2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
7 // Copyright (C) 2000-2001 Washington University School of Medicine
8 // and Howard Hughes Medical Institute
9 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
10 // All rights reserved
12 // This library is free software; you can redistribute it and/or
13 // modify it under the terms of the GNU Lesser General Public
14 // License as published by the Free Software Foundation; either
15 // version 2.1 of the License, or (at your option) any later version.
17 // This library is distributed in the hope that it will be useful,
18 // but WITHOUT ANY WARRANTY; without even the implied warranty of
19 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20 // Lesser General Public License for more details.
22 // You should have received a copy of the GNU Lesser General Public
23 // License along with this library; if not, write to the Free Software
24 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
26 // Contact: phylosoft @ gmail . com
27 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
29 package org.forester.archaeopteryx;
31 import java.awt.Color;
32 import java.io.BufferedReader;
34 import java.io.FileReader;
35 import java.io.IOException;
36 import java.io.InputStreamReader;
38 import java.util.Arrays;
39 import java.util.Hashtable;
41 import java.util.SortedMap;
42 import java.util.StringTokenizer;
43 import java.util.TreeMap;
45 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
46 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
47 import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE;
48 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
49 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
50 import org.forester.phylogeny.data.NodeData.NODE_DATA;
51 import org.forester.phylogeny.data.NodeVisualData;
52 import org.forester.phylogeny.data.NodeVisualData.NodeFill;
53 import org.forester.phylogeny.data.NodeVisualData.NodeShape;
54 import org.forester.util.ForesterUtil;
56 public final class Configuration {
58 final static String clickto_options[][] = {
59 { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
60 { "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "display" },
61 { "Colorize Node(s)", "display" }, { "Change Node Font(s)", "display" },
62 { "Colorize Subtree(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "display" },
63 { "Open Taxonomy DB", "display" }, { "Launch BLAST", "display" }, { "Cut Subtree", "display" },
64 { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" },
65 { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Sort Descendants", "display" },
66 { "Return", "display" }, { "Select Node(s)", "display" } };
67 final static int display_node_data = 0;
68 final static int collapse_uncollapse = 1;
69 final static int reroot = 2;
70 final static int subtree = 3;
71 final static int swap = 4;
72 final static int color_node_font = 5;
73 final static int change_node_font = 6;
74 final static int color_subtree = 7;
75 final static int open_seq_web = 8;
76 final static int open_pdb_web = 9;
77 final static int open_tax_web = 10;
78 final static int blast = 11;
79 final static int cut_subtree = 12;
80 final static int copy_subtree = 13;
81 final static int paste_subtree = 14;
82 final static int delete_subtree_or_node = 15;
83 final static int add_new_node = 16;
84 final static int edit_node_data = 17;
85 final static int sort_descendents = 18;
86 final static int get_ext_desc_data = 19;
87 final static int select_nodes = 20;
91 final static String display_options[][] = {
92 { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
93 { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" },
94 { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
95 { "Colorize by Sequence", "display", "no" },
96 { "Visual Styles/Branch Colors", "display", "no" }, { "Branch Widths", "display", "no" },
97 { "Protein Domains", "display", "no" }, { "Binary Characters", "nodisplay", "no" },
98 { "Binary Char Counts", "nodisplay", "no" }, { "Seq Name", "display", "yes" },
99 { "Seq Accession", "display", "no" }, { "Show Internal Data", "display", "yes" },
100 { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" },
101 { "Taxonomy Common", "display", "no" }, { "Colorize by Annotation", "display", "no" },
102 { "Seq Symbol", "display", "yes" }, { "Rollover", "display", "yes" },
103 { "Relation Confidence", "nodisplay", "no" }, { "Vector Data", "nodisplay", "no" },
104 { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" },
105 { "Gene Name", "display", "yes" } };
106 final static int display_as_phylogram = 0;
107 final static int show_node_names = 1;
108 final static int show_tax_code = 2;
109 final static int show_annotation = 3;
110 final static int write_confidence_values = 4;
111 final static int write_events = 5;
112 final static int color_according_to_species = 6;
113 final static int color_according_to_sequence = 7;
114 final static int use_style = 8;
115 final static int width_branches = 9;
116 final static int show_domain_architectures = 10;
117 final static int show_binary_characters = 11;
118 final static int show_binary_character_counts = 12;
119 final static int show_seq_names = 13;
120 final static int show_sequence_acc = 14;
121 final static int display_internal_data = 15;
122 final static int dynamically_hide_data = 16;
123 final static int show_taxonomy_scientific_names = 17;
124 final static int show_taxonomy_common_names = 18;
125 final static int color_according_to_annotation = 19;
126 final static int show_seq_symbols = 20;
127 final static int node_data_popup = 21;
128 final static int show_relation_confidence = 22;
129 final static int show_vector_data = 23;
130 final static int show_taxonomy_images = 24;
131 final static int show_properties = 25;
132 final static int show_gene_names = 26;
133 static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
134 private static Hashtable<String, Color> _sequence_colors;
137 private static Hashtable<String, Color> _annotation_colors;
138 private static Hashtable<String, Color> _domain_colors;
139 private static Hashtable<String, Color> _species_colors;
140 private static String DEFAULT_FONT_FAMILY = "";
141 private static final int DEPRECATED = -2;
142 private static final String DISPLAY_COLOR_KEY = "display_color";
143 // ---------------------------
