2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
7 // Copyright (C) 2000-2001 Washington University School of Medicine
8 // and Howard Hughes Medical Institute
9 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
10 // All rights reserved
12 // This library is free software; you can redistribute it and/or
13 // modify it under the terms of the GNU Lesser General Public
14 // License as published by the Free Software Foundation; either
15 // version 2.1 of the License, or (at your option) any later version.
17 // This library is distributed in the hope that it will be useful,
18 // but WITHOUT ANY WARRANTY; without even the implied warranty of
19 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20 // Lesser General Public License for more details.
22 // You should have received a copy of the GNU Lesser General Public
23 // License along with this library; if not, write to the Free Software
24 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
26 // Contact: phylosoft @ gmail . com
27 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
29 package org.forester.archaeopteryx;
31 import java.awt.Color;
32 import java.io.BufferedReader;
34 import java.io.FileReader;
35 import java.io.IOException;
36 import java.io.InputStreamReader;
38 import java.util.Arrays;
39 import java.util.Hashtable;
41 import java.util.SortedMap;
42 import java.util.StringTokenizer;
43 import java.util.TreeMap;
45 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
46 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
47 import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE;
48 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
49 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
50 import org.forester.phylogeny.data.NodeData.NODE_DATA;
51 import org.forester.phylogeny.data.NodeVisualData;
52 import org.forester.phylogeny.data.NodeVisualData.NodeFill;
53 import org.forester.phylogeny.data.NodeVisualData.NodeShape;
54 import org.forester.util.ForesterUtil;
56 public final class Configuration {
58 final static String clickto_options[][] = {
59 { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
60 { "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "display" },
61 { "Colorize Node(s)", "display" }, { "Change Node Font(s)", "display" },
62 { "Colorize Subtree(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "display" },
63 { "Open Taxonomy DB", "display" }, { "Launch BLAST", "display" }, { "Cut Subtree", "display" },
64 { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" },
65 { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Sort Descendants", "display" },
66 { "Return", "display" }, { "Select Node(s)", "display" } };
67 final static int display_node_data = 0;
68 final static int collapse_uncollapse = 1;
69 final static int reroot = 2;
70 final static int subtree = 3;
71 final static int swap = 4;
72 final static int color_node_font = 5;
73 final static int change_node_font = 6;
74 final static int color_subtree = 7;
75 final static int open_seq_web = 8;
76 final static int open_pdb_web = 9;
77 final static int open_tax_web = 10;
78 final static int blast = 11;
79 final static int cut_subtree = 12;
80 final static int copy_subtree = 13;
81 final static int paste_subtree = 14;
82 final static int delete_subtree_or_node = 15;
83 final static int add_new_node = 16;
84 final static int edit_node_data = 17;
85 final static int sort_descendents = 18;
86 final static int get_ext_desc_data = 19;
87 final static int select_nodes = 20;
91 final static String display_options[][] = {
92 { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
93 { "Seq Annotations", "nodisplay", "no" }, { "Confidence Values", "display", "?" },
94 { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
95 { "Visual Styles/Branch Colors", "display", "no" }, { "Branch Widths", "display", "no" },
96 { "Show Custom Nodes", "display", "yes" }, { "Protein Domains", "nodisplay", "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", "nodisplay", "no" }, { "Seq Symbol", "display", "yes" },
102 { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
103 { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
104 { "Properties", "nodisplay", "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 use_style = 7;
113 final static int width_branches = 8;
114 final static int show_custom_node_shapes = 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";
136 private static Hashtable<String, Color> _annotation_colors;
140 private static Hashtable<String, Color> _domain_colors;
144 private static Hashtable<String, Color> _species_colors;
145 private static String DEFAULT_FONT_FAMILY = "";
146 private static final int DEPRECATED = -2;
147 private static final String DISPLAY_COLOR_KEY = "display_color";
148 // ---------------------------
149 // Display options for trees
150 // ---------------------------
151 // ---------------------------------
152 // Pertaining to the config itself
153 // ---------------------------------
154 // Full path to config (may be URL)
155 String config_filename;
156 // This option is selected in the dropdown
157 int default_clickto = Configuration.display_node_data;
158 String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
162 TreeColorSet tree_color_set;
