2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
7 // Copyright (C) 2000-2001 Washington University School of Medicine
8 // and Howard Hughes Medical Institute
9 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
10 // All rights reserved
12 // This library is free software; you can redistribute it and/or
13 // modify it under the terms of the GNU Lesser General Public
14 // License as published by the Free Software Foundation; either
15 // version 2.1 of the License, or (at your option) any later version.
17 // This library is distributed in the hope that it will be useful,
18 // but WITHOUT ANY WARRANTY; without even the implied warranty of
19 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20 // Lesser General Public License for more details.
22 // You should have received a copy of the GNU Lesser General Public
23 // License along with this library; if not, write to the Free Software
24 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
26 // Contact: phylosoft @ gmail . com
27 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
29 package org.forester.archaeopteryx;
31 import java.awt.Color;
32 import java.io.BufferedReader;
34 import java.io.FileReader;
35 import java.io.IOException;
36 import java.io.InputStreamReader;
38 import java.util.Arrays;
39 import java.util.Hashtable;
41 import java.util.SortedMap;
42 import java.util.StringTokenizer;
43 import java.util.TreeMap;
45 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
46 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
47 import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE;
48 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
49 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
50 import org.forester.phylogeny.data.NodeData.NODE_DATA;
51 import org.forester.phylogeny.data.NodeVisualData;
52 import org.forester.phylogeny.data.NodeVisualData.NodeFill;
53 import org.forester.phylogeny.data.NodeVisualData.NodeShape;
54 import org.forester.util.ForesterUtil;
56 public final class Configuration {
58 final static String clickto_options[][] = {
59 { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
60 { "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "display" },
61 { "Colorize Node(s)", "display" }, { "Change Node Font(s)", "display" },
62 { "Colorize Subtree(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "display" },
63 { "Open Taxonomy DB", "display" }, { "Launch BLAST", "display" }, { "Cut Subtree", "display" },
64 { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" },
65 { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Sort Descendants", "display" },
66 { "Return", "display" }, { "Select Node(s)", "display" } };
67 final static int display_node_data = 0;
68 final static int collapse_uncollapse = 1;
69 final static int reroot = 2;
70 final static int subtree = 3;
71 final static int swap = 4;
72 final static int color_node_font = 5;
73 final static int change_node_font = 6;
74 final static int color_subtree = 7;
75 final static int open_seq_web = 8;
76 final static int open_pdb_web = 9;
77 final static int open_tax_web = 10;
78 final static int blast = 11;
79 final static int cut_subtree = 12;
80 final static int copy_subtree = 13;
81 final static int paste_subtree = 14;
82 final static int delete_subtree_or_node = 15;
83 final static int add_new_node = 16;
84 final static int edit_node_data = 17;
85 final static int sort_descendents = 18;
86 final static int get_ext_desc_data = 19;
87 final static int select_nodes = 20;
91 final static String display_options[][] = {
92 { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
93 { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" },
94 { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
95 { "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" },
96 { "Branch Widths", "display", "no" }, { "Domain Architectures", "display", "no" },
97 { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
98 { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" },
99 { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
100 { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
101 { "Colorize by Annotation", "display", "no" }, { "Seq Symbol", "display", "yes" },
102 { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
103 { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
104 { "Properties", "display", "no" }, { "Gene Name", "display", "yes" } };
105 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 boolean _editable = true;
174 private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
175 private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
176 private int _frame_x_size;
177 private int _frame_y_size;
178 private int _graphics_export_x = -1;
179 private int _graphics_export_y = -1;
180 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
181 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
182 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
183 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
184 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
185 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
186 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
187 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
188 private boolean _hide_controls_and_menus = false;
189 private boolean _internal_number_are_confidence_for_nh_parsing = false;
190 private String _label_for_get_ext_descendents_data = "";
191 private int _max_base_font_size = 20;
192 private boolean _midpoint_root = false;
193 private int _min_base_font_size = 2;
194 private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
195 private boolean _nh_parsing_replace_underscores = false;
196 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
197 private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
198 private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
199 private short _ov_max_height = 80;
200 private short _ov_max_width = 80;
201 private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
202 private File _path_to_local_fastme = null;
203 private File _path_to_local_mafft = null;