144 // Display options for trees
145 // ---------------------------
146 // ---------------------------------
147 // Pertaining to the config itself
148 // ---------------------------------
149 // Full path to config (may be URL)
150 String config_filename;
151 // This option is selected in the dropdown
152 int default_clickto = Configuration.display_node_data;
153 String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
157 TreeColorSet tree_color_set;
161 TreeFontSet tree_font_set;
162 boolean verbose = Constants.VERBOSE_DEFAULT;
163 private boolean _abbreviate_scientific_names = false;
164 private boolean _antialias_screen = true;
165 private boolean _background_color_gradient = false;
166 private String _base_font_family_name = "";
167 private int _base_font_size = -1;
168 private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
169 private boolean _color_labels_same_as_parent_branch = false;
170 private int _default_bootstrap_samples = -1;
171 private NodeFill _default_node_fill = NodeFill.SOLID;
172 private NodeShape _default_node_shape = NodeShape.RECTANGLE;
173 private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
174 private SortedMap<String, Color> _display_colors = null;
175 private boolean _display_sequence_relations = false;
176 private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
177 private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
178 private boolean _editable = true;
179 private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
180 private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
181 private int _frame_x_size;
182 private int _frame_y_size;
183 private int _graphics_export_x = -1;
184 private int _graphics_export_y = -1;
185 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
186 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
187 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
188 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
189 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
190 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
191 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
192 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
193 private boolean _hide_controls_and_menus = false;
194 private boolean _internal_number_are_confidence_for_nh_parsing = false;
195 private String _label_for_get_ext_descendents_data = "";
196 private int _max_base_font_size = 20;
197 private boolean _midpoint_root = false;
198 private int _min_base_font_size = 2;
199 private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
200 private boolean _nh_parsing_replace_underscores = false;
201 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
202 private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
203 private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
204 private short _ov_max_height = 80;
205 private short _ov_max_width = 80;
206 private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
207 private File _path_to_local_fastme = null;
208 private File _path_to_local_mafft = null;
209 private File _path_to_local_raxml = null;
210 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
211 private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
212 private boolean _show_annotation_ref_source = true;
213 private boolean _show_branch_length_values = false;
214 private boolean _show_default_node_shapes_external = false;
215 private boolean _show_default_node_shapes_internal = false;
216 private boolean _show_domain_labels = true;
217 private boolean _show_overview = true;
218 private boolean _show_scale = false;
219 private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
220 private UI _ui = UI.UNKNOWN;
221 private boolean _use_tabbed_display = false;
222 private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
224 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
225 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
226 DEFAULT_FONT_FAMILY = font_name;
230 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
231 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
235 public Configuration() {
236 this( null, false, false, false );
239 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
240 if ( ForesterUtil.isEmpty( cf ) ) {
241 config_filename = default_config_filename;
244 config_filename = cf;
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 public String getBaseFontFamilyName() {
300 return _base_font_family_name;
303 public int getDefaultBootstrapSamples() {
304 return _default_bootstrap_samples;
307 public NodeFill getDefaultNodeFill() {
308 return _default_node_fill;
311 public NodeShape getDefaultNodeShape() {
312 return _default_node_shape;
315 public short getDefaultNodeShapeSize() {
316 return _default_node_shape_size;
319 public Color getDomainStructureBaseColor() {
320 return _domain_structure_base_color;
323 public Color getDomainStructureFontColor() {
324 return _domain_structure_font_color;
327 public NODE_DATA getExtDescNodeDataToReturn() {
328 return _ext_desc_data_to_return;
331 public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
332 return _ext_node_data_return_on;
335 public int getFrameXSize() {
336 return _frame_x_size;
339 public int getFrameYSize() {
340 return _frame_y_size;
343 public String getLabelForGetExtDescendentsData() {
344 return _label_for_get_ext_descendents_data;
347 public File getPathToLocalFastme() {
348 return _path_to_local_fastme;
351 public File getpathToLocalMafft() {
352 return _path_to_local_mafft;
355 public File getPathToLocalRaxml() {
356 return _path_to_local_raxml;
359 public boolean isAbbreviateScientificTaxonNames() {
360 return _abbreviate_scientific_names;
363 public boolean isBackgroundColorGradient() {
364 return _background_color_gradient;
367 public boolean isColorByTaxonomicGroup() {
371 public boolean isColorLabelsSameAsParentBranch() {
372 return _color_labels_same_as_parent_branch;
375 public boolean isMidpointReroot() {
376 return _midpoint_root;
379 public boolean isShowAnnotationRefSource() {
380 return _show_annotation_ref_source;
383 public boolean isShowDefaultNodeShapesExternal() {
384 return _show_default_node_shapes_external;
387 public boolean isShowDefaultNodeShapesInternal() {
388 return _show_default_node_shapes_internal;
391 public boolean isShowDomainLabels() {
392 return _show_domain_labels;
