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" }, { "Visual Styles/Branch Colors", "display", "no" },
96 { "Branch Widths", "display", "no" }, { "Domain Architectures", "display", "no" },
97 { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
98 { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" },
99 { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
100 { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
101 { "Colorize by Annotation", "display", "no" }, { "Seq Symbol", "display", "yes" },
102 { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
103 { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
104 { "Properties", "display", "no" }, { "Gene Name", "display", "yes" },
105 { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" } };
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 final static int show_mol_seqs = 27;
134 final static int write_branch_length_values = 28;
135 static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
136 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 boolean _editable = true;
177 private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
178 private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
179 private int _frame_x_size;
180 private int _frame_y_size;
181 private int _graphics_export_x = -1;
182 private int _graphics_export_y = -1;
183 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
184 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
185 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
186 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
187 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
188 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
189 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
190 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
191 private boolean _hide_controls_and_menus = false;
192 private boolean _internal_number_are_confidence_for_nh_parsing = false;
193 private String _label_for_get_ext_descendents_data = "";
194 private int _max_base_font_size = 20;
195 private boolean _midpoint_root = false;
196 private int _min_base_font_size = 2;
197 private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
198 private boolean _nh_parsing_replace_underscores = false;
199 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
200 private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
201 private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
202 private short _ov_max_height = 80;
203 private short _ov_max_width = 80;
204 private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
205 private File _path_to_local_fastme = null;
206 private File _path_to_local_mafft = null;
207 private File _path_to_local_raxml = null;
208 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
209 private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
210 private boolean _show_annotation_ref_source = true;
211 private boolean _show_default_node_shapes_external = false;
212 private boolean _show_default_node_shapes_internal = false;
213 private boolean _show_domain_labels = true;
214 private boolean _show_overview = true;
215 private boolean _show_scale = false;
216 private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
217 private UI _ui = UI.UNKNOWN;
218 private boolean _use_tabbed_display = false;
219 private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
220 private Color _vector_data_min_color = Color.BLUE;
221 private Color _vector_data_max_color = Color.YELLOW;
222 private Color _vector_data_mean_color = Color.WHITE;
223 private double _vector_data_height = 12;
224 private int _vector_data_width = 120;
225 private boolean _line_up_renderable_node_data;
226 private boolean _right_align_domains;
228 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
229 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
230 DEFAULT_FONT_FAMILY = font_name;
234 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
235 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
239 public Configuration() {
240 this( null, false, false, false );
243 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
244 if ( ForesterUtil.isEmpty( cf ) ) {
245 config_filename = default_config_filename;
248 config_filename = cf;
250 setDisplayColors( new TreeMap<String, Color>() );
251 config_filename = config_filename.trim();
254 // If URL, open accordingly
256 u = new URL( config_filename );
258 final InputStreamReader isr = new InputStreamReader( u.openStream() );
259 final BufferedReader bf = new BufferedReader( isr );
262 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
263 + config_filename + "]" );
265 catch ( final Exception e ) {
266 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
267 + config_filename + "]: " + e.getLocalizedMessage() );
270 catch ( final Exception e ) {
271 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
272 + config_filename + "]" );
276 // Otherwise, open as a file
277 File f = new File( config_filename );
279 f = new File( config_filename + ".txt" );
281 if ( f.exists() && f.canRead() ) {
283 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
287 catch ( final Exception e ) {
289 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
290 + config_filename + "]: " + e );
296 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
297 + config_filename + "]" );
303 public String getBaseFontFamilyName() {
304 return _base_font_family_name;
307 public int getDefaultBootstrapSamples() {
308 return _default_bootstrap_samples;