204 private File _path_to_local_raxml = null;
205 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
206 private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
207 private boolean _show_annotation_ref_source = true;
208 private boolean _show_branch_length_values = false;
209 private boolean _show_default_node_shapes_external = false;
210 private boolean _show_default_node_shapes_internal = false;
211 private boolean _show_domain_labels = true;
212 private boolean _show_overview = true;
213 private boolean _show_scale = false;
214 private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
215 private UI _ui = UI.UNKNOWN;
216 private boolean _use_tabbed_display = false;
217 private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
218 private Color _vector_data_min_color = Color.BLUE;
219 private Color _vector_data_max_color = Color.YELLOW;
220 private Color _vector_data_mean_color = Color.WHITE;
221 private double _vector_data_height = 12;
222 private int _vector_data_width = 120;
223 private boolean _line_up_renderable_node_data;
224 private boolean _right_align_domains;
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 NODE_DATA getExtDescNodeDataToReturn() {
322 return _ext_desc_data_to_return;
325 public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
326 return _ext_node_data_return_on;
329 public int getFrameXSize() {
330 return _frame_x_size;
333 public int getFrameYSize() {
334 return _frame_y_size;
337 public String getLabelForGetExtDescendentsData() {
338 return _label_for_get_ext_descendents_data;
341 public File getPathToLocalFastme() {
342 return _path_to_local_fastme;
345 public File getPathToLocalMafft() {
346 return _path_to_local_mafft;
349 public File getPathToLocalRaxml() {
350 return _path_to_local_raxml;
353 public boolean isAbbreviateScientificTaxonNames() {
354 return _abbreviate_scientific_names;
357 public boolean isBackgroundColorGradient() {
358 return _background_color_gradient;
361 public boolean isColorByTaxonomicGroup() {
365 public boolean isColorLabelsSameAsParentBranch() {
366 return _color_labels_same_as_parent_branch;
369 public boolean isMidpointReroot() {
370 return _midpoint_root;
373 public boolean isShowAnnotationRefSource() {
374 return _show_annotation_ref_source;
377 public boolean isShowDefaultNodeShapesExternal() {
378 return _show_default_node_shapes_external;
381 public boolean isShowDefaultNodeShapesInternal() {
382 return _show_default_node_shapes_internal;
385 public boolean isShowDomainLabels() {
386 return _show_domain_labels;
389 public void putDisplayColors( final String key, final Color color ) {
390 getDisplayColors().put( key, color );
393 public void setAddTaxonomyImagesCB( final boolean b ) {
394 display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no";
397 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
398 _abbreviate_scientific_names = abbreviate_scientific_names;
401 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
402 _background_color_gradient = background_color_gradient;
405 public void setBaseFontFamilyName( final String base_font_family_name ) {
406 _base_font_family_name = base_font_family_name;
409 public void setBaseFontSize( final int base_font_size ) {
410 _base_font_size = base_font_size;
413 public void setColorizeBranches( final boolean b ) {
414 display_options[ use_style ][ 2 ] = b ? "yes" : "no";
417 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
418 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
421 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
422 _default_node_fill = default_node_fill;
425 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
426 _default_node_shape = default_node_shape;
429 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
430 _default_node_shape_size = default_node_shape_size;
433 public void setDisplayAsPhylogram( final boolean b ) {
434 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
437 public void setUseStyle( final boolean b ) {
438 display_options[ use_style ][ 2 ] = b ? "yes" : "no";
441 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
442 _display_colors = display_colors;
445 public void setDisplayConfidenceValues( final boolean b ) {
446 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
449 public void setDisplayInternalData( final boolean b ) {
450 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
453 public void setDisplayNodeNames( final boolean b ) {
454 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
457 public void setDisplaySequenceAcc( final boolean b ) {
458 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
461 public void setDisplaySequenceNames( final boolean b ) {
462 display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no";
465 public void setDisplayGeneNames( final boolean b ) {
466 display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
469 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
470 _display_sequence_relations = display_sequence_relations;
473 public void setDisplaySequenceSymbols( final boolean b ) {
474 display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no";
477 public void setDisplayTaxonomyCode( final boolean b ) {
478 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
481 public void setDisplayTaxonomyCommonNames( final boolean b ) {
482 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
485 public void setDisplayTaxonomyImages( final boolean b ) {
486 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
489 public void setDisplayTaxonomyScientificNames( final boolean b ) {
490 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
493 public void setDynamicallyHideData( final boolean b ) {
494 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
497 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
498 _ext_desc_data_to_return = ext_desc_data_to_return;
501 public void setFrameXSize( final int frame_x_size ) {
502 _frame_x_size = frame_x_size;
505 public void setFrameYSize( final int frame_y_size ) {
506 _frame_y_size = frame_y_size;
509 public void setMidpointReroot( final boolean midpoint_root ) {
