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.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 {
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", "?" }, { "Event", "display", "?" },
167 { "Taxonomy Colorize", "display", "no" }, { "Colorize Branches", "display", "no" },
168 { "Use Branch-Widths", "display", "no" }, { "Show Custom Nodes", "display", "yes" },
169 { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" },
170 { "Binary Char Counts", "nodisplay", "no" }, { "Prot/Gene Name", "display", "yes" },
171 { "Prot/Gene Acc", "display", "no" }, { "Show Internal Data", "display", "yes" },
172 { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" },
173 { "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" },
174 { "Prot/Gene Symbol", "display", "yes" }, { "Rollover", "display", "yes" },
175 { "Relation Confidence", "display", "no" }, { "Vector Data", "display", "no" },
176 { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" } };
177 final static String clickto_options[][] = {
178 { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
179 { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
180 { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Blast", "display" },
181 { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" },
182 { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" },
183 { "Sort Descendants", "display" }, { "Return", "display" }, { "Select Node(s)", "display" } };
184 // This option is selected in the dropdown
185 int default_clickto = Configuration.display_node_data;
189 TreeColorSet tree_color_set;
193 TreeFontSet tree_font_set;
197 private static Hashtable<String, Color> _species_colors;
201 private static Hashtable<String, Color> _domain_colors;
205 private static Hashtable<String, Color> _annotation_colors;
206 boolean verbose = Constants.VERBOSE_DEFAULT;
207 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
208 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
209 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
210 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
211 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
212 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
213 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
214 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
215 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
216 private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
217 private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
218 private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
219 private String _label_for_get_ext_descendents_data = "";
220 private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
221 private static String DEFAULT_FONT_FAMILY = "";
223 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
224 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
225 DEFAULT_FONT_FAMILY = font_name;
229 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
230 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
234 public Configuration() {
235 this( null, false, false, false );
238 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
239 if ( ForesterUtil.isEmpty( cf ) ) {
240 config_filename = default_config_filename;
243 config_filename = cf;
245 setWebLinks( new TreeMap<String, WebLink>() );
246 setDisplayColors( new TreeMap<String, Color>() );
247 config_filename = config_filename.trim();
250 // If URL, open accordingly
252 u = new URL( config_filename );
254 final InputStreamReader isr = new InputStreamReader( u.openStream() );
255 final BufferedReader bf = new BufferedReader( isr );
258 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
259 + config_filename + "]" );
261 catch ( final Exception e ) {
262 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
263 + config_filename + "]: " + e.getLocalizedMessage() );
266 catch ( final Exception e ) {
267 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
268 + config_filename + "]" );
272 // Otherwise, open as a file
273 File f = new File( config_filename );
275 f = new File( config_filename + ".txt" );
277 if ( f.exists() && f.canRead() ) {
279 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
283 catch ( final Exception e ) {
285 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
286 + config_filename + "]: " + e );
292 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
293 + config_filename + "]" );
299 private void createWebLink( final String url_str, final String desc, final String source_identifier ) {
300 WebLink weblink = null;
303 weblink = new WebLink( new URL( url_str.trim() ), desc.trim(), source_identifier.trim() );
305 catch ( final MalformedURLException e ) {
306 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not create URL from [" + url_str + "]" );
309 if ( !ex && ( weblink != null ) ) {
310 getWebLinks().put( weblink.getSourceIdentifier().toLowerCase(), weblink );
314 boolean displaySequenceRelations() {
315 return _display_sequence_relations;
318 boolean doCheckOption( final int which ) {
319 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
320 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
323 boolean doDisplayClickToOption( final int which ) {
324 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
327 boolean doDisplayOption( final int which ) {
328 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
332 * Will attempt to use the phylogeny to determine whether to check
333 * this or not (e.g. phylogram)
336 boolean doGuessCheckOption( final int which ) {
