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: www.phylosoft.org/forester
26 package org.forester.archaeopteryx;
30 import org.forester.util.ForesterUtil;
33 * This is to hold changeable options.
35 final public class Options {
37 static final double MIN_CONFIDENCE_DEFAULT = 0.0;
38 private boolean _show_branch_length_values;
39 private boolean _internal_number_are_confidence_for_nh_parsing;
40 private boolean _show_scale;
41 private boolean _show_overview;
42 private boolean _antialias_screen;
43 private boolean _antialias_print;
44 private boolean _graphics_export_visible_only;
45 private int _print_size_x;
46 private int _print_size_y;
47 private double _min_confidence_value;
48 private boolean _print_black_and_white;
49 private boolean _print_using_actual_size;
50 private boolean _graphics_export_using_actual_size;
51 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type;
52 private CLADOGRAM_TYPE _cladogram_type;
53 private OVERVIEW_PLACEMENT_TYPE _ov_placement;
54 private NODE_LABEL_DIRECTION _node_label_direction;
55 private Font _base_font;
56 private boolean _match_whole_terms_only;
57 private boolean _search_case_sensitive;
58 private float _print_line_width;
59 private boolean _inverse_search_result;
60 private double _scale_bar_length;
61 private short _number_of_digits_after_comma_for_confidence_values;
62 private short _number_of_digits_after_comma_for_branch_length_values;
63 private boolean _nh_parsing_replace_underscores;
64 private boolean _nh_parsing_extract_pfam_taxonomy_codes;
65 private boolean _editable;
66 private boolean _background_color_gradient;
67 private boolean _show_domain_labels;
68 private boolean _color_labels_same_as_parent_branch;
69 private boolean _abbreviate_scientific_names;
70 private NodeShape _default_node_shape;
71 private short _default_node_shape_size;
72 private boolean _taxonomy_colorize_node_shapes_instead_of_labels;
79 RECTANGLE_WITH_GRADIENT,
88 final Font getBaseFont() {
92 final CLADOGRAM_TYPE getCladogramType() {
93 return _cladogram_type;
96 final double getMinConfidenceValue() {
97 return _min_confidence_value;
100 final NODE_LABEL_DIRECTION getNodeLabelDirection() {
101 return _node_label_direction;
104 final short getNumberOfDigitsAfterCommaForBranchLengthValues() {
105 return _number_of_digits_after_comma_for_branch_length_values;
108 final short getNumberOfDigitsAfterCommaForConfidenceValues() {
109 return _number_of_digits_after_comma_for_confidence_values;
112 final OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
113 return _ov_placement;
116 final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
117 return _phylogeny_graphics_type;
120 final float getPrintLineWidth() {
121 return _print_line_width;
124 final int getPrintSizeX() {
125 return _print_size_x;
128 final int getPrintSizeY() {
129 return _print_size_y;
132 final double getScaleBarLength() {
133 return _scale_bar_length;
136 final private void init() {
137 _default_node_shape = NodeShape.RECTANGLE_WITH_GRADIENT;
138 _show_branch_length_values = false;
139 _internal_number_are_confidence_for_nh_parsing = false;
141 _antialias_screen = true;
142 _antialias_print = true;
143 _graphics_export_visible_only = false;
145 _background_color_gradient = false;
146 if ( Util.isUsOrCanada() ) {
147 _print_size_x = Constants.US_LETTER_SIZE_X;
148 _print_size_y = Constants.US_LETTER_SIZE_Y;
151 _print_size_x = Constants.A4_SIZE_X;
152 _print_size_y = Constants.A4_SIZE_Y;
154 _min_confidence_value = MIN_CONFIDENCE_DEFAULT;
155 _print_black_and_white = false;
156 _print_using_actual_size = false;
157 _graphics_export_using_actual_size = true;
158 _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
159 _base_font = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 10 );
160 _match_whole_terms_only = false;
161 _search_case_sensitive = false;
162 _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
163 _show_overview = true;
164 _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
165 _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
166 _inverse_search_result = false;
167 _scale_bar_length = 0.0;
168 _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
169 _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
170 _nh_parsing_replace_underscores = false;
171 _nh_parsing_extract_pfam_taxonomy_codes = false;
172 _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
173 _show_domain_labels = true;
174 setAbbreviateScientificTaxonNames( false );
175 _color_labels_same_as_parent_branch = false;
178 final boolean isAntialiasPrint() {
179 return _antialias_print;
182 final boolean isAntialiasScreen() {
183 return _antialias_screen;
