2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2009 Christian M. Zmasek
6 // Copyright (C) 2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.archaeopteryx;
30 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
31 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
32 import org.forester.phylogeny.data.NodeData;
33 import org.forester.phylogeny.data.NodeData.NODE_DATA;
34 import org.forester.phylogeny.data.NodeVisualization;
35 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
36 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
37 import org.forester.util.ForesterUtil;
40 * This is to hold changeable options.
42 final public class Options {
44 static final double MIN_CONFIDENCE_DEFAULT = 0.0;
45 private boolean _show_branch_length_values;
46 private boolean _internal_number_are_confidence_for_nh_parsing;
47 private boolean _show_scale;
48 private boolean _show_overview;
49 private boolean _antialias_screen;
50 private boolean _antialias_print;
51 private boolean _graphics_export_visible_only;
52 private int _print_size_x;
53 private int _print_size_y;
54 private double _min_confidence_value;
55 private boolean _print_black_and_white;
56 private boolean _print_using_actual_size;
57 private boolean _graphics_export_using_actual_size;
58 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type;
59 private CLADOGRAM_TYPE _cladogram_type;
60 private OVERVIEW_PLACEMENT_TYPE _ov_placement;
61 private NODE_LABEL_DIRECTION _node_label_direction;
62 private Font _base_font;
63 private boolean _match_whole_terms_only;
64 private boolean _search_case_sensitive;
65 private float _print_line_width;
66 private boolean _inverse_search_result;
67 private double _scale_bar_length;
68 private short _number_of_digits_after_comma_for_confidence_values;
69 private short _number_of_digits_after_comma_for_branch_length_values;
70 private boolean _nh_parsing_replace_underscores;
71 private TAXONOMY_EXTRACTION _taxonomy_extraction;
72 private boolean _editable;
73 private boolean _background_color_gradient;
74 private boolean _show_domain_labels;
75 private boolean _color_labels_same_as_parent_branch;
76 private boolean _abbreviate_scientific_names;
77 private NodeVisualization.NodeShape _default_node_shape;
78 private NodeVisualization.NodeFill _default_node_fill;
79 private short _default_node_shape_size;
80 private boolean _taxonomy_colorize_node_shapes;
81 private boolean _show_default_node_shapes;
82 private boolean _show_confidence_stddev;
83 private NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style;
84 private NODE_DATA _ext_desc_data_to_return;
90 final Font getBaseFont() {
94 final CLADOGRAM_TYPE getCladogramType() {
95 return _cladogram_type;
98 final NodeFill getDefaultNodeFill() {
99 return _default_node_fill;
102 final NodeShape getDefaultNodeShape() {
103 return _default_node_shape;
106 final short getDefaultNodeShapeSize() {
107 return _default_node_shape_size;
110 final double getMinConfidenceValue() {
111 return _min_confidence_value;
114 final NODE_LABEL_DIRECTION getNodeLabelDirection() {
115 return _node_label_direction;
118 final short getNumberOfDigitsAfterCommaForBranchLengthValues() {
119 return _number_of_digits_after_comma_for_branch_length_values;
122 final short getNumberOfDigitsAfterCommaForConfidenceValues() {
123 return _number_of_digits_after_comma_for_confidence_values;
126 final OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
127 return _ov_placement;
130 final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
131 return _phylogeny_graphics_type;
134 final float getPrintLineWidth() {
135 return _print_line_width;
138 final int getPrintSizeX() {
139 return _print_size_x;
142 final int getPrintSizeY() {
143 return _print_size_y;
146 final double getScaleBarLength() {
147 return _scale_bar_length;
150 final private void init() {
151 _default_node_shape = NodeShape.CIRCLE;
152 _default_node_fill = NodeFill.GRADIENT;
153 _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
154 _taxonomy_colorize_node_shapes = false;
155 _show_branch_length_values = false;
156 _internal_number_are_confidence_for_nh_parsing = false;
158 _antialias_screen = true;
159 _antialias_print = true;
160 _graphics_export_visible_only = false;
162 _background_color_gradient = false;