337 return display_options[ which ][ 2 ].equals( "?" );
340 Map<String, Color> getAnnotationColors() {
341 if ( _annotation_colors == null ) {
342 _annotation_colors = new Hashtable<String, Color>();
344 return _annotation_colors;
347 public String getBaseFontFamilyName() {
348 return _base_font_family_name;
351 int getBaseFontSize() {
352 return _base_font_size;
355 CLADOGRAM_TYPE getCladogramType() {
356 return _cladogram_type;
359 private int getClickToIndex( final String name ) {
361 if ( name.equals( "edit_info" ) ) {
362 index = Configuration.display_node_data;
364 .printWarningMessage( Constants.PRG_NAME,
365 "configuration key [edit_info] is deprecated, use [display node data] instead" );
367 else if ( name.equals( "display_node_data" ) ) {
368 index = Configuration.display_node_data;
370 else if ( name.equals( "collapse_uncollapse" ) ) {
371 index = Configuration.collapse_uncollapse;
373 else if ( name.equals( "reroot" ) ) {
374 index = Configuration.reroot;
376 else if ( name.equals( "subtree" ) ) {
377 index = Configuration.subtree;
379 else if ( name.equals( "swap" ) ) {
380 index = Configuration.swap;
382 else if ( name.equals( "sort_descendants" ) ) {
383 index = Configuration.sort_descendents;
385 else if ( name.equals( "get_ext_descendents_data" ) ) {
386 index = Configuration.get_ext_desc_data;
388 else if ( name.equals( "display_sequences" ) ) {
390 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
393 else if ( name.equals( "open_seq_web" ) ) {
394 index = Configuration.open_seq_web;
396 else if ( name.equals( "open_tax_web" ) ) {
397 index = Configuration.open_tax_web;
399 else if ( name.equals( "blast" ) ) {
400 index = Configuration.blast;
402 else if ( name.equals( "cut_subtree" ) ) {
403 index = Configuration.cut_subtree;
405 else if ( name.equals( "copy_subtree" ) ) {
406 index = Configuration.copy_subtree;
408 else if ( name.equals( "paste_subtree" ) ) {
409 index = Configuration.paste_subtree;
411 else if ( name.equals( "delete" ) ) {
412 index = Configuration.delete_subtree_or_node;
414 else if ( name.equals( "add_new_node" ) ) {
415 index = Configuration.add_new_node;
417 else if ( name.equals( "edit_node_data" ) ) {
418 index = Configuration.edit_node_data;
420 else if ( name.equals( "select_nodes" ) ) {
421 index = Configuration.select_nodes;
423 else if ( name.equals( "display_node_popup" ) ) {
424 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
425 "configuration key [display_node_popup] is deprecated" );
428 else if ( name.equals( "custom_option" ) ) {
429 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
432 else if ( name.equals( "color_subtree" ) ) {
433 index = Configuration.color_subtree;
435 else if ( name.equals( "go_to_swiss_prot" ) ) {
436 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" );
442 int getClickToOptionsCount() {
443 return clickto_options.length;
446 String getClickToTitle( final int which ) {
447 return clickto_options[ which ][ 0 ];
450 public int getDefaultBootstrapSamples() {
451 return _default_bootstrap_samples;
454 public File getpathToLocalMafft() {
455 return _path_to_local_mafft;
458 public File getPathToLocalFastme() {
459 return _path_to_local_fastme;
462 public File getPathToLocalRaxml() {
463 return _path_to_local_raxml;
466 int getDefaultDisplayClicktoOption() {
467 return default_clickto;
470 public NodeFill getDefaultNodeFill() {
471 return _default_node_fill;
474 public NodeShape getDefaultNodeShape() {
475 return _default_node_shape;
478 public short getDefaultNodeShapeSize() {
479 return _default_node_shape_size;
482 SortedMap<String, Color> getDisplayColors() {
483 return _display_colors;
486 String getDisplayTitle( final int which ) {
487 return display_options[ which ][ 0 ];
490 Map<String, Color> getDomainColors() {
491 if ( _domain_colors == null ) {
492 _domain_colors = new Hashtable<String, Color>();
494 return _domain_colors;
497 public Color getDomainStructureBaseColor() {
498 return _domain_structure_base_color;
501 public Color getDomainStructureFontColor() {
502 return _domain_structure_font_color;
505 int getGraphicsExportX() {
506 return _graphics_export_x;
509 int getGraphicsExportY() {
510 return _graphics_export_y;
513 Color getGuiBackgroundColor() {
514 return _gui_background_color;
517 Color getGuiButtonBackgroundColor() {
518 return _gui_button_background_color;
521 Color getGuiButtonBorderColor() {
522 return _gui_button_border_color;
525 Color getGuiButtonTextColor() {
526 return _gui_button_text_color;
529 Color getGuiCheckboxAndButtonActiveColor() {
530 return _gui_checkbox_and_button_active_color;
533 Color getGuiCheckboxTextColor() {
534 return _gui_checkbox_text_color;
537 Color getGuiMenuBackgroundColor() {
538 return _gui_menu_background_color;
541 Color getGuiMenuTextColor() {
542 return _gui_menu_text_color;
545 double getMinConfidenceValue() {
546 return _min_confidence_value;
549 NODE_LABEL_DIRECTION getNodeLabelDirection() {
550 return _node_label_direction;
553 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
554 return _number_of_digits_after_comma_for_branch_length_values;
557 short getNumberOfDigitsAfterCommaForConfidenceValues() {
558 return _number_of_digits_after_comma_for_confidence_values;
561 short getOvMaxHeight() {
562 return _ov_max_height;
565 short getOvMaxWidth() {
566 return _ov_max_width;
569 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
570 return _ov_placement;
573 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