186 final boolean isBackgroundColorGradient() {
187 return _background_color_gradient;
190 public final boolean isShowDomainLabels() {
191 return _show_domain_labels;
194 final boolean isColorLabelsSameAsParentBranch() {
195 return _color_labels_same_as_parent_branch;
198 final boolean isEditable() {
202 final boolean isExtractPfamTaxonomyCodesInNhParsing() {
203 return _nh_parsing_extract_pfam_taxonomy_codes;
206 final boolean isGraphicsExportUsingActualSize() {
207 return _graphics_export_using_actual_size;
210 final boolean isGraphicsExportVisibleOnly() {
211 return _graphics_export_visible_only;
214 final boolean isInternalNumberAreConfidenceForNhParsing() {
215 return _internal_number_are_confidence_for_nh_parsing;
218 final boolean isInverseSearchResult() {
219 return _inverse_search_result;
222 final boolean isMatchWholeTermsOnly() {
223 return _match_whole_terms_only;
226 final boolean isPrintBlackAndWhite() {
227 return _print_black_and_white;
230 final boolean isPrintUsingActualSize() {
231 return _print_using_actual_size;
234 final boolean isReplaceUnderscoresInNhParsing() {
235 return _nh_parsing_replace_underscores;
238 final boolean isSearchCaseSensitive() {
239 return _search_case_sensitive;
242 final boolean isShowBranchLengthValues() {
243 return _show_branch_length_values;
246 final NodeShape getDefaultNodeShape() {
247 return _default_node_shape;
250 final boolean isShowOverview() {
251 return _show_overview;
254 final boolean isShowScale() {
258 final void setAntialiasPrint( final boolean antialias_print ) {
259 _antialias_print = antialias_print;
262 final void setAntialiasScreen( final boolean antialias_screen ) {
263 _antialias_screen = antialias_screen;
266 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
267 _background_color_gradient = background_color_gradient;
270 public void setShowDomainLabels( final boolean show_domain_labels ) {
271 _show_domain_labels = show_domain_labels;
274 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
275 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
278 final void setBaseFont( final Font base_font ) {
279 _base_font = base_font;
282 final void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
283 _cladogram_type = cladogram_type;
286 final void setEditable( final boolean editable ) {
287 _editable = editable;
290 final void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) {
291 _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes;
294 final void setGraphicsExportUsingActualSize( final boolean graphics_export_using_actual_size ) {
295 _graphics_export_using_actual_size = graphics_export_using_actual_size;
296 if ( !graphics_export_using_actual_size ) {
297 setGraphicsExportVisibleOnly( false );
301 final void setGraphicsExportVisibleOnly( final boolean graphics_export_visible_only ) {
302 _graphics_export_visible_only = graphics_export_visible_only;
303 if ( graphics_export_visible_only ) {
304 setGraphicsExportUsingActualSize( true );
308 final void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
309 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
312 final void setInverseSearchResult( final boolean inverse_search_result ) {
313 _inverse_search_result = inverse_search_result;
316 final void setMatchWholeTermsOnly( final boolean search_whole_words_only ) {
317 _match_whole_terms_only = search_whole_words_only;
320 final void setMinConfidenceValue( final double min_confidence_value ) {
321 _min_confidence_value = min_confidence_value;
324 final void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
325 _node_label_direction = node_label_direction;
328 final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) {
329 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
332 final private void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
333 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
336 final void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
337 _ov_placement = ov_placement;
340 final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
341 _phylogeny_graphics_type = phylogeny_graphics_type;
344 final void setPrintBlackAndWhite( final boolean print_black_and_white ) {
345 _print_black_and_white = print_black_and_white;
348 final void setPrintLineWidth( final float print_line_width ) {
349 _print_line_width = print_line_width;
352 final void setPrintSizeX( final int print_size_x ) {
353 _print_size_x = print_size_x;
356 final void setPrintSizeY( final int print_size_y ) {
357 _print_size_y = print_size_y;
360 final void setPrintUsingActualSize( final boolean print_using_actual_size ) {
361 _print_using_actual_size = print_using_actual_size;