395 public void putDisplayColors( final String key, final Color color ) {
396 getDisplayColors().put( key, color );
399 public void setAddTaxonomyImagesCB( final boolean b ) {
400 display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no";
403 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
404 _abbreviate_scientific_names = abbreviate_scientific_names;
407 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
408 _background_color_gradient = background_color_gradient;
411 public void setBaseFontFamilyName( final String base_font_family_name ) {
412 _base_font_family_name = base_font_family_name;
415 public void setBaseFontSize( final int base_font_size ) {
416 _base_font_size = base_font_size;
419 public void setColorizeBranches( final boolean b ) {
420 display_options[ use_style ][ 2 ] = b ? "yes" : "no";
423 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
424 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
427 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
428 _default_node_fill = default_node_fill;
431 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
432 _default_node_shape = default_node_shape;
435 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
436 _default_node_shape_size = default_node_shape_size;
439 public void setDisplayAsPhylogram( final boolean b ) {
440 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
443 public void setUseStyle( final boolean b ) {
444 display_options[ use_style ][ 2 ] = b ? "yes" : "no";
447 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
448 _display_colors = display_colors;
451 public void setDisplayConfidenceValues( final boolean b ) {
452 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
455 public void setDisplayInternalData( final boolean b ) {
456 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
459 public void setDisplayNodeNames( final boolean b ) {
460 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
463 public void setDisplaySequenceAcc( final boolean b ) {
464 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
467 public void setDisplaySequenceNames( final boolean b ) {
468 display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no";
471 public void setDisplayGeneNames( final boolean b ) {
472 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
475 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
476 _display_sequence_relations = display_sequence_relations;
479 public void setDisplaySequenceSymbols( final boolean b ) {
480 display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no";
483 public void setDisplayTaxonomyCode( final boolean b ) {
484 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
487 public void setDisplayTaxonomyCommonNames( final boolean b ) {
488 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
491 public void setDisplayTaxonomyImages( final boolean b ) {
492 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
495 public void setDisplayTaxonomyScientificNames( final boolean b ) {
496 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
499 public void setDynamicallyHideData( final boolean b ) {
500 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
503 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
504 _ext_desc_data_to_return = ext_desc_data_to_return;
507 public void setFrameXSize( final int frame_x_size ) {
508 _frame_x_size = frame_x_size;
511 public void setFrameYSize( final int frame_y_size ) {
512 _frame_y_size = frame_y_size;
515 public void setMidpointReroot( final boolean midpoint_root ) {
516 _midpoint_root = midpoint_root;
519 public void setMinConfidenceValue( final double min_confidence_value ) {
520 _min_confidence_value = min_confidence_value;
523 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
524 _node_label_direction = node_label_direction;
527 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
528 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
531 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
532 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
535 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
536 _phylogeny_graphics_type = phylogeny_graphics_type;
539 public void setPrintLineWidth( final float print_line_width ) {
540 _print_line_width = print_line_width;
543 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
544 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
547 public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
548 _show_branch_length_values = show_branch_length_values;
551 public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
552 _show_default_node_shapes_external = show_default_node_shapes_external;
555 public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
556 _show_default_node_shapes_internal = show_default_node_shapes_internal;
559 public void setShowDomainLabels( final boolean show_domain_labels ) {
560 _show_domain_labels = show_domain_labels;
563 public void setShowScale( final boolean show_scale ) {
564 _show_scale = show_scale;
567 boolean displaySequenceRelations() {
568 return _display_sequence_relations;
571 boolean doCheckOption( final int which ) {
572 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
573 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
576 boolean doDisplayClickToOption( final int which ) {
577 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
580 boolean doDisplayOption( final int which ) {
581 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
585 * Will attempt to use the phylogeny to determine whether to check
586 * this or not (e.g. phylogram)
589 boolean doGuessCheckOption( final int which ) {
590 return display_options[ which ][ 2 ].equals( "?" );
593 Map<String, Color> getAnnotationColors() {
594 if ( _annotation_colors == null ) {
595 _annotation_colors = new Hashtable<String, Color>();
597 return _annotation_colors;
600 int getBaseFontSize() {
601 return _base_font_size;
604 CLADOGRAM_TYPE getCladogramType() {
605 return _cladogram_type;
608 int getClickToOptionsCount() {
609 return clickto_options.length;
612 String getClickToTitle( final int which ) {
613 return clickto_options[ which ][ 0 ];
616 int getDefaultDisplayClicktoOption() {
617 return default_clickto;
620 SortedMap<String, Color> getDisplayColors() {
621 return _display_colors;
624 String getDisplayTitle( final int which ) {
625 return display_options[ which ][ 0 ];
