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" }, { "Protein Domains", "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 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 color_according_to_sequence = 7;
113 final static int use_style = 8;
114 final static int width_branches = 9;
115 final static int show_domain_architectures = 10;
116 final static int show_binary_characters = 11;
117 final static int show_binary_character_counts = 12;
118 final static int show_seq_names = 13;
119 final static int show_sequence_acc = 14;
120 final static int display_internal_data = 15;
121 final static int dynamically_hide_data = 16;
122 final static int show_taxonomy_scientific_names = 17;
123 final static int show_taxonomy_common_names = 18;
124 final static int color_according_to_annotation = 19;
125 final static int show_seq_symbols = 20;
126 final static int node_data_popup = 21;
127 final static int show_relation_confidence = 22;
128 final static int show_vector_data = 23;
129 final static int show_taxonomy_images = 24;
130 final static int show_properties = 25;
131 final static int show_gene_names = 26;
132 static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
133 private static Hashtable<String, Color> _sequence_colors;
134 private static Hashtable<String, Color> _annotation_colors;
135 private static Hashtable<String, Color> _domain_colors;
136 private static Hashtable<String, Color> _species_colors;
137 private static String DEFAULT_FONT_FAMILY = "";
138 private static final int DEPRECATED = -2;
139 private static final String DISPLAY_COLOR_KEY = "display_color";
140 // ---------------------------
141 // Display options for trees
142 // ---------------------------
143 // ---------------------------------
144 // Pertaining to the config itself
145 // ---------------------------------
146 // Full path to config (may be URL)
147 String config_filename;
148 // This option is selected in the dropdown
149 int default_clickto = Configuration.display_node_data;
150 String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
154 TreeColorSet tree_color_set;
158 TreeFontSet tree_font_set;
159 boolean verbose = Constants.VERBOSE_DEFAULT;
160 private boolean _abbreviate_scientific_names = false;
161 private boolean _antialias_screen = true;
162 private boolean _background_color_gradient = false;
163 private String _base_font_family_name = "";
164 private int _base_font_size = -1;
165 private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
166 private boolean _color_labels_same_as_parent_branch = false;
167 private int _default_bootstrap_samples = -1;
168 private NodeFill _default_node_fill = NodeFill.SOLID;
169 private NodeShape _default_node_shape = NodeShape.RECTANGLE;
170 private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
171 private SortedMap<String, Color> _display_colors = null;
172 private boolean _display_sequence_relations = false;
173 private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
174 private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
175 private boolean _editable = true;
176 private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
177 private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
178 private int _frame_x_size;
179 private int _frame_y_size;
180 private int _graphics_export_x = -1;
181 private int _graphics_export_y = -1;
182 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
183 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
184 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
185 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
186 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
187 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
188 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
189 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
190 private boolean _hide_controls_and_menus = false;
191 private boolean _internal_number_are_confidence_for_nh_parsing = false;
192 private String _label_for_get_ext_descendents_data = "";
193 private int _max_base_font_size = 20;
194 private boolean _midpoint_root = false;
195 private int _min_base_font_size = 2;
196 private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
197 private boolean _nh_parsing_replace_underscores = false;
198 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
199 private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
200 private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
201 private short _ov_max_height = 80;
202 private short _ov_max_width = 80;
203 private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
204 private File _path_to_local_fastme = null;
205 private File _path_to_local_mafft = null;
206 private File _path_to_local_raxml = null;
207 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
208 private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
209 private boolean _show_annotation_ref_source = true;
210 private boolean _show_branch_length_values = false;
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;
226 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
227 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
228 DEFAULT_FONT_FAMILY = font_name;
232 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
233 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
237 public Configuration() {
238 this( null, false, false, false );
241 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
242 if ( ForesterUtil.isEmpty( cf ) ) {
243 config_filename = default_config_filename;
246 config_filename = cf;
248 setDisplayColors( new TreeMap<String, Color>() );
249 config_filename = config_filename.trim();
252 // If URL, open accordingly
254 u = new URL( config_filename );
256 final InputStreamReader isr = new InputStreamReader( u.openStream() );
257 final BufferedReader bf = new BufferedReader( isr );
260 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
261 + config_filename + "]" );
263 catch ( final Exception e ) {
264 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
265 + config_filename + "]: " + e.getLocalizedMessage() );