311 public NodeFill getDefaultNodeFill() {
312 return _default_node_fill;
315 public NodeShape getDefaultNodeShape() {
316 return _default_node_shape;
319 public short getDefaultNodeShapeSize() {
320 return _default_node_shape_size;
323 public NODE_DATA getExtDescNodeDataToReturn() {
324 return _ext_desc_data_to_return;
327 public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
328 return _ext_node_data_return_on;
331 public int getFrameXSize() {
332 return _frame_x_size;
335 public int getFrameYSize() {
336 return _frame_y_size;
339 public String getLabelForGetExtDescendentsData() {
340 return _label_for_get_ext_descendents_data;
343 public File getPathToLocalFastme() {
344 return _path_to_local_fastme;
347 public File getPathToLocalMafft() {
348 return _path_to_local_mafft;
351 public File getPathToLocalRaxml() {
352 return _path_to_local_raxml;
355 public boolean isAbbreviateScientificTaxonNames() {
356 return _abbreviate_scientific_names;
359 public boolean isBackgroundColorGradient() {
360 return _background_color_gradient;
363 public boolean isColorByTaxonomicGroup() {
367 public boolean isColorLabelsSameAsParentBranch() {
368 return _color_labels_same_as_parent_branch;
371 public boolean isMidpointReroot() {
372 return _midpoint_root;
375 public boolean isShowAnnotationRefSource() {
376 return _show_annotation_ref_source;
379 public boolean isShowDefaultNodeShapesExternal() {
380 return _show_default_node_shapes_external;
383 public boolean isShowDefaultNodeShapesInternal() {
384 return _show_default_node_shapes_internal;
387 public boolean isShowDomainLabels() {
388 return _show_domain_labels;
391 public void putDisplayColors( final String key, final Color color ) {
392 getDisplayColors().put( key, color );
395 public void setAddTaxonomyImagesCB( final boolean b ) {
396 display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no";
399 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
400 _abbreviate_scientific_names = abbreviate_scientific_names;
403 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
404 _background_color_gradient = background_color_gradient;
407 public void setBaseFontFamilyName( final String base_font_family_name ) {
408 _base_font_family_name = base_font_family_name;
411 public void setBaseFontSize( final int base_font_size ) {
412 _base_font_size = base_font_size;
415 public void setColorizeBranches( final boolean b ) {
416 display_options[ use_style ][ 2 ] = b ? "yes" : "no";
419 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
420 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
423 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
424 _default_node_fill = default_node_fill;
427 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
428 _default_node_shape = default_node_shape;
431 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
432 _default_node_shape_size = default_node_shape_size;
435 public void setDisplayAsPhylogram( final boolean b ) {
436 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
439 public void setUseStyle( final boolean b ) {
440 display_options[ use_style ][ 2 ] = b ? "yes" : "no";
443 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
444 _display_colors = display_colors;
447 public void setDisplayConfidenceValues( final boolean b ) {
448 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
451 public void setDisplayInternalData( final boolean b ) {
452 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
455 public void setDisplayNodeNames( final boolean b ) {
456 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
459 public void setDisplaySequenceAcc( final boolean b ) {
460 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
463 public void setDisplaySequenceNames( final boolean b ) {
464 display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no";
467 public void setDisplayGeneNames( final boolean b ) {
468 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
471 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
472 _display_sequence_relations = display_sequence_relations;
475 public void setDisplaySequenceSymbols( final boolean b ) {
476 display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no";
479 public void setDisplayTaxonomyCode( final boolean b ) {
480 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
483 public void setDisplayTaxonomyCommonNames( final boolean b ) {
484 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
487 public void setDisplayTaxonomyImages( final boolean b ) {
488 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
491 public void setDisplayTaxonomyScientificNames( final boolean b ) {
492 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
495 public void setDynamicallyHideData( final boolean b ) {
496 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
499 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
500 _ext_desc_data_to_return = ext_desc_data_to_return;
503 public void setFrameXSize( final int frame_x_size ) {
504 _frame_x_size = frame_x_size;
507 public void setFrameYSize( final int frame_y_size ) {
508 _frame_y_size = frame_y_size;
511 public void setMidpointReroot( final boolean midpoint_root ) {
512 _midpoint_root = midpoint_root;
515 public void setMinConfidenceValue( final double min_confidence_value ) {
516 _min_confidence_value = min_confidence_value;
519 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
520 _node_label_direction = node_label_direction;
523 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
