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", "nodisplay", "no" }, { "Confidence Values", "display", "?" },
94 { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
95 { "Visual Styles/Branch Colors", "display", "no" }, { "Branch Widths", "display", "no" },
96 { "Protein Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" },
97 { "Binary Char Counts", "nodisplay", "no" }, { "Seq Name", "display", "yes" },
98 { "Seq Accession", "display", "no" }, { "Show Internal Data", "display", "yes" },
99 { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" },
100 { "Taxonomy Common", "display", "no" }, { "Colorize by Annotation", "nodisplay", "no" },
101 { "Seq Symbol", "display", "yes" }, { "Rollover", "display", "yes" },
102 { "Relation Confidence", "nodisplay", "no" }, { "Vector Data", "nodisplay", "no" },
103 { "Taxonomy Images", "display", "no" }, { "Properties", "nodisplay", "no" },
104 { "Gene Name", "display", "yes" } };
105 final static int display_as_phylogram = 0;
106 final static int show_node_names = 1;
107 final static int show_tax_code = 2;
108 final static int show_annotation = 3;
109 final static int write_confidence_values = 4;
110 final static int write_events = 5;
111 final static int color_according_to_species = 6;
112 final static int use_style = 7;
113 final static int width_branches = 8;
114 final static int show_domain_architectures = 9;
115 final static int show_binary_characters = 10;
116 final static int show_binary_character_counts = 11;
117 final static int show_seq_names = 12;
118 final static int show_sequence_acc = 13;
119 final static int display_internal_data = 14;
120 final static int dynamically_hide_data = 15;
121 final static int show_taxonomy_scientific_names = 16;
122 final static int show_taxonomy_common_names = 17;
123 final static int color_according_to_annotation = 18;
124 final static int show_seq_symbols = 19;
125 final static int node_data_popup = 20;
126 final static int show_relation_confidence = 21;
127 final static int show_vector_data = 22;
128 final static int show_taxonomy_images = 23;
129 final static int show_properties = 24;
130 final static int show_gene_names = 25;
131 static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
135 private static Hashtable<String, Color> _annotation_colors;
139 private static Hashtable<String, Color> _domain_colors;
143 private static Hashtable<String, Color> _species_colors;
144 private static String DEFAULT_FONT_FAMILY = "";
145 private static final int DEPRECATED = -2;
146 private static final String DISPLAY_COLOR_KEY = "display_color";
147 // ---------------------------
148 // Display options for trees
149 // ---------------------------
150 // ---------------------------------
151 // Pertaining to the config itself
152 // ---------------------------------
153 // Full path to config (may be URL)
154 String config_filename;
155 // This option is selected in the dropdown
156 int default_clickto = Configuration.display_node_data;
157 String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
161 TreeColorSet tree_color_set;
165 TreeFontSet tree_font_set;
166 boolean verbose = Constants.VERBOSE_DEFAULT;
167 private boolean _abbreviate_scientific_names = false;
168 private boolean _antialias_screen = true;
169 private boolean _background_color_gradient = false;
170 private String _base_font_family_name = "";
171 private int _base_font_size = -1;
172 private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
173 private boolean _color_labels_same_as_parent_branch = false;
174 private int _default_bootstrap_samples = -1;
175 private NodeFill _default_node_fill = NodeFill.SOLID;
176 private NodeShape _default_node_shape = NodeShape.RECTANGLE;
177 private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
178 private SortedMap<String, Color> _display_colors = null;
179 private boolean _display_sequence_relations = false;
180 private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
181 private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
182 private boolean _editable = true;
183 private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
184 private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
185 private int _frame_x_size;
186 private int _frame_y_size;
187 private int _graphics_export_x = -1;
188 private int _graphics_export_y = -1;
189 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
190 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
191 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
192 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
193 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
194 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
195 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
196 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
197 private boolean _hide_controls_and_menus = false;
198 private boolean _internal_number_are_confidence_for_nh_parsing = false;
199 private String _label_for_get_ext_descendents_data = "";
200 private int _max_base_font_size = 20;
201 private boolean _midpoint_root = false;
202 private int _min_base_font_size = 2;
203 private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
204 private boolean _nh_parsing_replace_underscores = false;
205 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
206 private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
207 private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
208 private short _ov_max_height = 80;
209 private short _ov_max_width = 80;
210 private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
211 private File _path_to_local_fastme = null;
212 private File _path_to_local_mafft = null;
213 private File _path_to_local_raxml = null;
