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.NodeDataField;
33 import org.forester.phylogeny.data.NodeVisualData;
34 import org.forester.phylogeny.data.NodeVisualData.NodeFill;
35 import org.forester.phylogeny.data.NodeVisualData.NodeShape;
36 import org.forester.util.ForesterUtil;
39 * This is to hold changeable options.
41 final public class Options {
43 public static enum CLADOGRAM_TYPE {
44 LINED_UP, NON_LINED_UP;
47 public static enum NODE_LABEL_DIRECTION {
51 public static enum PHYLOGENY_GRAPHICS_TYPE {
52 CIRCULAR, CONVEX, CURVED, EURO_STYLE, RECTANGULAR, ROUNDED, TRIANGULAR, UNROOTED;
55 static enum OVERVIEW_PLACEMENT_TYPE {
56 LOWER_LEFT( "lower left" ),
57 LOWER_RIGHT( "lower right" ),
58 UPPER_LEFT( "upper left" ),
59 UPPER_RIGHT( "upper right" );
61 private final String _name;
63 private OVERVIEW_PLACEMENT_TYPE( final String name ) {
68 public String toString() {
72 public String toTag() {
73 return toString().replaceAll( " ", "_" );
76 static final double MIN_CONFIDENCE_DEFAULT = 0.0;
77 private boolean _abbreviate_scientific_names;
78 private boolean _allow_errors_in_distance_to_parent;
79 private boolean _antialias_print;
80 private boolean _antialias_screen;
81 private boolean _background_color_gradient;
82 private Font _base_font;
83 private CLADOGRAM_TYPE _cladogram_type;
84 private boolean _color_by_taxonomic_group;
85 private boolean _color_labels_same_as_parent_branch;
86 private NodeVisualData.NodeFill _default_node_fill;
87 private NodeVisualData.NodeShape _default_node_shape;
88 private short _default_node_shape_size;
89 private boolean _editable;
90 private NodeDataField _ext_desc_data_to_return;
91 private final boolean _graphics_export_using_actual_size = true;
92 private boolean _graphics_export_visible_only;
93 private boolean _internal_number_are_confidence_for_nh_parsing;
94 private boolean _inverse_search_result;
95 private boolean _match_whole_terms_only;
96 private boolean _search_with_regex;
97 private double _min_confidence_value;
98 private NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style;
99 private boolean _nh_parsing_replace_underscores;
100 private NODE_LABEL_DIRECTION _node_label_direction;
101 private short _number_of_digits_after_comma_for_branch_length_values;
102 private short _number_of_digits_after_comma_for_confidence_values;
103 private OVERVIEW_PLACEMENT_TYPE _ov_placement;
104 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type;
105 private boolean _print_black_and_white;
106 private float _print_line_width;
107 private final boolean _print_using_actual_size = true;
108 private double _scale_bar_length;
109 private boolean _search_case_sensitive;
110 private boolean _show_annotation_ref_source;
111 private boolean _show_confidence_stddev;
112 private boolean _show_default_node_shapes_for_marked_nodes;
113 private boolean _show_default_node_shapes_external;
114 private boolean _show_default_node_shapes_internal;
115 private boolean _show_domain_labels;
116 private boolean _show_overview;
117 private boolean _show_scale;
118 private TAXONOMY_EXTRACTION _taxonomy_extraction;
119 private boolean _line_up_renderable_node_data;
120 private boolean _right_align_domains;
121 private boolean _color_all_found_nodes_when_coloring_subtree;
122 private boolean _parse_beast_style_extended_nexus_tags;
123 private boolean _collapsed_with_average_height;
124 private boolean _show_abbreviated_labels_for_collapsed_nodes;
125 private boolean _align_ext_labels_in_phylogram;
131 public NodeDataField getExtDescNodeDataToReturn() {
132 return _ext_desc_data_to_return;
135 public boolean isAllowErrorsInDistanceToParent() {
136 return _allow_errors_in_distance_to_parent;
139 final public boolean isLineUpRendarableNodeData() {
140 return _line_up_renderable_node_data;
143 final public boolean isRightLineUpDomains() {
144 return _right_align_domains;
147 public final boolean isShowAnnotationRefSource() {
148 return _show_annotation_ref_source;
151 public final boolean isShowDomainLabels() {