524 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
527 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
528 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
531 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
532 _phylogeny_graphics_type = phylogeny_graphics_type;
535 public void setPrintLineWidth( final float print_line_width ) {
536 _print_line_width = print_line_width;
539 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
540 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
543 public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
544 _show_default_node_shapes_external = show_default_node_shapes_external;
547 public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
548 _show_default_node_shapes_internal = show_default_node_shapes_internal;
551 public void setShowDomainLabels( final boolean show_domain_labels ) {
552 _show_domain_labels = show_domain_labels;
555 public void setShowScale( final boolean show_scale ) {
556 _show_scale = show_scale;
559 boolean displaySequenceRelations() {
560 return _display_sequence_relations;
563 boolean doCheckOption( final int which ) {
564 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
565 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
568 boolean doDisplayClickToOption( final int which ) {
569 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
572 boolean doDisplayOption( final int which ) {
573 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
577 * Will attempt to use the phylogeny to determine whether to check
578 * this or not (e.g. phylogram)
581 boolean doGuessCheckOption( final int which ) {
582 return display_options[ which ][ 2 ].equals( "?" );
585 Map<String, Color> getAnnotationColors() {
586 if ( _annotation_colors == null ) {
587 _annotation_colors = new Hashtable<String, Color>();
589 return _annotation_colors;
592 int getBaseFontSize() {
593 return _base_font_size;
596 CLADOGRAM_TYPE getCladogramType() {
597 return _cladogram_type;
600 int getClickToOptionsCount() {
601 return clickto_options.length;
604 String getClickToTitle( final int which ) {
605 return clickto_options[ which ][ 0 ];
608 int getDefaultDisplayClicktoOption() {
609 return default_clickto;
612 SortedMap<String, Color> getDisplayColors() {
613 return _display_colors;
616 String getDisplayTitle( final int which ) {
617 return display_options[ which ][ 0 ];
620 Map<String, Color> getDomainColors() {
621 if ( _domain_colors == null ) {
622 _domain_colors = new Hashtable<String, Color>();
624 return _domain_colors;
627 int getGraphicsExportX() {
628 return _graphics_export_x;
631 int getGraphicsExportY() {
632 return _graphics_export_y;
635 Color getGuiBackgroundColor() {
636 return _gui_background_color;
639 Color getGuiButtonBackgroundColor() {
640 return _gui_button_background_color;
643 Color getGuiButtonBorderColor() {
644 return _gui_button_border_color;
647 Color getGuiButtonTextColor() {
648 return _gui_button_text_color;
651 Color getGuiCheckboxAndButtonActiveColor() {
652 return _gui_checkbox_and_button_active_color;
655 Color getGuiCheckboxTextColor() {
656 return _gui_checkbox_text_color;
659 Color getGuiMenuBackgroundColor() {
660 return _gui_menu_background_color;
663 Color getGuiMenuTextColor() {
664 return _gui_menu_text_color;
667 int getMaxBaseFontSize() {
668 return _max_base_font_size;
671 int getMinBaseFontSize() {
672 return _min_base_font_size;
675 double getMinConfidenceValue() {
676 return _min_confidence_value;
679 NODE_LABEL_DIRECTION getNodeLabelDirection() {
680 return _node_label_direction;
683 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
684 return _number_of_digits_after_comma_for_branch_length_values;
687 short getNumberOfDigitsAfterCommaForConfidenceValues() {
688 return _number_of_digits_after_comma_for_confidence_values;
691 short getOvMaxHeight() {
692 return _ov_max_height;
695 short getOvMaxWidth() {
696 return _ov_max_width;
699 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
700 return _ov_placement;
703 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
704 return _phylogeny_graphics_type;
707 float getPrintLineWidth() {
708 return _print_line_width;
711 Hashtable<String, Color> getSpeciesColors() {
712 if ( _species_colors == null ) {
713 _species_colors = new Hashtable<String, Color>();
715 return _species_colors;
718 Hashtable<String, Color> getSequenceColors() {
719 if ( _sequence_colors == null ) {
720 _sequence_colors = new Hashtable<String, Color>();
722 return _sequence_colors;
725 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
726 return _taxonomy_extraction;
729 boolean isAntialiasScreen() {
730 if ( ForesterUtil.isMac() ) {
731 //Apple Macintosh graphics are slow, turn off anti-alias.
734 return _antialias_screen;
738 * Convenience method.
740 * @return true if value in configuration file was 'yes'
742 boolean isDrawAsPhylogram() {
743 return doCheckOption( display_as_phylogram );
746 boolean isEditable() {
751 * Only used by ArchaeoptryxE.
754 boolean isHideControlPanelAndMenubar() {
755 return _hide_controls_and_menus;
758 boolean isInternalNumberAreConfidenceForNhParsing() {
759 return _internal_number_are_confidence_for_nh_parsing;
762 boolean isReplaceUnderscoresInNhParsing() {
763 return _nh_parsing_replace_underscores;
766 boolean isShowOverview() {
767 return _show_overview;
770 boolean isShowScale() {
774 final boolean isUseNativeUI() {
775 if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
778 return _ui == UI.NATIVE;
782 * Only used by ArchaeoptryxE.