166 TreeFontSet tree_font_set;
167 boolean verbose = Constants.VERBOSE_DEFAULT;
168 private boolean _abbreviate_scientific_names = false;
169 private boolean _antialias_screen = true;
170 private boolean _background_color_gradient = false;
171 private String _base_font_family_name = "";
172 private int _base_font_size = -1;
173 private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
174 private boolean _color_labels_same_as_parent_branch = false;
175 private int _default_bootstrap_samples = -1;
176 private NodeFill _default_node_fill = NodeFill.SOLID;
177 private NodeShape _default_node_shape = NodeShape.RECTANGLE;
178 private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
179 private SortedMap<String, Color> _display_colors = null;
180 private boolean _display_sequence_relations = false;
181 private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
182 private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
183 private boolean _editable = true;
184 private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
185 private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
186 private int _frame_x_size;
187 private int _frame_y_size;
188 private int _graphics_export_x = -1;
189 private int _graphics_export_y = -1;
190 private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
191 private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
192 private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
193 private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
194 private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
195 private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
196 private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
197 private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
198 private boolean _hide_controls_and_menus = false;
199 private boolean _internal_number_are_confidence_for_nh_parsing = false;
200 private String _label_for_get_ext_descendents_data = "";
201 private int _max_base_font_size = 20;
202 private boolean _midpoint_root = false;
203 private int _min_base_font_size = 2;
204 private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
205 private boolean _nh_parsing_replace_underscores = false;
206 private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
207 private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
208 private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
209 private short _ov_max_height = 80;
210 private short _ov_max_width = 80;
211 private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
212 private File _path_to_local_fastme = null;
213 private File _path_to_local_mafft = null;
214 private File _path_to_local_raxml = null;
215 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
216 private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
217 private boolean _show_annotation_ref_source = true;
218 private boolean _show_branch_length_values = false;
219 private boolean _show_default_node_shapes_external = false;
220 private boolean _show_default_node_shapes_internal = false;
221 private boolean _show_domain_labels = true;
222 private boolean _show_overview = true;
223 private boolean _show_scale = false;
224 private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
225 private UI _ui = UI.UNKNOWN;
226 private boolean _use_tabbed_display = false;
227 private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
229 for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
230 if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
231 DEFAULT_FONT_FAMILY = font_name;
235 if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
236 DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
240 public Configuration() {
241 this( null, false, false, false );
244 public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
245 if ( ForesterUtil.isEmpty( cf ) ) {
246 config_filename = default_config_filename;
249 config_filename = cf;
251 setDisplayColors( new TreeMap<String, Color>() );
252 config_filename = config_filename.trim();
255 // If URL, open accordingly
257 u = new URL( config_filename );
259 final InputStreamReader isr = new InputStreamReader( u.openStream() );
260 final BufferedReader bf = new BufferedReader( isr );
263 ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
264 + config_filename + "]" );
266 catch ( final Exception e ) {
267 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
268 + config_filename + "]: " + e.getLocalizedMessage() );
271 catch ( final Exception e ) {
272 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
273 + config_filename + "]" );
277 // Otherwise, open as a file
278 File f = new File( config_filename );
280 f = new File( config_filename + ".txt" );
282 if ( f.exists() && f.canRead() ) {
284 final BufferedReader bf = new BufferedReader( new FileReader( f ) );
288 catch ( final Exception e ) {
290 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
291 + config_filename + "]: " + e );
297 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
298 + config_filename + "]" );
304 public String getBaseFontFamilyName() {
305 return _base_font_family_name;
308 public int getDefaultBootstrapSamples() {
309 return _default_bootstrap_samples;
312 public NodeFill getDefaultNodeFill() {