152 return _show_domain_labels;
155 public final void setAllowErrorsInDistanceToParent( final boolean allow_errors_in_distance_to_parent ) {
156 _allow_errors_in_distance_to_parent = allow_errors_in_distance_to_parent;
159 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
160 _background_color_gradient = background_color_gradient;
163 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
164 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
167 public void setExtDescNodeDataToReturn( final NodeDataField ext_desc_data_to_return ) {
168 _ext_desc_data_to_return = ext_desc_data_to_return;
171 final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) {
172 _line_up_renderable_node_data = line_up_renderable_node_data;
175 final public void setRightLineUpDomains( final boolean right_align_domains ) {
176 _right_align_domains = right_align_domains;
179 public final void setShowAnnotationRefSource( final boolean show_annotation_ref_source ) {
180 _show_annotation_ref_source = show_annotation_ref_source;
183 public void setShowDomainLabels( final boolean show_domain_labels ) {
184 _show_domain_labels = show_domain_labels;
187 final private void init() {
188 _default_node_shape = NodeShape.CIRCLE;
189 _default_node_fill = NodeFill.GRADIENT;
190 _default_node_shape_size = AptxConstants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
191 _internal_number_are_confidence_for_nh_parsing = false;
193 _antialias_screen = true;
194 _antialias_print = true;
195 _graphics_export_visible_only = false;
197 _background_color_gradient = false;
198 _show_default_node_shapes_internal = false;
199 _show_default_node_shapes_external = false;
200 _show_default_node_shapes_for_marked_nodes = false;
201 _color_all_found_nodes_when_coloring_subtree = false;
202 _parse_beast_style_extended_nexus_tags= true;
203 _min_confidence_value = MIN_CONFIDENCE_DEFAULT;
204 _print_black_and_white = false;
205 _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
206 _base_font = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 10 );
207 _match_whole_terms_only = false;
208 _search_with_regex = false;
209 _search_case_sensitive = false;
210 _print_line_width = AptxConstants.PDF_LINE_WIDTH_DEFAULT;
211 _show_overview = true;
212 _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
213 _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
214 _inverse_search_result = false;
215 _scale_bar_length = 0.0;
216 _number_of_digits_after_comma_for_branch_length_values = AptxConstants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
217 _number_of_digits_after_comma_for_confidence_values = AptxConstants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
218 _nh_parsing_replace_underscores = false;
219 _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
220 _cladogram_type = AptxConstants.CLADOGRAM_TYPE_DEFAULT;
221 _show_domain_labels = true;
222 _show_annotation_ref_source = true;
223 setAbbreviateScientificTaxonNames( false );
224 _color_labels_same_as_parent_branch = false;
225 _show_confidence_stddev = false;
226 _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
227 _ext_desc_data_to_return = NodeDataField.UNKNOWN;
228 _line_up_renderable_node_data = true;
229 _right_align_domains = false;
230 _collapsed_with_average_height = true;
231 _show_abbreviated_labels_for_collapsed_nodes = true;
232 _align_ext_labels_in_phylogram = true;
235 final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) {
236 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
239 final private void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
240 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
243 final Font getBaseFont() {
247 final CLADOGRAM_TYPE getCladogramType() {
248 return _cladogram_type;
251 final NodeFill getDefaultNodeFill() {
252 return _default_node_fill;
255 final NodeShape getDefaultNodeShape() {
256 return _default_node_shape;
259 final short getDefaultNodeShapeSize() {
260 return _default_node_shape_size;
263 final double getMinConfidenceValue() {