268 catch ( final Exception e ) {
269 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
270 + config_filename + "]" );
274 // Otherwise, open as a file
275 File f = new File( config_filename );
277 f = new File( config_filename + ".txt" );
279 if ( f.exists() && f.canRead() ) {
281 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
285 catch ( final Exception e ) {
287 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
288 + config_filename + "]: " + e );
294 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
295 + config_filename + "]" );
301 public String getBaseFontFamilyName() {
302 return _base_font_family_name;
305 public int getDefaultBootstrapSamples() {
306 return _default_bootstrap_samples;
309 public NodeFill getDefaultNodeFill() {
310 return _default_node_fill;
313 public NodeShape getDefaultNodeShape() {
314 return _default_node_shape;
317 public short getDefaultNodeShapeSize() {
318 return _default_node_shape_size;
321 public Color getDomainStructureBaseColor() {
322 return _domain_structure_base_color;
325 public Color getDomainStructureFontColor() {
326 return _domain_structure_font_color;
329 public NODE_DATA getExtDescNodeDataToReturn() {
330 return _ext_desc_data_to_return;
333 public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
334 return _ext_node_data_return_on;
337 public int getFrameXSize() {
338 return _frame_x_size;
341 public int getFrameYSize() {
342 return _frame_y_size;
345 public String getLabelForGetExtDescendentsData() {
346 return _label_for_get_ext_descendents_data;
349 public File getPathToLocalFastme() {
350 return _path_to_local_fastme;
353 public File getPathToLocalMafft() {
354 return _path_to_local_mafft;
357 public File getPathToLocalRaxml() {
358 return _path_to_local_raxml;
361 public boolean isAbbreviateScientificTaxonNames() {
362 return _abbreviate_scientific_names;
365 public boolean isBackgroundColorGradient() {
366 return _background_color_gradient;
369 public boolean isColorByTaxonomicGroup() {
373 public boolean isColorLabelsSameAsParentBranch() {
374 return _color_labels_same_as_parent_branch;
377 public boolean isMidpointReroot() {
378 return _midpoint_root;
381 public boolean isShowAnnotationRefSource() {
382 return _show_annotation_ref_source;
385 public boolean isShowDefaultNodeShapesExternal() {
386 return _show_default_node_shapes_external;
389 public boolean isShowDefaultNodeShapesInternal() {
390 return _show_default_node_shapes_internal;
393 public boolean isShowDomainLabels() {
394 return _show_domain_labels;
397 public void putDisplayColors( final String key, final Color color ) {
398 getDisplayColors().put( key, color );
401 public void setAddTaxonomyImagesCB( final boolean b ) {
402 display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no";
405 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
406 _abbreviate_scientific_names = abbreviate_scientific_names;
409 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
410 _background_color_gradient = background_color_gradient;
413 public void setBaseFontFamilyName( final String base_font_family_name ) {
414 _base_font_family_name = base_font_family_name;
417 public void setBaseFontSize( final int base_font_size ) {
418 _base_font_size = base_font_size;
421 public void setColorizeBranches( final boolean b ) {
422 display_options[ use_style ][ 2 ] = b ? "yes" : "no";
425 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
426 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
429 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
430 _default_node_fill = default_node_fill;
433 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
434 _default_node_shape = default_node_shape;
437 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
438 _default_node_shape_size = default_node_shape_size;
441 public void setDisplayAsPhylogram( final boolean b ) {
442 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
445 public void setUseStyle( final boolean b ) {
446 display_options[ use_style ][ 2 ] = b ? "yes" : "no";
449 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
450 _display_colors = display_colors;
453 public void setDisplayConfidenceValues( final boolean b ) {
454 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
457 public void setDisplayInternalData( final boolean b ) {
458 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
461 public void setDisplayNodeNames( final boolean b ) {
462 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
465 public void setDisplaySequenceAcc( final boolean b ) {
466 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
469 public void setDisplaySequenceNames( final boolean b ) {
470 display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no";
473 public void setDisplayGeneNames( final boolean b ) {
474 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
477 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
478 _display_sequence_relations = display_sequence_relations;
481 public void setDisplaySequenceSymbols( final boolean b ) {
482 display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no";
485 public void setDisplayTaxonomyCode( final boolean b ) {
486 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
489 public void setDisplayTaxonomyCommonNames( final boolean b ) {
490 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
493 public void setDisplayTaxonomyImages( final boolean b ) {
494 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
497 public void setDisplayTaxonomyScientificNames( final boolean b ) {
498 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
501 public void setDynamicallyHideData( final boolean b ) {
502 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
505 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
506 _ext_desc_data_to_return = ext_desc_data_to_return;
509 public void setFrameXSize( final int frame_x_size ) {
510 _frame_x_size = frame_x_size;
513 public void setFrameYSize( final int frame_y_size ) {
514 _frame_y_size = frame_y_size;
517 public void setMidpointReroot( final boolean midpoint_root ) {
