NAME,
1125 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1127 else if ( key.equals( "hide_controls_and_menus" ) ) {
1128 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1130 else if ( key.equals( "use_tabbed_display" ) ) {
1131 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1133 else if ( key.equals( "overview_width" ) ) {
1134 final short i = parseShort( ( ( String ) st.nextElement() ) );
1137 else if ( key.equals( "overview_height" ) ) {
1138 final short i = parseShort( ( ( String ) st.nextElement() ) );
1139 setOvMaxHeight( i );
1141 else if ( key.equals( "overview_placement_type" ) ) {
1142 final String type_str = ( ( String ) st.nextElement() ).trim();
1143 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1144 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1146 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1147 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1149 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1150 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1152 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1153 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1156 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1157 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1158 + "] for [overview_placement_type]" );
1161 else if ( key.equals( "node_label_direction" ) ) {
1162 final String type_str = ( ( String ) st.nextElement() ).trim();
1163 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1164 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1166 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1167 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1170 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1171 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1172 + "] for [node_label_direction]" );
1175 else if ( key.equals( "branch_length_value_digits" ) ) {
1176 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1178 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1181 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1182 + "] for [branch_length_value_digits]" );
1185 else if ( key.equals( "confidence_value_digits" ) ) {
1186 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1188 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1191 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1192 + "] for [confidence_value_digits]" );
1195 else if ( key.equals( "allow_editing" ) ) {
1196 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1198 else if ( key.equals( "display_sequence_relations" ) ) {
1199 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1201 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1202 final boolean r = parseBoolean( ( String ) st.nextElement() );
1203 if ( r && isExtractPfamTaxonomyCodesInNhParsing() ) {
1205 .printWarningMessage( Constants.PRG_NAME,
1206 "attempt to extract taxonomies and replace underscores at the same time" );
1209 setReplaceUnderscoresInNhParsing( r );
1212 else if ( key.equals( "extract_taxonomy_codes_in_nh_parsing" ) ) {
1213 final boolean e = parseBoolean( ( String ) st.nextElement() );
1214 if ( e && isReplaceUnderscoresInNhParsing() ) {
1216 .printWarningMessage( Constants.PRG_NAME,
1217 "attempt to extract taxonomies and replace underscores at the same time" );
1220 setExtractPfamTaxonomyCodesInNhParsing( e );
1223 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1224 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1226 else if ( key.equals( "gui_background_color" ) ) {
1227 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1229 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1230 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1232 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1233 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1235 else if ( key.equals( "gui_button_text_color" ) ) {
1236 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1238 else if ( key.equals( "gui_button_background_color" ) ) {
1239 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1241 else if ( key.equals( "gui_menu_background_color" ) ) {
1242 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1244 else if ( key.equals( "gui_menu_text_color" ) ) {
1245 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1247 else if ( key.equals( "gui_button_border_color" ) ) {
1248 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1250 else if ( key.equals( "domain_structure_font_color" ) ) {
1251 _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
1253 else if ( key.equals( "domain_structure_base_color" ) ) {
1254 _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
1256 else if ( key.equals( "show_default_node_shapes" ) ) {
1257 setShowDefaultNodeShapes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1259 else if ( key.equals( "default_node_size" ) ) {
1260 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1261 setDefaultNodeShapeSize( i );
1263 else if ( key.equals( "default_node_fill" ) ) {
1264 final String fill_str = ( ( String ) st.nextElement() ).trim();
1265 if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.NONE.toString() ) ) {
1266 setDefaultNodeFill( NodeFill.NONE );
1268 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.GRADIENT.toString() ) ) {
1269 setDefaultNodeFill( NodeFill.GRADIENT );
1271 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.SOLID.toString() ) ) {
1272 setDefaultNodeFill( NodeFill.SOLID );
1275 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1276 + "] for [default_node_fill]" );
1279 else if ( key.equals( "default_node_shape" ) ) {
1280 final String shape_str = ( ( String ) st.nextElement() ).trim();
1281 if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.CIRCLE.toString() ) ) {
1282 setDefaultNodeShape( NodeShape.CIRCLE );
1284 else if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.RECTANGLE.toString() ) ) {
1285 setDefaultNodeShape( NodeShape.RECTANGLE );
1288 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1289 + "] for [default_node_shape]" );
1292 else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