214 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
215 private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
216 private boolean _show_annotation_ref_source = true;
217 private boolean _show_branch_length_values = false;
218 private boolean _show_default_node_shapes_external = false;
219 private boolean _show_default_node_shapes_internal = false;
220 private boolean _show_domain_labels = true;
221 private boolean _show_overview = true;
222 private boolean _show_scale = false;
223 private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
224 private UI _ui = UI.UNKNOWN;
225 private boolean _use_tabbed_display = false;
226 private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
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 Color getDomainStructureBaseColor() {
324 return _domain_structure_base_color;
327 public Color getDomainStructureFontColor() {
328 return _domain_structure_font_color;
331 public NODE_DATA getExtDescNodeDataToReturn() {
332 return _ext_desc_data_to_return;
335 public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
336 return _ext_node_data_return_on;
339 public int getFrameXSize() {
340 return _frame_x_size;
343 public int getFrameYSize() {
344 return _frame_y_size;
347 public String getLabelForGetExtDescendentsData() {
348 return _label_for_get_ext_descendents_data;
351 public File getPathToLocalFastme() {
352 return _path_to_local_fastme;
355 public File getpathToLocalMafft() {
356 return _path_to_local_mafft;
359 public File getPathToLocalRaxml() {
360 return _path_to_local_raxml;
363 public boolean isAbbreviateScientificTaxonNames() {
364 return _abbreviate_scientific_names;
367 public boolean isBackgroundColorGradient() {
368 return _background_color_gradient;
371 public boolean isColorByTaxonomicGroup() {
375 public boolean isColorLabelsSameAsParentBranch() {
376 return _color_labels_same_as_parent_branch;
379 public boolean isMidpointReroot() {
380 return _midpoint_root;
383 public boolean isShowAnnotationRefSource() {
384 return _show_annotation_ref_source;
387 public boolean isShowDefaultNodeShapesExternal() {
388 return _show_default_node_shapes_external;
391 public boolean isShowDefaultNodeShapesInternal() {
392 return _show_default_node_shapes_internal;
395 public boolean isShowDomainLabels() {
396 return _show_domain_labels;
399 public void putDisplayColors( final String key, final Color color ) {
400 getDisplayColors().put( key, color );
403 public void setAddTaxonomyImagesCB( final boolean b ) {
404 display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no";
407 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
408 _abbreviate_scientific_names = abbreviate_scientific_names;
411 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
412 _background_color_gradient = background_color_gradient;
415 public void setBaseFontFamilyName( final String base_font_family_name ) {
416 _base_font_family_name = base_font_family_name;
419 public void setBaseFontSize( final int base_font_size ) {
420 _base_font_size = base_font_size;
423 public void setColorizeBranches( final boolean b ) {
424 display_options[ use_style ][ 2 ] = b ? "yes" : "no";
427 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
428 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
431 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
432 _default_node_fill = default_node_fill;
435 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
436 _default_node_shape = default_node_shape;
439 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
440 _default_node_shape_size = default_node_shape_size;
443 public void setDisplayAsPhylogram( final boolean b ) {
444 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
447 public void setUseStyle( final boolean b ) {
448 display_options[ use_style ][ 2 ] = b ? "yes" : "no";
451 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
452 _display_colors = display_colors;
455 public void setDisplayConfidenceValues( final boolean b ) {
456 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
459 public void setDisplayInternalData( final boolean b ) {
460 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
463 public void setDisplayNodeNames( final boolean b ) {
464 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
467 public void setDisplaySequenceAcc( final boolean b ) {
468 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
471 public void setDisplaySequenceNames( final boolean b ) {
472 display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no";
475 public void setDisplayGeneNames( final boolean b ) {
476 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
479 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
480 _display_sequence_relations = display_sequence_relations;
483 public void setDisplaySequenceSymbols( final boolean b ) {
484 display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no";
487 public void setDisplayTaxonomyCode( final boolean b ) {
488 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
491 public void setDisplayTaxonomyCommonNames( final boolean b ) {
492 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
495 public void setDisplayTaxonomyImages( final boolean b ) {
496 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
499 public void setDisplayTaxonomyScientificNames( final boolean b ) {
500 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
503 public void setDynamicallyHideData( final boolean b ) {
504 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
507 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
508 _ext_desc_data_to_return = ext_desc_data_to_return;
511 public void setFrameXSize( final int frame_x_size ) {
