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 _abbreviate_scientific_names;
46 private boolean _allow_errors_in_distance_to_parent;
47 private boolean _antialias_print;
48 private boolean _antialias_screen;
49 private boolean _background_color_gradient;
50 private Font _base_font;
51 private CLADOGRAM_TYPE _cladogram_type;
52 private boolean _color_by_taxonomic_group;
53 private boolean _color_labels_same_as_parent_branch;
54 private NodeVisualization.NodeFill _default_node_fill;
55 private NodeVisualization.NodeShape _default_node_shape;
56 private short _default_node_shape_size;
57 private boolean _editable;
58 private NODE_DATA _ext_desc_data_to_return;
59 private boolean _graphics_export_using_actual_size;
60 private boolean _graphics_export_visible_only;
61 private boolean _internal_number_are_confidence_for_nh_parsing;
62 private boolean _inverse_search_result;
63 private boolean _match_whole_terms_only;
64 private double _min_confidence_value;
65 private NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style;
66 private boolean _nh_parsing_replace_underscores;
67 private NODE_LABEL_DIRECTION _node_label_direction;
68 private short _number_of_digits_after_comma_for_branch_length_values;
69 private short _number_of_digits_after_comma_for_confidence_values;
70 private OVERVIEW_PLACEMENT_TYPE _ov_placement;
71 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type;
72 private boolean _print_black_and_white;
73 private float _print_line_width;
74 private int _print_size_x;
75 private int _print_size_y;
76 private boolean _print_using_actual_size;
77 private double _scale_bar_length;
78 private boolean _search_case_sensitive;
79 private boolean _show_annotation_ref_source;
80 private boolean _show_branch_length_values;
81 private boolean _show_confidence_stddev;
82 private boolean _show_default_node_shapes_external;
83 private boolean _show_default_node_shapes_internal;
84 private boolean _show_domain_labels;
85 private boolean _show_overview;
86 private boolean _show_scale;
87 private TAXONOMY_EXTRACTION _taxonomy_extraction;
93 public NodeData.NODE_DATA getExtDescNodeDataToReturn() {
94 return _ext_desc_data_to_return;
97 public boolean isAllowErrorsInDistanceToParent() {
98 return _allow_errors_in_distance_to_parent;
101 public boolean isAllowFontSizeChange() {
105 public final boolean isShowAnnotationRefSource() {
106 return _show_annotation_ref_source;
109 public final boolean isShowDomainLabels() {
110 return _show_domain_labels;
113 public final void setAllowErrorsInDistanceToParent( final boolean allow_errors_in_distance_to_parent ) {
114 _allow_errors_in_distance_to_parent = allow_errors_in_distance_to_parent;
117 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
118 _background_color_gradient = background_color_gradient;
121 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
122 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
125 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
126 _ext_desc_data_to_return = ext_desc_data_to_return;
129 public final void setShowAnnotationRefSource( final boolean show_annotation_ref_source ) {
130 _show_annotation_ref_source = show_annotation_ref_source;
133 public void setShowDomainLabels( final boolean show_domain_labels ) {
134 _show_domain_labels = show_domain_labels;
137 final Font getBaseFont() {
141 final CLADOGRAM_TYPE getCladogramType() {
142 return _cladogram_type;
145 final NodeFill getDefaultNodeFill() {
146 return _default_node_fill;
149 final NodeShape getDefaultNodeShape() {
150 return _default_node_shape;
153 final short getDefaultNodeShapeSize() {
154 return _default_node_shape_size;
157 final double getMinConfidenceValue() {
158 return _min_confidence_value;
161 NH_CONVERSION_SUPPORT_VALUE_STYLE getNhConversionSupportValueStyle() {
162 return _nh_conversion_support_value_style;
165 final NODE_LABEL_DIRECTION getNodeLabelDirection() {
166 return _node_label_direction;
169 final short getNumberOfDigitsAfterCommaForBranchLengthValues() {
170 return _number_of_digits_after_comma_for_branch_length_values;
173 final short getNumberOfDigitsAfterCommaForConfidenceValues() {
174 return _number_of_digits_after_comma_for_confidence_values;
177 final OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
178 return _ov_placement;
181 final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
182 return _phylogeny_graphics_type;
185 final float getPrintLineWidth() {