1293 setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
1295 else if ( key.equals( "ext_descendents_data_to_return" ) ) {
1296 final String s = ( ( String ) st.nextElement() ).trim();
1297 if ( s.equalsIgnoreCase( "node_name" ) ) {
1298 setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
1300 else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
1301 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
1303 else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
1304 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
1306 else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
1307 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
1309 else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
1310 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
1312 else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
1313 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME );
1315 else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
1316 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
1318 else if ( s.equalsIgnoreCase( "user_selected" ) ) {
1319 setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
1322 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1323 + "] for [ext_descendents_data_to_return]" );
1326 else if ( key.equals( "label_for_get_ext_descendents_data" ) ) {
1327 final String s = ( ( String ) st.nextElement() ).trim();
1328 if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) {
1329 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s
1330 + "] for [label_for_get_ext_descendents_data]" );
1333 setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
1336 else if ( key.equals( "ext_descendents_data_to_return_on" ) ) {
1337 final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
1338 if ( s.equals( "console" ) ) {
1339 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
1341 else if ( s.equals( "window" ) ) {
1342 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
1345 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1346 + "] for [ext_descendents_data_to_return_on]" );
1349 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1352 if ( key.equals( "use_real_br_lengths" ) || key.equals( "phylogram" ) ) {
1353 key_index = Configuration.display_as_phylogram;
1354 if ( key.equals( "use_real_br_lengths" ) ) {
1356 .printWarningMessage( Constants.PRG_NAME,
1357 "configuration key [use_real_br_lengths] is deprecated, use [phylogram] instead" );
1360 else if ( key.equals( "rollover" ) ) {
1361 key_index = Configuration.node_data_popup;
1363 else if ( key.equals( "color_according_to_species" ) ) {
1364 key_index = Configuration.color_according_to_species;
1366 else if ( key.equals( "show_node_names" ) ) {
1367 key_index = Configuration.show_node_names;
1369 else if ( key.equals( "show_taxonomy" ) || key.equals( "show_taxonomy_code" ) ) {
1370 key_index = Configuration.show_tax_code;
1371 if ( key.equals( "show_taxonomy" ) ) {
1373 .printWarningMessage( Constants.PRG_NAME,
1374 "configuration key [show_taxonomy] is deprecated, use [show_taxonomy_code] instead" );
1377 else if ( key.equals( "write_br_length_values" ) ) {
1378 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1379 "configuration key [write_br_length_values] is deprecated" );
1380 key_index = DEPRECATED;
1382 else if ( key.equals( "write_bootstrap_values" ) || key.equals( "write_confidence_values" ) ) {
1383 key_index = Configuration.write_confidence_values;
1384 if ( key.equals( "write_bootstrap_values" ) ) {
1386 .printWarningMessage( Constants.PRG_NAME,
1387 "configuration key [write_bootstrap_values] is deprecated, use [write_confidence_values] instead" );
1390 else if ( key.equals( "write_events" ) || key.equals( "write_dup_spec" ) ) {
1391 key_index = Configuration.write_events;
1392 if ( key.equals( "write_dup_spec" ) ) {
1394 .printWarningMessage( Constants.PRG_NAME,
1395 "configuration key [write_dup_spec] is deprecated, use [write_events] instead" );
1398 else if ( key.equals( "color_branches" ) ) {
1399 key_index = Configuration.color_branches;
1401 else if ( key.equals( "width_branches" ) ) {
1402 key_index = Configuration.width_branches;
1404 else if ( key.equals( "color_orthologous" ) ) {
1405 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1406 "configuration key [color_orthologous] is deprecated" );
1408 else if ( key.equals( "color_subtree_neighbors" ) ) {
1409 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1410 "configuration key [color_subtree_neighbors] is deprecated" );
1412 else if ( key.equals( "color_super_orthologous" ) ) {
1413 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1414 "configuration key [color_super_orthologous] is deprecated" );
1416 else if ( key.equals( "mark_nodes_with_box" ) ) {
1417 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1418 "configuration key [mark_nodes_with_box] is deprecated" );
1419 key_index = DEPRECATED;
1421 else if ( key.equals( "show_domain_architectures" ) ) {
1422 key_index = Configuration.show_domain_architectures;
1424 else if ( key.equals( "show_annotations" ) ) {
1425 key_index = Configuration.show_annotation;
1427 else if ( key.equals( "show_binary_characters" ) ) {
1428 key_index = Configuration.show_binary_characters;
1430 else if ( key.equals( "show_binary_character_counts" ) ) {
1431 key_index = Configuration.show_binary_character_counts;
1433 else if ( key.equals( "show_gene_names" ) ) {
1434 key_index = Configuration.show_gene_names;
1436 else if ( key.equals( "show_gene_symbols" ) ) {
1437 key_index = Configuration.show_gene_symbols;
1439 else if ( key.equals( "show_sequence_acc" ) ) {
1440 key_index = Configuration.show_sequence_acc;
1442 else if ( key.equals( "show_node_ids" ) ) {
1444 .printWarningMessage( Constants.PRG_NAME, "configuration key [show_node_ids] is deprecated" );
1445 key_index = DEPRECATED;
1447 else if ( key.equals( "display_internal_data" ) ) {
1448 key_index = Configuration.display_internal_data;
1450 else if ( key.equals( "dynamically_hide_data" ) ) {