163 _show_default_node_shapes = false;
164 if ( AptxUtil.isUsOrCanada() ) {
165 _print_size_x = Constants.US_LETTER_SIZE_X;
166 _print_size_y = Constants.US_LETTER_SIZE_Y;
169 _print_size_x = Constants.A4_SIZE_X;
170 _print_size_y = Constants.A4_SIZE_Y;
172 _min_confidence_value = MIN_CONFIDENCE_DEFAULT;
173 _print_black_and_white = false;
174 _print_using_actual_size = false;
175 _graphics_export_using_actual_size = true;
176 _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
177 _base_font = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 10 );
178 _match_whole_terms_only = false;
179 _search_case_sensitive = false;
180 _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
181 _show_overview = true;
182 _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
183 _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
184 _inverse_search_result = false;
185 _scale_bar_length = 0.0;
186 _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
187 _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
188 _nh_parsing_replace_underscores = false;
189 _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
190 _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
191 _show_domain_labels = true;
192 setAbbreviateScientificTaxonNames( false );
193 _color_labels_same_as_parent_branch = false;
194 _show_confidence_stddev = true;
195 _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
196 _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
199 boolean isShowConfidenceStddev() {
200 return _show_confidence_stddev;
203 void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
204 _show_confidence_stddev = show_confidence_stddev;
207 NH_CONVERSION_SUPPORT_VALUE_STYLE getNhConversionSupportValueStyle() {
208 return _nh_conversion_support_value_style;
211 void setNhConversionSupportValueStyle( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_value_style ) {
212 _nh_conversion_support_value_style = nh_conversion_support_value_style;
215 final boolean isAbbreviateScientificTaxonNames() {
216 return _abbreviate_scientific_names;
219 boolean isAllowMagnificationOfTaxonomyImages() {
223 final boolean isAntialiasPrint() {
224 return _antialias_print;
227 final boolean isAntialiasScreen() {
228 return _antialias_screen;
231 final boolean isBackgroundColorGradient() {
232 return _background_color_gradient;
235 final boolean isColorLabelsSameAsParentBranch() {
236 return _color_labels_same_as_parent_branch;
239 final boolean isEditable() {
243 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
244 return _taxonomy_extraction;
247 final boolean isGraphicsExportUsingActualSize() {
248 return _graphics_export_using_actual_size;
251 final boolean isGraphicsExportVisibleOnly() {
252 return _graphics_export_visible_only;
255 final boolean isInternalNumberAreConfidenceForNhParsing() {
256 return _internal_number_are_confidence_for_nh_parsing;
259 final boolean isInverseSearchResult() {
260 return _inverse_search_result;
263 final boolean isMatchWholeTermsOnly() {
264 return _match_whole_terms_only;
267 final boolean isPrintBlackAndWhite() {
268 return _print_black_and_white;
271 final boolean isPrintUsingActualSize() {
272 return _print_using_actual_size;
275 final boolean isReplaceUnderscoresInNhParsing() {
276 return _nh_parsing_replace_underscores;
279 final boolean isSearchCaseSensitive() {
280 return _search_case_sensitive;
283 final boolean isShowBranchLengthValues() {
284 return _show_branch_length_values;
287 public final boolean isShowDomainLabels() {
288 return _show_domain_labels;
291 final boolean isShowOverview() {
292 return _show_overview;
295 final boolean isShowScale() {
299 boolean isTaxonomyColorizeNodeShapes() {
300 return _taxonomy_colorize_node_shapes;
303 final void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
304 _abbreviate_scientific_names = abbreviate_scientific_names;
307 final void setAntialiasPrint( final boolean antialias_print ) {
308 _antialias_print = antialias_print;
311 final void setAntialiasScreen( final boolean antialias_screen ) {
312 _antialias_screen = antialias_screen;
315 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
316 _background_color_gradient = background_color_gradient;
319 final void setBaseFont( final Font base_font ) {