186 return _print_line_width;
189 final int getPrintSizeX() {
190 return _print_size_x;
193 final int getPrintSizeY() {
194 return _print_size_y;
197 final double getScaleBarLength() {
198 return _scale_bar_length;
201 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
202 return _taxonomy_extraction;
205 final boolean isAbbreviateScientificTaxonNames() {
206 return _abbreviate_scientific_names;
209 boolean isAllowMagnificationOfTaxonomyImages() {
213 final boolean isAntialiasPrint() {
214 return _antialias_print;
217 final boolean isAntialiasScreen() {
218 return _antialias_screen;
221 final boolean isBackgroundColorGradient() {
222 return _background_color_gradient;
225 final boolean isColorByTaxonomicGroup() {
226 return _color_by_taxonomic_group;
229 final boolean isColorLabelsSameAsParentBranch() {
230 return _color_labels_same_as_parent_branch;
233 final boolean isEditable() {
237 final boolean isGraphicsExportUsingActualSize() {
238 return _graphics_export_using_actual_size;
241 final boolean isGraphicsExportVisibleOnly() {
242 return _graphics_export_visible_only;
245 final boolean isInternalNumberAreConfidenceForNhParsing() {
246 return _internal_number_are_confidence_for_nh_parsing;
249 final boolean isInverseSearchResult() {
250 return _inverse_search_result;
253 final boolean isMatchWholeTermsOnly() {
254 return _match_whole_terms_only;
257 final boolean isPrintBlackAndWhite() {
258 return _print_black_and_white;
261 final boolean isPrintUsingActualSize() {
262 return _print_using_actual_size;
265 final boolean isReplaceUnderscoresInNhParsing() {
266 return _nh_parsing_replace_underscores;
269 final boolean isSearchCaseSensitive() {
270 return _search_case_sensitive;
273 final boolean isShowBranchLengthValues() {
274 return _show_branch_length_values;
277 boolean isShowConfidenceStddev() {
278 return _show_confidence_stddev;
281 boolean isShowDefaultNodeShapesExternal() {
282 return _show_default_node_shapes_external;
285 boolean isShowDefaultNodeShapesInternal() {
286 return _show_default_node_shapes_internal;
289 final boolean isShowOverview() {
290 return _show_overview;
293 final boolean isShowScale() {
297 final void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
298 _abbreviate_scientific_names = abbreviate_scientific_names;
301 final void setAntialiasPrint( final boolean antialias_print ) {
302 _antialias_print = antialias_print;
305 final void setAntialiasScreen( final boolean antialias_screen ) {
306 _antialias_screen = antialias_screen;
309 final void setBaseFont( final Font base_font ) {
310 _base_font = base_font;
313 final void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
314 _cladogram_type = cladogram_type;
317 final void setColorByTaxonomicGroup( final boolean color_by_taxonomic_group ) {
318 _color_by_taxonomic_group = color_by_taxonomic_group;
321 final void setDefaultNodeFill( final NodeFill default_node_fill ) {
322 _default_node_fill = default_node_fill;
325 final void setDefaultNodeShape( final NodeShape default_node_shape ) {
326 _default_node_shape = default_node_shape;
329 final void setDefaultNodeShapeSize( final short default_node_shape_size ) {
330 _default_node_shape_size = default_node_shape_size;
333 final void setEditable( final boolean editable ) {
334 _editable = editable;
337 final void setGraphicsExportUsingActualSize( final boolean graphics_export_using_actual_size ) {
338 _graphics_export_using_actual_size = graphics_export_using_actual_size;
339 if ( !graphics_export_using_actual_size ) {
340 setGraphicsExportVisibleOnly( false );
344 final void setGraphicsExportVisibleOnly( final boolean graphics_export_visible_only ) {
345 _graphics_export_visible_only = graphics_export_visible_only;
346 if ( graphics_export_visible_only ) {
347 setGraphicsExportUsingActualSize( true );
351 final void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
352 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
355 final void setInverseSearchResult( final boolean inverse_search_result ) {
356 _inverse_search_result = inverse_search_result;
359 final void setMatchWholeTermsOnly( final boolean search_whole_words_only ) {
360 _match_whole_terms_only = search_whole_words_only;
363 final void setMinConfidenceValue( final double min_confidence_value ) {
364 _min_confidence_value = min_confidence_value;
367 void setNhConversionSupportValueStyle( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_value_style ) {