628 Map<String, Color> getDomainColors() {
629 if ( _domain_colors == null ) {
630 _domain_colors = new Hashtable<String, Color>();
632 return _domain_colors;
635 int getGraphicsExportX() {
636 return _graphics_export_x;
639 int getGraphicsExportY() {
640 return _graphics_export_y;
643 Color getGuiBackgroundColor() {
644 return _gui_background_color;
647 Color getGuiButtonBackgroundColor() {
648 return _gui_button_background_color;
651 Color getGuiButtonBorderColor() {
652 return _gui_button_border_color;
655 Color getGuiButtonTextColor() {
656 return _gui_button_text_color;
659 Color getGuiCheckboxAndButtonActiveColor() {
660 return _gui_checkbox_and_button_active_color;
663 Color getGuiCheckboxTextColor() {
664 return _gui_checkbox_text_color;
667 Color getGuiMenuBackgroundColor() {
668 return _gui_menu_background_color;
671 Color getGuiMenuTextColor() {
672 return _gui_menu_text_color;
675 int getMaxBaseFontSize() {
676 return _max_base_font_size;
679 int getMinBaseFontSize() {
680 return _min_base_font_size;
683 double getMinConfidenceValue() {
684 return _min_confidence_value;
687 NODE_LABEL_DIRECTION getNodeLabelDirection() {
688 return _node_label_direction;
691 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
692 return _number_of_digits_after_comma_for_branch_length_values;
695 short getNumberOfDigitsAfterCommaForConfidenceValues() {
696 return _number_of_digits_after_comma_for_confidence_values;
699 short getOvMaxHeight() {
700 return _ov_max_height;
703 short getOvMaxWidth() {
704 return _ov_max_width;
707 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
708 return _ov_placement;
711 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
712 return _phylogeny_graphics_type;
715 float getPrintLineWidth() {
716 return _print_line_width;
719 Hashtable<String, Color> getSpeciesColors() {
720 if ( _species_colors == null ) {
721 _species_colors = new Hashtable<String, Color>();
723 return _species_colors;
726 Hashtable<String, Color> getSequenceColors() {
727 if ( _sequence_colors == null ) {
728 _sequence_colors = new Hashtable<String, Color>();
730 return _sequence_colors;
733 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
734 return _taxonomy_extraction;
737 boolean isAntialiasScreen() {
738 if ( ForesterUtil.isMac() ) {
739 //Apple Macintosh graphics are slow, turn off anti-alias.
742 return _antialias_screen;
746 * Convenience method.
748 * @return true if value in configuration file was 'yes'
750 boolean isDrawAsPhylogram() {
751 return doCheckOption( display_as_phylogram );
754 boolean isEditable() {
759 * Only used by ArchaeoptryxE.
762 boolean isHideControlPanelAndMenubar() {
763 return _hide_controls_and_menus;
766 boolean isInternalNumberAreConfidenceForNhParsing() {
767 return _internal_number_are_confidence_for_nh_parsing;
770 boolean isReplaceUnderscoresInNhParsing() {
771 return _nh_parsing_replace_underscores;
774 boolean isShowBranchLengthValues() {
775 return _show_branch_length_values;
778 boolean isShowOverview() {
779 return _show_overview;
782 boolean isShowScale() {
786 final boolean isUseNativeUI() {
787 if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
790 return _ui == UI.NATIVE;
794 * Only used by ArchaeoptryxE.
797 boolean isUseTabbedDisplay() {
798 return _use_tabbed_display;
801 boolean isValidatePhyloXmlAgainstSchema() {
802 return _validate_against_phyloxml_xsd_schema;
805 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
806 _taxonomy_extraction = taxonomy_extraction;
809 private int getClickToIndex( final String name ) {
811 if ( name.equals( "edit_info" ) ) {
812 index = Configuration.display_node_data;
814 .printWarningMessage( Constants.PRG_NAME,
815 "configuration key [edit_info] is deprecated, use [display node data] instead" );
817 else if ( name.equals( "display_node_data" ) ) {
818 index = Configuration.display_node_data;
820 else if ( name.equals( "collapse_uncollapse" ) ) {
821 index = Configuration.collapse_uncollapse;
823 else if ( name.equals( "reroot" ) ) {
824 index = Configuration.reroot;
826 else if ( name.equals( "subtree" ) ) {
827 index = Configuration.subtree;
829 else if ( name.equals( "swap" ) ) {
830 index = Configuration.swap;
832 else if ( name.equals( "sort_descendants" ) ) {
833 index = Configuration.sort_descendents;
835 else if ( name.equals( "get_ext_descendents_data" ) ) {
836 index = Configuration.get_ext_desc_data;
838 else if ( name.equals( "display_sequences" ) ) {
840 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
843 else if ( name.equals( "open_seq_web" ) ) {
844 index = Configuration.open_seq_web;
846 else if ( name.equals( "open_pdb_web" ) ) {
847 index = Configuration.open_pdb_web;
849 else if ( name.equals( "open_tax_web" ) ) {
850 index = Configuration.open_tax_web;
852 else if ( name.equals( "blast" ) ) {
853 index = Configuration.blast;
855 else if ( name.equals( "cut_subtree" ) ) {
856 index = Configuration.cut_subtree;
858 else if ( name.equals( "copy_subtree" ) ) {
859 index = Configuration.copy_subtree;
861 else if ( name.equals( "paste_subtree" ) ) {
862 index = Configuration.paste_subtree;
864 else if ( name.equals( "delete" ) ) {
865 index = Configuration.delete_subtree_or_node;
867 else if ( name.equals( "add_new_node" ) ) {
868 index = Configuration.add_new_node;
870 else if ( name.equals( "edit_node_data" ) ) {
871 index = Configuration.edit_node_data;
873 else if ( name.equals( "select_nodes" ) ) {
874 index = Configuration.select_nodes;
876 else if ( name.equals( "display_node_popup" ) ) {
877 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
878 "configuration key [display_node_popup] is deprecated" );
881 else if ( name.equals( "custom_option" ) ) {
882 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
885 else if ( name.equals( "color_subtree" ) ) {
886 index = Configuration.color_subtree;
888 else if ( name.equals( "change_node_font" ) ) {
889 index = Configuration.change_node_font;
891 else if ( name.equals( "color_node_font" ) ) {
892 index = Configuration.color_node_font;
894 else if ( name.equals( "color_subtree" ) ) {
895 index = Configuration.color_subtree;
900 private boolean parseBoolean( final String str ) {
901 final String my_str = str.trim().toLowerCase();
902 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
905 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
