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