518 _midpoint_root = midpoint_root;
521 public void setMinConfidenceValue( final double min_confidence_value ) {
522 _min_confidence_value = min_confidence_value;
525 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
526 _node_label_direction = node_label_direction;
529 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
530 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
533 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
534 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
537 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
538 _phylogeny_graphics_type = phylogeny_graphics_type;
541 public void setPrintLineWidth( final float print_line_width ) {
542 _print_line_width = print_line_width;
545 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
546 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
549 public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
550 _show_branch_length_values = show_branch_length_values;
553 public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
554 _show_default_node_shapes_external = show_default_node_shapes_external;
557 public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
558 _show_default_node_shapes_internal = show_default_node_shapes_internal;
561 public void setShowDomainLabels( final boolean show_domain_labels ) {
562 _show_domain_labels = show_domain_labels;
565 public void setShowScale( final boolean show_scale ) {
566 _show_scale = show_scale;
569 boolean displaySequenceRelations() {
570 return _display_sequence_relations;
573 boolean doCheckOption( final int which ) {
574 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
575 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
578 boolean doDisplayClickToOption( final int which ) {
579 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
582 boolean doDisplayOption( final int which ) {
583 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
587 * Will attempt to use the phylogeny to determine whether to check
588 * this or not (e.g. phylogram)
591 boolean doGuessCheckOption( final int which ) {
592 return display_options[ which ][ 2 ].equals( "?" );
595 Map<String, Color> getAnnotationColors() {
596 if ( _annotation_colors == null ) {
597 _annotation_colors = new Hashtable<String, Color>();
599 return _annotation_colors;
602 int getBaseFontSize() {
603 return _base_font_size;
606 CLADOGRAM_TYPE getCladogramType() {
607 return _cladogram_type;
610 int getClickToOptionsCount() {
611 return clickto_options.length;
614 String getClickToTitle( final int which ) {
615 return clickto_options[ which ][ 0 ];
618 int getDefaultDisplayClicktoOption() {
619 return default_clickto;
622 SortedMap<String, Color> getDisplayColors() {
623 return _display_colors;
626 String getDisplayTitle( final int which ) {
627 return display_options[ which ][ 0 ];
630 Map<String, Color> getDomainColors() {
631 if ( _domain_colors == null ) {
632 _domain_colors = new Hashtable<String, Color>();
634 return _domain_colors;
637 int getGraphicsExportX() {
638 return _graphics_export_x;
641 int getGraphicsExportY() {
642 return _graphics_export_y;
645 Color getGuiBackgroundColor() {
646 return _gui_background_color;
649 Color getGuiButtonBackgroundColor() {
650 return _gui_button_background_color;
653 Color getGuiButtonBorderColor() {
654 return _gui_button_border_color;
657 Color getGuiButtonTextColor() {
658 return _gui_button_text_color;
661 Color getGuiCheckboxAndButtonActiveColor() {
662 return _gui_checkbox_and_button_active_color;
665 Color getGuiCheckboxTextColor() {
666 return _gui_checkbox_text_color;
669 Color getGuiMenuBackgroundColor() {
670 return _gui_menu_background_color;
673 Color getGuiMenuTextColor() {
674 return _gui_menu_text_color;
677 int getMaxBaseFontSize() {
678 return _max_base_font_size;
681 int getMinBaseFontSize() {
682 return _min_base_font_size;
685 double getMinConfidenceValue() {
686 return _min_confidence_value;
689 NODE_LABEL_DIRECTION getNodeLabelDirection() {
690 return _node_label_direction;
693 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
694 return _number_of_digits_after_comma_for_branch_length_values;
697 short getNumberOfDigitsAfterCommaForConfidenceValues() {
698 return _number_of_digits_after_comma_for_confidence_values;
701 short getOvMaxHeight() {
702 return _ov_max_height;
705 short getOvMaxWidth() {
706 return _ov_max_width;
709 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
710 return _ov_placement;
713 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
714 return _phylogeny_graphics_type;
717 float getPrintLineWidth() {
718 return _print_line_width;
721 Hashtable<String, Color> getSpeciesColors() {
722 if ( _species_colors == null ) {
723 _species_colors = new Hashtable<String, Color>();
725 return _species_colors;
728 Hashtable<String, Color> getSequenceColors() {
729 if ( _sequence_colors == null ) {
730 _sequence_colors = new Hashtable<String, Color>();
732 return _sequence_colors;
735 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
736 return _taxonomy_extraction;
739 boolean isAntialiasScreen() {
740 if ( ForesterUtil.isMac() ) {
741 //Apple Macintosh graphics are slow, turn off anti-alias.
744 return _antialias_screen;
748 * Convenience method.
750 * @return true if value in configuration file was 'yes'
752 boolean isDrawAsPhylogram() {
753 return doCheckOption( display_as_phylogram );
756 boolean isEditable() {
761 * Only used by ArchaeoptryxE.
764 boolean isHideControlPanelAndMenubar() {
765 return _hide_controls_and_menus;
768 boolean isInternalNumberAreConfidenceForNhParsing() {
769 return _internal_number_are_confidence_for_nh_parsing;
772 boolean isReplaceUnderscoresInNhParsing() {
773 return _nh_parsing_replace_underscores;
776 boolean isShowBranchLengthValues() {
777 return _show_branch_length_values;
780 boolean isShowOverview() {
781 return _show_overview;
784 boolean isShowScale() {
788 final boolean isUseNativeUI() {
789 if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
792 return _ui == UI.NATIVE;
796 * Only used by ArchaeoptryxE.