320 _base_font = base_font;
323 final void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
324 _cladogram_type = cladogram_type;
327 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
328 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
331 final void setDefaultNodeFill( final NodeFill default_node_fill ) {
332 _default_node_fill = default_node_fill;
335 final void setDefaultNodeShape( final NodeShape default_node_shape ) {
336 _default_node_shape = default_node_shape;
339 final void setDefaultNodeShapeSize( final short default_node_shape_size ) {
340 _default_node_shape_size = default_node_shape_size;
343 final void setEditable( final boolean editable ) {
344 _editable = editable;
347 final void setTaxonomyExtractio( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
348 _taxonomy_extraction = taxonomy_extraction;
351 final void setGraphicsExportUsingActualSize( final boolean graphics_export_using_actual_size ) {
352 _graphics_export_using_actual_size = graphics_export_using_actual_size;
353 if ( !graphics_export_using_actual_size ) {
354 setGraphicsExportVisibleOnly( false );
358 final void setGraphicsExportVisibleOnly( final boolean graphics_export_visible_only ) {
359 _graphics_export_visible_only = graphics_export_visible_only;
360 if ( graphics_export_visible_only ) {
361 setGraphicsExportUsingActualSize( true );
365 final void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
366 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
369 final void setInverseSearchResult( final boolean inverse_search_result ) {
370 _inverse_search_result = inverse_search_result;
373 final void setMatchWholeTermsOnly( final boolean search_whole_words_only ) {
374 _match_whole_terms_only = search_whole_words_only;
377 final void setMinConfidenceValue( final double min_confidence_value ) {
378 _min_confidence_value = min_confidence_value;
381 final void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
382 _node_label_direction = node_label_direction;
385 final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) {
386 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
389 final private void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
390 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
393 final void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
394 _ov_placement = ov_placement;
397 final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
398 _phylogeny_graphics_type = phylogeny_graphics_type;
401 final void setPrintBlackAndWhite( final boolean print_black_and_white ) {
402 _print_black_and_white = print_black_and_white;
405 final void setPrintLineWidth( final float print_line_width ) {
406 _print_line_width = print_line_width;
409 final void setPrintSizeX( final int print_size_x ) {
410 _print_size_x = print_size_x;
413 final void setPrintSizeY( final int print_size_y ) {
414 _print_size_y = print_size_y;
417 final void setPrintUsingActualSize( final boolean print_using_actual_size ) {
418 _print_using_actual_size = print_using_actual_size;
421 final void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
422 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
425 final void setScaleBarLength( final double scale_bar_length ) {
426 _scale_bar_length = scale_bar_length;
429 final void setSearchCaseSensitive( final boolean search_case_sensitive ) {
430 _search_case_sensitive = search_case_sensitive;
433 final void setShowBranchLengthValues( final boolean show_branch_length_values ) {
434 _show_branch_length_values = show_branch_length_values;
437 public void setShowDomainLabels( final boolean show_domain_labels ) {
438 _show_domain_labels = show_domain_labels;
441 final void setShowOverview( final boolean show_overview ) {
442 _show_overview = show_overview;
445 final void setShowScale( final boolean show_scale ) {
446 _show_scale = show_scale;
449 void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
450 _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
453 final static Options createDefaultInstance() {
454 return new Options();
457 boolean isShowDefaultNodeShapes() {
458 return _show_default_node_shapes;
461 void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
462 _show_default_node_shapes = show_default_node_shapes;