510 _midpoint_root = midpoint_root;
513 public void setMinConfidenceValue( final double min_confidence_value ) {
514 _min_confidence_value = min_confidence_value;
517 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
518 _node_label_direction = node_label_direction;
521 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
522 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
525 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
526 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
529 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
530 _phylogeny_graphics_type = phylogeny_graphics_type;
533 public void setPrintLineWidth( final float print_line_width ) {
534 _print_line_width = print_line_width;
537 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
538 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
541 public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
542 _show_branch_length_values = show_branch_length_values;
545 public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
546 _show_default_node_shapes_external = show_default_node_shapes_external;
549 public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
550 _show_default_node_shapes_internal = show_default_node_shapes_internal;
553 public void setShowDomainLabels( final boolean show_domain_labels ) {
554 _show_domain_labels = show_domain_labels;
557 public void setShowScale( final boolean show_scale ) {
558 _show_scale = show_scale;
561 boolean displaySequenceRelations() {
562 return _display_sequence_relations;
565 boolean doCheckOption( final int which ) {
566 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
567 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
570 boolean doDisplayClickToOption( final int which ) {
571 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
574 boolean doDisplayOption( final int which ) {
575 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
579 * Will attempt to use the phylogeny to determine whether to check
580 * this or not (e.g. phylogram)
583 boolean doGuessCheckOption( final int which ) {
584 return display_options[ which ][ 2 ].equals( "?" );
587 Map<String, Color> getAnnotationColors() {
588 if ( _annotation_colors == null ) {
589 _annotation_colors = new Hashtable<String, Color>();
591 return _annotation_colors;
594 int getBaseFontSize() {
595 return _base_font_size;
598 CLADOGRAM_TYPE getCladogramType() {
599 return _cladogram_type;
602 int getClickToOptionsCount() {
603 return clickto_options.length;
606 String getClickToTitle( final int which ) {
607 return clickto_options[ which ][ 0 ];
610 int getDefaultDisplayClicktoOption() {
611 return default_clickto;
614 SortedMap<String, Color> getDisplayColors() {
615 return _display_colors;
618 String getDisplayTitle( final int which ) {
619 return display_options[ which ][ 0 ];
622 Map<String, Color> getDomainColors() {
623 if ( _domain_colors == null ) {
624 _domain_colors = new Hashtable<String, Color>();
626 return _domain_colors;
629 int getGraphicsExportX() {
630 return _graphics_export_x;
633 int getGraphicsExportY() {
634 return _graphics_export_y;
637 Color getGuiBackgroundColor() {
638 return _gui_background_color;
641 Color getGuiButtonBackgroundColor() {
642 return _gui_button_background_color;
645 Color getGuiButtonBorderColor() {
646 return _gui_button_border_color;
649 Color getGuiButtonTextColor() {
650 return _gui_button_text_color;
653 Color getGuiCheckboxAndButtonActiveColor() {
654 return _gui_checkbox_and_button_active_color;
657 Color getGuiCheckboxTextColor() {
658 return _gui_checkbox_text_color;
661 Color getGuiMenuBackgroundColor() {
662 return _gui_menu_background_color;
665 Color getGuiMenuTextColor() {
666 return _gui_menu_text_color;
669 int getMaxBaseFontSize() {
670 return _max_base_font_size;
673 int getMinBaseFontSize() {
674 return _min_base_font_size;
677 double getMinConfidenceValue() {
678 return _min_confidence_value;
681 NODE_LABEL_DIRECTION getNodeLabelDirection() {
682 return _node_label_direction;
685 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
686 return _number_of_digits_after_comma_for_branch_length_values;
689 short getNumberOfDigitsAfterCommaForConfidenceValues() {
690 return _number_of_digits_after_comma_for_confidence_values;
693 short getOvMaxHeight() {
694 return _ov_max_height;
697 short getOvMaxWidth() {
698 return _ov_max_width;
701 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
702 return _ov_placement;
705 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
706 return _phylogeny_graphics_type;
709 float getPrintLineWidth() {
710 return _print_line_width;
713 Hashtable<String, Color> getSpeciesColors() {
714 if ( _species_colors == null ) {
715 _species_colors = new Hashtable<String, Color>();
717 return _species_colors;
720 Hashtable<String, Color> getSequenceColors() {
721 if ( _sequence_colors == null ) {
722 _sequence_colors = new Hashtable<String, Color>();
724 return _sequence_colors;
727 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
728 return _taxonomy_extraction;
731 boolean isAntialiasScreen() {
732 if ( ForesterUtil.isMac() ) {
733 //Apple Macintosh graphics are slow, turn off anti-alias.
736 return _antialias_screen;
740 * Convenience method.
742 * @return true if value in configuration file was 'yes'
744 boolean isDrawAsPhylogram() {
745 return doCheckOption( display_as_phylogram );
748 boolean isEditable() {
753 * Only used by ArchaeoptryxE.
756 boolean isHideControlPanelAndMenubar() {
757 return _hide_controls_and_menus;
760 boolean isInternalNumberAreConfidenceForNhParsing() {
761 return _internal_number_are_confidence_for_nh_parsing;
764 boolean isReplaceUnderscoresInNhParsing() {
765 return _nh_parsing_replace_underscores;
768 boolean isShowBranchLengthValues() {
769 return _show_branch_length_values;
772 boolean isShowOverview() {
773 return _show_overview;
776 boolean isShowScale() {
780 final boolean isUseNativeUI() {
781 if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
784 return _ui == UI.NATIVE;
788 * Only used by ArchaeoptryxE.