574 return _phylogeny_graphics_type;
577 float getPrintLineWidth() {
578 return _print_line_width;
581 Hashtable<String, Color> getSpeciesColors() {
582 if ( _species_colors == null ) {
583 _species_colors = new Hashtable<String, Color>();
585 return _species_colors;
588 TreeColorSet getTreeColorSet() {
592 TreeFontSet getTreeFontSet() {
596 WebLink getWebLink( final String source ) {
597 return getWebLinks().get( source );
600 Map<String, WebLink> getWebLinks() {
604 public boolean isAbbreviateScientificTaxonNames() {
605 return _abbreviate_scientific_names;
608 boolean isAntialiasScreen() {
609 return _antialias_screen;
612 public boolean isBackgroundColorGradient() {
613 return _background_color_gradient;
616 public boolean isColorLabelsSameAsParentBranch() {
617 return _color_labels_same_as_parent_branch;
621 * Convenience method.
623 * @return true if value in configuration file was 'yes'
625 boolean isDrawAsPhylogram() {
626 return doCheckOption( display_as_phylogram );
629 boolean isEditable() {
633 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
634 return _taxonomy_extraction;
637 boolean isHasWebLink( final String source ) {
638 return getWebLinks().containsKey( source );
642 * Only used by ArchaeoptryxE.
645 boolean isHideControlPanelAndMenubar() {
646 return _hide_controls_and_menus;
649 boolean isInternalNumberAreConfidenceForNhParsing() {
650 return _internal_number_are_confidence_for_nh_parsing;
653 boolean isReplaceUnderscoresInNhParsing() {
654 return _nh_parsing_replace_underscores;
657 boolean isShowBranchLengthValues() {
658 return _show_branch_length_values;
661 public boolean isShowDefaultNodeShapes() {
662 return _show_default_node_shapes;
665 public boolean isShowDomainLabels() {
666 return _show_domain_labels;
669 boolean isShowOverview() {
670 return _show_overview;
673 boolean isShowScale() {
677 public boolean isTaxonomyColorizeNodeShapes() {
678 return _taxonomy_colorize_node_shapes;
681 final boolean isUseNativeUI() {
682 if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) {
685 return _ui == UI.NATIVE;
689 * Only used by ArchaeoptryxE.
692 boolean isUseTabbedDisplay() {
693 return _use_tabbed_display;
696 boolean isValidatePhyloXmlAgainstSchema() {
697 return _validate_against_phyloxml_xsd_schema;
700 private boolean parseBoolean( final String str ) {
701 final String my_str = str.trim().toLowerCase();
702 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
705 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
709 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
714 private double parseDouble( final String str ) {
717 d = Double.parseDouble( str.trim() );
719 catch ( final Exception e ) {
720 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
726 private float parseFloat( final String str ) {
729 f = Float.parseFloat( str.trim() );
731 catch ( final Exception e ) {
732 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
738 private int parseInt( final String str ) {
741 i = Integer.parseInt( str.trim() );
743 catch ( final Exception e ) {
744 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
750 private short parseShort( final String str ) {
753 i = Short.parseShort( str.trim() );
755 catch ( final Exception e ) {
756 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
762 private void processFontFamily( final StringTokenizer st ) {
763 setBaseFontFamilyName( "" );
764 final String font_str = ( ( String ) st.nextElement() ).trim();
765 final String[] fonts = font_str.split( ",+" );
766 for( String font : fonts ) {
767 font = font.replace( '_', ' ' ).trim();
768 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
769 setBaseFontFamilyName( font );
775 public void putDisplayColors( final String key, final Color color ) {
776 getDisplayColors().put( key, color );
780 * read each line of config file, process non-comment lines
781 * @throws IOException
783 private void readConfig( final BufferedReader conf_in ) throws IOException {
786 line = conf_in.readLine();
787 if ( line != null ) {
789 // skip comments and blank lines
790 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
791 // convert runs of spaces to tabs
792 line = line.replaceAll( "\\s+", "\t" );
793 final StringTokenizer st = new StringTokenizer( line, "\t" );
797 } while ( line != null );
800 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
801 _abbreviate_scientific_names = abbreviate_scientific_names;
804 private void setAntialiasScreen( final boolean antialias_screen ) {
805 _antialias_screen = antialias_screen;
808 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
809 _background_color_gradient = background_color_gradient;
812 public void setBaseFontFamilyName( final String base_font_family_name ) {
813 _base_font_family_name = base_font_family_name;
816 public void setBaseFontSize( final int base_font_size ) {
817 _base_font_size = base_font_size;
820 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
821 _cladogram_type = cladogram_type;
824 public void setColorizeBranches( final boolean b ) {
825 display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
828 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
829 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
832 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
833 _default_bootstrap_samples = default_bootstrap_samples;
836 private void setPathToLocalMafft( final File path_to_local_mafft ) {
837 _path_to_local_mafft = path_to_local_mafft;
840 private void setPathToLocalFastme( final File path_to_local_fastme ) {