264 return _min_confidence_value;
267 NH_CONVERSION_SUPPORT_VALUE_STYLE getNhConversionSupportValueStyle() {
268 return _nh_conversion_support_value_style;
271 final NODE_LABEL_DIRECTION getNodeLabelDirection() {
272 return _node_label_direction;
275 final short getNumberOfDigitsAfterCommaForBranchLengthValues() {
276 return _number_of_digits_after_comma_for_branch_length_values;
279 final short getNumberOfDigitsAfterCommaForConfidenceValues() {
280 return _number_of_digits_after_comma_for_confidence_values;
283 final OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
284 return _ov_placement;
287 final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
288 return _phylogeny_graphics_type;
291 final float getPrintLineWidth() {
292 return _print_line_width;
295 final double getScaleBarLength() {
296 return _scale_bar_length;
299 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
300 return _taxonomy_extraction;
303 final boolean isAbbreviateScientificTaxonNames() {
304 return _abbreviate_scientific_names;
307 boolean isAllowMagnificationOfTaxonomyImages() {
311 final boolean isAntialiasPrint() {
312 return _antialias_print;
315 final boolean isAntialiasScreen() {
316 return _antialias_screen;
319 final boolean isBackgroundColorGradient() {
320 return _background_color_gradient;
323 final boolean isColorByTaxonomicGroup() {
324 return _color_by_taxonomic_group;
327 final boolean isColorLabelsSameAsParentBranch() {
328 return _color_labels_same_as_parent_branch;
331 final boolean isEditable() {
335 final boolean isGraphicsExportUsingActualSize() {
336 return _graphics_export_using_actual_size;
339 final boolean isGraphicsExportVisibleOnly() {
340 return _graphics_export_visible_only;
343 final boolean isInternalNumberAreConfidenceForNhParsing() {
344 return _internal_number_are_confidence_for_nh_parsing;
347 final boolean isInverseSearchResult() {
348 return _inverse_search_result;
351 final boolean isMatchWholeTermsOnly() {
352 return _match_whole_terms_only;
355 final boolean isPrintBlackAndWhite() {
356 return _print_black_and_white;
359 final boolean isPrintUsingActualSize() {
360 return _print_using_actual_size;
363 final boolean isReplaceUnderscoresInNhParsing() {
364 return _nh_parsing_replace_underscores;
367 final boolean isSearchCaseSensitive() {
368 return _search_case_sensitive;
371 final boolean isSearchWithRegex() {
372 return _search_with_regex;
375 boolean isShowConfidenceStddev() {
376 return _show_confidence_stddev;
379 boolean isShowDefaultNodeShapesExternal() {
380 return _show_default_node_shapes_external;
383 boolean isShowDefaultNodeShapesForMarkedNodes() {
384 return _show_default_node_shapes_for_marked_nodes;
387 boolean isShowDefaultNodeShapesInternal() {
388 return _show_default_node_shapes_internal;
391 final boolean isShowOverview() {
392 return _show_overview;
395 final boolean isShowScale() {
399 final void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
400 _abbreviate_scientific_names = abbreviate_scientific_names;
403 final void setAntialiasPrint( final boolean antialias_print ) {
404 _antialias_print = antialias_print;
407 final void setAntialiasScreen( final boolean antialias_screen ) {
408 _antialias_screen = antialias_screen;
411 final void setBaseFont( final Font base_font ) {
412 _base_font = base_font;
415 final void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
416 _cladogram_type = cladogram_type;
419 final void setColorByTaxonomicGroup( final boolean color_by_taxonomic_group ) {
420 _color_by_taxonomic_group = color_by_taxonomic_group;
423 final void setDefaultNodeFill( final NodeFill default_node_fill ) {
424 _default_node_fill = default_node_fill;
427 final void setDefaultNodeShape( final NodeShape default_node_shape ) {
428 _default_node_shape = default_node_shape;
431 final void setDefaultNodeShapeSize( final short default_node_shape_size ) {
432 _default_node_shape_size = default_node_shape_size;
435 final void setEditable( final boolean editable ) {
436 _editable = editable;