512 _frame_x_size = frame_x_size;
515 public void setFrameYSize( final int frame_y_size ) {
516 _frame_y_size = frame_y_size;
519 public void setMidpointReroot( final boolean midpoint_root ) {
520 _midpoint_root = midpoint_root;
523 public void setMinConfidenceValue( final double min_confidence_value ) {
524 _min_confidence_value = min_confidence_value;
527 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
528 _node_label_direction = node_label_direction;
531 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
532 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
535 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
536 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
539 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
540 _phylogeny_graphics_type = phylogeny_graphics_type;
543 public void setPrintLineWidth( final float print_line_width ) {
544 _print_line_width = print_line_width;
547 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
548 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
551 public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
552 _show_branch_length_values = show_branch_length_values;
555 public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
556 _show_default_node_shapes_external = show_default_node_shapes_external;
559 public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
560 _show_default_node_shapes_internal = show_default_node_shapes_internal;
563 public void setShowDomainLabels( final boolean show_domain_labels ) {
564 _show_domain_labels = show_domain_labels;
567 public void setShowScale( final boolean show_scale ) {
568 _show_scale = show_scale;
571 public void setTaxonomyColorize( final boolean b ) {
572 display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
575 public void setUseBranchesWidths( final boolean b ) {
576 display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
579 boolean displaySequenceRelations() {
580 return _display_sequence_relations;
583 boolean doCheckOption( final int which ) {
584 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
585 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
588 boolean doDisplayClickToOption( final int which ) {
589 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
592 boolean doDisplayOption( final int which ) {
593 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
597 * Will attempt to use the phylogeny to determine whether to check
598 * this or not (e.g. phylogram)
601 boolean doGuessCheckOption( final int which ) {
602 return display_options[ which ][ 2 ].equals( "?" );
605 Map<String, Color> getAnnotationColors() {
606 if ( _annotation_colors == null ) {
607 _annotation_colors = new Hashtable<String, Color>();
609 return _annotation_colors;
612 int getBaseFontSize() {
613 return _base_font_size;
616 CLADOGRAM_TYPE getCladogramType() {
617 return _cladogram_type;
620 int getClickToOptionsCount() {
621 return clickto_options.length;
624 String getClickToTitle( final int which ) {
625 return clickto_options[ which ][ 0 ];
628 int getDefaultDisplayClicktoOption() {
629 return default_clickto;
632 SortedMap<String, Color> getDisplayColors() {
633 return _display_colors;
636 String getDisplayTitle( final int which ) {
637 return display_options[ which ][ 0 ];
640 Map<String, Color> getDomainColors() {
641 if ( _domain_colors == null ) {
642 _domain_colors = new Hashtable<String, Color>();
644 return _domain_colors;
647 int getGraphicsExportX() {
648 return _graphics_export_x;
651 int getGraphicsExportY() {
652 return _graphics_export_y;
655 Color getGuiBackgroundColor() {
656 return _gui_background_color;
659 Color getGuiButtonBackgroundColor() {
660 return _gui_button_background_color;
663 Color getGuiButtonBorderColor() {
664 return _gui_button_border_color;
667 Color getGuiButtonTextColor() {
668 return _gui_button_text_color;
671 Color getGuiCheckboxAndButtonActiveColor() {
672 return _gui_checkbox_and_button_active_color;
675 Color getGuiCheckboxTextColor() {
676 return _gui_checkbox_text_color;
679 Color getGuiMenuBackgroundColor() {
680 return _gui_menu_background_color;
683 Color getGuiMenuTextColor() {
684 return _gui_menu_text_color;
687 int getMaxBaseFontSize() {
688 return _max_base_font_size;
691 int getMinBaseFontSize() {
692 return _min_base_font_size;
695 double getMinConfidenceValue() {
696 return _min_confidence_value;
699 NODE_LABEL_DIRECTION getNodeLabelDirection() {
700 return _node_label_direction;
703 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
704 return _number_of_digits_after_comma_for_branch_length_values;
707 short getNumberOfDigitsAfterCommaForConfidenceValues() {
708 return _number_of_digits_after_comma_for_confidence_values;
711 short getOvMaxHeight() {
712 return _ov_max_height;
715 short getOvMaxWidth() {
716 return _ov_max_width;
719 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
720 return _ov_placement;
723 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
724 return _phylogeny_graphics_type;
727 float getPrintLineWidth() {
728 return _print_line_width;
731 Hashtable<String, Color> getSpeciesColors() {
732 if ( _species_colors == null ) {
733 _species_colors = new Hashtable<String, Color>();
735 return _species_colors;
738 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
739 return _taxonomy_extraction;
742 boolean isAntialiasScreen() {
743 if ( ForesterUtil.isMac() ) {
744 //Apple Macintosh graphics are slow, turn off anti-alias.
747 return _antialias_screen;
751 * Convenience method.
753 * @return true if value in configuration file was 'yes'
755 boolean isDrawAsPhylogram() {
756 return doCheckOption( display_as_phylogram );
759 boolean isEditable() {
764 * Only used by ArchaeoptryxE.