799 boolean isUseTabbedDisplay() {
800 return _use_tabbed_display;
803 boolean isValidatePhyloXmlAgainstSchema() {
804 return _validate_against_phyloxml_xsd_schema;
807 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
808 _taxonomy_extraction = taxonomy_extraction;
811 private int getClickToIndex( final String name ) {
813 if ( name.equals( "edit_info" ) ) {
814 index = Configuration.display_node_data;
816 .printWarningMessage( Constants.PRG_NAME,
817 "configuration key [edit_info] is deprecated, use [display node data] instead" );
819 else if ( name.equals( "display_node_data" ) ) {
820 index = Configuration.display_node_data;
822 else if ( name.equals( "collapse_uncollapse" ) ) {
823 index = Configuration.collapse_uncollapse;
825 else if ( name.equals( "reroot" ) ) {
826 index = Configuration.reroot;
828 else if ( name.equals( "subtree" ) ) {
829 index = Configuration.subtree;
831 else if ( name.equals( "swap" ) ) {
832 index = Configuration.swap;
834 else if ( name.equals( "sort_descendants" ) ) {
835 index = Configuration.sort_descendents;
837 else if ( name.equals( "get_ext_descendents_data" ) ) {
838 index = Configuration.get_ext_desc_data;
840 else if ( name.equals( "display_sequences" ) ) {
842 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
845 else if ( name.equals( "open_seq_web" ) ) {
846 index = Configuration.open_seq_web;
848 else if ( name.equals( "open_pdb_web" ) ) {
849 index = Configuration.open_pdb_web;
851 else if ( name.equals( "open_tax_web" ) ) {
852 index = Configuration.open_tax_web;
854 else if ( name.equals( "blast" ) ) {
855 index = Configuration.blast;
857 else if ( name.equals( "cut_subtree" ) ) {
858 index = Configuration.cut_subtree;
860 else if ( name.equals( "copy_subtree" ) ) {
861 index = Configuration.copy_subtree;
863 else if ( name.equals( "paste_subtree" ) ) {
864 index = Configuration.paste_subtree;
866 else if ( name.equals( "delete" ) ) {
867 index = Configuration.delete_subtree_or_node;
869 else if ( name.equals( "add_new_node" ) ) {
870 index = Configuration.add_new_node;
872 else if ( name.equals( "edit_node_data" ) ) {
873 index = Configuration.edit_node_data;
875 else if ( name.equals( "select_nodes" ) ) {
876 index = Configuration.select_nodes;
878 else if ( name.equals( "display_node_popup" ) ) {
879 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
880 "configuration key [display_node_popup] is deprecated" );
883 else if ( name.equals( "custom_option" ) ) {
884 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
887 else if ( name.equals( "color_subtree" ) ) {
888 index = Configuration.color_subtree;
890 else if ( name.equals( "change_node_font" ) ) {
891 index = Configuration.change_node_font;
893 else if ( name.equals( "color_node_font" ) ) {
894 index = Configuration.color_node_font;
896 else if ( name.equals( "color_subtree" ) ) {
897 index = Configuration.color_subtree;
902 private boolean parseBoolean( final String str ) {
903 final String my_str = str.trim().toLowerCase();
904 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
907 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
911 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
916 private double parseDouble( final String str ) {
919 d = Double.parseDouble( str.trim() );
921 catch ( final Exception e ) {
922 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
928 private float parseFloat( final String str ) {
931 f = Float.parseFloat( str.trim() );
933 catch ( final Exception e ) {
934 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
940 private int parseInt( final String str ) {
943 i = Integer.parseInt( str.trim() );
945 catch ( final Exception e ) {
946 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
952 private short parseShort( final String str ) {
955 i = Short.parseShort( str.trim() );
957 catch ( final Exception e ) {
958 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
964 private void processFontFamily( final StringTokenizer st ) {
965 setBaseFontFamilyName( "" );
966 final String font_str = ( ( String ) st.nextElement() ).trim();
967 final String[] fonts = font_str.split( ",+" );
968 for( String font : fonts ) {
969 font = font.replace( '_', ' ' ).trim();
970 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
971 setBaseFontFamilyName( font );
978 * read each line of config file, process non-comment lines
979 * @throws IOException
981 private void readConfig( final BufferedReader conf_in ) throws IOException {
984 line = conf_in.readLine();
985 if ( line != null ) {
987 // skip comments and blank lines
988 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
989 // convert runs of spaces to tabs
990 line = line.replaceAll( "\\s+", "\t" );
991 final StringTokenizer st = new StringTokenizer( line, "\t" );
995 } while ( line != null );
998 private void setAntialiasScreen( final boolean antialias_screen ) {
999 _antialias_screen = antialias_screen;
1002 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
1003 _cladogram_type = cladogram_type;
1006 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
1007 _default_bootstrap_samples = default_bootstrap_samples;
1010 private void setEditable( final boolean editable ) {
1011 _editable = editable;
1014 private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
1015 _ext_node_data_return_on = ext_node_data_return_on;
1018 private void setGraphicsExportX( final int graphics_export_x ) {
1019 _graphics_export_x = graphics_export_x;
1022 private void setGraphicsExportY( final int graphics_export_y ) {
1023 _graphics_export_y = graphics_export_y;
1026 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
1027 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
1031 * Set a key-value(s) tuple
1033 private void setKeyValue( final StringTokenizer st ) {
1034 final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
1035 if ( !st.hasMoreElements() ) {
1038 // Handle single value settings first:
