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_internal;
82 private boolean _show_default_node_shapes_external;
83 private boolean _show_confidence_stddev;
84 private NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style;
85 private NODE_DATA _ext_desc_data_to_return;
91 public NodeData.NODE_DATA getExtDescNodeDataToReturn() {
92 return _ext_desc_data_to_return;
95 public final boolean isShowDomainLabels() {
96 return _show_domain_labels;
99 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
100 _background_color_gradient = background_color_gradient;
103 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
104 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
107 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
108 _ext_desc_data_to_return = ext_desc_data_to_return;
111 public void setShowDomainLabels( final boolean show_domain_labels ) {
112 _show_domain_labels = show_domain_labels;
115 final Font getBaseFont() {
119 final CLADOGRAM_TYPE getCladogramType() {
120 return _cladogram_type;
123 final NodeFill getDefaultNodeFill() {
124 return _default_node_fill;
127 final NodeShape getDefaultNodeShape() {
128 return _default_node_shape;
131 final short getDefaultNodeShapeSize() {
132 return _default_node_shape_size;
135 final double getMinConfidenceValue() {
136 return _min_confidence_value;
139 NH_CONVERSION_SUPPORT_VALUE_STYLE getNhConversionSupportValueStyle() {
140 return _nh_conversion_support_value_style;
143 final NODE_LABEL_DIRECTION getNodeLabelDirection() {
144 return _node_label_direction;
147 final short getNumberOfDigitsAfterCommaForBranchLengthValues() {
148 return _number_of_digits_after_comma_for_branch_length_values;
151 final short getNumberOfDigitsAfterCommaForConfidenceValues() {
152 return _number_of_digits_after_comma_for_confidence_values;
155 final OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
156 return _ov_placement;
159 final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
160 return _phylogeny_graphics_type;
163 final float getPrintLineWidth() {
164 return _print_line_width;
167 final int getPrintSizeX() {
168 return _print_size_x;
171 final int getPrintSizeY() {
172 return _print_size_y;
175 final double getScaleBarLength() {
176 return _scale_bar_length;
179 final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
180 return _taxonomy_extraction;
183 final boolean isAbbreviateScientificTaxonNames() {
184 return _abbreviate_scientific_names;
187 boolean isAllowMagnificationOfTaxonomyImages() {
191 final boolean isAntialiasPrint() {
192 return _antialias_print;
195 final boolean isAntialiasScreen() {
196 return _antialias_screen;
199 final boolean isBackgroundColorGradient() {
200 return _background_color_gradient;
203 final boolean isColorLabelsSameAsParentBranch() {
204 return _color_labels_same_as_parent_branch;
207 final boolean isEditable() {
211 final boolean isGraphicsExportUsingActualSize() {
212 return _graphics_export_using_actual_size;
215 final boolean isGraphicsExportVisibleOnly() {
216 return _graphics_export_visible_only;
219 final boolean isInternalNumberAreConfidenceForNhParsing() {
220 return _internal_number_are_confidence_for_nh_parsing;
223 final boolean isInverseSearchResult() {
224 return _inverse_search_result;
227 final boolean isMatchWholeTermsOnly() {
228 return _match_whole_terms_only;
231 final boolean isPrintBlackAndWhite() {
232 return _print_black_and_white;
235 final boolean isPrintUsingActualSize() {
236 return _print_using_actual_size;
239 final boolean isReplaceUnderscoresInNhParsing() {
240 return _nh_parsing_replace_underscores;
243 final boolean isSearchCaseSensitive() {
244 return _search_case_sensitive;
247 final boolean isShowBranchLengthValues() {
248 return _show_branch_length_values;
251 boolean isShowConfidenceStddev() {
252 return _show_confidence_stddev;
255 boolean isShowDefaultNodeShapesExternal() {
256 return _show_default_node_shapes_external;
259 boolean isShowDefaultNodeShapesInternal() {
260 return _show_default_node_shapes_internal;
263 final boolean isShowOverview() {
264 return _show_overview;
267 final boolean isShowScale() {
271 boolean isTaxonomyColorizeNodeShapes() {
272 return _taxonomy_colorize_node_shapes;
275 final void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
276 _abbreviate_scientific_names = abbreviate_scientific_names;
279 final void setAntialiasPrint( final boolean antialias_print ) {
280 _antialias_print = antialias_print;
283 final void setAntialiasScreen( final boolean antialias_screen ) {
284 _antialias_screen = antialias_screen;
287 final void setBaseFont( final Font base_font ) {
288 _base_font = base_font;
291 final void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
292 _cladogram_type = cladogram_type;
295 final void setDefaultNodeFill( final NodeFill default_node_fill ) {
296 _default_node_fill = default_node_fill;
299 final void setDefaultNodeShape( final NodeShape default_node_shape ) {
300 _default_node_shape = default_node_shape;
303 final void setDefaultNodeShapeSize( final short default_node_shape_size ) {