767 boolean isHideControlPanelAndMenubar() {
768 return _hide_controls_and_menus;
771 boolean isInternalNumberAreConfidenceForNhParsing() {
772 return _internal_number_are_confidence_for_nh_parsing;
775 boolean isReplaceUnderscoresInNhParsing() {
776 return _nh_parsing_replace_underscores;
779 boolean isShowBranchLengthValues() {
780 return _show_branch_length_values;
783 boolean isShowOverview() {
784 return _show_overview;
787 boolean isShowScale() {
791 final boolean isUseNativeUI() {
792 if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
795 return _ui == UI.NATIVE;
799 * Only used by ArchaeoptryxE.
802 boolean isUseTabbedDisplay() {
803 return _use_tabbed_display;
806 boolean isValidatePhyloXmlAgainstSchema() {
807 return _validate_against_phyloxml_xsd_schema;
810 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
811 _taxonomy_extraction = taxonomy_extraction;
814 private int getClickToIndex( final String name ) {
816 if ( name.equals( "edit_info" ) ) {
817 index = Configuration.display_node_data;
819 .printWarningMessage( Constants.PRG_NAME,
820 "configuration key [edit_info] is deprecated, use [display node data] instead" );
822 else if ( name.equals( "display_node_data" ) ) {
823 index = Configuration.display_node_data;
825 else if ( name.equals( "collapse_uncollapse" ) ) {
826 index = Configuration.collapse_uncollapse;
828 else if ( name.equals( "reroot" ) ) {
829 index = Configuration.reroot;
831 else if ( name.equals( "subtree" ) ) {
832 index = Configuration.subtree;
834 else if ( name.equals( "swap" ) ) {
835 index = Configuration.swap;
837 else if ( name.equals( "sort_descendants" ) ) {
838 index = Configuration.sort_descendents;
840 else if ( name.equals( "get_ext_descendents_data" ) ) {
841 index = Configuration.get_ext_desc_data;
843 else if ( name.equals( "display_sequences" ) ) {
845 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
848 else if ( name.equals( "open_seq_web" ) ) {
849 index = Configuration.open_seq_web;
851 else if ( name.equals( "open_pdb_web" ) ) {
852 index = Configuration.open_pdb_web;
854 else if ( name.equals( "open_tax_web" ) ) {
855 index = Configuration.open_tax_web;
857 else if ( name.equals( "blast" ) ) {
858 index = Configuration.blast;
860 else if ( name.equals( "cut_subtree" ) ) {
861 index = Configuration.cut_subtree;
863 else if ( name.equals( "copy_subtree" ) ) {
864 index = Configuration.copy_subtree;
866 else if ( name.equals( "paste_subtree" ) ) {
867 index = Configuration.paste_subtree;
869 else if ( name.equals( "delete" ) ) {
870 index = Configuration.delete_subtree_or_node;
872 else if ( name.equals( "add_new_node" ) ) {
873 index = Configuration.add_new_node;
875 else if ( name.equals( "edit_node_data" ) ) {
876 index = Configuration.edit_node_data;
878 else if ( name.equals( "select_nodes" ) ) {
879 index = Configuration.select_nodes;
881 else if ( name.equals( "display_node_popup" ) ) {
882 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
883 "configuration key [display_node_popup] is deprecated" );
886 else if ( name.equals( "custom_option" ) ) {
887 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
890 else if ( name.equals( "color_subtree" ) ) {
891 index = Configuration.color_subtree;
893 else if ( name.equals( "change_node_font" ) ) {
894 index = Configuration.change_node_font;
896 else if ( name.equals( "color_node_font" ) ) {
897 index = Configuration.color_node_font;
899 else if ( name.equals( "color_subtree" ) ) {
900 index = Configuration.color_subtree;
905 private boolean parseBoolean( final String str ) {
906 final String my_str = str.trim().toLowerCase();
907 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
910 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
914 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
919 private double parseDouble( final String str ) {
922 d = Double.parseDouble( str.trim() );
924 catch ( final Exception e ) {
925 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
931 private float parseFloat( final String str ) {
934 f = Float.parseFloat( str.trim() );
936 catch ( final Exception e ) {
937 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
943 private int parseInt( final String str ) {
946 i = Integer.parseInt( str.trim() );
948 catch ( final Exception e ) {
949 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
955 private short parseShort( final String str ) {
958 i = Short.parseShort( str.trim() );
960 catch ( final Exception e ) {
961 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
967 private void processFontFamily( final StringTokenizer st ) {
968 setBaseFontFamilyName( "" );
969 final String font_str = ( ( String ) st.nextElement() ).trim();
970 final String[] fonts = font_str.split( ",+" );
971 for( String font : fonts ) {
972 font = font.replace( '_', ' ' ).trim();
973 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
974 setBaseFontFamilyName( font );
981 * read each line of config file, process non-comment lines
982 * @throws IOException
984 private void readConfig( final BufferedReader conf_in ) throws IOException {
987 line = conf_in.readLine();
988 if ( line != null ) {
990 // skip comments and blank lines
991 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
992 // convert runs of spaces to tabs
993 line = line.replaceAll( "\\s+", "\t" );
994 final StringTokenizer st = new StringTokenizer( line, "\t" );
998 } while ( line != null );
1001 private void setAntialiasScreen( final boolean antialias_screen ) {
1002 _antialias_screen = antialias_screen;
1005 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
1006 _cladogram_type = cladogram_type;
1009 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
1010 _default_bootstrap_samples = default_bootstrap_samples;