1039 if ( key.equals( "default_click_to" ) ) {
1040 final String clickto_name = ( String ) st.nextElement();
1041 default_clickto = getClickToIndex( clickto_name );
1042 if ( default_clickto == -1 ) {
1043 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
1044 + "] for [default_click_to]" );
1045 default_clickto = 0;
1047 else if ( default_clickto == DEPRECATED ) {
1051 else if ( key.equals( "native_ui" ) ) {
1052 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
1053 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
1056 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
1057 _ui = UI.CROSSPLATFORM;
1059 else if ( my_str.equals( "?" ) ) {
1063 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
1068 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
1069 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
1071 else if ( key.equals( "antialias_screen" ) ) {
1072 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
1074 else if ( key.equals( "phylogeny_graphics_type" ) ) {
1075 final String type_str = ( ( String ) st.nextElement() ).trim();
1076 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
1077 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1079 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
1080 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1082 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
1083 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1085 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
1086 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1088 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
1089 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1091 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
1092 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1094 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
1095 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1097 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
1098 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1101 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1102 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1103 + "] for [phylogeny_graphics_type]" );
1106 else if ( key.equals( "min_confidence_value" ) ) {
1107 final String mcv_str = ( ( String ) st.nextElement() ).trim();
1108 final double d = parseDouble( mcv_str );
1109 setMinConfidenceValue( d );
1111 else if ( key.equals( "font_family" ) ) {
1112 processFontFamily( st );
1114 else if ( key.equals( "font_size" ) ) {
1115 final String size_str = ( ( String ) st.nextElement() ).trim();
1116 final int i = parseInt( size_str );
1118 setBaseFontSize( i );
1121 else if ( key.equals( "font_size_min" ) ) {
1122 final String size_str = ( ( String ) st.nextElement() ).trim();
1123 final int i = parseInt( size_str );
1125 setMinBaseFontSize( i );
1128 else if ( key.equals( "font_size_max" ) ) {
1129 final String size_str = ( ( String ) st.nextElement() ).trim();
1130 final int i = parseInt( size_str );
1132 setMaxBaseFontSize( i );
1135 else if ( key.equals( "graphics_export_x" ) ) {
1136 final String str = ( ( String ) st.nextElement() ).trim();
1137 final int i = parseInt( str );
1139 setGraphicsExportX( i );
1142 else if ( key.equals( "graphics_export_y" ) ) {
1143 final String str = ( ( String ) st.nextElement() ).trim();
1144 final int i = parseInt( str );
1146 setGraphicsExportY( i );
1149 else if ( key.equals( "pdf_export_line_width" ) ) {
1150 final String str = ( ( String ) st.nextElement() ).trim();
1151 final float f = parseFloat( str );
1153 setPrintLineWidth( f );
1156 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1157 "value for [pdf_export_line_width] cannot be zero or negative" );
1160 else if ( key.equals( "window_initial_size_x" ) ) {
1161 final String str = ( ( String ) st.nextElement() ).trim();
1162 final int i = parseInt( str );
1167 else if ( key.equals( "window_initial_size_y" ) ) {
1168 final String str = ( ( String ) st.nextElement() ).trim();
1169 final int i = parseInt( str );
1174 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1175 final String str = ( ( String ) st.nextElement() ).trim();
1176 final int i = parseInt( str );
1178 setDefaultBootstrapSamples( i );
1182 .printWarningMessage( Constants.PRG_NAME,
1183 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1186 else if ( key.equals( "mafft_local" ) ) {
1187 final String str = ( ( String ) st.nextElement() ).trim();
1188 if ( !ForesterUtil.isEmpty( str ) ) {
1189 setPathToLocalMafft( new File( str ) );
1192 else if ( key.equals( "fastme_local" ) ) {
1193 final String str = ( ( String ) st.nextElement() ).trim();
1194 if ( !ForesterUtil.isEmpty( str ) ) {
1195 setPathToLocalFastme( new File( str ) );
1198 else if ( key.equals( "raxml_local" ) ) {
1199 final String str = ( ( String ) st.nextElement() ).trim();
1200 if ( !ForesterUtil.isEmpty( str ) ) {
1201 setPathToLocalRaxml( new File( str ) );
1204 else if ( key.equals( "show_scale" ) ) {
1205 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1207 else if ( key.equals( "show_overview" ) ) {
1208 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1210 else if ( key.equals( "show_branch_length_values" ) ) {
1211 setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
1213 else if ( key.equals( "background_gradient" ) ) {
1214 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1216 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1217 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1219 else if ( key.equals( "show_domain_labels" ) ) {
1220 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1222 else if ( key.equals( "show_seq_annotation_ref_sources" ) ) {
1223 setShowAnnotationRefSource( parseBoolean( ( String ) st.nextElement() ) );
1225 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1226 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1228 else if ( key.equals( "cladogram_type" ) ) {