313 return _default_node_fill;
316 public NodeShape getDefaultNodeShape() {
317 return _default_node_shape;
320 public short getDefaultNodeShapeSize() {
321 return _default_node_shape_size;
324 public Color getDomainStructureBaseColor() {
325 return _domain_structure_base_color;
328 public Color getDomainStructureFontColor() {
329 return _domain_structure_font_color;
332 public NODE_DATA getExtDescNodeDataToReturn() {
333 return _ext_desc_data_to_return;
336 public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
337 return _ext_node_data_return_on;
340 public int getFrameXSize() {
341 return _frame_x_size;
344 public int getFrameYSize() {
345 return _frame_y_size;
348 public String getLabelForGetExtDescendentsData() {
349 return _label_for_get_ext_descendents_data;
352 public File getPathToLocalFastme() {
353 return _path_to_local_fastme;
356 public File getpathToLocalMafft() {
357 return _path_to_local_mafft;
360 public File getPathToLocalRaxml() {
361 return _path_to_local_raxml;
364 public boolean isAbbreviateScientificTaxonNames() {
365 return _abbreviate_scientific_names;
368 public boolean isBackgroundColorGradient() {
369 return _background_color_gradient;
372 public boolean isColorByTaxonomicGroup() {
376 public boolean isColorLabelsSameAsParentBranch() {
377 return _color_labels_same_as_parent_branch;
380 public boolean isMidpointReroot() {
381 return _midpoint_root;
384 public boolean isShowAnnotationRefSource() {
385 return _show_annotation_ref_source;
388 public boolean isShowDefaultNodeShapesExternal() {
389 return _show_default_node_shapes_external;
392 public boolean isShowDefaultNodeShapesInternal() {
393 return _show_default_node_shapes_internal;
396 public boolean isShowDomainLabels() {
397 return _show_domain_labels;
400 public void putDisplayColors( final String key, final Color color ) {
401 getDisplayColors().put( key, color );
404 public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
405 _abbreviate_scientific_names = abbreviate_scientific_names;
408 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
409 _background_color_gradient = background_color_gradient;
412 public void setBaseFontFamilyName( final String base_font_family_name ) {
413 _base_font_family_name = base_font_family_name;
416 public void setBaseFontSize( final int base_font_size ) {
417 _base_font_size = base_font_size;
420 public void setColorizeBranches( final boolean b ) {
421 display_options[ use_style ][ 2 ] = b ? "yes" : "no";
424 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
425 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
428 public void setDefaultNodeFill( final NodeFill default_node_fill ) {
429 _default_node_fill = default_node_fill;
432 public void setDefaultNodeShape( final NodeShape default_node_shape ) {
433 _default_node_shape = default_node_shape;
436 public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
437 _default_node_shape_size = default_node_shape_size;
440 public void setDisplayAsPhylogram( final boolean b ) {
441 display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
444 public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
445 _display_colors = display_colors;
448 public void setDisplayConfidenceValues( final boolean b ) {
449 display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
452 public void setDisplayInternalData( final boolean b ) {
453 display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
456 public void setDisplayNodeNames( final boolean b ) {
457 display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
460 public void setDisplaySequenceAcc( final boolean b ) {
461 display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
464 public void setDisplaySequenceNames( final boolean b ) {
465 display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no";
468 public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
469 _display_sequence_relations = display_sequence_relations;
472 public void setDisplaySequenceSymbols( final boolean b ) {
473 display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no";
476 public void setDisplayTaxonomyCode( final boolean b ) {
477 display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
480 public void setDisplayTaxonomyCommonNames( final boolean b ) {
481 display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
484 public void setDisplayTaxonomyImages( final boolean b ) {
485 display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
488 public void setDisplayTaxonomyScientificNames( final boolean b ) {
489 display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
492 public void setDynamicallyHideData( final boolean b ) {
493 display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
496 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
497 _ext_desc_data_to_return = ext_desc_data_to_return;
500 public void setFrameXSize( final int frame_x_size ) {
501 _frame_x_size = frame_x_size;
504 public void setFrameYSize( final int frame_y_size ) {
505 _frame_y_size = frame_y_size;
508 public void setMidpointReroot( final boolean midpoint_root ) {
509 _midpoint_root = midpoint_root;
512 public void setMinConfidenceValue( final double min_confidence_value ) {
513 _min_confidence_value = min_confidence_value;