909 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
914 private double parseDouble( final String str ) {
917 d = Double.parseDouble( str.trim() );
919 catch ( final Exception e ) {
920 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
926 private float parseFloat( final String str ) {
929 f = Float.parseFloat( str.trim() );
931 catch ( final Exception e ) {
932 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
938 private int parseInt( final String str ) {
941 i = Integer.parseInt( str.trim() );
943 catch ( final Exception e ) {
944 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
950 private short parseShort( final String str ) {
953 i = Short.parseShort( str.trim() );
955 catch ( final Exception e ) {
956 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
962 private void processFontFamily( final StringTokenizer st ) {
963 setBaseFontFamilyName( "" );
964 final String font_str = ( ( String ) st.nextElement() ).trim();
965 final String[] fonts = font_str.split( ",+" );
966 for( String font : fonts ) {
967 font = font.replace( '_', ' ' ).trim();
968 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
969 setBaseFontFamilyName( font );
976 * read each line of config file, process non-comment lines
977 * @throws IOException
979 private void readConfig( final BufferedReader conf_in ) throws IOException {
982 line = conf_in.readLine();
983 if ( line != null ) {
985 // skip comments and blank lines
986 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
987 // convert runs of spaces to tabs
988 line = line.replaceAll( "\\s+", "\t" );
989 final StringTokenizer st = new StringTokenizer( line, "\t" );
993 } while ( line != null );
996 private void setAntialiasScreen( final boolean antialias_screen ) {
997 _antialias_screen = antialias_screen;
1000 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
1001 _cladogram_type = cladogram_type;
1004 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
1005 _default_bootstrap_samples = default_bootstrap_samples;
1008 private void setEditable( final boolean editable ) {
1009 _editable = editable;
1012 private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
1013 _ext_node_data_return_on = ext_node_data_return_on;
1016 private void setGraphicsExportX( final int graphics_export_x ) {
1017 _graphics_export_x = graphics_export_x;
1020 private void setGraphicsExportY( final int graphics_export_y ) {
1021 _graphics_export_y = graphics_export_y;
1024 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
1025 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
1029 * Set a key-value(s) tuple
1031 private void setKeyValue( final StringTokenizer st ) {
1032 final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
1033 if ( !st.hasMoreElements() ) {
1036 // Handle single value settings first:
1037 if ( key.equals( "default_click_to" ) ) {
1038 final String clickto_name = ( String ) st.nextElement();
1039 default_clickto = getClickToIndex( clickto_name );
1040 if ( default_clickto == -1 ) {
1041 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
1042 + "] for [default_click_to]" );
1043 default_clickto = 0;
1045 else if ( default_clickto == DEPRECATED ) {
1049 else if ( key.equals( "native_ui" ) ) {
1050 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
1051 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
1054 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
1055 _ui = UI.CROSSPLATFORM;
1057 else if ( my_str.equals( "?" ) ) {
1061 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
1066 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
1067 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
1069 else if ( key.equals( "antialias_screen" ) ) {
1070 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
1072 else if ( key.equals( "phylogeny_graphics_type" ) ) {
1073 final String type_str = ( ( String ) st.nextElement() ).trim();
1074 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
1075 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1077 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
1078 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1080 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
1081 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1083 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
1084 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1086 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
1087 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1089 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
1090 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1092 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
1093 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1095 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
1096 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1099 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1100 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1101 + "] for [phylogeny_graphics_type]" );
1104 else if ( key.equals( "min_confidence_value" ) ) {
1105 final String mcv_str = ( ( String ) st.nextElement() ).trim();
1106 final double d = parseDouble( mcv_str );
1107 setMinConfidenceValue( d );
1109 else if ( key.equals( "font_family" ) ) {
1110 processFontFamily( st );
1112 else if ( key.equals( "font_size" ) ) {
1113 final String size_str = ( ( String ) st.nextElement() ).trim();
1114 final int i = parseInt( size_str );
1116 setBaseFontSize( i );
1119 else if ( key.equals( "font_size_min" ) ) {
1120 final String size_str = ( ( String ) st.nextElement() ).trim();
1121 final int i = parseInt( size_str );
1123 setMinBaseFontSize( i );
1126 else if ( key.equals( "font_size_max" ) ) {
1127 final String size_str = ( ( String ) st.nextElement() ).trim();
1128 final int i = parseInt( size_str );
1130 setMaxBaseFontSize( i );
1133 else if ( key.equals( "graphics_export_x" ) ) {
1134 final String str = ( ( String ) st.nextElement() ).trim();
1135 final int i = parseInt( str );
1137 setGraphicsExportX( i );
1140 else if ( key.equals( "graphics_export_y" ) ) {
1141 final String str = ( ( String ) st.nextElement() ).trim();
1142 final int i = parseInt( str );
1144 setGraphicsExportY( i );
1147 else if ( key.equals( "pdf_export_line_width" ) ) {
1148 final String str = ( ( String ) st.nextElement() ).trim();