841 _path_to_local_fastme = path_to_local_fastme;
844 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
845 _path_to_local_raxml = path_to_local_raxml;
848 public File getPathToLocalClustalOmega() {
849 return _path_to_local_clustalo;
852 public void setPathToLocalClustalOmega( final File path_to_local_clustalo ) {
853 _path_to_local_clustalo = path_to_local_clustalo;
856 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
857 _default_node_fill = default_node_fill;
860 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
861 _default_node_shape = default_node_shape;
864 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
865 _default_node_shape_size = default_node_shape_size;
868 public void setDisplayAsPhylogram( final boolean b ) {
869 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
872 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
873 _display_colors = display_colors;
876 public void setDisplayConfidenceValues( final boolean b ) {
877 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
880 public void setDisplayInternalData( final boolean b ) {
881 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
884 public void setDisplayNodeNames( final boolean b ) {
885 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
888 public void setDisplaySequenceAcc( final boolean b ) {
889 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
892 public void setDisplaySequenceNames( final boolean b ) {
893 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
896 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
897 _display_sequence_relations = display_sequence_relations;
900 public void setDisplaySequenceSymbols( final boolean b ) {
901 display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no";
904 public void setDisplayTaxonomyCode( final boolean b ) {
905 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
908 public void setDisplayTaxonomyCommonNames( final boolean b ) {
909 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
912 public void setDisplayTaxonomyImages( final boolean b ) {
913 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
916 public void setDisplayTaxonomyScientificNames( final boolean b ) {
917 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
920 public void setDynamicallyHideData( final boolean b ) {
921 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
924 private void setEditable( final boolean editable ) {
925 _editable = editable;
928 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
929 _taxonomy_extraction = taxonomy_extraction;
932 private void setGraphicsExportX( final int graphics_export_x ) {
933 _graphics_export_x = graphics_export_x;
936 private void setGraphicsExportY( final int graphics_export_y ) {
937 _graphics_export_y = graphics_export_y;
940 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
941 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
945 * Set a key-value(s) tuple
947 private void setKeyValue( final StringTokenizer st ) {
948 final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
949 if ( !st.hasMoreElements() ) {
952 // Handle single value settings first:
953 if ( key.equals( "default_click_to" ) ) {
954 final String clickto_name = ( String ) st.nextElement();
955 default_clickto = getClickToIndex( clickto_name );
956 if ( default_clickto == -1 ) {
957 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
958 + "] for [default_click_to]" );
961 else if ( default_clickto == DEPRECATED ) {
965 else if ( key.equals( "native_ui" ) ) {
966 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
967 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
970 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
971 _ui = UI.CROSSPLATFORM;
973 else if ( my_str.equals( "?" ) ) {
977 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
982 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
983 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
985 else if ( key.equals( "antialias_screen" ) ) {
986 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
988 else if ( key.equals( "phylogeny_graphics_type" ) ) {
989 final String type_str = ( ( String ) st.nextElement() ).trim();
990 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
991 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
993 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
994 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
996 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
997 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
999 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
1000 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1002 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
1003 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1005 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
1006 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1008 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
1009 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1011 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
1012 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1015 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1016 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1017 + "] for [phylogeny_graphics_type]" );
1020 else if ( key.equals( "min_confidence_value" ) ) {
1021 final String mcv_str = ( ( String ) st.nextElement() ).trim();
1022 final double d = parseDouble( mcv_str );
1023 setMinConfidenceValue( d );
1025 else if ( key.equals( "font_family" ) ) {