1229 final String type_str = ( ( String ) st.nextElement() ).trim();
1230 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1231 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1233 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1234 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1236 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1237 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1240 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1241 + "] for [cladogram_type]" );
1244 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1246 .printWarningMessage( Constants.PRG_NAME,
1247 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1249 else if ( key.equals( "hide_controls_and_menus" ) ) {
1250 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1252 else if ( key.equals( "use_tabbed_display" ) ) {
1253 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1255 else if ( key.equals( "overview_width" ) ) {
1256 final short i = parseShort( ( ( String ) st.nextElement() ) );
1259 else if ( key.equals( "overview_height" ) ) {
1260 final short i = parseShort( ( ( String ) st.nextElement() ) );
1261 setOvMaxHeight( i );
1263 else if ( key.equals( "overview_placement_type" ) ) {
1264 final String type_str = ( ( String ) st.nextElement() ).trim();
1265 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1266 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1268 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1269 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1271 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1272 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1274 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1275 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1278 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1279 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1280 + "] for [overview_placement_type]" );
1283 else if ( key.equals( "node_label_direction" ) ) {
1284 final String type_str = ( ( String ) st.nextElement() ).trim();
1285 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1286 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1288 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1289 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1292 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1293 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1294 + "] for [node_label_direction]" );
1297 else if ( key.equals( "branch_length_value_digits" ) ) {
1298 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1300 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1303 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1304 + "] for [branch_length_value_digits]" );
1307 else if ( key.equals( "confidence_value_digits" ) ) {
1308 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1310 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1313 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1314 + "] for [confidence_value_digits]" );
1317 else if ( key.equals( "allow_editing" ) ) {
1318 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1320 else if ( key.equals( "display_sequence_relations" ) ) {
1321 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1323 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1324 final boolean r = parseBoolean( ( String ) st.nextElement() );
1325 if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
1327 .printWarningMessage( Constants.PRG_NAME,
1328 "attempt to extract taxonomies and replace underscores at the same time" );
1331 setReplaceUnderscoresInNhParsing( r );
1334 else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
1335 final String s = ( String ) st.nextElement();
1336 if ( s.equalsIgnoreCase( "no" ) ) {
1337 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1339 else if ( s.equalsIgnoreCase( "pfam_relaxed" ) ) {
1340 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1342 else if ( s.equalsIgnoreCase( "pfam_strict" ) ) {
1343 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1345 else if ( s.equalsIgnoreCase( "aggressive" ) ) {
1346 setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
1350 .printWarningMessage( Constants.PRG_NAME,
1351 "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
1353 + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
1355 if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
1357 .printWarningMessage( Constants.PRG_NAME,
1358 "attempt to extract taxonomies and replace underscores at the same time" );
1361 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1362 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1364 else if ( key.equals( "gui_background_color" ) ) {
1365 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1367 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1368 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1370 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1371 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1373 else if ( key.equals( "gui_button_text_color" ) ) {
1374 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1376 else if ( key.equals( "gui_button_background_color" ) ) {
1377 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1379 else if ( key.equals( "gui_menu_background_color" ) ) {
1380 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1382 else if ( key.equals( "gui_menu_text_color" ) ) {
1383 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1385 else if ( key.equals( "gui_button_border_color" ) ) {
1386 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1388 else if ( key.equals( "domain_structure_font_color" ) ) {
1389 _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
1391 else if ( key.equals( "domain_structure_base_color" ) ) {
1392 _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
1394 else if ( key.equals( "show_default_node_shapes" ) ) {
1396 .printWarningMessage( Constants.PRG_NAME,
1397 "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" );