364 final void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
365 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
368 final void setScaleBarLength( final double scale_bar_length ) {
369 _scale_bar_length = scale_bar_length;
372 final void setSearchCaseSensitive( final boolean search_case_sensitive ) {
373 _search_case_sensitive = search_case_sensitive;
376 final void setShowBranchLengthValues( final boolean show_branch_length_values ) {
377 _show_branch_length_values = show_branch_length_values;
380 final void setDefaultNodeShape( final NodeShape default_node_shape ) {
381 _default_node_shape = default_node_shape;
384 final void setShowOverview( final boolean show_overview ) {
385 _show_overview = show_overview;
388 final void setShowScale( final boolean show_scale ) {
389 _show_scale = show_scale;
392 final static Options createDefaultInstance() {
393 return new Options();
396 final static Options createInstance( final Configuration configuration ) {
397 final Options instance = createDefaultInstance();
398 if ( configuration != null ) {
399 instance.setAntialiasScreen( configuration.isAntialiasScreen() );
400 instance.setShowScale( configuration.isShowScale() );
401 instance.setShowBranchLengthValues( configuration.isShowBranchLengthValues() );
402 instance.setShowOverview( configuration.isShowOverview() );
403 instance.setCladogramType( configuration.getCladogramType() );
404 instance.setOvPlacement( configuration.getOvPlacement() );
405 instance.setPrintLineWidth( configuration.getPrintLineWidth() );
406 instance.setNodeLabelDirection( configuration.getNodeLabelDirection() );
407 instance.setBackgroundColorGradient( configuration.isBackgroundColorGradient() );
408 if ( configuration.getNumberOfDigitsAfterCommaForBranchLengthValues() >= 0 ) {
409 instance.setNumberOfDigitsAfterCommaForBranchLength( configuration
410 .getNumberOfDigitsAfterCommaForBranchLengthValues() );
412 if ( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() >= 0 ) {
413 instance.setNumberOfDigitsAfterCommaForConfidenceValues( configuration
414 .getNumberOfDigitsAfterCommaForConfidenceValues() );
416 instance.setExtractPfamTaxonomyCodesInNhParsing( configuration.isExtractPfamTaxonomyCodesInNhParsing() );
417 instance.setReplaceUnderscoresInNhParsing( configuration.isReplaceUnderscoresInNhParsing() );
418 instance.setInternalNumberAreConfidenceForNhParsing( configuration
419 .isInternalNumberAreConfidenceForNhParsing() );
420 instance.setEditable( configuration.isEditable() );
421 instance.setColorLabelsSameAsParentBranch( configuration.isColorLabelsSameAsParentBranch() );
422 instance.setShowDomainLabels( configuration.isShowDomainLabels() );
423 instance.setAbbreviateScientificTaxonNames( configuration.isAbbreviateScientificTaxonNames() );
424 if ( configuration.getMinConfidenceValue() != MIN_CONFIDENCE_DEFAULT ) {
425 instance.setMinConfidenceValue( configuration.getMinConfidenceValue() );
427 if ( configuration.getGraphicsExportX() > 0 ) {
428 instance.setPrintSizeX( configuration.getGraphicsExportX() );
430 if ( configuration.getGraphicsExportY() > 0 ) {
431 instance.setPrintSizeY( configuration.getGraphicsExportY() );
433 if ( configuration.getBaseFontSize() > 0 ) {
434 instance.setBaseFont( instance.getBaseFont().deriveFont( ( float ) configuration.getBaseFontSize() ) );
436 if ( !ForesterUtil.isEmpty( configuration.getBaseFontFamilyName() ) ) {
437 instance.setBaseFont( new Font( configuration.getBaseFontFamilyName(), Font.PLAIN, instance
438 .getBaseFont().getSize() ) );
440 if ( configuration.getPhylogenyGraphicsType() != null ) {
441 instance.setPhylogenyGraphicsType( configuration.getPhylogenyGraphicsType() );
447 final void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
448 _abbreviate_scientific_names = abbreviate_scientific_names;
451 final boolean isAbbreviateScientificTaxonNames() {
452 return _abbreviate_scientific_names;
455 static enum CLADOGRAM_TYPE {
456 NON_LINED_UP, EXT_NODE_SUM_DEP, TOTAL_NODE_SUM_DEP;
459 static enum NODE_LABEL_DIRECTION {
463 static enum OVERVIEW_PLACEMENT_TYPE {
464 UPPER_LEFT( "upper left" ),
465 UPPER_RIGHT( "upper right" ),
466 LOWER_LEFT( "lower left" ),
467 LOWER_RIGHT( "lower right" );
469 private final String _name;
471 private OVERVIEW_PLACEMENT_TYPE( final String name ) {
476 public String toString() {
480 public String toTag() {
481 return toString().replaceAll( " ", "_" );
485 static enum PHYLOGENY_GRAPHICS_TYPE {
486 RECTANGULAR, TRIANGULAR, EURO_STYLE, ROUNDED, CONVEX, CURVED, UNROOTED, CIRCULAR;
489 boolean isAllowMagnificationOfTaxonomyImages() {
493 int getDefaultNodeBoxSize() {
494 // TODO make variable ~~