785 boolean isUseTabbedDisplay() {
786 return _use_tabbed_display;
789 boolean isValidatePhyloXmlAgainstSchema() {
790 return _validate_against_phyloxml_xsd_schema;
793 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
794 _taxonomy_extraction = taxonomy_extraction;
797 private int getClickToIndex( final String name ) {
799 if ( name.equals( "edit_info" ) ) {
800 index = Configuration.display_node_data;
802 .printWarningMessage( Constants.PRG_NAME,
803 "configuration key [edit_info] is deprecated, use [display node data] instead" );
805 else if ( name.equals( "display_node_data" ) ) {
806 index = Configuration.display_node_data;
808 else if ( name.equals( "collapse_uncollapse" ) ) {
809 index = Configuration.collapse_uncollapse;
811 else if ( name.equals( "reroot" ) ) {
812 index = Configuration.reroot;
814 else if ( name.equals( "subtree" ) ) {
815 index = Configuration.subtree;
817 else if ( name.equals( "swap" ) ) {
818 index = Configuration.swap;
820 else if ( name.equals( "sort_descendants" ) ) {
821 index = Configuration.sort_descendents;
823 else if ( name.equals( "get_ext_descendents_data" ) ) {
824 index = Configuration.get_ext_desc_data;
826 else if ( name.equals( "display_sequences" ) ) {
828 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
831 else if ( name.equals( "open_seq_web" ) ) {
832 index = Configuration.open_seq_web;
834 else if ( name.equals( "open_pdb_web" ) ) {
835 index = Configuration.open_pdb_web;
837 else if ( name.equals( "open_tax_web" ) ) {
838 index = Configuration.open_tax_web;
840 else if ( name.equals( "blast" ) ) {
841 index = Configuration.blast;
843 else if ( name.equals( "cut_subtree" ) ) {
844 index = Configuration.cut_subtree;
846 else if ( name.equals( "copy_subtree" ) ) {
847 index = Configuration.copy_subtree;
849 else if ( name.equals( "paste_subtree" ) ) {
850 index = Configuration.paste_subtree;
852 else if ( name.equals( "delete" ) ) {
853 index = Configuration.delete_subtree_or_node;
855 else if ( name.equals( "add_new_node" ) ) {
856 index = Configuration.add_new_node;
858 else if ( name.equals( "edit_node_data" ) ) {
859 index = Configuration.edit_node_data;
861 else if ( name.equals( "select_nodes" ) ) {
862 index = Configuration.select_nodes;
864 else if ( name.equals( "display_node_popup" ) ) {
865 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
866 "configuration key [display_node_popup] is deprecated" );
869 else if ( name.equals( "custom_option" ) ) {
870 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
873 else if ( name.equals( "color_subtree" ) ) {
874 index = Configuration.color_subtree;
876 else if ( name.equals( "change_node_font" ) ) {
877 index = Configuration.change_node_font;
879 else if ( name.equals( "color_node_font" ) ) {
880 index = Configuration.color_node_font;
882 else if ( name.equals( "color_subtree" ) ) {
883 index = Configuration.color_subtree;
888 private boolean parseBoolean( final String str ) {
889 final String my_str = str.trim().toLowerCase();
890 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
893 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
897 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
902 private double parseDouble( final String str ) {
905 d = Double.parseDouble( str.trim() );
907 catch ( final Exception e ) {
908 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
914 private float parseFloat( final String str ) {
917 f = Float.parseFloat( str.trim() );
919 catch ( final Exception e ) {
920 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
926 private int parseInt( final String str ) {
929 i = Integer.parseInt( str.trim() );
931 catch ( final Exception e ) {
932 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
938 private short parseShort( final String str ) {
941 i = Short.parseShort( str.trim() );
943 catch ( final Exception e ) {
944 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
950 private void processFontFamily( final StringTokenizer st ) {
951 setBaseFontFamilyName( "" );
952 final String font_str = ( ( String ) st.nextElement() ).trim();
953 final String[] fonts = font_str.split( ",+" );
954 for( String font : fonts ) {
955 font = font.replace( '_', ' ' ).trim();
956 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
957 setBaseFontFamilyName( font );
964 * read each line of config file, process non-comment lines
965 * @throws IOException
967 private void readConfig( final BufferedReader conf_in ) throws IOException {
970 line = conf_in.readLine();
971 if ( line != null ) {
973 // skip comments and blank lines
974 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
975 // convert runs of spaces to tabs
976 line = line.replaceAll( "\\s+", "\t" );
977 final StringTokenizer st = new StringTokenizer( line, "\t" );
981 } while ( line != null );
984 private void setAntialiasScreen( final boolean antialias_screen ) {
985 _antialias_screen = antialias_screen;
988 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
989 _cladogram_type = cladogram_type;
992 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
993 _default_bootstrap_samples = default_bootstrap_samples;
996 private void setEditable( final boolean editable ) {
997 _editable = editable;
1000 private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
1001 _ext_node_data_return_on = ext_node_data_return_on;
1004 private void setGraphicsExportX( final int graphics_export_x ) {
1005 _graphics_export_x = graphics_export_x;
1008 private void setGraphicsExportY( final int graphics_export_y ) {
1009 _graphics_export_y = graphics_export_y;
1012 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
1013 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
1017 * Set a key-value(s) tuple
1019 private void setKeyValue( final StringTokenizer st ) {
1020 final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
1021 if ( !st.hasMoreElements() ) {
1024 // Handle single value settings first:
1025 if ( key.equals( "default_click_to" ) ) {
1026 final String clickto_name = ( String ) st.nextElement();