791 boolean isUseTabbedDisplay() {
792 return _use_tabbed_display;
795 boolean isValidatePhyloXmlAgainstSchema() {
796 return _validate_against_phyloxml_xsd_schema;
799 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
800 _taxonomy_extraction = taxonomy_extraction;
803 private int getClickToIndex( final String name ) {
805 if ( name.equals( "edit_info" ) ) {
806 index = Configuration.display_node_data;
808 .printWarningMessage( Constants.PRG_NAME,
809 "configuration key [edit_info] is deprecated, use [display node data] instead" );
811 else if ( name.equals( "display_node_data" ) ) {
812 index = Configuration.display_node_data;
814 else if ( name.equals( "collapse_uncollapse" ) ) {
815 index = Configuration.collapse_uncollapse;
817 else if ( name.equals( "reroot" ) ) {
818 index = Configuration.reroot;
820 else if ( name.equals( "subtree" ) ) {
821 index = Configuration.subtree;
823 else if ( name.equals( "swap" ) ) {
824 index = Configuration.swap;
826 else if ( name.equals( "sort_descendants" ) ) {
827 index = Configuration.sort_descendents;
829 else if ( name.equals( "get_ext_descendents_data" ) ) {
830 index = Configuration.get_ext_desc_data;
832 else if ( name.equals( "display_sequences" ) ) {
834 .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
837 else if ( name.equals( "open_seq_web" ) ) {
838 index = Configuration.open_seq_web;
840 else if ( name.equals( "open_pdb_web" ) ) {
841 index = Configuration.open_pdb_web;
843 else if ( name.equals( "open_tax_web" ) ) {
844 index = Configuration.open_tax_web;
846 else if ( name.equals( "blast" ) ) {
847 index = Configuration.blast;
849 else if ( name.equals( "cut_subtree" ) ) {
850 index = Configuration.cut_subtree;
852 else if ( name.equals( "copy_subtree" ) ) {
853 index = Configuration.copy_subtree;
855 else if ( name.equals( "paste_subtree" ) ) {
856 index = Configuration.paste_subtree;
858 else if ( name.equals( "delete" ) ) {
859 index = Configuration.delete_subtree_or_node;
861 else if ( name.equals( "add_new_node" ) ) {
862 index = Configuration.add_new_node;
864 else if ( name.equals( "edit_node_data" ) ) {
865 index = Configuration.edit_node_data;
867 else if ( name.equals( "select_nodes" ) ) {
868 index = Configuration.select_nodes;
870 else if ( name.equals( "display_node_popup" ) ) {
871 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
872 "configuration key [display_node_popup] is deprecated" );
875 else if ( name.equals( "custom_option" ) ) {
876 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
879 else if ( name.equals( "color_subtree" ) ) {
880 index = Configuration.color_subtree;
882 else if ( name.equals( "change_node_font" ) ) {
883 index = Configuration.change_node_font;
885 else if ( name.equals( "color_node_font" ) ) {
886 index = Configuration.color_node_font;
888 else if ( name.equals( "color_subtree" ) ) {
889 index = Configuration.color_subtree;
894 private boolean parseBoolean( final String str ) {
895 final String my_str = str.trim().toLowerCase();
896 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
899 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
903 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
908 private double parseDouble( final String str ) {
911 d = Double.parseDouble( str.trim() );
913 catch ( final Exception e ) {
914 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
920 private float parseFloat( final String str ) {
923 f = Float.parseFloat( str.trim() );
925 catch ( final Exception e ) {
926 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
932 private int parseInt( final String str ) {
935 i = Integer.parseInt( str.trim() );
937 catch ( final Exception e ) {
938 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
944 private short parseShort( final String str ) {
947 i = Short.parseShort( str.trim() );
949 catch ( final Exception e ) {
950 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
956 private void processFontFamily( final StringTokenizer st ) {
957 setBaseFontFamilyName( "" );
958 final String font_str = ( ( String ) st.nextElement() ).trim();
959 final String[] fonts = font_str.split( ",+" );
960 for( String font : fonts ) {
961 font = font.replace( '_', ' ' ).trim();
962 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
963 setBaseFontFamilyName( font );
970 * read each line of config file, process non-comment lines
971 * @throws IOException
973 private void readConfig( final BufferedReader conf_in ) throws IOException {
976 line = conf_in.readLine();
977 if ( line != null ) {
979 // skip comments and blank lines
980 if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
981 // convert runs of spaces to tabs
982 line = line.replaceAll( "\\s+", "\t" );
983 final StringTokenizer st = new StringTokenizer( line, "\t" );
987 } while ( line != null );
990 private void setAntialiasScreen( final boolean antialias_screen ) {
991 _antialias_screen = antialias_screen;
994 private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
995 _cladogram_type = cladogram_type;
998 private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
999 _default_bootstrap_samples = default_bootstrap_samples;
1002 private void setEditable( final boolean editable ) {
1003 _editable = editable;
1006 private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
1007 _ext_node_data_return_on = ext_node_data_return_on;
1010 private void setGraphicsExportX( final int graphics_export_x ) {
1011 _graphics_export_x = graphics_export_x;
1014 private void setGraphicsExportY( final int graphics_export_y ) {
1015 _graphics_export_y = graphics_export_y;
1018 private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
1019 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
1023 * Set a key-value(s) tuple
1025 private void setKeyValue( final StringTokenizer st ) {
1026 final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
1027 if ( !st.hasMoreElements() ) {
1030 // Handle single value settings first:
1031 if ( key.equals( "default_click_to" ) ) {
1032 final String clickto_name = ( String ) st.nextElement();
1033 default_clickto = getClickToIndex( clickto_name );