1026 processFontFamily( st );
1028 else if ( key.equals( "font_size" ) ) {
1029 final String size_str = ( ( String ) st.nextElement() ).trim();
1030 final int i = parseInt( size_str );
1031 setBaseFontSize( i );
1033 else if ( key.equals( "graphics_export_x" ) ) {
1034 final String str = ( ( String ) st.nextElement() ).trim();
1035 final int i = parseInt( str );
1036 setGraphicsExportX( i );
1038 else if ( key.equals( "graphics_export_y" ) ) {
1039 final String str = ( ( String ) st.nextElement() ).trim();
1040 final int i = parseInt( str );
1041 setGraphicsExportY( i );
1043 else if ( key.equals( "pdf_export_line_width" ) ) {
1044 final String str = ( ( String ) st.nextElement() ).trim();
1045 final float f = parseFloat( str );
1047 setPrintLineWidth( f );
1050 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1051 "value for [pdf_export_line_width] cannot be zero or negative" );
1054 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1055 final String str = ( ( String ) st.nextElement() ).trim();
1056 final int i = parseInt( str );
1058 setDefaultBootstrapSamples( i );
1062 .printWarningMessage( Constants.PRG_NAME,
1063 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1066 else if ( key.equals( "clustalo_local" ) ) {
1067 final String str = ( ( String ) st.nextElement() ).trim();
1068 if ( !ForesterUtil.isEmpty( str ) ) {
1069 setPathToLocalClustalOmega( new File( str ) );
1072 else if ( key.equals( "mafft_local" ) ) {
1073 final String str = ( ( String ) st.nextElement() ).trim();
1074 if ( !ForesterUtil.isEmpty( str ) ) {
1075 setPathToLocalMafft( new File( str ) );
1078 else if ( key.equals( "fastme_local" ) ) {
1079 final String str = ( ( String ) st.nextElement() ).trim();
1080 if ( !ForesterUtil.isEmpty( str ) ) {
1081 setPathToLocalFastme( new File( str ) );
1084 else if ( key.equals( "raxml_local" ) ) {
1085 final String str = ( ( String ) st.nextElement() ).trim();
1086 if ( !ForesterUtil.isEmpty( str ) ) {
1087 setPathToLocalRaxml( new File( str ) );
1090 else if ( key.equals( "show_scale" ) ) {
1091 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1093 else if ( key.equals( "show_overview" ) ) {
1094 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1096 else if ( key.equals( "show_branch_length_values" ) ) {
1097 setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
1099 else if ( key.equals( "background_gradient" ) ) {
1100 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1102 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1103 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1105 else if ( key.equals( "show_domain_labels" ) ) {
1106 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1108 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1109 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1111 else if ( key.equals( "cladogram_type" ) ) {
1112 final String type_str = ( ( String ) st.nextElement() ).trim();
1113 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1114 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1116 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1117 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1119 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1120 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1123 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1124 + "] for [cladogram_type]" );
1127 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1129 .printWarningMessage( Constants.PRG_NAME,
1130 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1132 else if ( key.equals( "hide_controls_and_menus" ) ) {
1133 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1135 else if ( key.equals( "use_tabbed_display" ) ) {
1136 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1138 else if ( key.equals( "overview_width" ) ) {
1139 final short i = parseShort( ( ( String ) st.nextElement() ) );
1142 else if ( key.equals( "overview_height" ) ) {
1143 final short i = parseShort( ( ( String ) st.nextElement() ) );
1144 setOvMaxHeight( i );
1146 else if ( key.equals( "overview_placement_type" ) ) {
1147 final String type_str = ( ( String ) st.nextElement() ).trim();
1148 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1149 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1151 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1152 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1154 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1155 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1157 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1158 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1161 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1162 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1163 + "] for [overview_placement_type]" );
1166 else if ( key.equals( "node_label_direction" ) ) {
1167 final String type_str = ( ( String ) st.nextElement() ).trim();
1168 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1169 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1171 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1172 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1175 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1176 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1177 + "] for [node_label_direction]" );
1180 else if ( key.equals( "branch_length_value_digits" ) ) {
1181 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1183 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1186 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1187 + "] for [branch_length_value_digits]" );