465 public final static Options createInstance( final Configuration configuration ) {
466 final Options instance = createDefaultInstance();
467 if ( configuration != null ) {
468 instance.setAntialiasScreen( configuration.isAntialiasScreen() );
469 instance.setShowScale( configuration.isShowScale() );
470 instance.setShowBranchLengthValues( configuration.isShowBranchLengthValues() );
471 instance.setShowOverview( configuration.isShowOverview() );
472 instance.setCladogramType( configuration.getCladogramType() );
473 instance.setOvPlacement( configuration.getOvPlacement() );
474 instance.setPrintLineWidth( configuration.getPrintLineWidth() );
475 instance.setNodeLabelDirection( configuration.getNodeLabelDirection() );
476 instance.setBackgroundColorGradient( configuration.isBackgroundColorGradient() );
477 if ( configuration.getNumberOfDigitsAfterCommaForBranchLengthValues() >= 0 ) {
478 instance.setNumberOfDigitsAfterCommaForBranchLength( configuration
479 .getNumberOfDigitsAfterCommaForBranchLengthValues() );
481 if ( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() >= 0 ) {
482 instance.setNumberOfDigitsAfterCommaForConfidenceValues( configuration
483 .getNumberOfDigitsAfterCommaForConfidenceValues() );
485 instance.setTaxonomyExtractio( configuration.getTaxonomyExtraction() );
486 instance.setReplaceUnderscoresInNhParsing( configuration.isReplaceUnderscoresInNhParsing() );
487 instance.setInternalNumberAreConfidenceForNhParsing( configuration
488 .isInternalNumberAreConfidenceForNhParsing() );
489 instance.setEditable( configuration.isEditable() );
490 instance.setColorLabelsSameAsParentBranch( configuration.isColorLabelsSameAsParentBranch() );
491 instance.setShowDomainLabels( configuration.isShowDomainLabels() );
492 instance.setAbbreviateScientificTaxonNames( configuration.isAbbreviateScientificTaxonNames() );
493 if ( configuration.getMinConfidenceValue() != MIN_CONFIDENCE_DEFAULT ) {
494 instance.setMinConfidenceValue( configuration.getMinConfidenceValue() );
496 if ( configuration.getGraphicsExportX() > 0 ) {
497 instance.setPrintSizeX( configuration.getGraphicsExportX() );
499 if ( configuration.getGraphicsExportY() > 0 ) {
500 instance.setPrintSizeY( configuration.getGraphicsExportY() );
502 if ( configuration.getBaseFontSize() > 0 ) {
503 instance.setBaseFont( instance.getBaseFont().deriveFont( ( float ) configuration.getBaseFontSize() ) );
505 if ( !ForesterUtil.isEmpty( configuration.getBaseFontFamilyName() ) ) {
506 instance.setBaseFont( new Font( configuration.getBaseFontFamilyName(), Font.PLAIN, instance
507 .getBaseFont().getSize() ) );
509 if ( configuration.getPhylogenyGraphicsType() != null ) {
510 instance.setPhylogenyGraphicsType( configuration.getPhylogenyGraphicsType() );
512 if ( configuration.getDefaultNodeFill() != null ) {
513 instance.setDefaultNodeFill( configuration.getDefaultNodeFill() );
515 if ( configuration.getDefaultNodeShape() != null ) {
516 instance.setDefaultNodeShape( configuration.getDefaultNodeShape() );
518 if ( configuration.getDefaultNodeShapeSize() >= 0 ) {
519 instance.setDefaultNodeShapeSize( configuration.getDefaultNodeShapeSize() );
521 instance.setTaxonomyColorizeNodeShapes( configuration.isTaxonomyColorizeNodeShapes() );
522 instance.setShowDefaultNodeShapes( configuration.isShowDefaultNodeShapes() );
523 if ( configuration.getExtDescNodeDataToReturn() != null ) {
524 instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() );
530 public static enum CLADOGRAM_TYPE {
531 NON_LINED_UP, EXT_NODE_SUM_DEP, TOTAL_NODE_SUM_DEP;
534 public static enum NODE_LABEL_DIRECTION {
538 static enum OVERVIEW_PLACEMENT_TYPE {
539 UPPER_LEFT( "upper left" ),
540 UPPER_RIGHT( "upper right" ),
541 LOWER_LEFT( "lower left" ),
542 LOWER_RIGHT( "lower right" );
544 private final String _name;
546 private OVERVIEW_PLACEMENT_TYPE( final String name ) {
551 public String toString() {
555 public String toTag() {
556 return toString().replaceAll( " ", "_" );
560 public static enum PHYLOGENY_GRAPHICS_TYPE {
561 RECTANGULAR, TRIANGULAR, EURO_STYLE, ROUNDED, CONVEX, CURVED, UNROOTED, CIRCULAR;
564 public NodeData.NODE_DATA getExtDescNodeDataToReturn() {
565 return _ext_desc_data_to_return;
568 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
569 _ext_desc_data_to_return = ext_desc_data_to_return;