368 _nh_conversion_support_value_style = nh_conversion_support_value_style;
371 final void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
372 _node_label_direction = node_label_direction;
375 final void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
376 _ov_placement = ov_placement;
379 final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
380 _phylogeny_graphics_type = phylogeny_graphics_type;
383 final void setPrintBlackAndWhite( final boolean print_black_and_white ) {
384 _print_black_and_white = print_black_and_white;
387 final void setPrintLineWidth( final float print_line_width ) {
388 _print_line_width = print_line_width;
391 final void setPrintSizeX( final int print_size_x ) {
392 _print_size_x = print_size_x;
395 final void setPrintSizeY( final int print_size_y ) {
396 _print_size_y = print_size_y;
399 final void setPrintUsingActualSize( final boolean print_using_actual_size ) {
400 _print_using_actual_size = print_using_actual_size;
403 final void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
404 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
407 final void setScaleBarLength( final double scale_bar_length ) {
408 _scale_bar_length = scale_bar_length;
411 final void setSearchCaseSensitive( final boolean search_case_sensitive ) {
412 _search_case_sensitive = search_case_sensitive;
415 final void setShowBranchLengthValues( final boolean show_branch_length_values ) {
416 _show_branch_length_values = show_branch_length_values;
419 void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
420 _show_confidence_stddev = show_confidence_stddev;
423 void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
424 _show_default_node_shapes_external = show_default_node_shapes_external;
427 void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
428 _show_default_node_shapes_internal = show_default_node_shapes_internal;
431 final void setShowOverview( final boolean show_overview ) {
432 _show_overview = show_overview;
435 final void setShowScale( final boolean show_scale ) {
436 _show_scale = show_scale;
439 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
440 _taxonomy_extraction = taxonomy_extraction;
443 final private void init() {
444 _default_node_shape = NodeShape.CIRCLE;
445 _default_node_fill = NodeFill.GRADIENT;
446 _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
447 _show_branch_length_values = false;
448 _internal_number_are_confidence_for_nh_parsing = false;
450 _antialias_screen = true;
451 _antialias_print = true;
452 _graphics_export_visible_only = false;
454 _background_color_gradient = false;
455 _show_default_node_shapes_internal = false;
456 _show_default_node_shapes_external = false;
457 if ( AptxUtil.isUsOrCanada() ) {
458 _print_size_x = Constants.US_LETTER_SIZE_X;
459 _print_size_y = Constants.US_LETTER_SIZE_Y;
462 _print_size_x = Constants.A4_SIZE_X;
463 _print_size_y = Constants.A4_SIZE_Y;
465 _min_confidence_value = MIN_CONFIDENCE_DEFAULT;
466 _print_black_and_white = false;
467 _print_using_actual_size = false;
468 _graphics_export_using_actual_size = true;
469 _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
470 _base_font = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 10 );
471 _match_whole_terms_only = false;
472 _search_case_sensitive = false;
473 _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
474 _show_overview = true;
475 _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
476 _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
477 _inverse_search_result = false;
478 _scale_bar_length = 0.0;
479 _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
480 _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
481 _nh_parsing_replace_underscores = false;
482 _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
483 _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
484 _show_domain_labels = true;
485 _show_annotation_ref_source = true;
486 setAbbreviateScientificTaxonNames( false );
487 _color_labels_same_as_parent_branch = false;
488 _show_confidence_stddev = true;
489 _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
490 _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
493 final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) {
494 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
497 final private void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
498 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