1190 else if ( key.equals( "confidence_value_digits" ) ) {
1191 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1193 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1196 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1197 + "] for [confidence_value_digits]" );
1200 else if ( key.equals( "allow_editing" ) ) {
1201 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1203 else if ( key.equals( "display_sequence_relations" ) ) {
1204 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1206 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1207 final boolean r = parseBoolean( ( String ) st.nextElement() );
1208 if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
1210 .printWarningMessage( Constants.PRG_NAME,
1211 "attempt to extract taxonomies and replace underscores at the same time" );
1214 setReplaceUnderscoresInNhParsing( r );
1217 else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
1218 final String s = ( String ) st.nextElement();
1219 if ( s.equalsIgnoreCase( "no" ) ) {
1220 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1222 else if ( s.equalsIgnoreCase( "yes" ) ) {
1223 setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES );
1225 else if ( s.equalsIgnoreCase( "pfam" ) ) {
1226 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
1229 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1230 "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + s );
1232 if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
1234 .printWarningMessage( Constants.PRG_NAME,
1235 "attempt to extract taxonomies and replace underscores at the same time" );
1238 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1239 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1241 else if ( key.equals( "gui_background_color" ) ) {
1242 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1244 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1245 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1247 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1248 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1250 else if ( key.equals( "gui_button_text_color" ) ) {
1251 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1253 else if ( key.equals( "gui_button_background_color" ) ) {
1254 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1256 else if ( key.equals( "gui_menu_background_color" ) ) {
1257 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1259 else if ( key.equals( "gui_menu_text_color" ) ) {
1260 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1262 else if ( key.equals( "gui_button_border_color" ) ) {
1263 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1265 else if ( key.equals( "domain_structure_font_color" ) ) {
1266 _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
1268 else if ( key.equals( "domain_structure_base_color" ) ) {
1269 _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
1271 else if ( key.equals( "show_default_node_shapes" ) ) {
1272 setShowDefaultNodeShapes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1274 else if ( key.equals( "default_node_size" ) ) {
1275 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1276 setDefaultNodeShapeSize( i );
1278 else if ( key.equals( "default_node_fill" ) ) {
1279 final String fill_str = ( ( String ) st.nextElement() ).trim();
1280 if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.NONE.toString() ) ) {
1281 setDefaultNodeFill( NodeFill.NONE );
1283 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.GRADIENT.toString() ) ) {
1284 setDefaultNodeFill( NodeFill.GRADIENT );
1286 else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.SOLID.toString() ) ) {
1287 setDefaultNodeFill( NodeFill.SOLID );
1290 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1291 + "] for [default_node_fill]" );
1294 else if ( key.equals( "default_node_shape" ) ) {
1295 final String shape_str = ( ( String ) st.nextElement() ).trim();
1296 if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.CIRCLE.toString() ) ) {
1297 setDefaultNodeShape( NodeShape.CIRCLE );
1299 else if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.RECTANGLE.toString() ) ) {
1300 setDefaultNodeShape( NodeShape.RECTANGLE );
1303 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1304 + "] for [default_node_shape]" );
1307 else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
1308 setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
1310 else if ( key.equals( "ext_descendents_data_to_return" ) ) {
1311 final String s = ( ( String ) st.nextElement() ).trim();
1312 if ( s.equalsIgnoreCase( "node_name" ) ) {
1313 setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
1315 else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
1316 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
1318 else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
1319 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
1321 else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
1322 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
1324 else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
1325 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
1327 else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
1328 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME );
1330 else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
1331 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
1333 else if ( s.equalsIgnoreCase( "user_selected" ) ) {