1034 if ( default_clickto == -1 ) {
1035 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
1036 + "] for [default_click_to]" );
1037 default_clickto = 0;
1039 else if ( default_clickto == DEPRECATED ) {
1043 else if ( key.equals( "native_ui" ) ) {
1044 final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
1045 if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
1048 else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
1049 _ui = UI.CROSSPLATFORM;
1051 else if ( my_str.equals( "?" ) ) {
1055 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
1060 else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
1061 setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
1063 else if ( key.equals( "antialias_screen" ) ) {
1064 setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
1066 else if ( key.equals( "phylogeny_graphics_type" ) ) {
1067 final String type_str = ( ( String ) st.nextElement() ).trim();
1068 if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
1069 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1071 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
1072 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1074 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
1075 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1077 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
1078 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1080 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
1081 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1083 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
1084 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1086 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
1087 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1089 else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
1090 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1093 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1094 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1095 + "] for [phylogeny_graphics_type]" );
1098 else if ( key.equals( "min_confidence_value" ) ) {
1099 final String mcv_str = ( ( String ) st.nextElement() ).trim();
1100 final double d = parseDouble( mcv_str );
1101 setMinConfidenceValue( d );
1103 else if ( key.equals( "font_family" ) ) {
1104 processFontFamily( st );
1106 else if ( key.equals( "font_size" ) ) {
1107 final String size_str = ( ( String ) st.nextElement() ).trim();
1108 final int i = parseInt( size_str );
1110 setBaseFontSize( i );
1113 else if ( key.equals( "font_size_min" ) ) {
1114 final String size_str = ( ( String ) st.nextElement() ).trim();
1115 final int i = parseInt( size_str );
1117 setMinBaseFontSize( i );
1120 else if ( key.equals( "font_size_max" ) ) {
1121 final String size_str = ( ( String ) st.nextElement() ).trim();
1122 final int i = parseInt( size_str );
1124 setMaxBaseFontSize( i );
1127 else if ( key.equals( "graphics_export_x" ) ) {
1128 final String str = ( ( String ) st.nextElement() ).trim();
1129 final int i = parseInt( str );
1131 setGraphicsExportX( i );
1134 else if ( key.equals( "graphics_export_y" ) ) {
1135 final String str = ( ( String ) st.nextElement() ).trim();
1136 final int i = parseInt( str );
1138 setGraphicsExportY( i );
1141 else if ( key.equals( "pdf_export_line_width" ) ) {
1142 final String str = ( ( String ) st.nextElement() ).trim();
1143 final float f = parseFloat( str );
1145 setPrintLineWidth( f );
1148 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1149 "value for [pdf_export_line_width] cannot be zero or negative" );
1152 else if ( key.equals( "window_initial_size_x" ) ) {
1153 final String str = ( ( String ) st.nextElement() ).trim();
1154 final int i = parseInt( str );
1159 else if ( key.equals( "window_initial_size_y" ) ) {
1160 final String str = ( ( String ) st.nextElement() ).trim();
1161 final int i = parseInt( str );
1166 else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
1167 final String str = ( ( String ) st.nextElement() ).trim();
1168 final int i = parseInt( str );
1170 setDefaultBootstrapSamples( i );
1174 .printWarningMessage( Constants.PRG_NAME,
1175 "value for [default_number_of_bootstrap_resamples] cannot be negative" );
1178 else if ( key.equals( "mafft_local" ) ) {
1179 final String str = ( ( String ) st.nextElement() ).trim();
1180 if ( !ForesterUtil.isEmpty( str ) ) {
1181 setPathToLocalMafft( new File( str ) );
1184 else if ( key.equals( "fastme_local" ) ) {
1185 final String str = ( ( String ) st.nextElement() ).trim();
1186 if ( !ForesterUtil.isEmpty( str ) ) {
1187 setPathToLocalFastme( new File( str ) );
1190 else if ( key.equals( "raxml_local" ) ) {
1191 final String str = ( ( String ) st.nextElement() ).trim();
1192 if ( !ForesterUtil.isEmpty( str ) ) {
1193 setPathToLocalRaxml( new File( str ) );
1196 else if ( key.equals( "show_scale" ) ) {
1197 setShowScale( parseBoolean( ( String ) st.nextElement() ) );
1199 else if ( key.equals( "show_overview" ) ) {
1200 setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
1202 else if ( key.equals( "show_branch_length_values" ) ) {
1203 setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
1205 else if ( key.equals( "background_gradient" ) ) {
1206 setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
1208 else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
1209 setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
1211 else if ( key.equals( "show_domain_labels" ) ) {
1212 setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
1214 else if ( key.equals( "show_seq_annotation_ref_sources" ) ) {
1215 setShowAnnotationRefSource( parseBoolean( ( String ) st.nextElement() ) );
1217 else if ( key.equals( "abbreviate_scientific_names" ) ) {
1218 setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) );
1220 else if ( key.equals( "cladogram_type" ) ) {
1221 final String type_str = ( ( String ) st.nextElement() ).trim();
1222 if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
1223 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
1225 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