516 public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
517 _node_label_direction = node_label_direction;
520 public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
521 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
524 public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
525 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
528 public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
529 _phylogeny_graphics_type = phylogeny_graphics_type;
532 public void setPrintLineWidth( final float print_line_width ) {
533 _print_line_width = print_line_width;
536 public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
537 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
540 public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
541 _show_branch_length_values = show_branch_length_values;
544 public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
545 _show_default_node_shapes_external = show_default_node_shapes_external;
548 public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
549 _show_default_node_shapes_internal = show_default_node_shapes_internal;
552 public void setShowDomainLabels( final boolean show_domain_labels ) {
553 _show_domain_labels = show_domain_labels;
556 public void setShowScale( final boolean show_scale ) {
557 _show_scale = show_scale;
560 public void setTaxonomyColorize( final boolean b ) {
561 display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
564 public void setUseBranchesWidths( final boolean b ) {
565 display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
568 boolean displaySequenceRelations() {
569 return _display_sequence_relations;
572 boolean doCheckOption( final int which ) {
573 return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
574 || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
577 boolean doDisplayClickToOption( final int which ) {
578 return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
581 boolean doDisplayOption( final int which ) {
582 return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
586 * Will attempt to use the phylogeny to determine whether to check
587 * this or not (e.g. phylogram)
590 boolean doGuessCheckOption( final int which ) {
591 return display_options[ which ][ 2 ].equals( "?" );
594 Map<String, Color> getAnnotationColors() {
595 if ( _annotation_colors == null ) {
596 _annotation_colors = new Hashtable<String, Color>();
598 return _annotation_colors;
601 int getBaseFontSize() {
602 return _base_font_size;
605 CLADOGRAM_TYPE getCladogramType() {
606 return _cladogram_type;
609 int getClickToOptionsCount() {
610 return clickto_options.length;
613 String getClickToTitle( final int which ) {
614 return clickto_options[ which ][ 0 ];
617 int getDefaultDisplayClicktoOption() {
618 return default_clickto;
621 SortedMap<String, Color> getDisplayColors() {
622 return _display_colors;
625 String getDisplayTitle( final int which ) {
626 return display_options[ which ][ 0 ];
629 Map<String, Color> getDomainColors() {
630 if ( _domain_colors == null ) {
631 _domain_colors = new Hashtable<String, Color>();
633 return _domain_colors;
636 int getGraphicsExportX() {
637 return _graphics_export_x;
640 int getGraphicsExportY() {
641 return _graphics_export_y;
644 Color getGuiBackgroundColor() {
645 return _gui_background_color;
648 Color getGuiButtonBackgroundColor() {
649 return _gui_button_background_color;
652 Color getGuiButtonBorderColor() {
653 return _gui_button_border_color;
656 Color getGuiButtonTextColor() {
657 return _gui_button_text_color;
660 Color getGuiCheckboxAndButtonActiveColor() {
661 return _gui_checkbox_and_button_active_color;
664 Color getGuiCheckboxTextColor() {
665 return _gui_checkbox_text_color;
668 Color getGuiMenuBackgroundColor() {
669 return _gui_menu_background_color;
672 Color getGuiMenuTextColor() {
673 return _gui_menu_text_color;
676 int getMaxBaseFontSize() {
677 return _max_base_font_size;
680 int getMinBaseFontSize() {
681 return _min_base_font_size;
684 double getMinConfidenceValue() {
685 return _min_confidence_value;
688 NODE_LABEL_DIRECTION getNodeLabelDirection() {
689 return _node_label_direction;
692 short getNumberOfDigitsAfterCommaForBranchLengthValues() {
693 return _number_of_digits_after_comma_for_branch_length_values;
696 short getNumberOfDigitsAfterCommaForConfidenceValues() {
697 return _number_of_digits_after_comma_for_confidence_values;
700 short getOvMaxHeight() {
701 return _ov_max_height;
704 short getOvMaxWidth() {
705 return _ov_max_width;
708 OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
709 return _ov_placement;
712 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
713 return _phylogeny_graphics_type;
716 float getPrintLineWidth() {
717 return _print_line_width;
720 Hashtable<String, Color> getSpeciesColors() {
721 if ( _species_colors == null ) {
722 _species_colors = new Hashtable<String, Color>();
724 return _species_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( "domain_structure_font_color" ) ) {
1381 _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
1383 else if ( key.equals( "domain_structure_base_color" ) ) {
1384 _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
1386 else if ( key.equals( "show_default_node_shapes" ) ) {