1013 private void setEditable( final boolean editable ) {
1014 _editable = editable;
1017 private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
1018 _ext_node_data_return_on = ext_node_data_return_on;
1021 private void setGraphicsExportX( final int graphics_export_x ) {
1022 _graphics_export_x = graphics_export_x;
1025 private void setGraphicsExportY( final int graphics_export_y ) {
1026 _graphics_export_y = graphics_export_y;
1029 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
1030 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
1034 * Set a key-value(s) tuple
1036 private void setKeyValue( final StringTokenizer st ) {
1037 final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
1038 if ( !st.hasMoreElements() ) {
1041 // Handle single value settings first:
1042 if ( key.equals( "default_click_to" ) ) {
1043 final String clickto_name = ( String ) st.nextElement();
1044 default_clickto = getClickToIndex( clickto_name );
1045 if ( default_clickto == -1 ) {
1046 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
1047 + "] for [default_click_to]" );
1048 default_clickto = 0;
1050 else if ( default_clickto == DEPRECATED ) {
1054 else if ( key.equals( "native_ui" ) ) {
1055 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
1056 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
1059 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
1060 _ui = UI.CROSSPLATFORM;
1062 else if ( my_str.equals( "?" ) ) {
1066 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
1071 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
1072 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
1074 else if ( key.equals( "antialias_screen" ) ) {
1075 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
1077 else if ( key.equals( "phylogeny_graphics_type" ) ) {
1078 final String type_str = ( ( String ) st.nextElement() ).trim();
1079 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
1080 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1082 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
1083 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1085 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
1086 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1088 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
1089 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1091 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
1092 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1094 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
1095 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1097 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
1098 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1100 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
1101 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1104 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1105 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1106 + "] for [phylogeny_graphics_type]" );
1109 else if ( key.equals( "min_confidence_value" ) ) {
1110 final String mcv_str = ( ( String ) st.nextElement() ).trim();
1111 final double d = parseDouble( mcv_str );
1112 setMinConfidenceValue( d );
1114 else if ( key.equals( "font_family" ) ) {
1115 processFontFamily( st );
1117 else if ( key.equals( "font_size" ) ) {
1118 final String size_str = ( ( String ) st.nextElement() ).trim();
1119 final int i = parseInt( size_str );
1121 setBaseFontSize( i );
1124 else if ( key.equals( "font_size_min" ) ) {
1125 final String size_str = ( ( String ) st.nextElement() ).trim();
1126 final int i = parseInt( size_str );
1128 setMinBaseFontSize( i );
1131 else if ( key.equals( "font_size_max" ) ) {
1132 final String size_str = ( ( String ) st.nextElement() ).trim();
1133 final int i = parseInt( size_str );
1135 setMaxBaseFontSize( i );
1138 else if ( key.equals( "graphics_export_x" ) ) {
1139 final String str = ( ( String ) st.nextElement() ).trim();
1140 final int i = parseInt( str );
1142 setGraphicsExportX( i );
1145 else if ( key.equals( "graphics_export_y" ) ) {
1146 final String str = ( ( String ) st.nextElement() ).trim();
1147 final int i = parseInt( str );
1149 setGraphicsExportY( i );
1152 else if ( key.equals( "pdf_export_line_width" ) ) {
1153 final String str = ( ( String ) st.nextElement() ).trim();
1154 final float f = parseFloat( str );
1156 setPrintLineWidth( f );
1159 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1160 "value for [pdf_export_line_width] cannot be zero or negative" );
1163 else if ( key.equals( "window_initial_size_x" ) ) {
1164 final String str = ( ( String ) st.nextElement() ).trim();
1165 final int i = parseInt( str );
1170 else if ( key.equals( "window_initial_size_y" ) ) {
1171 final String str = ( ( String ) st.nextElement() ).trim();
1172 final int i = parseInt( str );
1177 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1178 final String str = ( ( String ) st.nextElement() ).trim();
1179 final int i = parseInt( str );
1181 setDefaultBootstrapSamples( i );
1185 .printWarningMessage( Constants.PRG_NAME,
1186 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1189 else if ( key.equals( "mafft_local" ) ) {
1190 final String str = ( ( String ) st.nextElement() ).trim();
1191 if ( !ForesterUtil.isEmpty( str ) ) {
1192 setPathToLocalMafft( new File( str ) );
1195 else if ( key.equals( "fastme_local" ) ) {
1196 final String str = ( ( String ) st.nextElement() ).trim();
1197 if ( !ForesterUtil.isEmpty( str ) ) {
1198 setPathToLocalFastme( new File( str ) );
1201 else if ( key.equals( "raxml_local" ) ) {
1202 final String str = ( ( String ) st.nextElement() ).trim();
1203 if ( !ForesterUtil.isEmpty( str ) ) {
1204 setPathToLocalRaxml( new File( str ) );
1207 else if ( key.equals( "show_scale" ) ) {