1226 setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1228 else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
1229 setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1232 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1233 + "] for [cladogram_type]" );
1236 else if ( key.equals( "non_lined_up_cladogram" ) ) {
1238 .printWarningMessage( Constants.PRG_NAME,
1239 "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
1241 else if ( key.equals( "hide_controls_and_menus" ) ) {
1242 _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
1244 else if ( key.equals( "use_tabbed_display" ) ) {
1245 _use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
1247 else if ( key.equals( "overview_width" ) ) {
1248 final short i = parseShort( ( ( String ) st.nextElement() ) );
1251 else if ( key.equals( "overview_height" ) ) {
1252 final short i = parseShort( ( ( String ) st.nextElement() ) );
1253 setOvMaxHeight( i );
1255 else if ( key.equals( "overview_placement_type" ) ) {
1256 final String type_str = ( ( String ) st.nextElement() ).trim();
1257 if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
1258 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1260 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
1261 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1263 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
1264 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1266 else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
1267 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1270 setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1271 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1272 + "] for [overview_placement_type]" );
1275 else if ( key.equals( "node_label_direction" ) ) {
1276 final String type_str = ( ( String ) st.nextElement() ).trim();
1277 if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
1278 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1280 else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
1281 setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1284 setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1285 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
1286 + "] for [node_label_direction]" );
1289 else if ( key.equals( "branch_length_value_digits" ) ) {
1290 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1292 setNumberOfDigitsAfterCommaForBranchLengthValue( i );
1295 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1296 + "] for [branch_length_value_digits]" );
1299 else if ( key.equals( "confidence_value_digits" ) ) {
1300 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1302 setNumberOfDigitsAfterCommaForConfidenceValues( i );
1305 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
1306 + "] for [confidence_value_digits]" );
1309 else if ( key.equals( "allow_editing" ) ) {
1310 setEditable( parseBoolean( ( String ) st.nextElement() ) );
1312 else if ( key.equals( "display_sequence_relations" ) ) {
1313 setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
1315 else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
1316 final boolean r = parseBoolean( ( String ) st.nextElement() );
1317 if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
1319 .printWarningMessage( Constants.PRG_NAME,
1320 "attempt to extract taxonomies and replace underscores at the same time" );
1323 setReplaceUnderscoresInNhParsing( r );
1326 else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
1327 final String s = ( String ) st.nextElement();
1328 if ( s.equalsIgnoreCase( "no" ) ) {
1329 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1331 else if ( s.equalsIgnoreCase( "pfam_relaxed" ) ) {
1332 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1334 else if ( s.equalsIgnoreCase( "pfam_strict" ) ) {
1335 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1337 else if ( s.equalsIgnoreCase( "aggressive" ) ) {
1338 setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
1342 .printWarningMessage( Constants.PRG_NAME,
1343 "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
1345 + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
1347 if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
1349 .printWarningMessage( Constants.PRG_NAME,
1350 "attempt to extract taxonomies and replace underscores at the same time" );
1353 else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
1354 setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
1356 else if ( key.equals( "gui_background_color" ) ) {
1357 _gui_background_color = Color.decode( ( String ) st.nextElement() );
1359 else if ( key.equals( "gui_checkbox_text_color" ) ) {
1360 _gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
1362 else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
1363 _gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
1365 else if ( key.equals( "gui_button_text_color" ) ) {
1366 _gui_button_text_color = Color.decode( ( String ) st.nextElement() );
1368 else if ( key.equals( "gui_button_background_color" ) ) {
1369 _gui_button_background_color = Color.decode( ( String ) st.nextElement() );
1371 else if ( key.equals( "gui_menu_background_color" ) ) {
1372 _gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
1374 else if ( key.equals( "gui_menu_text_color" ) ) {
1375 _gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
1377 else if ( key.equals( "gui_button_border_color" ) ) {
1378 _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
1380 else if ( key.equals( "show_default_node_shapes" ) ) {
1382 .printWarningMessage( Constants.PRG_NAME,
1383 "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" );
1384 final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() );
1385 setShowDefaultNodeShapesInternal( b );
1386 setShowDefaultNodeShapesExternal( b );
1388 else if ( key.equals( "show_default_node_shapes_internal" ) ) {
1389 setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1391 else if ( key.equals( "show_default_node_shapes_external" ) ) {
1392 setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1394 else if ( key.equals( "default_node_size" ) ) {