304 _default_node_shape_size = default_node_shape_size;
307 final void setEditable( final boolean editable ) {
308 _editable = editable;
311 final void setGraphicsExportUsingActualSize( final boolean graphics_export_using_actual_size ) {
312 _graphics_export_using_actual_size = graphics_export_using_actual_size;
313 if ( !graphics_export_using_actual_size ) {
314 setGraphicsExportVisibleOnly( false );
318 final void setGraphicsExportVisibleOnly( final boolean graphics_export_visible_only ) {
319 _graphics_export_visible_only = graphics_export_visible_only;
320 if ( graphics_export_visible_only ) {
321 setGraphicsExportUsingActualSize( true );
325 final void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
326 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
329 final void setInverseSearchResult( final boolean inverse_search_result ) {
330 _inverse_search_result = inverse_search_result;
333 final void setMatchWholeTermsOnly( final boolean search_whole_words_only ) {
334 _match_whole_terms_only = search_whole_words_only;
337 final void setMinConfidenceValue( final double min_confidence_value ) {
338 _min_confidence_value = min_confidence_value;
341 void setNhConversionSupportValueStyle( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_value_style ) {
342 _nh_conversion_support_value_style = nh_conversion_support_value_style;
345 final void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
346 _node_label_direction = node_label_direction;
349 final void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
350 _ov_placement = ov_placement;
353 final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
354 _phylogeny_graphics_type = phylogeny_graphics_type;
357 final void setPrintBlackAndWhite( final boolean print_black_and_white ) {
358 _print_black_and_white = print_black_and_white;
361 final void setPrintLineWidth( final float print_line_width ) {
362 _print_line_width = print_line_width;
365 final void setPrintSizeX( final int print_size_x ) {
366 _print_size_x = print_size_x;
369 final void setPrintSizeY( final int print_size_y ) {
370 _print_size_y = print_size_y;
373 final void setPrintUsingActualSize( final boolean print_using_actual_size ) {
374 _print_using_actual_size = print_using_actual_size;
377 final void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
378 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
381 final void setScaleBarLength( final double scale_bar_length ) {
382 _scale_bar_length = scale_bar_length;
385 final void setSearchCaseSensitive( final boolean search_case_sensitive ) {
386 _search_case_sensitive = search_case_sensitive;
389 final void setShowBranchLengthValues( final boolean show_branch_length_values ) {
390 _show_branch_length_values = show_branch_length_values;
393 void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
394 _show_confidence_stddev = show_confidence_stddev;
397 void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
398 _show_default_node_shapes_external = show_default_node_shapes_external;
401 void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
402 _show_default_node_shapes_internal = show_default_node_shapes_internal;
405 final void setShowOverview( final boolean show_overview ) {
406 _show_overview = show_overview;
409 final void setShowScale( final boolean show_scale ) {
410 _show_scale = show_scale;
413 void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
414 _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
417 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
418 _taxonomy_extraction = taxonomy_extraction;
421 final private void init() {
422 _default_node_shape = NodeShape.CIRCLE;
423 _default_node_fill = NodeFill.GRADIENT;
424 _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
425 _taxonomy_colorize_node_shapes = false;
426 _show_branch_length_values = false;
427 _internal_number_are_confidence_for_nh_parsing = false;
429 _antialias_screen = false;
430 _antialias_print = true;
431 _graphics_export_visible_only = false;
433 _background_color_gradient = false;
434 _show_default_node_shapes_internal = false;
435 _show_default_node_shapes_external = false;
436 if ( AptxUtil.isUsOrCanada() ) {
437 _print_size_x = Constants.US_LETTER_SIZE_X;
438 _print_size_y = Constants.US_LETTER_SIZE_Y;
441 _print_size_x = Constants.A4_SIZE_X;
442 _print_size_y = Constants.A4_SIZE_Y;
444 _min_confidence_value = MIN_CONFIDENCE_DEFAULT;
445 _print_black_and_white = false;
446 _print_using_actual_size = false;
447 _graphics_export_using_actual_size = true;
448 _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
449 _base_font = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 10 );
450 _match_whole_terms_only = false;
451 _search_case_sensitive = false;
452 _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
453 _show_overview = true;
454 _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
455 _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
456 _inverse_search_result = false;
457 _scale_bar_length = 0.0;
458 _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
