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_node_boxes;
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 final Font getBaseFont() {
80 final CLADOGRAM_TYPE getCladogramType() {
81 return _cladogram_type;
84 final double getMinConfidenceValue() {
85 return _min_confidence_value;
88 final NODE_LABEL_DIRECTION getNodeLabelDirection() {
89 return _node_label_direction;
92 final short getNumberOfDigitsAfterCommaForBranchLengthValues() {
93 return _number_of_digits_after_comma_for_branch_length_values;
96 final short getNumberOfDigitsAfterCommaForConfidenceValues() {
97 return _number_of_digits_after_comma_for_confidence_values;
100 final OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
101 return _ov_placement;
104 final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
105 return _phylogeny_graphics_type;
108 final float getPrintLineWidth() {
109 return _print_line_width;
112 final int getPrintSizeX() {
113 return _print_size_x;
116 final int getPrintSizeY() {
117 return _print_size_y;
120 final double getScaleBarLength() {
121 return _scale_bar_length;
124 final private void init() {
125 _show_node_boxes = false;
126 _show_branch_length_values = false;
127 _internal_number_are_confidence_for_nh_parsing = false;
129 _antialias_screen = true;
130 _antialias_print = true;
131 _graphics_export_visible_only = false;
133 _background_color_gradient = false;
134 if ( Util.isUsOrCanada() ) {
135 _print_size_x = Constants.US_LETTER_SIZE_X;
136 _print_size_y = Constants.US_LETTER_SIZE_Y;
139 _print_size_x = Constants.A4_SIZE_X;
140 _print_size_y = Constants.A4_SIZE_Y;
142 _min_confidence_value = MIN_CONFIDENCE_DEFAULT;
143 _print_black_and_white = false;
144 _print_using_actual_size = false;
145 _graphics_export_using_actual_size = true;
146 _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
147 _base_font = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 10 );
148 _match_whole_terms_only = false;
149 _search_case_sensitive = false;
150 _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
151 _show_overview = true;
152 _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
153 _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
154 _inverse_search_result = false;
155 _scale_bar_length = 0.0;
156 _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
157 _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
158 _nh_parsing_replace_underscores = false;
159 _nh_parsing_extract_pfam_taxonomy_codes = false;
160 _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
161 _show_domain_labels = true;
162 setAbbreviateScientificTaxonNames( false );
163 _color_labels_same_as_parent_branch = false;
166 final boolean isAntialiasPrint() {
167 return _antialias_print;
170 final boolean isAntialiasScreen() {
171 return _antialias_screen;
174 final boolean isBackgroundColorGradient() {
175 return _background_color_gradient;
178 public final boolean isShowDomainLabels() {
179 return _show_domain_labels;
182 final boolean isColorLabelsSameAsParentBranch() {
183 return _color_labels_same_as_parent_branch;
186 final boolean isEditable() {
190 final boolean isExtractPfamTaxonomyCodesInNhParsing() {
191 return _nh_parsing_extract_pfam_taxonomy_codes;
194 final boolean isGraphicsExportUsingActualSize() {
195 return _graphics_export_using_actual_size;
198 final boolean isGraphicsExportVisibleOnly() {
199 return _graphics_export_visible_only;
202 final boolean isInternalNumberAreConfidenceForNhParsing() {
203 return _internal_number_are_confidence_for_nh_parsing;
206 final boolean isInverseSearchResult() {
207 return _inverse_search_result;
210 final boolean isMatchWholeTermsOnly() {
211 return _match_whole_terms_only;
214 final boolean isPrintBlackAndWhite() {
215 return _print_black_and_white;
218 final boolean isPrintUsingActualSize() {
219 return _print_using_actual_size;
222 final boolean isReplaceUnderscoresInNhParsing() {
223 return _nh_parsing_replace_underscores;
226 final boolean isSearchCaseSensitive() {
227 return _search_case_sensitive;