1388 .printWarningMessage( Constants.PRG_NAME,
1389 "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" );
1390 final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() );
1391 setShowDefaultNodeShapesInternal( b );
1392 setShowDefaultNodeShapesExternal( b );
1394 else if ( key.equals( "show_default_node_shapes_internal" ) ) {
1395 setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1397 else if ( key.equals( "show_default_node_shapes_external" ) ) {
1398 setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
1400 else if ( key.equals( "default_node_size" ) ) {
1401 final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
1402 setDefaultNodeShapeSize( i );
1404 else if ( key.equals( "default_node_fill" ) ) {
1405 final String fill_str = ( ( String ) st.nextElement() ).trim();
1406 if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.NONE.toString() ) ) {
1407 setDefaultNodeFill( NodeFill.NONE );
1409 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.GRADIENT.toString() ) ) {
1410 setDefaultNodeFill( NodeFill.GRADIENT );
1412 else if ( fill_str.equalsIgnoreCase( NodeVisualData.NodeFill.SOLID.toString() ) ) {
1413 setDefaultNodeFill( NodeFill.SOLID );
1416 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
1417 + "] for [default_node_fill]" );
1420 else if ( key.equals( "default_node_shape" ) ) {
1421 final String shape_str = ( ( String ) st.nextElement() ).trim();
1422 if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.CIRCLE.toString() ) ) {
1423 setDefaultNodeShape( NodeShape.CIRCLE );
1425 else if ( shape_str.equalsIgnoreCase( NodeVisualData.NodeShape.RECTANGLE.toString() ) ) {
1426 setDefaultNodeShape( NodeShape.RECTANGLE );
1429 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
1430 + "] for [default_node_shape]" );
1433 else if ( key.equals( "midpoint_reroot" ) ) {
1434 setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) );
1436 else if ( key.equals( "ext_descendents_data_to_return" ) ) {
1437 final String s = ( ( String ) st.nextElement() ).trim();
1438 if ( s.equalsIgnoreCase( "node_name" ) ) {
1439 setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
1441 else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
1442 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
1444 else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) {
1445 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ_FASTA );
1447 else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
1448 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
1450 else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
1451 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
1453 else if ( s.equalsIgnoreCase( "gene_name" ) ) {
1454 setExtDescNodeDataToReturn( NODE_DATA.GENE_NAME );
1456 else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
1457 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
1459 else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
1460 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME );
1462 else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
1463 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
1465 else if ( s.equalsIgnoreCase( "taxonomy_common_name" ) ) {
1466 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_COMM0N_NAME );
1468 else if ( s.equalsIgnoreCase( "user_selected" ) ) {
1469 setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
1472 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1473 + "] for [ext_descendents_data_to_return]" );
1476 else if ( key.equals( "label_for_get_ext_descendents_data" ) ) {
1477 final String s = ( ( String ) st.nextElement() ).trim();
1478 if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) {
1479 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s
1480 + "] for [label_for_get_ext_descendents_data]" );
1483 setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
1486 else if ( key.equals( "ext_descendents_data_to_return_on" ) ) {
1487 final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
1488 if ( s.equals( "console" ) ) {
1489 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
1491 else if ( s.equals( "window" ) ) {
1492 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
1494 else if ( s.equals( "buffer_only" ) ) {
1495 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
1498 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
1499 + "] for [ext_descendents_data_to_return_on]" );
1502 else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
1505 if ( key.equals( "phylogram" ) ) {
1506 key_index = Configuration.display_as_phylogram;
1508 else if ( key.equals( "rollover" ) ) {
1509 key_index = Configuration.node_data_popup;
1511 else if ( key.equals( "color_according_to_species" ) ) {
1512 key_index = Configuration.color_according_to_species;
1514 else if ( key.equals( "show_node_names" ) ) {
1515 key_index = Configuration.show_node_names;
1517 else if ( key.equals( "show_taxonomy_code" ) ) {
1518 key_index = Configuration.show_tax_code;
1520 else if ( key.equals( "write_confidence_values" ) ) {
1521 key_index = Configuration.write_confidence_values;
1523 else if ( key.equals( "write_events" ) ) {
1524 key_index = Configuration.write_events;
1526 else if ( key.equals( "use_visual_styles" ) ) {
1527 key_index = Configuration.use_style;