459 _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
460 _nh_parsing_replace_underscores = false;
461 _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
462 _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
463 _show_domain_labels = true;
464 setAbbreviateScientificTaxonNames( false );
465 _color_labels_same_as_parent_branch = false;
466 _show_confidence_stddev = true;
467 _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
468 _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
471 final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) {
472 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
475 final private void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
476 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
479 public final static Options createInstance( final Configuration configuration ) {
480 final Options instance = createDefaultInstance();
481 if ( configuration != null ) {
482 instance.setAntialiasScreen( configuration.isAntialiasScreen() );
483 instance.setShowScale( configuration.isShowScale() );
484 instance.setShowBranchLengthValues( configuration.isShowBranchLengthValues() );
485 instance.setShowOverview( configuration.isShowOverview() );
486 instance.setCladogramType( configuration.getCladogramType() );
487 instance.setOvPlacement( configuration.getOvPlacement() );
488 instance.setPrintLineWidth( configuration.getPrintLineWidth() );
489 instance.setNodeLabelDirection( configuration.getNodeLabelDirection() );
490 instance.setBackgroundColorGradient( configuration.isBackgroundColorGradient() );
491 if ( configuration.getNumberOfDigitsAfterCommaForBranchLengthValues() >= 0 ) {
492 instance.setNumberOfDigitsAfterCommaForBranchLength( configuration
493 .getNumberOfDigitsAfterCommaForBranchLengthValues() );
495 if ( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() >= 0 ) {
496 instance.setNumberOfDigitsAfterCommaForConfidenceValues( configuration
497 .getNumberOfDigitsAfterCommaForConfidenceValues() );
499 instance.setTaxonomyExtraction( configuration.getTaxonomyExtraction() );
500 instance.setReplaceUnderscoresInNhParsing( configuration.isReplaceUnderscoresInNhParsing() );
501 instance.setInternalNumberAreConfidenceForNhParsing( configuration
502 .isInternalNumberAreConfidenceForNhParsing() );
503 instance.setEditable( configuration.isEditable() );
504 instance.setColorLabelsSameAsParentBranch( configuration.isColorLabelsSameAsParentBranch() );
505 instance.setShowDomainLabels( configuration.isShowDomainLabels() );
506 instance.setAbbreviateScientificTaxonNames( configuration.isAbbreviateScientificTaxonNames() );
507 if ( configuration.getMinConfidenceValue() != MIN_CONFIDENCE_DEFAULT ) {
508 instance.setMinConfidenceValue( configuration.getMinConfidenceValue() );
510 if ( configuration.getGraphicsExportX() > 0 ) {
511 instance.setPrintSizeX( configuration.getGraphicsExportX() );
513 if ( configuration.getGraphicsExportY() > 0 ) {
514 instance.setPrintSizeY( configuration.getGraphicsExportY() );
516 if ( configuration.getBaseFontSize() > 0 ) {
517 instance.setBaseFont( instance.getBaseFont().deriveFont( ( float ) configuration.getBaseFontSize() ) );
519 if ( !ForesterUtil.isEmpty( configuration.getBaseFontFamilyName() ) ) {
520 instance.setBaseFont( new Font( configuration.getBaseFontFamilyName(), Font.PLAIN, instance
521 .getBaseFont().getSize() ) );
523 if ( configuration.getPhylogenyGraphicsType() != null ) {
524 instance.setPhylogenyGraphicsType( configuration.getPhylogenyGraphicsType() );
526 if ( configuration.getDefaultNodeFill() != null ) {
527 instance.setDefaultNodeFill( configuration.getDefaultNodeFill() );
529 if ( configuration.getDefaultNodeShape() != null ) {
530 instance.setDefaultNodeShape( configuration.getDefaultNodeShape() );
532 if ( configuration.getDefaultNodeShapeSize() >= 0 ) {
533 instance.setDefaultNodeShapeSize( configuration.getDefaultNodeShapeSize() );
535 instance.setTaxonomyColorizeNodeShapes( configuration.isTaxonomyColorizeNodeShapes() );
536 instance.setShowDefaultNodeShapesInternal( configuration.isShowDefaultNodeShapesInternal() );
537 instance.setShowDefaultNodeShapesExternal( configuration.isShowDefaultNodeShapesExternal() );
538 if ( configuration.getExtDescNodeDataToReturn() != null ) {
539 instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() );
545 final static Options createDefaultInstance() {
546 return new Options();
549 public static enum CLADOGRAM_TYPE {
550 NON_LINED_UP, EXT_NODE_SUM_DEP, TOTAL_NODE_SUM_DEP;
553 public static enum NODE_LABEL_DIRECTION {
557 public static enum PHYLOGENY_GRAPHICS_TYPE {
558 RECTANGULAR, TRIANGULAR, EURO_STYLE, ROUNDED, CONVEX, CURVED, UNROOTED, CIRCULAR;
561 static enum OVERVIEW_PLACEMENT_TYPE {
562 UPPER_LEFT( "upper left" ),
563 UPPER_RIGHT( "upper right" ),
564 LOWER_LEFT( "lower left" ),
565 LOWER_RIGHT( "lower right" );
567 private final String _name;
569 private OVERVIEW_PLACEMENT_TYPE( final String name ) {
574 public String toString() {
578 public String toTag() {
579 return toString().replaceAll( " ", "_" );
583 public boolean isAllowFontSizeChange() {