1395 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1396 setDefaultNodeShapeSize( i );
1398 else if ( key.equals( "default_node_fill" ) ) {
1399 final String fill_str = ( ( String ) st.nextElement() ).trim();
1400 if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.NONE.toString() ) ) {
1401 setDefaultNodeFill( NodeFill.NONE );
1403 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.GRADIENT.toString() ) ) {
1404 setDefaultNodeFill( NodeFill.GRADIENT );
1406 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.SOLID.toString() ) ) {
1407 setDefaultNodeFill( NodeFill.SOLID );
1410 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1411 + "] for [default_node_fill]" );
1414 else if ( key.equals( "default_node_shape" ) ) {
1415 final String shape_str = ( ( String ) st.nextElement() ).trim();
1416 if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.CIRCLE.toString() ) ) {
1417 setDefaultNodeShape( NodeShape.CIRCLE );
1419 else if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.RECTANGLE.toString() ) ) {
1420 setDefaultNodeShape( NodeShape.RECTANGLE );
1423 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1424 + "] for [default_node_shape]" );
1427 else if ( key.equals( "midpoint_reroot" ) ) {
1428 setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) );
1430 else if ( key.equals( "ext_descendents_data_to_return" ) ) {
1431 final String s = ( ( String ) st.nextElement() ).trim();
1432 if ( s.equalsIgnoreCase( "node_name" ) ) {
1433 setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
1435 else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
1436 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
1438 else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) {
1439 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ_FASTA );
1441 else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
1442 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
1444 else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
1445 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
1447 else if ( s.equalsIgnoreCase( "gene_name" ) ) {
1448 setExtDescNodeDataToReturn( NODE_DATA.GENE_NAME );
1450 else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
1451 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
1453 else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
1454 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME );
1456 else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
1457 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
1459 else if ( s.equalsIgnoreCase( "taxonomy_common_name" ) ) {
1460 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_COMM0N_NAME );
1462 else if ( s.equalsIgnoreCase( "user_selected" ) ) {
1463 setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
1466 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1467 + "] for [ext_descendents_data_to_return]" );
1470 else if ( key.equals( "label_for_get_ext_descendents_data" ) ) {
1471 final String s = ( ( String ) st.nextElement() ).trim();
1472 if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) {
1473 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s
1474 + "] for [label_for_get_ext_descendents_data]" );
1477 setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
1480 else if ( key.equals( "ext_descendents_data_to_return_on" ) ) {
1481 final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
1482 if ( s.equals( "console" ) ) {
1483 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
1485 else if ( s.equals( "window" ) ) {
1486 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
1488 else if ( s.equals( "buffer_only" ) ) {
1489 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
1492 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1493 + "] for [ext_descendents_data_to_return_on]" );
1496 else if ( key.equals( "vector_data_min_color" ) ) {
1497 _vector_data_min_color = Color.decode( ( String ) st.nextElement() );
1499 else if ( key.equals( "vector_data_max_color" ) ) {
1500 _vector_data_max_color = Color.decode( ( String ) st.nextElement() );
1502 else if ( key.equals( "vector_data_mean_color" ) ) {
1503 _vector_data_mean_color = Color.decode( ( String ) st.nextElement() );
1505 else if ( key.equals( "vector_data_width" ) ) {
1506 _vector_data_width = parseShort( ( String ) st.nextElement() );
1507 if ( _vector_data_width < 1 ) {
1508 _vector_data_width = 120;
1511 else if ( key.equals( "vector_data_height" ) ) {
1512 _vector_data_height = parseShort( ( String ) st.nextElement() );
1513 if ( _vector_data_height < 1 ) {
1514 _vector_data_height = 12;
1517 else if ( key.equals( "line_up_renderable_data" ) ) {
1518 setLineUpRendarableNodeData( parseBoolean( ( String ) st.nextElement() ) );
1520 else if ( key.equals( "right_align_domain_architectures" ) ) {
1521 setRightLineUpDomains( parseBoolean( ( String ) st.nextElement() ) );
1523 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1526 if ( key.equals( "phylogram" ) ) {
1527 key_index = Configuration.display_as_phylogram;
1529 else if ( key.equals( "rollover" ) ) {
1530 key_index = Configuration.node_data_popup;
1532 else if ( key.equals( "color_according_to_species" ) ) {
1533 key_index = Configuration.color_according_to_species;
1535 else if ( key.equals( "color_according_to_sequence" ) ) {
1536 key_index = Configuration.color_according_to_sequence;
1538 else if ( key.equals( "show_node_names" ) ) {
1539 key_index = Configuration.show_node_names;
1541 else if ( key.equals( "show_taxonomy_code" ) ) {
1542 key_index = Configuration.show_tax_code;
1544 else if ( key.equals( "write_confidence_values" ) ) {
1545 key_index = Configuration.write_confidence_values;
1547 else if ( key.equals( "write_events" ) ) {
1548 key_index = Configuration.write_events;
1550 else if ( key.equals( "use_visual_styles" ) ) {
1551 key_index = Configuration.use_style;
1553 else if ( key.equals( "color_branches" ) ) {
1554 key_index = Configuration.use_style;
1556 .printWarningMessage( Constants.PRG_NAME,
1557 "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" );