1027 default_clickto = getClickToIndex( clickto_name );
1028 if ( default_clickto == -1 ) {
1029 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
1030 + "] for [default_click_to]" );
1031 default_clickto = 0;
1033 else if ( default_clickto == DEPRECATED ) {
1037 else if ( key.equals( "native_ui" ) ) {
1038 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
1039 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
1042 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
1043 _ui = UI.CROSSPLATFORM;
1045 else if ( my_str.equals( "?" ) ) {
1049 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
1054 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
1055 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
1057 else if ( key.equals( "antialias_screen" ) ) {
1058 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
1060 else if ( key.equals( "phylogeny_graphics_type" ) ) {
1061 final String type_str = ( ( String ) st.nextElement() ).trim();
1062 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
1063 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1065 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
1066 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1068 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
1069 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1071 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
1072 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1074 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
1075 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1077 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
1078 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1080 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
1081 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1083 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
1084 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1087 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1088 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1089 + "] for [phylogeny_graphics_type]" );
1092 else if ( key.equals( "min_confidence_value" ) ) {
1093 final String mcv_str = ( ( String ) st.nextElement() ).trim();
1094 final double d = parseDouble( mcv_str );
1095 setMinConfidenceValue( d );
1097 else if ( key.equals( "font_family" ) ) {
1098 processFontFamily( st );
1100 else if ( key.equals( "font_size" ) ) {
1101 final String size_str = ( ( String ) st.nextElement() ).trim();
1102 final int i = parseInt( size_str );
1104 setBaseFontSize( i );
1107 else if ( key.equals( "font_size_min" ) ) {
1108 final String size_str = ( ( String ) st.nextElement() ).trim();
1109 final int i = parseInt( size_str );
1111 setMinBaseFontSize( i );
1114 else if ( key.equals( "font_size_max" ) ) {
1115 final String size_str = ( ( String ) st.nextElement() ).trim();
1116 final int i = parseInt( size_str );
1118 setMaxBaseFontSize( i );
1121 else if ( key.equals( "graphics_export_x" ) ) {
1122 final String str = ( ( String ) st.nextElement() ).trim();
1123 final int i = parseInt( str );
1125 setGraphicsExportX( i );
1128 else if ( key.equals( "graphics_export_y" ) ) {
1129 final String str = ( ( String ) st.nextElement() ).trim();
1130 final int i = parseInt( str );
1132 setGraphicsExportY( i );
1135 else if ( key.equals( "pdf_export_line_width" ) ) {
1136 final String str = ( ( String ) st.nextElement() ).trim();
1137 final float f = parseFloat( str );
1139 setPrintLineWidth( f );
1142 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1143 "value for [pdf_export_line_width] cannot be zero or negative" );
1146 else if ( key.equals( "window_initial_size_x" ) ) {
1147 final String str = ( ( String ) st.nextElement() ).trim();
1148 final int i = parseInt( str );
1153 else if ( key.equals( "window_initial_size_y" ) ) {
1154 final String str = ( ( String ) st.nextElement() ).trim();
1155 final int i = parseInt( str );
1160 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1161 final String str = ( ( String ) st.nextElement() ).trim();
1162 final int i = parseInt( str );
1164 setDefaultBootstrapSamples( i );
1168 .printWarningMessage( Constants.PRG_NAME,
1169 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1172 else if ( key.equals( "mafft_local" ) ) {
1173 final String str = ( ( String ) st.nextElement() ).trim();
1174 if ( !ForesterUtil.isEmpty( str ) ) {
1175 setPathToLocalMafft( new File( str ) );
1178 else if ( key.equals( "fastme_local" ) ) {
1179 final String str = ( ( String ) st.nextElement() ).trim();
1180 if ( !ForesterUtil.isEmpty( str ) ) {
1181 setPathToLocalFastme( new File( str ) );
1184 else if ( key.equals( "raxml_local" ) ) {
1185 final String str = ( ( String ) st.nextElement() ).trim();
1186 if ( !ForesterUtil.isEmpty( str ) ) {
1187 setPathToLocalRaxml( new File( str ) );
1190 else if ( key.equals( "show_scale" ) ) {
1191 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1193 else if ( key.equals( "show_overview" ) ) {
1194 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1196 else if ( key.equals( "background_gradient" ) ) {
1197 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1199 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1200 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1202 else if ( key.equals( "show_domain_labels" ) ) {
1203 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1205 else if ( key.equals( "show_seq_annotation_ref_sources" ) ) {
1206 setShowAnnotationRefSource( parseBoolean( ( String ) st.nextElement() ) );
1208 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1209 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1211 else if ( key.equals( "cladogram_type" ) ) {
1212 final String type_str = ( ( String ) st.nextElement() ).trim();
1213 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1214 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1216 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1217 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1219 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1220 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1223 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1224 + "] for [cladogram_type]" );
