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.NodeVisualData;
35 import org.forester.phylogeny.data.NodeVisualData.NodeFill;
36 import org.forester.phylogeny.data.NodeVisualData.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 NodeVisualData.NodeFill _default_node_fill;
55 private NodeVisualData.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_confidence_stddev;
81 private boolean _show_default_node_shapes_external;
82 private boolean _show_default_node_shapes_internal;
83 private boolean _show_domain_labels;
84 private boolean _show_overview;
85 private boolean _show_scale;
86 private TAXONOMY_EXTRACTION _taxonomy_extraction;
87 private boolean _line_up_renderable_node_data;
88 private boolean _right_align_domains;
94 public NodeData.NODE_DATA getExtDescNodeDataToReturn() {
95 return _ext_desc_data_to_return;
98 public boolean isAllowErrorsInDistanceToParent() {
99 return _allow_errors_in_distance_to_parent;
102 public boolean isAllowFontSizeChange() {
106 public final boolean isShowAnnotationRefSource() {
107 return _show_annotation_ref_source;
110 public final boolean isShowDomainLabels() {
111 return _show_domain_labels;
114 public final void setAllowErrorsInDistanceToParent( final boolean allow_errors_in_distance_to_parent ) {
115 _allow_errors_in_distance_to_parent = allow_errors_in_distance_to_parent;
118 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
119 _background_color_gradient = background_color_gradient;
122 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
123 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
126 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
127 _ext_desc_data_to_return = ext_desc_data_to_return;
130 public final void setShowAnnotationRefSource( final boolean show_annotation_ref_source ) {
131 _show_annotation_ref_source = show_annotation_ref_source;
134 public void setShowDomainLabels( final boolean show_domain_labels ) {
135 _show_domain_labels = show_domain_labels;
138 final Font getBaseFont() {
142 final CLADOGRAM_TYPE getCladogramType() {
143 return _cladogram_type;
146 final NodeFill getDefaultNodeFill() {
147 return _default_node_fill;
150 final NodeShape getDefaultNodeShape() {
151 return _default_node_shape;
154 final short getDefaultNodeShapeSize() {
155 return _default_node_shape_size;
158 final double getMinConfidenceValue() {
159 return _min_confidence_value;
162 NH_CONVERSION_SUPPORT_VALUE_STYLE getNhConversionSupportValueStyle() {
163 return _nh_conversion_support_value_style;
166 final NODE_LABEL_DIRECTION getNodeLabelDirection() {
167 return _node_label_direction;
170 final short getNumberOfDigitsAfterCommaForBranchLengthValues() {
171 return _number_of_digits_after_comma_for_branch_length_values;
174 final short getNumberOfDigitsAfterCommaForConfidenceValues() {
175 return _number_of_digits_after_comma_for_confidence_values;
178 final OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
179 return _ov_placement;
182 final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
183 return _phylogeny_graphics_type;
186 final float getPrintLineWidth() {
187 return _print_line_width;
190 final int getPrintSizeX() {
191 return _print_size_x;
194 final int getPrintSizeY() {
195 return _print_size_y;
198 final double getScaleBarLength() {
199 return _scale_bar_length;
202 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
203 return _taxonomy_extraction;
206 final boolean isAbbreviateScientificTaxonNames() {
207 return _abbreviate_scientific_names;
210 boolean isAllowMagnificationOfTaxonomyImages() {
214 final boolean isAntialiasPrint() {
215 return _antialias_print;
218 final boolean isAntialiasScreen() {
219 return _antialias_screen;
222 final boolean isBackgroundColorGradient() {
223 return _background_color_gradient;
226 final boolean isColorByTaxonomicGroup() {
227 return _color_by_taxonomic_group;
230 final boolean isColorLabelsSameAsParentBranch() {
231 return _color_labels_same_as_parent_branch;
234 final boolean isEditable() {
238 final boolean isGraphicsExportUsingActualSize() {
239 return _graphics_export_using_actual_size;
242 final boolean isGraphicsExportVisibleOnly() {
243 return _graphics_export_visible_only;