1559 else if ( key.equals( "width_branches" ) ) {
1560 key_index = Configuration.width_branches;
1562 else if ( key.equals( "show_domain_architectures" ) ) {
1563 key_index = Configuration.show_domain_architectures;
1565 else if ( key.equals( "show_annotations" ) ) {
1566 key_index = Configuration.show_annotation;
1568 else if ( key.equals( "show_binary_characters" ) ) {
1569 key_index = Configuration.show_binary_characters;
1571 else if ( key.equals( "show_binary_character_counts" ) ) {
1572 key_index = Configuration.show_binary_character_counts;
1574 else if ( key.equals( "show_seq_names" ) ) {
1575 key_index = Configuration.show_seq_names;
1577 else if ( key.equals( "show_gene_names" ) ) {
1578 key_index = Configuration.show_gene_names;
1580 else if ( key.equals( "show_seq_symbols" ) ) {
1581 key_index = Configuration.show_seq_symbols;
1583 else if ( key.equals( "show_seq_acc" ) ) {
1584 key_index = Configuration.show_sequence_acc;
1586 else if ( key.equals( "display_internal_data" ) ) {
1587 key_index = Configuration.display_internal_data;
1589 else if ( key.equals( "dynamically_hide_data" ) ) {
1590 key_index = Configuration.dynamically_hide_data;
1592 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1593 key_index = Configuration.show_taxonomy_scientific_names;
1595 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1596 key_index = Configuration.show_taxonomy_common_names;
1598 else if ( key.equals( "show_taxonomy_images" ) ) {
1599 key_index = Configuration.show_taxonomy_images;
1601 else if ( key.equals( "color_according_to_annotation" ) ) {
1602 key_index = Configuration.color_according_to_annotation;
1604 else if ( key.equals( "show_vector_data" ) ) {
1605 key_index = Configuration.show_vector_data;
1607 else if ( key.equals( "show_properties" ) ) {
1608 key_index = Configuration.show_properties;
1610 else if ( key.equals( "show_relation_confidence" ) ) {
1611 key_index = Configuration.show_relation_confidence;
1613 // If we've found the key, set the values
1614 if ( key_index >= 0 ) {
1615 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1616 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1617 // otherwise, keep looking
1620 if ( key_index == DEPRECATED ) {
1623 else if ( key.equals( "click_to" ) ) {
1624 final String click_to_name = ( String ) st.nextElement();
1625 key_index = getClickToIndex( click_to_name );
1626 if ( key_index >= 0 ) {
1627 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1629 else if ( key_index == DEPRECATED ) {
1633 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1637 else if ( key.equals( "species_color" ) ) {
1638 getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
1639 Color.decode( ( String ) st.nextElement() ) );
1641 else if ( key.equals( "sequence_color" ) ) {
1642 getSequenceColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
1643 Color.decode( ( String ) st.nextElement() ) );
1645 else if ( key.equals( "domain_color" ) ) {
1646 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1648 else if ( key.equals( "annotation_color" ) ) {
1649 getAnnotationColors()
1650 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1652 else if ( key.equals( "function_color" ) ) {
1653 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1654 "configuration key [function_color] is deprecated" );
1656 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1657 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1660 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1661 + "] in: " + config_filename );
1666 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1667 + config_filename );
1671 private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
1672 _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
1675 private void setMaxBaseFontSize( final int max_base_font_size ) {
1676 _max_base_font_size = max_base_font_size;
1679 private void setMinBaseFontSize( final int min_base_font_size ) {
1680 _min_base_font_size = min_base_font_size;
1683 private void setOvMaxHeight( final short ov_max_height ) {
1684 _ov_max_height = ov_max_height;
1687 private void setOvMaxWidth( final short ov_max_width ) {
1688 _ov_max_width = ov_max_width;
1691 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1692 _ov_placement = ov_placement;
1695 private void setPathToLocalFastme( final File path_to_local_fastme ) {
1696 _path_to_local_fastme = path_to_local_fastme;
1699 private void setPathToLocalMafft( final File path_to_local_mafft ) {
1700 _path_to_local_mafft = path_to_local_mafft;
1703 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
1704 _path_to_local_raxml = path_to_local_raxml;
1707 private void setShowAnnotationRefSource( final boolean b ) {
1708 _show_annotation_ref_source = b;
1711 private void setShowOverview( final boolean show_overview ) {
1712 _show_overview = show_overview;
1715 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1716 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1719 static String getDefaultFontFamilyName() {
1720 return DEFAULT_FONT_FAMILY;
1723 public enum EXT_NODE_DATA_RETURN_ON {
1724 BUFFER_ONLY, CONSOLE, WINODW;
1728 CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN
1731 static enum TRIPLET {
1732 FALSE, TRUE, UNKNOWN
1735 public Color getVectorDataMinColor() {
1736 return _vector_data_min_color;
1739 public Color getVectorDataMaxColor() {
1740 return _vector_data_max_color;
1743 public Color getVectorDataMeanColor() {
1744 return _vector_data_mean_color;
1747 public double getVectorDataHeight() {
1748 return _vector_data_height;
1751 public int getVectorDataWidth() {
1752 return _vector_data_width;
1755 final public boolean isLineUpRendarableNodeData() {
1756 return _line_up_renderable_node_data;
1759 final public boolean isRightLineUpDomains() {
1760 return _right_align_domains;
1763 final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) {
1764 _line_up_renderable_node_data = line_up_renderable_node_data;
1767 final public void setRightLineUpDomains( final boolean right_align_domains ) {
1768 _right_align_domains = right_align_domains;