439 final void setGraphicsExportVisibleOnly( final boolean graphics_export_visible_only ) {
440 _graphics_export_visible_only = graphics_export_visible_only;
443 final void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
444 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
447 final void setInverseSearchResult( final boolean inverse_search_result ) {
448 _inverse_search_result = inverse_search_result;
451 final void setMatchWholeTermsOnly( final boolean search_whole_words_only ) {
452 _match_whole_terms_only = search_whole_words_only;
455 final void setMinConfidenceValue( final double min_confidence_value ) {
456 _min_confidence_value = min_confidence_value;
459 void setNhConversionSupportValueStyle( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_value_style ) {
460 _nh_conversion_support_value_style = nh_conversion_support_value_style;
463 final void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
464 _node_label_direction = node_label_direction;
467 final void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
468 _ov_placement = ov_placement;
471 final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
472 _phylogeny_graphics_type = phylogeny_graphics_type;
475 final void setPrintBlackAndWhite( final boolean print_black_and_white ) {
476 _print_black_and_white = print_black_and_white;
479 final void setPrintLineWidth( final float print_line_width ) {
480 _print_line_width = print_line_width;
483 final void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
484 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
487 final void setScaleBarLength( final double scale_bar_length ) {
488 _scale_bar_length = scale_bar_length;
491 final void setSearchCaseSensitive( final boolean search_case_sensitive ) {
492 _search_case_sensitive = search_case_sensitive;
495 final void setSearchWithRegex( final boolean search_with_regex ) {
496 _search_with_regex = search_with_regex;
499 void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
500 _show_confidence_stddev = show_confidence_stddev;
503 void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
504 _show_default_node_shapes_external = show_default_node_shapes_external;
507 void setShowDefaultNodeShapesForMarkedNodes( final boolean show_default_node_shapes_for_marked_nodes ) {
508 _show_default_node_shapes_for_marked_nodes = show_default_node_shapes_for_marked_nodes;
511 void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
512 _show_default_node_shapes_internal = show_default_node_shapes_internal;
515 final void setShowOverview( final boolean show_overview ) {
516 _show_overview = show_overview;
519 final void setShowScale( final boolean show_scale ) {
520 _show_scale = show_scale;
523 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
524 _taxonomy_extraction = taxonomy_extraction;
527 public final static Options createInstance( final Configuration configuration ) {
528 final Options instance = createDefaultInstance();
529 if ( configuration != null ) {
530 instance.setAntialiasScreen( configuration.isAntialiasScreen() );
531 instance.setShowScale( configuration.isShowScale() );
532 instance.setShowOverview( configuration.isShowOverview() );
533 instance.setColorByTaxonomicGroup( configuration.isColorByTaxonomicGroup() );
534 instance.setCladogramType( configuration.getCladogramType() );
535 instance.setOvPlacement( configuration.getOvPlacement() );
536 instance.setPrintLineWidth( configuration.getPrintLineWidth() );
537 instance.setNodeLabelDirection( configuration.getNodeLabelDirection() );
538 instance.setBackgroundColorGradient( configuration.isBackgroundColorGradient() );
539 if ( configuration.getNumberOfDigitsAfterCommaForBranchLengthValues() >= 0 ) {
540 instance.setNumberOfDigitsAfterCommaForBranchLength( configuration
541 .getNumberOfDigitsAfterCommaForBranchLengthValues() );
543 if ( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() >= 0 ) {
544 instance.setNumberOfDigitsAfterCommaForConfidenceValues( configuration