246 final boolean isInternalNumberAreConfidenceForNhParsing() {
247 return _internal_number_are_confidence_for_nh_parsing;
250 final boolean isInverseSearchResult() {
251 return _inverse_search_result;
254 final boolean isMatchWholeTermsOnly() {
255 return _match_whole_terms_only;
258 final boolean isPrintBlackAndWhite() {
259 return _print_black_and_white;
262 final boolean isPrintUsingActualSize() {
263 return _print_using_actual_size;
266 final boolean isReplaceUnderscoresInNhParsing() {
267 return _nh_parsing_replace_underscores;
270 final boolean isSearchCaseSensitive() {
271 return _search_case_sensitive;
274 boolean isShowConfidenceStddev() {
275 return _show_confidence_stddev;
278 boolean isShowDefaultNodeShapesExternal() {
279 return _show_default_node_shapes_external;
282 boolean isShowDefaultNodeShapesInternal() {
283 return _show_default_node_shapes_internal;
286 final boolean isShowOverview() {
287 return _show_overview;
290 final boolean isShowScale() {
294 final void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
295 _abbreviate_scientific_names = abbreviate_scientific_names;
298 final void setAntialiasPrint( final boolean antialias_print ) {
299 _antialias_print = antialias_print;
302 final void setAntialiasScreen( final boolean antialias_screen ) {
303 _antialias_screen = antialias_screen;
306 final void setBaseFont( final Font base_font ) {
307 _base_font = base_font;
310 final void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
311 _cladogram_type = cladogram_type;
314 final void setColorByTaxonomicGroup( final boolean color_by_taxonomic_group ) {
315 _color_by_taxonomic_group = color_by_taxonomic_group;
318 final void setDefaultNodeFill( final NodeFill default_node_fill ) {
319 _default_node_fill = default_node_fill;
322 final void setDefaultNodeShape( final NodeShape default_node_shape ) {
323 _default_node_shape = default_node_shape;
326 final void setDefaultNodeShapeSize( final short default_node_shape_size ) {
327 _default_node_shape_size = default_node_shape_size;
330 final void setEditable( final boolean editable ) {
331 _editable = editable;
334 final void setGraphicsExportUsingActualSize( final boolean graphics_export_using_actual_size ) {
335 _graphics_export_using_actual_size = graphics_export_using_actual_size;
336 if ( !graphics_export_using_actual_size ) {
337 setGraphicsExportVisibleOnly( false );
341 final void setGraphicsExportVisibleOnly( final boolean graphics_export_visible_only ) {
342 _graphics_export_visible_only = graphics_export_visible_only;
343 if ( graphics_export_visible_only ) {
344 setGraphicsExportUsingActualSize( true );
348 final void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
349 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
352 final void setInverseSearchResult( final boolean inverse_search_result ) {
353 _inverse_search_result = inverse_search_result;
356 final void setMatchWholeTermsOnly( final boolean search_whole_words_only ) {
357 _match_whole_terms_only = search_whole_words_only;
360 final void setMinConfidenceValue( final double min_confidence_value ) {
361 _min_confidence_value = min_confidence_value;
364 void setNhConversionSupportValueStyle( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_value_style ) {
365 _nh_conversion_support_value_style = nh_conversion_support_value_style;
368 final void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
369 _node_label_direction = node_label_direction;
372 final void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
373 _ov_placement = ov_placement;
376 final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
377 _phylogeny_graphics_type = phylogeny_graphics_type;
380 final void setPrintBlackAndWhite( final boolean print_black_and_white ) {
381 _print_black_and_white = print_black_and_white;
384 final void setPrintLineWidth( final float print_line_width ) {
385 _print_line_width = print_line_width;
388 final void setPrintSizeX( final int print_size_x ) {
389 _print_size_x = print_size_x;
392 final void setPrintSizeY( final int print_size_y ) {
393 _print_size_y = print_size_y;
396 final void setPrintUsingActualSize( final boolean print_using_actual_size ) {