1529 else if ( key.equals( "width_branches" ) ) {
1530 key_index = Configuration.width_branches;
1532 else if ( key.equals( "show_domain_architectures" ) ) {
1533 key_index = Configuration.show_domain_architectures;
1535 else if ( key.equals( "show_annotations" ) ) {
1536 key_index = Configuration.show_annotation;
1538 else if ( key.equals( "show_binary_characters" ) ) {
1539 key_index = Configuration.show_binary_characters;
1541 else if ( key.equals( "show_binary_character_counts" ) ) {
1542 key_index = Configuration.show_binary_character_counts;
1544 else if ( key.equals( "show_seq_names" ) ) {
1545 key_index = Configuration.show_seq_names;
1547 else if ( key.equals( "show_gene_names" ) ) {
1548 key_index = Configuration.show_gene_names;
1550 else if ( key.equals( "show_seq_symbols" ) ) {
1551 key_index = Configuration.show_seq_symbols;
1553 else if ( key.equals( "show_seq_acc" ) ) {
1554 key_index = Configuration.show_sequence_acc;
1556 else if ( key.equals( "display_internal_data" ) ) {
1557 key_index = Configuration.display_internal_data;
1559 else if ( key.equals( "dynamically_hide_data" ) ) {
1560 key_index = Configuration.dynamically_hide_data;
1562 else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
1563 key_index = Configuration.show_taxonomy_scientific_names;
1565 else if ( key.equals( "show_taxonomy_common_names" ) ) {
1566 key_index = Configuration.show_taxonomy_common_names;
1568 else if ( key.equals( "show_taxonomy_images" ) ) {
1569 key_index = Configuration.show_taxonomy_images;
1571 else if ( key.equals( "color_according_to_annotation" ) ) {
1572 key_index = Configuration.color_according_to_annotation;
1574 else if ( key.equals( "show_vector_data" ) ) {
1575 key_index = Configuration.show_vector_data;
1577 else if ( key.equals( "show_properties" ) ) {
1578 key_index = Configuration.show_properties;
1580 else if ( key.equals( "show_relation_confidence" ) ) {
1581 key_index = Configuration.show_relation_confidence;
1583 else if ( key.equals( "show_custom_node_shapes" ) ) {
1584 key_index = Configuration.show_custom_node_shapes;
1586 // If we've found the key, set the values
1587 if ( key_index >= 0 ) {
1588 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1589 display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
1590 // otherwise, keep looking
1593 if ( key_index == DEPRECATED ) {
1596 else if ( key.equals( "click_to" ) ) {
1597 final String click_to_name = ( String ) st.nextElement();
1598 key_index = getClickToIndex( click_to_name );
1599 if ( key_index >= 0 ) {
1600 clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
1602 else if ( key_index == DEPRECATED ) {
1606 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
1610 else if ( key.equals( "species_color" ) ) {
1611 getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
1612 Color.decode( ( String ) st.nextElement() ) );
1614 else if ( key.equals( "domain_color" ) ) {
1615 getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1617 else if ( key.equals( "annotation_color" ) ) {
1618 getAnnotationColors()
1619 .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1621 else if ( key.equals( "function_color" ) ) {
1622 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
1623 "configuration key [function_color] is deprecated" );
1625 else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
1626 putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
1629 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
1630 + "] in: " + config_filename );
1635 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
1636 + config_filename );
1640 private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
1641 _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
1644 private void setMaxBaseFontSize( final int max_base_font_size ) {
1645 _max_base_font_size = max_base_font_size;
1648 private void setMinBaseFontSize( final int min_base_font_size ) {
1649 _min_base_font_size = min_base_font_size;
1652 private void setOvMaxHeight( final short ov_max_height ) {
1653 _ov_max_height = ov_max_height;
1656 private void setOvMaxWidth( final short ov_max_width ) {
1657 _ov_max_width = ov_max_width;
1660 private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
1661 _ov_placement = ov_placement;
1664 private void setPathToLocalFastme( final File path_to_local_fastme ) {
1665 _path_to_local_fastme = path_to_local_fastme;
1668 private void setPathToLocalMafft( final File path_to_local_mafft ) {
1669 _path_to_local_mafft = path_to_local_mafft;
1672 private void setPathToLocalRaxml( final File path_to_local_raxml ) {
1673 _path_to_local_raxml = path_to_local_raxml;
1676 private void setShowAnnotationRefSource( final boolean b ) {
1677 _show_annotation_ref_source = b;
1680 private void setShowOverview( final boolean show_overview ) {
1681 _show_overview = show_overview;
1684 private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
1685 _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
1688 static String getDefaultFontFamilyName() {
1689 return DEFAULT_FONT_FAMILY;
1692 public enum EXT_NODE_DATA_RETURN_ON {
1693 BUFFER_ONLY, CONSOLE, WINODW;
1697 CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN
1700 static enum TRIPLET {
1701 FALSE, TRUE, UNKNOWN