545 .getNumberOfDigitsAfterCommaForConfidenceValues() );
547 instance.setTaxonomyExtraction( configuration.getTaxonomyExtraction() );
548 instance.setReplaceUnderscoresInNhParsing( configuration.isReplaceUnderscoresInNhParsing() );
549 instance.setInternalNumberAreConfidenceForNhParsing( configuration
550 .isInternalNumberAreConfidenceForNhParsing() );
551 instance.setEditable( configuration.isEditable() );
552 instance.setColorLabelsSameAsParentBranch( configuration.isColorLabelsSameAsParentBranch() );
553 instance.setShowDomainLabels( configuration.isShowDomainLabels() );
554 instance.setShowAnnotationRefSource( configuration.isShowAnnotationRefSource() );
555 instance.setAbbreviateScientificTaxonNames( configuration.isAbbreviateScientificTaxonNames() );
556 if ( configuration.getMinConfidenceValue() != MIN_CONFIDENCE_DEFAULT ) {
557 instance.setMinConfidenceValue( configuration.getMinConfidenceValue() );
559 if ( configuration.getBaseFontSize() > 0 ) {
560 instance.setBaseFont( instance.getBaseFont().deriveFont( ( float ) configuration.getBaseFontSize() ) );
562 if ( !ForesterUtil.isEmpty( configuration.getBaseFontFamilyName() ) ) {
563 instance.setBaseFont( new Font( configuration.getBaseFontFamilyName(), Font.PLAIN, instance
564 .getBaseFont().getSize() ) );
566 if ( configuration.getPhylogenyGraphicsType() != null ) {
567 instance.setPhylogenyGraphicsType( configuration.getPhylogenyGraphicsType() );
569 if ( configuration.getDefaultNodeFill() != null ) {
570 instance.setDefaultNodeFill( configuration.getDefaultNodeFill() );
572 if ( configuration.getDefaultNodeShape() != null ) {
573 instance.setDefaultNodeShape( configuration.getDefaultNodeShape() );
575 if ( configuration.getDefaultNodeShapeSize() >= 0 ) {
576 instance.setDefaultNodeShapeSize( configuration.getDefaultNodeShapeSize() );
578 instance.setShowDefaultNodeShapesInternal( configuration.isShowDefaultNodeShapesInternal() );
579 instance.setShowDefaultNodeShapesExternal( configuration.isShowDefaultNodeShapesExternal() );
580 instance.setShowDefaultNodeShapesForMarkedNodes( configuration.isShowDefaultNodeShapesForMarkedNodes() );
581 if ( configuration.getExtDescNodeDataToReturn() != null ) {
582 instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() );
584 instance.setRightLineUpDomains( configuration.isRightLineUpDomains() );
585 instance.setLineUpRendarableNodeData( configuration.isLineUpRendarableNodeData() );
586 instance.setAllowErrorsInDistanceToParent( false );
591 final static Options createDefaultInstance() {
592 return new Options();
595 final boolean isColorAllFoundNodesWhenColoringSubtree() {
596 return _color_all_found_nodes_when_coloring_subtree;
599 final void setColorAllFoundNodesWhenColoringSubtree( final boolean color_all_found_nodes_when_coloring_subtree ) {
600 _color_all_found_nodes_when_coloring_subtree = color_all_found_nodes_when_coloring_subtree;
603 final boolean isParseBeastStyleExtendedNexusTags() {
604 return _parse_beast_style_extended_nexus_tags;
607 final void setParseBeastStyleExtendedNexusTags( final boolean parse_beast_style_extended_nexus_tags ) {
608 _parse_beast_style_extended_nexus_tags = parse_beast_style_extended_nexus_tags;
611 final boolean isCollapsedWithAverageHeigh() {
612 return _collapsed_with_average_height;
615 final void setCollapsedWithAverageHeigh( final boolean collapsed_with_average_height ) {
616 _collapsed_with_average_height = collapsed_with_average_height;
619 final boolean isShowAbbreviatedLabelsForCollapsedNodes() {
620 return _show_abbreviated_labels_for_collapsed_nodes;
623 final void setShowAbbreviatedLabelsForCollapsedNodes(final boolean show_abbreviated_labels_for_collapsed_nodes) {
624 _show_abbreviated_labels_for_collapsed_nodes = show_abbreviated_labels_for_collapsed_nodes;
627 final boolean isAlignExtLabelsInPhylogram() {
628 return _align_ext_labels_in_phylogram;
631 final void setAlignExtLabelsInPhylogram( final boolean align_ext_labels_in_phylogram ) {
632 _align_ext_labels_in_phylogram = align_ext_labels_in_phylogram;