397 _print_using_actual_size = print_using_actual_size;
400 final void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
401 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
404 final void setScaleBarLength( final double scale_bar_length ) {
405 _scale_bar_length = scale_bar_length;
408 final void setSearchCaseSensitive( final boolean search_case_sensitive ) {
409 _search_case_sensitive = search_case_sensitive;
412 void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
413 _show_confidence_stddev = show_confidence_stddev;
416 void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
417 _show_default_node_shapes_external = show_default_node_shapes_external;
420 void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
421 _show_default_node_shapes_internal = show_default_node_shapes_internal;
424 final void setShowOverview( final boolean show_overview ) {
425 _show_overview = show_overview;
428 final void setShowScale( final boolean show_scale ) {
429 _show_scale = show_scale;
432 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
433 _taxonomy_extraction = taxonomy_extraction;
436 final private void init() {
437 _default_node_shape = NodeShape.CIRCLE;
438 _default_node_fill = NodeFill.GRADIENT;
439 _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
440 _internal_number_are_confidence_for_nh_parsing = false;
442 _antialias_screen = true;
443 _antialias_print = true;
444 _graphics_export_visible_only = false;
446 _background_color_gradient = false;
447 _show_default_node_shapes_internal = false;
448 _show_default_node_shapes_external = false;
449 if ( AptxUtil.isUsOrCanada() ) {
450 _print_size_x = Constants.US_LETTER_SIZE_X;
451 _print_size_y = Constants.US_LETTER_SIZE_Y;
454 _print_size_x = Constants.A4_SIZE_X;
455 _print_size_y = Constants.A4_SIZE_Y;
457 _min_confidence_value = MIN_CONFIDENCE_DEFAULT;
458 _print_black_and_white = false;
459 _print_using_actual_size = true;
460 _graphics_export_using_actual_size = true;
461 _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
462 _base_font = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 10 );
463 _match_whole_terms_only = false;
464 _search_case_sensitive = false;
465 _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
466 _show_overview = true;
467 _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
468 _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
469 _inverse_search_result = false;
470 _scale_bar_length = 0.0;
471 _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
472 _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
473 _nh_parsing_replace_underscores = false;
474 _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
475 _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
476 _show_domain_labels = true;
477 _show_annotation_ref_source = true;
478 setAbbreviateScientificTaxonNames( false );
479 _color_labels_same_as_parent_branch = false;
480 _show_confidence_stddev = true;
481 _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
482 _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
483 _line_up_renderable_node_data = false;
484 _right_align_domains = false;
487 final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) {
488 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
491 final private void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
492 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
495 public final static Options createInstance( final Configuration configuration ) {
496 final Options instance = createDefaultInstance();
497 if ( configuration != null ) {
498 instance.setAntialiasScreen( configuration.isAntialiasScreen() );
499 instance.setShowScale( configuration.isShowScale() );
500 instance.setShowOverview( configuration.isShowOverview() );
501 instance.setColorByTaxonomicGroup( configuration.isColorByTaxonomicGroup() );
502 instance.setCladogramType( configuration.getCladogramType() );
503 instance.setOvPlacement( configuration.getOvPlacement() );
504 instance.setPrintLineWidth( configuration.getPrintLineWidth() );
505 instance.setNodeLabelDirection( configuration.getNodeLabelDirection() );
506 instance.setBackgroundColorGradient( configuration.isBackgroundColorGradient() );