1398 final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() );
1399 setShowDefaultNodeShapesInternal( b );
1400 setShowDefaultNodeShapesExternal( b );
1402 else if ( key.equals( "show_default_node_shapes_internal" ) ) {
1403 setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1405 else if ( key.equals( "show_default_node_shapes_external" ) ) {
1406 setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1408 else if ( key.equals( "default_node_size" ) ) {
1409 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1410 setDefaultNodeShapeSize( i );
1412 else if ( key.equals( "default_node_fill" ) ) {
1413 final String fill_str = ( ( String ) st.nextElement() ).trim();
1414 if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.NONE.toString() ) ) {
1415 setDefaultNodeFill( NodeFill.NONE );
1417 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.GRADIENT.toString() ) ) {
1418 setDefaultNodeFill( NodeFill.GRADIENT );
1420 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.SOLID.toString() ) ) {
1421 setDefaultNodeFill( NodeFill.SOLID );
1424 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1425 + "] for [default_node_fill]" );
1428 else if ( key.equals( "default_node_shape" ) ) {
1429 final String shape_str = ( ( String ) st.nextElement() ).trim();
1430 if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.CIRCLE.toString() ) ) {
1431 setDefaultNodeShape( NodeShape.CIRCLE );
1433 else if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.RECTANGLE.toString() ) ) {
1434 setDefaultNodeShape( NodeShape.RECTANGLE );
1437 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1438 + "] for [default_node_shape]" );
1441 else if ( key.equals( "midpoint_reroot" ) ) {
1442 setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) );
1444 else if ( key.equals( "ext_descendents_data_to_return" ) ) {
1445 final String s = ( ( String ) st.nextElement() ).trim();
1446 if ( s.equalsIgnoreCase( "node_name" ) ) {
1447 setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
1449 else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
1450 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
1452 else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) {
1453 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ_FASTA );
1455 else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
1456 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
1458 else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
1459 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
1461 else if ( s.equalsIgnoreCase( "gene_name" ) ) {
1462 setExtDescNodeDataToReturn( NODE_DATA.GENE_NAME );
1464 else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
1465 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
1467 else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
1468 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME );
1470 else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
1471 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
1473 else if ( s.equalsIgnoreCase( "taxonomy_common_name" ) ) {
1474 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_COMM0N_NAME );
1476 else if ( s.equalsIgnoreCase( "user_selected" ) ) {
1477 setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
1480 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1481 + "] for [ext_descendents_data_to_return]" );
1484 else if ( key.equals( "label_for_get_ext_descendents_data" ) ) {
1485 final String s = ( ( String ) st.nextElement() ).trim();
1486 if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) {
1487 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s
1488 + "] for [label_for_get_ext_descendents_data]" );
1491 setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
1494 else if ( key.equals( "ext_descendents_data_to_return_on" ) ) {
1495 final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
1496 if ( s.equals( "console" ) ) {
1497 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
1499 else if ( s.equals( "window" ) ) {
1500 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
1502 else if ( s.equals( "buffer_only" ) ) {
1503 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
1506 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1507 + "] for [ext_descendents_data_to_return_on]" );
1511 else if ( key.equals( "vector_data_min_color" ) ) {
1512 _vector_data_min_color = Color.decode( ( String ) st.nextElement() );
1514 else if ( key.equals( "vector_data_max_color" ) ) {
1515 _vector_data_max_color = Color.decode( ( String ) st.nextElement() );
1517 else if ( key.equals( "vector_data_mean_color" ) ) {
1518 _vector_data_mean_color = Color.decode( ( String ) st.nextElement() );
1521 else if ( key.equals( "vector_data_width" ) ) {
1522 _vector_data_width = parseShort( ( String ) st.nextElement() );
1523 if ( _vector_data_width < 1 ) {
1524 _vector_data_width = 120;
1527 else if ( key.equals( "vector_data_height" ) ) {
1528 _vector_data_height = parseShort( ( String ) st.nextElement() );
1529 if ( _vector_data_height < 1 ) {
1530 _vector_data_height = 12;
1534 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1537 if ( key.equals( "phylogram" ) ) {
1538 key_index = Configuration.display_as_phylogram;
1540 else if ( key.equals( "rollover" ) ) {
1541 key_index = Configuration.node_data_popup;
1543 else if ( key.equals( "color_according_to_species" ) ) {
1544 key_index = Configuration.color_according_to_species;
1546 else if ( key.equals( "color_according_to_sequence" ) ) {
1547 key_index = Configuration.color_according_to_sequence;
1549 else if ( key.equals( "show_node_names" ) ) {
1550 key_index = Configuration.show_node_names;
1552 else if ( key.equals( "show_taxonomy_code" ) ) {
1553 key_index = Configuration.show_tax_code;
1555 else if ( key.equals( "write_confidence_values" ) ) {
1556 key_index = Configuration.write_confidence_values;
1558 else if ( key.equals( "write_events" ) ) {
1559 key_index = Configuration.write_events;