1334 setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
1337 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1338 + "] for [ext_descendents_data_to_return]" );
1341 else if ( key.equals( "label_for_get_ext_descendents_data" ) ) {
1342 final String s = ( ( String ) st.nextElement() ).trim();
1343 if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) {
1344 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s
1345 + "] for [label_for_get_ext_descendents_data]" );
1348 setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
1351 else if ( key.equals( "ext_descendents_data_to_return_on" ) ) {
1352 final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
1353 if ( s.equals( "console" ) ) {
1354 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
1356 else if ( s.equals( "window" ) ) {
1357 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
1360 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1361 + "] for [ext_descendents_data_to_return_on]" );
1364 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1367 if ( key.equals( "use_real_br_lengths" ) || key.equals( "phylogram" ) ) {
1368 key_index = Configuration.display_as_phylogram;
1369 if ( key.equals( "use_real_br_lengths" ) ) {
1371 .printWarningMessage( Constants.PRG_NAME,
1372 "configuration key [use_real_br_lengths] is deprecated, use [phylogram] instead" );
1375 else if ( key.equals( "rollover" ) ) {
1376 key_index = Configuration.node_data_popup;
1378 else if ( key.equals( "color_according_to_species" ) ) {
1379 key_index = Configuration.color_according_to_species;
1381 else if ( key.equals( "show_node_names" ) ) {
1382 key_index = Configuration.show_node_names;
1384 else if ( key.equals( "show_taxonomy" ) || key.equals( "show_taxonomy_code" ) ) {
1385 key_index = Configuration.show_tax_code;
1386 if ( key.equals( "show_taxonomy" ) ) {
1388 .printWarningMessage( Constants.PRG_NAME,
1389 "configuration key [show_taxonomy] is deprecated, use [show_taxonomy_code] instead" );
1392 else if ( key.equals( "write_br_length_values" ) ) {
1393 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1394 "configuration key [write_br_length_values] is deprecated" );
1395 key_index = DEPRECATED;
1397 else if ( key.equals( "write_bootstrap_values" ) || key.equals( "write_confidence_values" ) ) {
1398 key_index = Configuration.write_confidence_values;
1399 if ( key.equals( "write_bootstrap_values" ) ) {
1401 .printWarningMessage( Constants.PRG_NAME,
1402 "configuration key [write_bootstrap_values] is deprecated, use [write_confidence_values] instead" );
1405 else if ( key.equals( "write_events" ) || key.equals( "write_dup_spec" ) ) {
1406 key_index = Configuration.write_events;
1407 if ( key.equals( "write_dup_spec" ) ) {
1409 .printWarningMessage( Constants.PRG_NAME,
1410 "configuration key [write_dup_spec] is deprecated, use [write_events] instead" );
1413 else if ( key.equals( "color_branches" ) ) {
1414 key_index = Configuration.color_branches;
1416 else if ( key.equals( "width_branches" ) ) {
1417 key_index = Configuration.width_branches;
1419 else if ( key.equals( "color_orthologous" ) ) {
1420 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1421 "configuration key [color_orthologous] is deprecated" );
1423 else if ( key.equals( "color_subtree_neighbors" ) ) {
1424 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1425 "configuration key [color_subtree_neighbors] is deprecated" );
1427 else if ( key.equals( "color_super_orthologous" ) ) {
1428 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1429 "configuration key [color_super_orthologous] is deprecated" );
1431 else if ( key.equals( "mark_nodes_with_box" ) ) {
1432 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1433 "configuration key [mark_nodes_with_box] is deprecated" );
1434 key_index = DEPRECATED;
1436 else if ( key.equals( "show_domain_architectures" ) ) {
1437 key_index = Configuration.show_domain_architectures;
1439 else if ( key.equals( "show_annotations" ) ) {
1440 key_index = Configuration.show_annotation;
1442 else if ( key.equals( "show_binary_characters" ) ) {
1443 key_index = Configuration.show_binary_characters;
1445 else if ( key.equals( "show_binary_character_counts" ) ) {
1446 key_index = Configuration.show_binary_character_counts;
1448 else if ( key.equals( "show_gene_names" ) ) {
1449 key_index = Configuration.show_gene_names;
1451 else if ( key.equals( "show_gene_symbols" ) ) {
1452 key_index = Configuration.show_gene_symbols;
1454 else if ( key.equals( "show_sequence_acc" ) ) {
1455 key_index = Configuration.show_sequence_acc;
1457 else if ( key.equals( "show_node_ids" ) ) {
1459 .printWarningMessage( Constants.PRG_NAME, "configuration key [show_node_ids] is deprecated" );
1460 key_index = DEPRECATED;
1462 else if ( key.equals( "display_internal_data" ) ) {
1463 key_index = Configuration.display_internal_data;
1465 else if ( key.equals( "dynamically_hide_data" ) ) {
1466 key_index = Configuration.dynamically_hide_data;
1468 else if ( key.equals( "show_taxonomy_names" ) ) {
1469 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1470 "configuration key [show_taxonomy_names] is deprecated" );
1471 key_index = DEPRECATED;
1473 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1474 key_index = Configuration.show_taxonomy_scientific_names;
1476 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1477 key_index = Configuration.show_taxonomy_common_names;
1479 else if ( key.equals( "show_taxonomy_images" ) ) {