1208 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1210 else if ( key.equals( "show_overview" ) ) {
1211 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1213 else if ( key.equals( "show_branch_length_values" ) ) {
1214 setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
1216 else if ( key.equals( "background_gradient" ) ) {
1217 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1219 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1220 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1222 else if ( key.equals( "show_domain_labels" ) ) {
1223 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1225 else if ( key.equals( "show_seq_annotation_ref_sources" ) ) {
1226 setShowAnnotationRefSource( parseBoolean( ( String ) st.nextElement() ) );
1228 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1229 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1231 else if ( key.equals( "cladogram_type" ) ) {
1232 final String type_str = ( ( String ) st.nextElement() ).trim();
1233 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1234 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1236 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1237 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1239 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1240 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1243 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1244 + "] for [cladogram_type]" );
1247 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1249 .printWarningMessage( Constants.PRG_NAME,
1250 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1252 else if ( key.equals( "hide_controls_and_menus" ) ) {
1253 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1255 else if ( key.equals( "use_tabbed_display" ) ) {
1256 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1258 else if ( key.equals( "overview_width" ) ) {
1259 final short i = parseShort( ( ( String ) st.nextElement() ) );
1262 else if ( key.equals( "overview_height" ) ) {
1263 final short i = parseShort( ( ( String ) st.nextElement() ) );
1264 setOvMaxHeight( i );
1266 else if ( key.equals( "overview_placement_type" ) ) {
1267 final String type_str = ( ( String ) st.nextElement() ).trim();
1268 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1269 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1271 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1272 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1274 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1275 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1277 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1278 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1281 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1282 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1283 + "] for [overview_placement_type]" );
1286 else if ( key.equals( "node_label_direction" ) ) {
1287 final String type_str = ( ( String ) st.nextElement() ).trim();
1288 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1289 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1291 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1292 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1295 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1296 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1297 + "] for [node_label_direction]" );
1300 else if ( key.equals( "branch_length_value_digits" ) ) {
1301 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1303 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1306 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1307 + "] for [branch_length_value_digits]" );
1310 else if ( key.equals( "confidence_value_digits" ) ) {
1311 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1313 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1316 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1317 + "] for [confidence_value_digits]" );
1320 else if ( key.equals( "allow_editing" ) ) {
1321 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1323 else if ( key.equals( "display_sequence_relations" ) ) {
1324 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1326 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1327 final boolean r = parseBoolean( ( String ) st.nextElement() );
1328 if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
1330 .printWarningMessage( Constants.PRG_NAME,
1331 "attempt to extract taxonomies and replace underscores at the same time" );
1334 setReplaceUnderscoresInNhParsing( r );
1337 else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
1338 final String s = ( String ) st.nextElement();
1339 if ( s.equalsIgnoreCase( "no" ) ) {
1340 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1342 else if ( s.equalsIgnoreCase( "pfam_relaxed" ) ) {
1343 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1345 else if ( s.equalsIgnoreCase( "pfam_strict" ) ) {
1346 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1348 else if ( s.equalsIgnoreCase( "aggressive" ) ) {
1349 setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
1353 .printWarningMessage( Constants.PRG_NAME,
1354 "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
1356 + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
1358 if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
1360 .printWarningMessage( Constants.PRG_NAME,
1361 "attempt to extract taxonomies and replace underscores at the same time" );
1364 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1365 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1367 else if ( key.equals( "gui_background_color" ) ) {