1149 final float f = parseFloat( str );
1151 setPrintLineWidth( f );
1154 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1155 "value for [pdf_export_line_width] cannot be zero or negative" );
1158 else if ( key.equals( "window_initial_size_x" ) ) {
1159 final String str = ( ( String ) st.nextElement() ).trim();
1160 final int i = parseInt( str );
1165 else if ( key.equals( "window_initial_size_y" ) ) {
1166 final String str = ( ( String ) st.nextElement() ).trim();
1167 final int i = parseInt( str );
1172 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1173 final String str = ( ( String ) st.nextElement() ).trim();
1174 final int i = parseInt( str );
1176 setDefaultBootstrapSamples( i );
1180 .printWarningMessage( Constants.PRG_NAME,
1181 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1184 else if ( key.equals( "mafft_local" ) ) {
1185 final String str = ( ( String ) st.nextElement() ).trim();
1186 if ( !ForesterUtil.isEmpty( str ) ) {
1187 setPathToLocalMafft( new File( str ) );
1190 else if ( key.equals( "fastme_local" ) ) {
1191 final String str = ( ( String ) st.nextElement() ).trim();
1192 if ( !ForesterUtil.isEmpty( str ) ) {
1193 setPathToLocalFastme( new File( str ) );
1196 else if ( key.equals( "raxml_local" ) ) {
1197 final String str = ( ( String ) st.nextElement() ).trim();
1198 if ( !ForesterUtil.isEmpty( str ) ) {
1199 setPathToLocalRaxml( new File( str ) );
1202 else if ( key.equals( "show_scale" ) ) {
1203 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1205 else if ( key.equals( "show_overview" ) ) {
1206 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1208 else if ( key.equals( "show_branch_length_values" ) ) {
1209 setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
1211 else if ( key.equals( "background_gradient" ) ) {
1212 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1214 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1215 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1217 else if ( key.equals( "show_domain_labels" ) ) {
1218 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1220 else if ( key.equals( "show_seq_annotation_ref_sources" ) ) {
1221 setShowAnnotationRefSource( parseBoolean( ( String ) st.nextElement() ) );
1223 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1224 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1226 else if ( key.equals( "cladogram_type" ) ) {
1227 final String type_str = ( ( String ) st.nextElement() ).trim();
1228 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1229 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1231 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1232 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1234 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1235 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1238 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1239 + "] for [cladogram_type]" );
1242 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1244 .printWarningMessage( Constants.PRG_NAME,
1245 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1247 else if ( key.equals( "hide_controls_and_menus" ) ) {
1248 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1250 else if ( key.equals( "use_tabbed_display" ) ) {
1251 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1253 else if ( key.equals( "overview_width" ) ) {
1254 final short i = parseShort( ( ( String ) st.nextElement() ) );
1257 else if ( key.equals( "overview_height" ) ) {
1258 final short i = parseShort( ( ( String ) st.nextElement() ) );
1259 setOvMaxHeight( i );
1261 else if ( key.equals( "overview_placement_type" ) ) {
1262 final String type_str = ( ( String ) st.nextElement() ).trim();
1263 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1264 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1266 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1267 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1269 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1270 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1272 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1273 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1276 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1277 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1278 + "] for [overview_placement_type]" );
1281 else if ( key.equals( "node_label_direction" ) ) {
1282 final String type_str = ( ( String ) st.nextElement() ).trim();
1283 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1284 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1286 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1287 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1290 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1291 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1292 + "] for [node_label_direction]" );
1295 else if ( key.equals( "branch_length_value_digits" ) ) {
1296 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1298 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1301 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1302 + "] for [branch_length_value_digits]" );
1305 else if ( key.equals( "confidence_value_digits" ) ) {
1306 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1308 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1311 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1312 + "] for [confidence_value_digits]" );
1315 else if ( key.equals( "allow_editing" ) ) {
1316 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1318 else if ( key.equals( "display_sequence_relations" ) ) {
1319 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1321 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1322 final boolean r = parseBoolean( ( String ) st.nextElement() );
1323 if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
1325 .printWarningMessage( Constants.PRG_NAME,
1326 "attempt to extract taxonomies and replace underscores at the same time" );
1329 setReplaceUnderscoresInNhParsing( r );
1332 else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
1333 final String s = ( String ) st.nextElement();
1334 if ( s.equalsIgnoreCase( "no" ) ) {
1335 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1337 else if ( s.equalsIgnoreCase( "pfam_relaxed" ) ) {
1338 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1340 else if ( s.equalsIgnoreCase( "pfam_strict" ) ) {