1227 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1229 .printWarningMessage( Constants.PRG_NAME,
1230 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1232 else if ( key.equals( "hide_controls_and_menus" ) ) {
1233 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1235 else if ( key.equals( "use_tabbed_display" ) ) {
1236 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1238 else if ( key.equals( "overview_width" ) ) {
1239 final short i = parseShort( ( ( String ) st.nextElement() ) );
1242 else if ( key.equals( "overview_height" ) ) {
1243 final short i = parseShort( ( ( String ) st.nextElement() ) );
1244 setOvMaxHeight( i );
1246 else if ( key.equals( "overview_placement_type" ) ) {
1247 final String type_str = ( ( String ) st.nextElement() ).trim();
1248 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1249 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1251 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1252 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1254 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1255 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1257 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1258 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1261 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1262 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1263 + "] for [overview_placement_type]" );
1266 else if ( key.equals( "node_label_direction" ) ) {
1267 final String type_str = ( ( String ) st.nextElement() ).trim();
1268 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1269 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1271 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1272 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1275 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1276 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1277 + "] for [node_label_direction]" );
1280 else if ( key.equals( "branch_length_value_digits" ) ) {
1281 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1283 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1286 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1287 + "] for [branch_length_value_digits]" );
1290 else if ( key.equals( "confidence_value_digits" ) ) {
1291 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1293 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1296 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1297 + "] for [confidence_value_digits]" );
1300 else if ( key.equals( "allow_editing" ) ) {
1301 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1303 else if ( key.equals( "display_sequence_relations" ) ) {
1304 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1306 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1307 final boolean r = parseBoolean( ( String ) st.nextElement() );
1308 if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
1310 .printWarningMessage( Constants.PRG_NAME,
1311 "attempt to extract taxonomies and replace underscores at the same time" );
1314 setReplaceUnderscoresInNhParsing( r );
1317 else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
1318 final String s = ( String ) st.nextElement();
1319 if ( s.equalsIgnoreCase( "no" ) ) {
1320 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1322 else if ( s.equalsIgnoreCase( "pfam_relaxed" ) ) {
1323 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1325 else if ( s.equalsIgnoreCase( "pfam_strict" ) ) {
1326 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1328 else if ( s.equalsIgnoreCase( "aggressive" ) ) {
1329 setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
1333 .printWarningMessage( Constants.PRG_NAME,
1334 "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
1336 + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
1338 if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
1340 .printWarningMessage( Constants.PRG_NAME,
1341 "attempt to extract taxonomies and replace underscores at the same time" );
1344 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1345 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1347 else if ( key.equals( "gui_background_color" ) ) {
1348 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1350 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1351 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1353 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1354 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1356 else if ( key.equals( "gui_button_text_color" ) ) {
1357 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1359 else if ( key.equals( "gui_button_background_color" ) ) {
1360 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1362 else if ( key.equals( "gui_menu_background_color" ) ) {
1363 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1365 else if ( key.equals( "gui_menu_text_color" ) ) {
1366 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1368 else if ( key.equals( "gui_button_border_color" ) ) {
1369 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1371 else if ( key.equals( "show_default_node_shapes" ) ) {
1373 .printWarningMessage( Constants.PRG_NAME,
1374 "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" );
1375 final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() );
1376 setShowDefaultNodeShapesInternal( b );
1377 setShowDefaultNodeShapesExternal( b );
1379 else if ( key.equals( "show_default_node_shapes_internal" ) ) {
1380 setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1382 else if ( key.equals( "show_default_node_shapes_external" ) ) {
1383 setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1385 else if ( key.equals( "default_node_size" ) ) {
1386 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1387 setDefaultNodeShapeSize( i );
1389 else if ( key.equals( "default_node_fill" ) ) {
1390 final String fill_str = ( ( String ) st.nextElement() ).trim();