1368 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1370 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1371 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1373 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1374 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1376 else if ( key.equals( "gui_button_text_color" ) ) {
1377 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1379 else if ( key.equals( "gui_button_background_color" ) ) {
1380 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1382 else if ( key.equals( "gui_menu_background_color" ) ) {
1383 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1385 else if ( key.equals( "gui_menu_text_color" ) ) {
1386 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1388 else if ( key.equals( "gui_button_border_color" ) ) {
1389 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1391 else if ( key.equals( "domain_structure_font_color" ) ) {
1392 _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
1394 else if ( key.equals( "domain_structure_base_color" ) ) {
1395 _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
1397 else if ( key.equals( "show_default_node_shapes" ) ) {
1399 .printWarningMessage( Constants.PRG_NAME,
1400 "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" );
1401 final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() );
1402 setShowDefaultNodeShapesInternal( b );
1403 setShowDefaultNodeShapesExternal( b );
1405 else if ( key.equals( "show_default_node_shapes_internal" ) ) {
1406 setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1408 else if ( key.equals( "show_default_node_shapes_external" ) ) {
1409 setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1411 else if ( key.equals( "default_node_size" ) ) {
1412 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1413 setDefaultNodeShapeSize( i );
1415 else if ( key.equals( "default_node_fill" ) ) {
1416 final String fill_str = ( ( String ) st.nextElement() ).trim();
1417 if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.NONE.toString() ) ) {
1418 setDefaultNodeFill( NodeFill.NONE );
1420 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.GRADIENT.toString() ) ) {
1421 setDefaultNodeFill( NodeFill.GRADIENT );
1423 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.SOLID.toString() ) ) {
1424 setDefaultNodeFill( NodeFill.SOLID );
1427 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1428 + "] for [default_node_fill]" );
1431 else if ( key.equals( "default_node_shape" ) ) {
1432 final String shape_str = ( ( String ) st.nextElement() ).trim();
1433 if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.CIRCLE.toString() ) ) {
1434 setDefaultNodeShape( NodeShape.CIRCLE );
1436 else if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.RECTANGLE.toString() ) ) {
1437 setDefaultNodeShape( NodeShape.RECTANGLE );
1440 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1441 + "] for [default_node_shape]" );
1444 else if ( key.equals( "midpoint_reroot" ) ) {
1445 setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) );
1447 else if ( key.equals( "ext_descendents_data_to_return" ) ) {
1448 final String s = ( ( String ) st.nextElement() ).trim();
1449 if ( s.equalsIgnoreCase( "node_name" ) ) {
1450 setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
1452 else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
1453 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
1455 else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) {
1456 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ_FASTA );
1458 else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
1459 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
1461 else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
1462 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
1464 else if ( s.equalsIgnoreCase( "gene_name" ) ) {
1465 setExtDescNodeDataToReturn( NODE_DATA.GENE_NAME );
1467 else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
1468 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
1470 else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
1471 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME );
1473 else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
1474 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
1476 else if ( s.equalsIgnoreCase( "taxonomy_common_name" ) ) {
1477 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_COMM0N_NAME );
1479 else if ( s.equalsIgnoreCase( "user_selected" ) ) {
1480 setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
1483 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1484 + "] for [ext_descendents_data_to_return]" );
1487 else if ( key.equals( "label_for_get_ext_descendents_data" ) ) {
1488 final String s = ( ( String ) st.nextElement() ).trim();
1489 if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) {
1490 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s
1491 + "] for [label_for_get_ext_descendents_data]" );
1494 setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
1497 else if ( key.equals( "ext_descendents_data_to_return_on" ) ) {
1498 final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
1499 if ( s.equals( "console" ) ) {
1500 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
1502 else if ( s.equals( "window" ) ) {
1503 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
1505 else if ( s.equals( "buffer_only" ) ) {
1506 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
1509 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1510 + "] for [ext_descendents_data_to_return_on]" );
1513 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1516 if ( key.equals( "phylogram" ) ) {
1517 key_index = Configuration.display_as_phylogram;
1519 else if ( key.equals( "rollover" ) ) {
1520 key_index = Configuration.node_data_popup;
1522 else if ( key.equals( "color_according_to_species" ) ) {
1523 key_index = Configuration.color_according_to_species;