230 final boolean isShowBranchLengthValues() {
231 return _show_branch_length_values;
234 final boolean isShowNodeBoxes() {
235 return _show_node_boxes;
238 final boolean isShowOverview() {
239 return _show_overview;
242 final boolean isShowScale() {
246 final void setAntialiasPrint( final boolean antialias_print ) {
247 _antialias_print = antialias_print;
250 final void setAntialiasScreen( final boolean antialias_screen ) {
251 _antialias_screen = antialias_screen;
254 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
255 _background_color_gradient = background_color_gradient;
258 public void setShowDomainLabels( final boolean show_domain_labels ) {
259 _show_domain_labels = show_domain_labels;
262 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
263 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
266 final void setBaseFont( final Font base_font ) {
267 _base_font = base_font;
270 final void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
271 _cladogram_type = cladogram_type;
274 final void setEditable( final boolean editable ) {
275 _editable = editable;
278 final void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) {
279 _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes;
282 final void setGraphicsExportUsingActualSize( final boolean graphics_export_using_actual_size ) {
283 _graphics_export_using_actual_size = graphics_export_using_actual_size;
284 if ( !graphics_export_using_actual_size ) {
285 setGraphicsExportVisibleOnly( false );
289 final void setGraphicsExportVisibleOnly( final boolean graphics_export_visible_only ) {
290 _graphics_export_visible_only = graphics_export_visible_only;
291 if ( graphics_export_visible_only ) {
292 setGraphicsExportUsingActualSize( true );
296 final void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
297 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
300 final void setInverseSearchResult( final boolean inverse_search_result ) {
301 _inverse_search_result = inverse_search_result;
304 final void setMatchWholeTermsOnly( final boolean search_whole_words_only ) {
305 _match_whole_terms_only = search_whole_words_only;
308 final void setMinConfidenceValue( final double min_confidence_value ) {
309 _min_confidence_value = min_confidence_value;
312 final void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
313 _node_label_direction = node_label_direction;
316 final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) {
317 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
320 final private void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
321 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
324 final void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
325 _ov_placement = ov_placement;
328 final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
329 _phylogeny_graphics_type = phylogeny_graphics_type;
332 final void setPrintBlackAndWhite( final boolean print_black_and_white ) {
333 _print_black_and_white = print_black_and_white;
336 final void setPrintLineWidth( final float print_line_width ) {
337 _print_line_width = print_line_width;
340 final void setPrintSizeX( final int print_size_x ) {
341 _print_size_x = print_size_x;
344 final void setPrintSizeY( final int print_size_y ) {
345 _print_size_y = print_size_y;
348 final void setPrintUsingActualSize( final boolean print_using_actual_size ) {
349 _print_using_actual_size = print_using_actual_size;
352 final void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
353 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
356 final void setScaleBarLength( final double scale_bar_length ) {
357 _scale_bar_length = scale_bar_length;
360 final void setSearchCaseSensitive( final boolean search_case_sensitive ) {
361 _search_case_sensitive = search_case_sensitive;
364 final void setShowBranchLengthValues( final boolean show_branch_length_values ) {
365 _show_branch_length_values = show_branch_length_values;
368 final void setShowNodeBoxes( final boolean show_node_boxes ) {