1451 key_index = Configuration.dynamically_hide_data;
1453 else if ( key.equals( "show_taxonomy_names" ) ) {
1454 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1455 "configuration key [show_taxonomy_names] is deprecated" );
1456 key_index = DEPRECATED;
1458 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1459 key_index = Configuration.show_taxonomy_scientific_names;
1461 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1462 key_index = Configuration.show_taxonomy_common_names;
1464 else if ( key.equals( "show_taxonomy_images" ) ) {
1465 key_index = Configuration.show_taxonomy_images;
1467 else if ( key.equals( "color_according_to_annotation" ) ) {
1468 key_index = Configuration.color_according_to_annotation;
1470 else if ( key.equals( "show_vector_data" ) ) {
1471 key_index = Configuration.show_vector_data;
1473 else if ( key.equals( "show_properties" ) ) {
1474 key_index = Configuration.show_properties;
1476 else if ( key.equals( "show_relation_confidence" ) ) {
1477 key_index = Configuration.show_relation_confidence;
1479 else if ( key.equals( "show_custom_node_shapes" ) ) {
1480 key_index = Configuration.show_custom_node_shapes;
1482 // If we've found the key, set the values
1483 if ( key_index >= 0 ) {
1484 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1485 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1486 // otherwise, keep looking
1489 if ( key_index == DEPRECATED ) {
1492 else if ( key.equals( "click_to" ) ) {
1493 final String click_to_name = ( String ) st.nextElement();
1494 key_index = getClickToIndex( click_to_name );
1495 if ( key_index >= 0 ) {
1496 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1498 else if ( key_index == DEPRECATED ) {
1502 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1506 else if ( key.equals( "species_color" ) ) {
1507 getSpeciesColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1509 else if ( key.equals( "domain_color" ) ) {
1510 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1512 else if ( key.equals( "annotation_color" ) ) {
1513 getAnnotationColors()
1514 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1516 else if ( key.equals( "function_color" ) ) {
1517 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1518 "configuration key [function_color] is deprecated" );
1520 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1521 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1523 else if ( key.equals( WEB_LINK_KEY ) ) {
1524 if ( st.countTokens() == 3 ) {
1525 createWebLink( ( String ) st.nextElement(),
1526 ( String ) st.nextElement(),
1527 ( String ) st.nextElement() );
1530 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1531 "illegal format in configuration file for key [" + key + "]" );
1535 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1536 + "] in: " + config_filename );
1541 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1542 + config_filename );
1546 private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
1547 _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
1550 public String getLabelForGetExtDescendentsData() {
1551 return _label_for_get_ext_descendents_data;
1554 public void setMinConfidenceValue( final double min_confidence_value ) {
1555 _min_confidence_value = min_confidence_value;
1558 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
1559 _node_label_direction = node_label_direction;
1562 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
1563 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
1566 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
1567 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
1570 private void setOvMaxHeight( final short ov_max_height ) {
1571 _ov_max_height = ov_max_height;
1574 private void setOvMaxWidth( final short ov_max_width ) {
1575 _ov_max_width = ov_max_width;
1578 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1579 _ov_placement = ov_placement;
1582 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
1583 _phylogeny_graphics_type = phylogeny_graphics_type;
1586 public void setPrintLineWidth( final float print_line_width ) {
1587 _print_line_width = print_line_width;
1590 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
1591 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
1594 public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
1595 _show_branch_length_values = show_branch_length_values;
1598 public void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
1599 _show_default_node_shapes = show_default_node_shapes;
1602 public void setShowDomainLabels( final boolean show_domain_labels ) {
1603 _show_domain_labels = show_domain_labels;
1606 private void setShowOverview( final boolean show_overview ) {
1607 _show_overview = show_overview;
1610 public void setShowScale( final boolean show_scale ) {
1611 _show_scale = show_scale;
1614 public void setTaxonomyColorize( final boolean b ) {
1615 display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
1618 public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
1619 _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
1622 public void setUseBranchesWidths( final boolean b ) {
1623 display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
1626 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1627 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1630 void setWebLinks( final SortedMap<String, WebLink> weblinks ) {
1631 _weblinks = weblinks;
1634 static String getDefaultFontFamilyName() {
1635 return DEFAULT_FONT_FAMILY;
1638 static enum TRIPLET {
1639 TRUE, FALSE, UNKNOWN
1643 NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN
1646 public NODE_DATA getExtDescNodeDataToReturn() {
1647 return _ext_desc_data_to_return;
1650 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
1651 _ext_desc_data_to_return = ext_desc_data_to_return;
1654 public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
1655 return _ext_node_data_return_on;
1658 private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
1659 _ext_node_data_return_on = ext_node_data_return_on;