1341 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1343 else if ( s.equalsIgnoreCase( "aggressive" ) ) {
1344 setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
1348 .printWarningMessage( Constants.PRG_NAME,
1349 "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
1351 + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
1353 if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
1355 .printWarningMessage( Constants.PRG_NAME,
1356 "attempt to extract taxonomies and replace underscores at the same time" );
1359 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1360 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1362 else if ( key.equals( "gui_background_color" ) ) {
1363 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1365 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1366 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1368 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1369 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1371 else if ( key.equals( "gui_button_text_color" ) ) {
1372 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1374 else if ( key.equals( "gui_button_background_color" ) ) {
1375 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1377 else if ( key.equals( "gui_menu_background_color" ) ) {
1378 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1380 else if ( key.equals( "gui_menu_text_color" ) ) {
1381 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1383 else if ( key.equals( "gui_button_border_color" ) ) {
1384 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1386 else if ( key.equals( "domain_structure_font_color" ) ) {
1387 _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
1389 else if ( key.equals( "domain_structure_base_color" ) ) {
1390 _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
1392 else if ( key.equals( "show_default_node_shapes" ) ) {
1394 .printWarningMessage( Constants.PRG_NAME,
1395 "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" );
1396 final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() );
1397 setShowDefaultNodeShapesInternal( b );
1398 setShowDefaultNodeShapesExternal( b );
1400 else if ( key.equals( "show_default_node_shapes_internal" ) ) {
1401 setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1403 else if ( key.equals( "show_default_node_shapes_external" ) ) {
1404 setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1406 else if ( key.equals( "default_node_size" ) ) {
1407 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1408 setDefaultNodeShapeSize( i );
1410 else if ( key.equals( "default_node_fill" ) ) {
1411 final String fill_str = ( ( String ) st.nextElement() ).trim();
1412 if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.NONE.toString() ) ) {
1413 setDefaultNodeFill( NodeFill.NONE );
1415 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.GRADIENT.toString() ) ) {
1416 setDefaultNodeFill( NodeFill.GRADIENT );
1418 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.SOLID.toString() ) ) {
1419 setDefaultNodeFill( NodeFill.SOLID );
1422 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1423 + "] for [default_node_fill]" );
1426 else if ( key.equals( "default_node_shape" ) ) {
1427 final String shape_str = ( ( String ) st.nextElement() ).trim();
1428 if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.CIRCLE.toString() ) ) {
1429 setDefaultNodeShape( NodeShape.CIRCLE );
1431 else if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.RECTANGLE.toString() ) ) {
1432 setDefaultNodeShape( NodeShape.RECTANGLE );
1435 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1436 + "] for [default_node_shape]" );
1439 else if ( key.equals( "midpoint_reroot" ) ) {
1440 setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) );
1442 else if ( key.equals( "ext_descendents_data_to_return" ) ) {
1443 final String s = ( ( String ) st.nextElement() ).trim();
1444 if ( s.equalsIgnoreCase( "node_name" ) ) {
1445 setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
1447 else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
1448 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
1450 else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) {
1451 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ_FASTA );
1453 else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
1454 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
1456 else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
1457 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
1459 else if ( s.equalsIgnoreCase( "gene_name" ) ) {
1460 setExtDescNodeDataToReturn( NODE_DATA.GENE_NAME );
1462 else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
1463 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
1465 else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
1466 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME );
1468 else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
1469 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
1471 else if ( s.equalsIgnoreCase( "taxonomy_common_name" ) ) {
1472 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_COMM0N_NAME );
1474 else if ( s.equalsIgnoreCase( "user_selected" ) ) {
1475 setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
1478 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1479 + "] for [ext_descendents_data_to_return]" );
1482 else if ( key.equals( "label_for_get_ext_descendents_data" ) ) {
1483 final String s = ( ( String ) st.nextElement() ).trim();
1484 if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) {
1485 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s
1486 + "] for [label_for_get_ext_descendents_data]" );
1489 setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
1492 else if ( key.equals( "ext_descendents_data_to_return_on" ) ) {
1493 final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
1494 if ( s.equals( "console" ) ) {
1495 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
1497 else if ( s.equals( "window" ) ) {
1498 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
1500 else if ( s.equals( "buffer_only" ) ) {
1501 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
1504 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1505 + "] for [ext_descendents_data_to_return_on]" );
1508 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1511 if ( key.equals( "phylogram" ) ) {