1525 else if ( key.equals( "show_node_names" ) ) {
1526 key_index = Configuration.show_node_names;
1528 else if ( key.equals( "show_taxonomy_code" ) ) {
1529 key_index = Configuration.show_tax_code;
1531 else if ( key.equals( "write_confidence_values" ) ) {
1532 key_index = Configuration.write_confidence_values;
1534 else if ( key.equals( "write_events" ) ) {
1535 key_index = Configuration.write_events;
1537 else if ( key.equals( "use_visual_styles" ) ) {
1538 key_index = Configuration.use_style;
1540 else if ( key.equals( "color_branches" ) ) {
1541 key_index = Configuration.use_style;
1543 .printWarningMessage( Constants.PRG_NAME,
1544 "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" );
1546 else if ( key.equals( "width_branches" ) ) {
1547 key_index = Configuration.width_branches;
1549 else if ( key.equals( "show_domain_architectures" ) ) {
1550 key_index = Configuration.show_domain_architectures;
1552 else if ( key.equals( "show_annotations" ) ) {
1553 key_index = Configuration.show_annotation;
1555 else if ( key.equals( "show_binary_characters" ) ) {
1556 key_index = Configuration.show_binary_characters;
1558 else if ( key.equals( "show_binary_character_counts" ) ) {
1559 key_index = Configuration.show_binary_character_counts;
1561 else if ( key.equals( "show_seq_names" ) ) {
1562 key_index = Configuration.show_seq_names;
1564 else if ( key.equals( "show_gene_names" ) ) {
1565 key_index = Configuration.show_gene_names;
1567 else if ( key.equals( "show_seq_symbols" ) ) {
1568 key_index = Configuration.show_seq_symbols;
1570 else if ( key.equals( "show_seq_acc" ) ) {
1571 key_index = Configuration.show_sequence_acc;
1573 else if ( key.equals( "display_internal_data" ) ) {
1574 key_index = Configuration.display_internal_data;
1576 else if ( key.equals( "dynamically_hide_data" ) ) {
1577 key_index = Configuration.dynamically_hide_data;
1579 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1580 key_index = Configuration.show_taxonomy_scientific_names;
1582 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1583 key_index = Configuration.show_taxonomy_common_names;
1585 else if ( key.equals( "show_taxonomy_images" ) ) {
1586 key_index = Configuration.show_taxonomy_images;
1588 else if ( key.equals( "color_according_to_annotation" ) ) {
1589 key_index = Configuration.color_according_to_annotation;
1591 else if ( key.equals( "show_vector_data" ) ) {
1592 key_index = Configuration.show_vector_data;
1594 else if ( key.equals( "show_properties" ) ) {
1595 key_index = Configuration.show_properties;
1597 else if ( key.equals( "show_relation_confidence" ) ) {
1598 key_index = Configuration.show_relation_confidence;
1600 // If we've found the key, set the values
1601 if ( key_index >= 0 ) {
1602 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1603 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1604 // otherwise, keep looking
1607 if ( key_index == DEPRECATED ) {
1610 else if ( key.equals( "click_to" ) ) {
1611 final String click_to_name = ( String ) st.nextElement();
1612 key_index = getClickToIndex( click_to_name );
1613 if ( key_index >= 0 ) {
1614 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1616 else if ( key_index == DEPRECATED ) {
1620 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1624 else if ( key.equals( "species_color" ) ) {
1625 getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
1626 Color.decode( ( String ) st.nextElement() ) );
1628 else if ( key.equals( "domain_color" ) ) {
1629 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1631 else if ( key.equals( "annotation_color" ) ) {
1632 getAnnotationColors()
1633 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1635 else if ( key.equals( "function_color" ) ) {
1636 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1637 "configuration key [function_color] is deprecated" );
1639 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1640 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1643 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1644 + "] in: " + config_filename );
1649 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1650 + config_filename );
1654 private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
1655 _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
1658 private void setMaxBaseFontSize( final int max_base_font_size ) {
1659 _max_base_font_size = max_base_font_size;
1662 private void setMinBaseFontSize( final int min_base_font_size ) {
1663 _min_base_font_size = min_base_font_size;
1666 private void setOvMaxHeight( final short ov_max_height ) {
1667 _ov_max_height = ov_max_height;
1670 private void setOvMaxWidth( final short ov_max_width ) {
1671 _ov_max_width = ov_max_width;
1674 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1675 _ov_placement = ov_placement;
1678 private void setPathToLocalFastme( final File path_to_local_fastme ) {
1679 _path_to_local_fastme = path_to_local_fastme;
1682 private void setPathToLocalMafft( final File path_to_local_mafft ) {
1683 _path_to_local_mafft = path_to_local_mafft;
1686 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
1687 _path_to_local_raxml = path_to_local_raxml;
1690 private void setShowAnnotationRefSource( final boolean b ) {
1691 _show_annotation_ref_source = b;
1694 private void setShowOverview( final boolean show_overview ) {
1695 _show_overview = show_overview;
1698 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1699 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1702 static String getDefaultFontFamilyName() {
1703 return DEFAULT_FONT_FAMILY;
1706 public enum EXT_NODE_DATA_RETURN_ON {
1707 BUFFER_ONLY, CONSOLE, WINODW;
1711 CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN
1714 static enum TRIPLET {
1715 FALSE, TRUE, UNKNOWN