1391 if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.NONE.toString() ) ) {
1392 setDefaultNodeFill( NodeFill.NONE );
1394 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.GRADIENT.toString() ) ) {
1395 setDefaultNodeFill( NodeFill.GRADIENT );
1397 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.SOLID.toString() ) ) {
1398 setDefaultNodeFill( NodeFill.SOLID );
1401 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1402 + "] for [default_node_fill]" );
1405 else if ( key.equals( "default_node_shape" ) ) {
1406 final String shape_str = ( ( String ) st.nextElement() ).trim();
1407 if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.CIRCLE.toString() ) ) {
1408 setDefaultNodeShape( NodeShape.CIRCLE );
1410 else if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.RECTANGLE.toString() ) ) {
1411 setDefaultNodeShape( NodeShape.RECTANGLE );
1414 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1415 + "] for [default_node_shape]" );
1418 else if ( key.equals( "midpoint_reroot" ) ) {
1419 setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) );
1421 else if ( key.equals( "ext_descendents_data_to_return" ) ) {
1422 final String s = ( ( String ) st.nextElement() ).trim();
1423 if ( s.equalsIgnoreCase( "node_name" ) ) {
1424 setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
1426 else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
1427 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
1429 else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) {
1430 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ_FASTA );
1432 else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
1433 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
1435 else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
1436 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
1438 else if ( s.equalsIgnoreCase( "gene_name" ) ) {
1439 setExtDescNodeDataToReturn( NODE_DATA.GENE_NAME );
1441 else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
1442 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
1444 else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
1445 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME );
1447 else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
1448 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
1450 else if ( s.equalsIgnoreCase( "taxonomy_common_name" ) ) {
1451 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_COMM0N_NAME );
1453 else if ( s.equalsIgnoreCase( "user_selected" ) ) {
1454 setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
1457 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1458 + "] for [ext_descendents_data_to_return]" );
1461 else if ( key.equals( "label_for_get_ext_descendents_data" ) ) {
1462 final String s = ( ( String ) st.nextElement() ).trim();
1463 if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) {
1464 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s
1465 + "] for [label_for_get_ext_descendents_data]" );
1468 setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
1471 else if ( key.equals( "ext_descendents_data_to_return_on" ) ) {
1472 final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
1473 if ( s.equals( "console" ) ) {
1474 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
1476 else if ( s.equals( "window" ) ) {
1477 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
1479 else if ( s.equals( "buffer_only" ) ) {
1480 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
1483 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1484 + "] for [ext_descendents_data_to_return_on]" );
1487 else if ( key.equals( "vector_data_min_color" ) ) {
1488 _vector_data_min_color = Color.decode( ( String ) st.nextElement() );
1490 else if ( key.equals( "vector_data_max_color" ) ) {
1491 _vector_data_max_color = Color.decode( ( String ) st.nextElement() );
1493 else if ( key.equals( "vector_data_mean_color" ) ) {
1494 _vector_data_mean_color = Color.decode( ( String ) st.nextElement() );
1496 else if ( key.equals( "vector_data_width" ) ) {
1497 _vector_data_width = parseShort( ( String ) st.nextElement() );
1498 if ( _vector_data_width < 1 ) {
1499 _vector_data_width = 120;
1502 else if ( key.equals( "vector_data_height" ) ) {
1503 _vector_data_height = parseShort( ( String ) st.nextElement() );
1504 if ( _vector_data_height < 1 ) {
1505 _vector_data_height = 12;
1508 else if ( key.equals( "line_up_renderable_data" ) ) {
1509 setLineUpRendarableNodeData( parseBoolean( ( String ) st.nextElement() ) );
1511 else if ( key.equals( "right_align_domain_architectures" ) ) {
1512 setRightLineUpDomains( parseBoolean( ( String ) st.nextElement() ) );
1514 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1517 if ( key.equals( "phylogram" ) ) {
1518 key_index = Configuration.display_as_phylogram;
1520 else if ( key.equals( "rollover" ) ) {
1521 key_index = Configuration.node_data_popup;
1523 else if ( key.equals( "color_according_to_species" ) ) {
1524 key_index = Configuration.color_according_to_species;
1526 else if ( key.equals( "color_according_to_sequence" ) ) {
1527 key_index = Configuration.color_according_to_sequence;
1529 else if ( key.equals( "show_node_names" ) ) {
1530 key_index = Configuration.show_node_names;
1532 else if ( key.equals( "show_taxonomy_code" ) ) {
1533 key_index = Configuration.show_tax_code;
1535 else if ( key.equals( "write_confidence_values" ) ) {
1536 key_index = Configuration.write_confidence_values;
1538 else if ( key.equals( "write_branch_length_values" ) ) {
1539 key_index = Configuration.write_branch_length_values;
1541 else if ( key.equals( "write_events" ) ) {
1542 key_index = Configuration.write_events;
1544 else if ( key.equals( "use_visual_styles" ) ) {
1545 key_index = Configuration.use_style;
1547 else if ( key.equals( "color_branches" ) ) {
1548 key_index = Configuration.use_style;
1550 .printWarningMessage( Constants.PRG_NAME,
1551 "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" );
1553 else if ( key.equals( "width_branches" ) ) {
1554 key_index = Configuration.width_branches;