507 if ( configuration.getNumberOfDigitsAfterCommaForBranchLengthValues() >= 0 ) {
508 instance.setNumberOfDigitsAfterCommaForBranchLength( configuration
509 .getNumberOfDigitsAfterCommaForBranchLengthValues() );
511 if ( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() >= 0 ) {
512 instance.setNumberOfDigitsAfterCommaForConfidenceValues( configuration
513 .getNumberOfDigitsAfterCommaForConfidenceValues() );
515 instance.setTaxonomyExtraction( configuration.getTaxonomyExtraction() );
516 instance.setReplaceUnderscoresInNhParsing( configuration.isReplaceUnderscoresInNhParsing() );
517 instance.setInternalNumberAreConfidenceForNhParsing( configuration
518 .isInternalNumberAreConfidenceForNhParsing() );
519 instance.setEditable( configuration.isEditable() );
520 instance.setColorLabelsSameAsParentBranch( configuration.isColorLabelsSameAsParentBranch() );
521 instance.setShowDomainLabels( configuration.isShowDomainLabels() );
522 instance.setShowAnnotationRefSource( configuration.isShowAnnotationRefSource() );
523 instance.setAbbreviateScientificTaxonNames( configuration.isAbbreviateScientificTaxonNames() );
524 if ( configuration.getMinConfidenceValue() != MIN_CONFIDENCE_DEFAULT ) {
525 instance.setMinConfidenceValue( configuration.getMinConfidenceValue() );
527 if ( configuration.getGraphicsExportX() > 0 ) {
528 instance.setPrintSizeX( configuration.getGraphicsExportX() );
530 if ( configuration.getGraphicsExportY() > 0 ) {
531 instance.setPrintSizeY( configuration.getGraphicsExportY() );
533 if ( configuration.getBaseFontSize() > 0 ) {
534 instance.setBaseFont( instance.getBaseFont().deriveFont( ( float ) configuration.getBaseFontSize() ) );
536 if ( !ForesterUtil.isEmpty( configuration.getBaseFontFamilyName() ) ) {
537 instance.setBaseFont( new Font( configuration.getBaseFontFamilyName(), Font.PLAIN, instance
538 .getBaseFont().getSize() ) );
540 if ( configuration.getPhylogenyGraphicsType() != null ) {
541 instance.setPhylogenyGraphicsType( configuration.getPhylogenyGraphicsType() );
543 if ( configuration.getDefaultNodeFill() != null ) {
544 instance.setDefaultNodeFill( configuration.getDefaultNodeFill() );
546 if ( configuration.getDefaultNodeShape() != null ) {
547 instance.setDefaultNodeShape( configuration.getDefaultNodeShape() );
549 if ( configuration.getDefaultNodeShapeSize() >= 0 ) {
550 instance.setDefaultNodeShapeSize( configuration.getDefaultNodeShapeSize() );
552 instance.setShowDefaultNodeShapesInternal( configuration.isShowDefaultNodeShapesInternal() );
553 instance.setShowDefaultNodeShapesExternal( configuration.isShowDefaultNodeShapesExternal() );
554 if ( configuration.getExtDescNodeDataToReturn() != null ) {
555 instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() );
557 instance.setRightLineUpDomains( configuration.isRightLineUpDomains() );
558 instance.setLineUpRendarableNodeData( configuration.isLineUpRendarableNodeData() );
559 instance.setAllowErrorsInDistanceToParent( false );
564 final static Options createDefaultInstance() {
565 return new Options();
568 public static enum CLADOGRAM_TYPE {
569 EXT_NODE_SUM_DEP, NON_LINED_UP, TOTAL_NODE_SUM_DEP;
572 public static enum NODE_LABEL_DIRECTION {
576 public static enum PHYLOGENY_GRAPHICS_TYPE {
577 CIRCULAR, CONVEX, CURVED, EURO_STYLE, RECTANGULAR, ROUNDED, TRIANGULAR, UNROOTED;
580 static enum OVERVIEW_PLACEMENT_TYPE {
581 LOWER_LEFT( "lower left" ),
582 LOWER_RIGHT( "lower right" ),
583 UPPER_LEFT( "upper left" ),
584 UPPER_RIGHT( "upper right" );
586 private final String _name;
588 private OVERVIEW_PLACEMENT_TYPE( final String name ) {
593 public String toString() {
597 public String toTag() {
598 return toString().replaceAll( " ", "_" );
602 final public boolean isLineUpRendarableNodeData() {
603 return _line_up_renderable_node_data;
606 final public boolean isRightLineUpDomains() {
607 return _right_align_domains;
610 final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) {
611 _line_up_renderable_node_data = line_up_renderable_node_data;
614 final public void setRightLineUpDomains( final boolean right_align_domains ) {
615 _right_align_domains = right_align_domains;