1480 key_index = Configuration.show_taxonomy_images;
1482 else if ( key.equals( "color_according_to_annotation" ) ) {
1483 key_index = Configuration.color_according_to_annotation;
1485 else if ( key.equals( "show_vector_data" ) ) {
1486 key_index = Configuration.show_vector_data;
1488 else if ( key.equals( "show_properties" ) ) {
1489 key_index = Configuration.show_properties;
1491 else if ( key.equals( "show_relation_confidence" ) ) {
1492 key_index = Configuration.show_relation_confidence;
1494 else if ( key.equals( "show_custom_node_shapes" ) ) {
1495 key_index = Configuration.show_custom_node_shapes;
1497 // If we've found the key, set the values
1498 if ( key_index >= 0 ) {
1499 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1500 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1501 // otherwise, keep looking
1504 if ( key_index == DEPRECATED ) {
1507 else if ( key.equals( "click_to" ) ) {
1508 final String click_to_name = ( String ) st.nextElement();
1509 key_index = getClickToIndex( click_to_name );
1510 if ( key_index >= 0 ) {
1511 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1513 else if ( key_index == DEPRECATED ) {
1517 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1521 else if ( key.equals( "species_color" ) ) {
1522 getSpeciesColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1524 else if ( key.equals( "domain_color" ) ) {
1525 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1527 else if ( key.equals( "annotation_color" ) ) {
1528 getAnnotationColors()
1529 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1531 else if ( key.equals( "function_color" ) ) {
1532 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1533 "configuration key [function_color] is deprecated" );
1535 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1536 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1538 else if ( key.equals( WEB_LINK_KEY ) ) {
1539 if ( st.countTokens() == 3 ) {
1540 createWebLink( ( String ) st.nextElement(),
1541 ( String ) st.nextElement(),
1542 ( String ) st.nextElement() );
1545 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1546 "illegal format in configuration file for key [" + key + "]" );
1550 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1551 + "] in: " + config_filename );
1556 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1557 + config_filename );
1561 private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
1562 _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
1565 public String getLabelForGetExtDescendentsData() {
1566 return _label_for_get_ext_descendents_data;
1569 public void setMinConfidenceValue( final double min_confidence_value ) {
1570 _min_confidence_value = min_confidence_value;
1573 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
1574 _node_label_direction = node_label_direction;
1577 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
1578 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
1581 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
1582 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
1585 private void setOvMaxHeight( final short ov_max_height ) {
1586 _ov_max_height = ov_max_height;
1589 private void setOvMaxWidth( final short ov_max_width ) {
1590 _ov_max_width = ov_max_width;
1593 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1594 _ov_placement = ov_placement;
1597 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
1598 _phylogeny_graphics_type = phylogeny_graphics_type;
1601 public void setPrintLineWidth( final float print_line_width ) {
1602 _print_line_width = print_line_width;
1605 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
1606 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
1609 public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
1610 _show_branch_length_values = show_branch_length_values;
1613 public void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
1614 _show_default_node_shapes = show_default_node_shapes;
1617 public void setShowDomainLabels( final boolean show_domain_labels ) {
1618 _show_domain_labels = show_domain_labels;
1621 private void setShowOverview( final boolean show_overview ) {
1622 _show_overview = show_overview;
1625 public void setShowScale( final boolean show_scale ) {
1626 _show_scale = show_scale;
1629 public void setTaxonomyColorize( final boolean b ) {
1630 display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
1633 public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
1634 _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
1637 public void setUseBranchesWidths( final boolean b ) {
1638 display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
1641 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1642 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1645 void setWebLinks( final SortedMap<String, WebLink> weblinks ) {
1646 _weblinks = weblinks;
1649 static String getDefaultFontFamilyName() {
1650 return DEFAULT_FONT_FAMILY;
1653 static enum TRIPLET {
1654 TRUE, FALSE, UNKNOWN
1658 NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN
1661 public NODE_DATA getExtDescNodeDataToReturn() {
1662 return _ext_desc_data_to_return;
1665 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
1666 _ext_desc_data_to_return = ext_desc_data_to_return;
1669 public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
1670 return _ext_node_data_return_on;
1673 private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
1674 _ext_node_data_return_on = ext_node_data_return_on;