1561 else if ( key.equals( "use_visual_styles" ) ) {
1562 key_index = Configuration.use_style;
1564 else if ( key.equals( "color_branches" ) ) {
1565 key_index = Configuration.use_style;
1567 .printWarningMessage( Constants.PRG_NAME,
1568 "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" );
1570 else if ( key.equals( "width_branches" ) ) {
1571 key_index = Configuration.width_branches;
1573 else if ( key.equals( "show_domain_architectures" ) ) {
1574 key_index = Configuration.show_domain_architectures;
1576 else if ( key.equals( "show_annotations" ) ) {
1577 key_index = Configuration.show_annotation;
1579 else if ( key.equals( "show_binary_characters" ) ) {
1580 key_index = Configuration.show_binary_characters;
1582 else if ( key.equals( "show_binary_character_counts" ) ) {
1583 key_index = Configuration.show_binary_character_counts;
1585 else if ( key.equals( "show_seq_names" ) ) {
1586 key_index = Configuration.show_seq_names;
1588 else if ( key.equals( "show_gene_names" ) ) {
1589 key_index = Configuration.show_gene_names;
1591 else if ( key.equals( "show_seq_symbols" ) ) {
1592 key_index = Configuration.show_seq_symbols;
1594 else if ( key.equals( "show_seq_acc" ) ) {
1595 key_index = Configuration.show_sequence_acc;
1597 else if ( key.equals( "display_internal_data" ) ) {
1598 key_index = Configuration.display_internal_data;
1600 else if ( key.equals( "dynamically_hide_data" ) ) {
1601 key_index = Configuration.dynamically_hide_data;
1603 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1604 key_index = Configuration.show_taxonomy_scientific_names;
1606 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1607 key_index = Configuration.show_taxonomy_common_names;
1609 else if ( key.equals( "show_taxonomy_images" ) ) {
1610 key_index = Configuration.show_taxonomy_images;
1612 else if ( key.equals( "color_according_to_annotation" ) ) {
1613 key_index = Configuration.color_according_to_annotation;
1615 else if ( key.equals( "show_vector_data" ) ) {
1616 key_index = Configuration.show_vector_data;
1618 else if ( key.equals( "show_properties" ) ) {
1619 key_index = Configuration.show_properties;
1621 else if ( key.equals( "show_relation_confidence" ) ) {
1622 key_index = Configuration.show_relation_confidence;
1624 // If we've found the key, set the values
1625 if ( key_index >= 0 ) {
1626 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1627 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1628 // otherwise, keep looking
1631 if ( key_index == DEPRECATED ) {
1634 else if ( key.equals( "click_to" ) ) {
1635 final String click_to_name = ( String ) st.nextElement();
1636 key_index = getClickToIndex( click_to_name );
1637 if ( key_index >= 0 ) {
1638 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1640 else if ( key_index == DEPRECATED ) {
1644 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1648 else if ( key.equals( "species_color" ) ) {
1649 getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
1650 Color.decode( ( String ) st.nextElement() ) );
1652 else if ( key.equals( "sequence_color" ) ) {
1653 getSequenceColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
1654 Color.decode( ( String ) st.nextElement() ) );
1656 else if ( key.equals( "domain_color" ) ) {
1657 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1659 else if ( key.equals( "annotation_color" ) ) {
1660 getAnnotationColors()
1661 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1663 else if ( key.equals( "function_color" ) ) {
1664 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1665 "configuration key [function_color] is deprecated" );
1667 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1668 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1671 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1672 + "] in: " + config_filename );
1677 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1678 + config_filename );
1682 private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
1683 _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
1686 private void setMaxBaseFontSize( final int max_base_font_size ) {
1687 _max_base_font_size = max_base_font_size;
1690 private void setMinBaseFontSize( final int min_base_font_size ) {
1691 _min_base_font_size = min_base_font_size;
1694 private void setOvMaxHeight( final short ov_max_height ) {
1695 _ov_max_height = ov_max_height;
1698 private void setOvMaxWidth( final short ov_max_width ) {
1699 _ov_max_width = ov_max_width;
1702 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1703 _ov_placement = ov_placement;
1706 private void setPathToLocalFastme( final File path_to_local_fastme ) {
1707 _path_to_local_fastme = path_to_local_fastme;
1710 private void setPathToLocalMafft( final File path_to_local_mafft ) {
1711 _path_to_local_mafft = path_to_local_mafft;
1714 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
1715 _path_to_local_raxml = path_to_local_raxml;
1718 private void setShowAnnotationRefSource( final boolean b ) {
1719 _show_annotation_ref_source = b;
1722 private void setShowOverview( final boolean show_overview ) {
1723 _show_overview = show_overview;
1726 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1727 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1730 static String getDefaultFontFamilyName() {
1731 return DEFAULT_FONT_FAMILY;
1734 public enum EXT_NODE_DATA_RETURN_ON {
1735 BUFFER_ONLY, CONSOLE, WINODW;
1739 CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN
1742 static enum TRIPLET {
1743 FALSE, TRUE, UNKNOWN
1746 public Color getVectorDataMinColor() {
1747 return _vector_data_min_color;
1750 public Color getVectorDataMaxColor() {
1751 return _vector_data_max_color;
1754 public Color getVectorDataMeanColor() {
1755 return _vector_data_mean_color;
1758 public double getVectorDataHeight() {
1759 return _vector_data_height;
1762 public int getVectorDataWidth() {
1763 return _vector_data_width;