501 public final static Options createInstance( final Configuration configuration ) {
502 final Options instance = createDefaultInstance();
503 if ( configuration != null ) {
504 instance.setAntialiasScreen( configuration.isAntialiasScreen() );
505 instance.setShowScale( configuration.isShowScale() );
506 instance.setShowBranchLengthValues( configuration.isShowBranchLengthValues() );
507 instance.setShowOverview( configuration.isShowOverview() );
508 instance.setColorByTaxonomicGroup( configuration.isColorByTaxonomicGroup() );
509 instance.setCladogramType( configuration.getCladogramType() );
510 instance.setOvPlacement( configuration.getOvPlacement() );
511 instance.setPrintLineWidth( configuration.getPrintLineWidth() );
512 instance.setNodeLabelDirection( configuration.getNodeLabelDirection() );
513 instance.setBackgroundColorGradient( configuration.isBackgroundColorGradient() );
514 if ( configuration.getNumberOfDigitsAfterCommaForBranchLengthValues() >= 0 ) {
515 instance.setNumberOfDigitsAfterCommaForBranchLength( configuration
516 .getNumberOfDigitsAfterCommaForBranchLengthValues() );
518 if ( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() >= 0 ) {
519 instance.setNumberOfDigitsAfterCommaForConfidenceValues( configuration
520 .getNumberOfDigitsAfterCommaForConfidenceValues() );
522 instance.setTaxonomyExtraction( configuration.getTaxonomyExtraction() );
523 instance.setReplaceUnderscoresInNhParsing( configuration.isReplaceUnderscoresInNhParsing() );
524 instance.setInternalNumberAreConfidenceForNhParsing( configuration
525 .isInternalNumberAreConfidenceForNhParsing() );
526 instance.setEditable( configuration.isEditable() );
527 instance.setColorLabelsSameAsParentBranch( configuration.isColorLabelsSameAsParentBranch() );
528 instance.setShowDomainLabels( configuration.isShowDomainLabels() );
529 instance.setShowAnnotationRefSource( configuration.isShowAnnotationRefSource() );
530 instance.setAbbreviateScientificTaxonNames( configuration.isAbbreviateScientificTaxonNames() );
531 if ( configuration.getMinConfidenceValue() != MIN_CONFIDENCE_DEFAULT ) {
532 instance.setMinConfidenceValue( configuration.getMinConfidenceValue() );
534 if ( configuration.getGraphicsExportX() > 0 ) {
535 instance.setPrintSizeX( configuration.getGraphicsExportX() );
537 if ( configuration.getGraphicsExportY() > 0 ) {
538 instance.setPrintSizeY( configuration.getGraphicsExportY() );
540 if ( configuration.getBaseFontSize() > 0 ) {
541 instance.setBaseFont( instance.getBaseFont().deriveFont( ( float ) configuration.getBaseFontSize() ) );
543 if ( !ForesterUtil.isEmpty( configuration.getBaseFontFamilyName() ) ) {
544 instance.setBaseFont( new Font( configuration.getBaseFontFamilyName(), Font.PLAIN, instance
545 .getBaseFont().getSize() ) );
547 if ( configuration.getPhylogenyGraphicsType() != null ) {
548 instance.setPhylogenyGraphicsType( configuration.getPhylogenyGraphicsType() );
550 if ( configuration.getDefaultNodeFill() != null ) {
551 instance.setDefaultNodeFill( configuration.getDefaultNodeFill() );
553 if ( configuration.getDefaultNodeShape() != null ) {
554 instance.setDefaultNodeShape( configuration.getDefaultNodeShape() );
556 if ( configuration.getDefaultNodeShapeSize() >= 0 ) {
557 instance.setDefaultNodeShapeSize( configuration.getDefaultNodeShapeSize() );
559 instance.setShowDefaultNodeShapesInternal( configuration.isShowDefaultNodeShapesInternal() );
560 instance.setShowDefaultNodeShapesExternal( configuration.isShowDefaultNodeShapesExternal() );
561 if ( configuration.getExtDescNodeDataToReturn() != null ) {
562 instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() );
564 instance.setAllowErrorsInDistanceToParent( false );
569 final static Options createDefaultInstance() {
570 return new Options();
573 public static enum CLADOGRAM_TYPE {
574 EXT_NODE_SUM_DEP, NON_LINED_UP, TOTAL_NODE_SUM_DEP;
577 public static enum NODE_LABEL_DIRECTION {
581 public static enum PHYLOGENY_GRAPHICS_TYPE {
582 CIRCULAR, CONVEX, CURVED, EURO_STYLE, RECTANGULAR, ROUNDED, TRIANGULAR, UNROOTED;
585 static enum OVERVIEW_PLACEMENT_TYPE {
586 LOWER_LEFT( "lower left" ),
587 LOWER_RIGHT( "lower right" ),
588 UPPER_LEFT( "upper left" ),
589 UPPER_RIGHT( "upper right" );
591 private final String _name;
593 private OVERVIEW_PLACEMENT_TYPE( final String name ) {
598 public String toString() {
602 public String toTag() {
603 return toString().replaceAll( " ", "_" );