1512 key_index = Configuration.display_as_phylogram;
1514 else if ( key.equals( "rollover" ) ) {
1515 key_index = Configuration.node_data_popup;
1517 else if ( key.equals( "color_according_to_species" ) ) {
1518 key_index = Configuration.color_according_to_species;
1520 else if ( key.equals( "color_according_to_sequence" ) ) {
1521 key_index = Configuration.color_according_to_sequence;
1523 else if ( key.equals( "show_node_names" ) ) {
1524 key_index = Configuration.show_node_names;
1526 else if ( key.equals( "show_taxonomy_code" ) ) {
1527 key_index = Configuration.show_tax_code;
1529 else if ( key.equals( "write_confidence_values" ) ) {
1530 key_index = Configuration.write_confidence_values;
1532 else if ( key.equals( "write_events" ) ) {
1533 key_index = Configuration.write_events;
1535 else if ( key.equals( "use_visual_styles" ) ) {
1536 key_index = Configuration.use_style;
1538 else if ( key.equals( "color_branches" ) ) {
1539 key_index = Configuration.use_style;
1541 .printWarningMessage( Constants.PRG_NAME,
1542 "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" );
1544 else if ( key.equals( "width_branches" ) ) {
1545 key_index = Configuration.width_branches;
1547 else if ( key.equals( "show_domain_architectures" ) ) {
1548 key_index = Configuration.show_domain_architectures;
1550 else if ( key.equals( "show_annotations" ) ) {
1551 key_index = Configuration.show_annotation;
1553 else if ( key.equals( "show_binary_characters" ) ) {
1554 key_index = Configuration.show_binary_characters;
1556 else if ( key.equals( "show_binary_character_counts" ) ) {
1557 key_index = Configuration.show_binary_character_counts;
1559 else if ( key.equals( "show_seq_names" ) ) {
1560 key_index = Configuration.show_seq_names;
1562 else if ( key.equals( "show_gene_names" ) ) {
1563 key_index = Configuration.show_gene_names;
1565 else if ( key.equals( "show_seq_symbols" ) ) {
1566 key_index = Configuration.show_seq_symbols;
1568 else if ( key.equals( "show_seq_acc" ) ) {
1569 key_index = Configuration.show_sequence_acc;
1571 else if ( key.equals( "display_internal_data" ) ) {
1572 key_index = Configuration.display_internal_data;
1574 else if ( key.equals( "dynamically_hide_data" ) ) {
1575 key_index = Configuration.dynamically_hide_data;
1577 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1578 key_index = Configuration.show_taxonomy_scientific_names;
1580 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1581 key_index = Configuration.show_taxonomy_common_names;
1583 else if ( key.equals( "show_taxonomy_images" ) ) {
1584 key_index = Configuration.show_taxonomy_images;
1586 else if ( key.equals( "color_according_to_annotation" ) ) {
1587 key_index = Configuration.color_according_to_annotation;
1589 else if ( key.equals( "show_vector_data" ) ) {
1590 key_index = Configuration.show_vector_data;
1592 else if ( key.equals( "show_properties" ) ) {
1593 key_index = Configuration.show_properties;
1595 else if ( key.equals( "show_relation_confidence" ) ) {
1596 key_index = Configuration.show_relation_confidence;
1598 // If we've found the key, set the values
1599 if ( key_index >= 0 ) {
1600 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1601 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1602 // otherwise, keep looking
1605 if ( key_index == DEPRECATED ) {
1608 else if ( key.equals( "click_to" ) ) {
1609 final String click_to_name = ( String ) st.nextElement();
1610 key_index = getClickToIndex( click_to_name );
1611 if ( key_index >= 0 ) {
1612 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1614 else if ( key_index == DEPRECATED ) {
1618 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1622 else if ( key.equals( "species_color" ) ) {
1623 getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
1624 Color.decode( ( String ) st.nextElement() ) );
1626 else if ( key.equals( "sequence_color" ) ) {
1627 getSequenceColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
1628 Color.decode( ( String ) st.nextElement() ) );
1630 else if ( key.equals( "domain_color" ) ) {
1631 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1633 else if ( key.equals( "annotation_color" ) ) {
1634 getAnnotationColors()
1635 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1637 else if ( key.equals( "function_color" ) ) {
1638 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1639 "configuration key [function_color] is deprecated" );
1641 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1642 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1645 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1646 + "] in: " + config_filename );
1651 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1652 + config_filename );
1656 private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
1657 _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
1660 private void setMaxBaseFontSize( final int max_base_font_size ) {
1661 _max_base_font_size = max_base_font_size;
1664 private void setMinBaseFontSize( final int min_base_font_size ) {
1665 _min_base_font_size = min_base_font_size;
1668 private void setOvMaxHeight( final short ov_max_height ) {
1669 _ov_max_height = ov_max_height;
1672 private void setOvMaxWidth( final short ov_max_width ) {
1673 _ov_max_width = ov_max_width;
1676 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1677 _ov_placement = ov_placement;
1680 private void setPathToLocalFastme( final File path_to_local_fastme ) {
1681 _path_to_local_fastme = path_to_local_fastme;
1684 private void setPathToLocalMafft( final File path_to_local_mafft ) {
1685 _path_to_local_mafft = path_to_local_mafft;
1688 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
1689 _path_to_local_raxml = path_to_local_raxml;
1692 private void setShowAnnotationRefSource( final boolean b ) {
1693 _show_annotation_ref_source = b;
1696 private void setShowOverview( final boolean show_overview ) {
1697 _show_overview = show_overview;
1700 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1701 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1704 static String getDefaultFontFamilyName() {
1705 return DEFAULT_FONT_FAMILY;
1708 public enum EXT_NODE_DATA_RETURN_ON {
1709 BUFFER_ONLY, CONSOLE, WINODW;
1713 CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN
1716 static enum TRIPLET {
1717 FALSE, TRUE, UNKNOWN