369 _show_node_boxes = show_node_boxes;
372 final void setShowOverview( final boolean show_overview ) {
373 _show_overview = show_overview;
376 final void setShowScale( final boolean show_scale ) {
377 _show_scale = show_scale;
380 final static Options createDefaultInstance() {
381 return new Options();
384 final static Options createInstance( final Configuration configuration ) {
385 final Options instance = createDefaultInstance();
386 if ( configuration != null ) {
387 instance.setAntialiasScreen( configuration.isAntialiasScreen() );
388 instance.setShowScale( configuration.isShowScale() );
389 instance.setShowBranchLengthValues( configuration.isShowBranchLengthValues() );
390 instance.setShowOverview( configuration.isShowOverview() );
391 instance.setCladogramType( configuration.getCladogramType() );
392 instance.setOvPlacement( configuration.getOvPlacement() );
393 instance.setPrintLineWidth( configuration.getPrintLineWidth() );
394 instance.setNodeLabelDirection( configuration.getNodeLabelDirection() );
395 instance.setBackgroundColorGradient( configuration.isBackgroundColorGradient() );
396 if ( configuration.getNumberOfDigitsAfterCommaForBranchLengthValues() >= 0 ) {
397 instance.setNumberOfDigitsAfterCommaForBranchLength( configuration
398 .getNumberOfDigitsAfterCommaForBranchLengthValues() );
400 if ( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() >= 0 ) {
401 instance.setNumberOfDigitsAfterCommaForConfidenceValues( configuration
402 .getNumberOfDigitsAfterCommaForConfidenceValues() );
404 instance.setExtractPfamTaxonomyCodesInNhParsing( configuration.isExtractPfamTaxonomyCodesInNhParsing() );
405 instance.setReplaceUnderscoresInNhParsing( configuration.isReplaceUnderscoresInNhParsing() );
406 instance.setInternalNumberAreConfidenceForNhParsing( configuration
407 .isInternalNumberAreConfidenceForNhParsing() );
408 instance.setEditable( configuration.isEditable() );
409 instance.setColorLabelsSameAsParentBranch( configuration.isColorLabelsSameAsParentBranch() );
410 instance.setShowDomainLabels( configuration.isShowDomainLabels() );
411 instance.setAbbreviateScientificTaxonNames( configuration.isAbbreviateScientificTaxonNames() );
412 if ( configuration.getMinConfidenceValue() != MIN_CONFIDENCE_DEFAULT ) {
413 instance.setMinConfidenceValue( configuration.getMinConfidenceValue() );
415 if ( configuration.getGraphicsExportX() > 0 ) {
416 instance.setPrintSizeX( configuration.getGraphicsExportX() );
418 if ( configuration.getGraphicsExportY() > 0 ) {
419 instance.setPrintSizeY( configuration.getGraphicsExportY() );
421 if ( configuration.getBaseFontSize() > 0 ) {
422 instance.setBaseFont( instance.getBaseFont().deriveFont( ( float ) configuration.getBaseFontSize() ) );
424 if ( !ForesterUtil.isEmpty( configuration.getBaseFontFamilyName() ) ) {
425 instance.setBaseFont( new Font( configuration.getBaseFontFamilyName(), Font.PLAIN, instance
426 .getBaseFont().getSize() ) );
428 if ( configuration.getPhylogenyGraphicsType() != null ) {
429 instance.setPhylogenyGraphicsType( configuration.getPhylogenyGraphicsType() );
435 final void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
436 _abbreviate_scientific_names = abbreviate_scientific_names;
439 final boolean isAbbreviateScientificTaxonNames() {
440 return _abbreviate_scientific_names;
443 static enum CLADOGRAM_TYPE {
444 NON_LINED_UP, EXT_NODE_SUM_DEP, TOTAL_NODE_SUM_DEP;
447 static enum NODE_LABEL_DIRECTION {
451 static enum OVERVIEW_PLACEMENT_TYPE {
452 UPPER_LEFT( "upper left" ),
453 UPPER_RIGHT( "upper right" ),
454 LOWER_LEFT( "lower left" ),
455 LOWER_RIGHT( "lower right" );
457 private final String _name;
459 private OVERVIEW_PLACEMENT_TYPE( final String name ) {
464 public String toString() {
468 public String toTag() {
469 return toString().replaceAll( " ", "_" );
473 static enum PHYLOGENY_GRAPHICS_TYPE {
474 RECTANGULAR, TRIANGULAR, EURO_STYLE, ROUNDED, CONVEX, CURVED, UNROOTED, CIRCULAR;
477 boolean isAllowMagnificationOfTaxonomyImages() {
478 // TODO Auto-generated method stub