1556 else if ( key.equals( "show_domain_architectures" ) ) {
1557 key_index = Configuration.show_domain_architectures;
1559 else if ( key.equals( "show_msa" ) ) {
1560 key_index = Configuration.show_mol_seqs;
1562 else if ( key.equals( "show_annotations" ) ) {
1563 key_index = Configuration.show_annotation;
1565 else if ( key.equals( "show_binary_characters" ) ) {
1566 key_index = Configuration.show_binary_characters;
1568 else if ( key.equals( "show_binary_character_counts" ) ) {
1569 key_index = Configuration.show_binary_character_counts;
1571 else if ( key.equals( "show_seq_names" ) ) {
1572 key_index = Configuration.show_seq_names;
1574 else if ( key.equals( "show_gene_names" ) ) {
1575 key_index = Configuration.show_gene_names;
1577 else if ( key.equals( "show_seq_symbols" ) ) {
1578 key_index = Configuration.show_seq_symbols;
1580 else if ( key.equals( "show_seq_acc" ) ) {
1581 key_index = Configuration.show_sequence_acc;
1583 else if ( key.equals( "display_internal_data" ) ) {
1584 key_index = Configuration.display_internal_data;
1586 else if ( key.equals( "dynamically_hide_data" ) ) {
1587 key_index = Configuration.dynamically_hide_data;
1589 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1590 key_index = Configuration.show_taxonomy_scientific_names;
1592 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1593 key_index = Configuration.show_taxonomy_common_names;
1595 else if ( key.equals( "show_taxonomy_images" ) ) {
1596 key_index = Configuration.show_taxonomy_images;
1598 else if ( key.equals( "color_according_to_annotation" ) ) {
1599 key_index = Configuration.color_according_to_annotation;
1601 else if ( key.equals( "show_vector_data" ) ) {
1602 key_index = Configuration.show_vector_data;
1604 else if ( key.equals( "show_properties" ) ) {
1605 key_index = Configuration.show_properties;
1607 else if ( key.equals( "show_relation_confidence" ) ) {
1608 key_index = Configuration.show_relation_confidence;
1610 // If we've found the key, set the values
1611 if ( key_index >= 0 ) {
1612 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1613 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1614 // otherwise, keep looking
1617 if ( key_index == DEPRECATED ) {
1620 else if ( key.equals( "click_to" ) ) {
1621 final String click_to_name = ( String ) st.nextElement();
1622 key_index = getClickToIndex( click_to_name );
1623 if ( key_index >= 0 ) {
1624 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1626 else if ( key_index == DEPRECATED ) {
1630 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1634 else if ( key.equals( "species_color" ) ) {
1635 getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
1636 Color.decode( ( String ) st.nextElement() ) );
1638 else if ( key.equals( "sequence_color" ) ) {
1639 getSequenceColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
1640 Color.decode( ( String ) st.nextElement() ) );
1642 else if ( key.equals( "domain_color" ) ) {
1643 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1645 else if ( key.equals( "annotation_color" ) ) {
1646 getAnnotationColors()
1647 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1649 else if ( key.equals( "function_color" ) ) {
1650 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1651 "configuration key [function_color] is deprecated" );
1653 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1654 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1657 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1658 + "] in: " + config_filename );
1663 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1664 + config_filename );
1668 private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
1669 _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
1672 private void setMaxBaseFontSize( final int max_base_font_size ) {
1673 _max_base_font_size = max_base_font_size;
1676 private void setMinBaseFontSize( final int min_base_font_size ) {
1677 _min_base_font_size = min_base_font_size;
1680 private void setOvMaxHeight( final short ov_max_height ) {
1681 _ov_max_height = ov_max_height;
1684 private void setOvMaxWidth( final short ov_max_width ) {
1685 _ov_max_width = ov_max_width;
1688 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1689 _ov_placement = ov_placement;
1692 private void setPathToLocalFastme( final File path_to_local_fastme ) {
1693 _path_to_local_fastme = path_to_local_fastme;
1696 private void setPathToLocalMafft( final File path_to_local_mafft ) {
1697 _path_to_local_mafft = path_to_local_mafft;
1700 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
1701 _path_to_local_raxml = path_to_local_raxml;
1704 private void setShowAnnotationRefSource( final boolean b ) {
1705 _show_annotation_ref_source = b;
1708 private void setShowOverview( final boolean show_overview ) {
1709 _show_overview = show_overview;
1712 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1713 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1716 static String getDefaultFontFamilyName() {
1717 return DEFAULT_FONT_FAMILY;
1720 public enum EXT_NODE_DATA_RETURN_ON {
1721 BUFFER_ONLY, CONSOLE, WINODW;
1725 CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN
1728 static enum TRIPLET {
1729 FALSE, TRUE, UNKNOWN
1732 public Color getVectorDataMinColor() {
1733 return _vector_data_min_color;
1736 public Color getVectorDataMaxColor() {
1737 return _vector_data_max_color;
1740 public Color getVectorDataMeanColor() {
1741 return _vector_data_mean_color;
1744 public double getVectorDataHeight() {
1745 return _vector_data_height;
1748 public int getVectorDataWidth() {
1749 return _vector_data_width;
1752 final public boolean isLineUpRendarableNodeData() {
1753 return _line_up_renderable_node_data;
1756 final public boolean isRightLineUpDomains() {
1757 return _right_align_domains;
1760 final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) {
1761 _line_up_renderable_node_data = line_up_renderable_node_data;
1764 final public void setRightLineUpDomains( final boolean right_align_domains ) {
1765 _right_align_domains = right_align_domains;