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.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
31 import org.forester.phylogeny.data.NodeData;
32 import org.forester.phylogeny.data.NodeData.NODE_DATA;
33 import org.forester.phylogeny.data.NodeVisualization;
34 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
35 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
36 import org.forester.util.ForesterUtil;
39 * This is to hold changeable options.
41 final public class Options {
43 static final double MIN_CONFIDENCE_DEFAULT = 0.0;
44 private boolean _show_branch_length_values;
45 private boolean _internal_number_are_confidence_for_nh_parsing;
46 private boolean _show_scale;
47 private boolean _show_overview;
48 private boolean _antialias_screen;
49 private boolean _antialias_print;
50 private boolean _graphics_export_visible_only;
51 private int _print_size_x;
52 private int _print_size_y;
53 private double _min_confidence_value;
54 private boolean _print_black_and_white;
55 private boolean _print_using_actual_size;
56 private boolean _graphics_export_using_actual_size;
57 private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type;
58 private CLADOGRAM_TYPE _cladogram_type;
59 private OVERVIEW_PLACEMENT_TYPE _ov_placement;
60 private NODE_LABEL_DIRECTION _node_label_direction;
61 private Font _base_font;
62 private boolean _match_whole_terms_only;
63 private boolean _search_case_sensitive;
64 private float _print_line_width;
65 private boolean _inverse_search_result;
66 private double _scale_bar_length;
67 private short _number_of_digits_after_comma_for_confidence_values;
68 private short _number_of_digits_after_comma_for_branch_length_values;
69 private boolean _nh_parsing_replace_underscores;
70 private boolean _nh_parsing_extract_pfam_taxonomy_codes;
71 private boolean _editable;
72 private boolean _background_color_gradient;
73 private boolean _show_domain_labels;
74 private boolean _color_labels_same_as_parent_branch;
75 private boolean _abbreviate_scientific_names;
76 private NodeVisualization.NodeShape _default_node_shape;
77 private NodeVisualization.NodeFill _default_node_fill;
78 private short _default_node_shape_size;
79 private boolean _taxonomy_colorize_node_shapes;
80 private boolean _show_default_node_shapes;
81 private boolean _show_confidence_stddev;
82 private NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style;
83 private NODE_DATA _ext_desc_data_to_return;
89 final Font getBaseFont() {
93 final CLADOGRAM_TYPE getCladogramType() {
94 return _cladogram_type;
97 final NodeFill getDefaultNodeFill() {
98 return _default_node_fill;
101 final NodeShape getDefaultNodeShape() {
102 return _default_node_shape;
105 final short getDefaultNodeShapeSize() {
106 return _default_node_shape_size;
109 final double getMinConfidenceValue() {
110 return _min_confidence_value;
113 final NODE_LABEL_DIRECTION getNodeLabelDirection() {
114 return _node_label_direction;
117 final short getNumberOfDigitsAfterCommaForBranchLengthValues() {
118 return _number_of_digits_after_comma_for_branch_length_values;
121 final short getNumberOfDigitsAfterCommaForConfidenceValues() {
122 return _number_of_digits_after_comma_for_confidence_values;
125 final OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
126 return _ov_placement;
129 final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
130 return _phylogeny_graphics_type;
133 final float getPrintLineWidth() {
134 return _print_line_width;
137 final int getPrintSizeX() {
138 return _print_size_x;
141 final int getPrintSizeY() {
142 return _print_size_y;
145 final double getScaleBarLength() {
146 return _scale_bar_length;
149 final private void init() {
150 _default_node_shape = NodeShape.CIRCLE;
151 _default_node_fill = NodeFill.GRADIENT;
152 _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
153 _taxonomy_colorize_node_shapes = false;
154 _show_branch_length_values = false;
155 _internal_number_are_confidence_for_nh_parsing = false;
157 _antialias_screen = true;
158 _antialias_print = true;
159 _graphics_export_visible_only = false;
161 _background_color_gradient = false;
162 _show_default_node_shapes = false;
163 if ( AptxUtil.isUsOrCanada() ) {
164 _print_size_x = Constants.US_LETTER_SIZE_X;
165 _print_size_y = Constants.US_LETTER_SIZE_Y;
168 _print_size_x = Constants.A4_SIZE_X;
169 _print_size_y = Constants.A4_SIZE_Y;
171 _min_confidence_value = MIN_CONFIDENCE_DEFAULT;
172 _print_black_and_white = false;
173 _print_using_actual_size = false;
174 _graphics_export_using_actual_size = true;
175 _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
176 _base_font = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 10 );
177 _match_whole_terms_only = false;
178 _search_case_sensitive = false;
179 _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
180 _show_overview = true;
181 _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
182 _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
183 _inverse_search_result = false;
184 _scale_bar_length = 0.0;
185 _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
186 _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
187 _nh_parsing_replace_underscores = false;
188 _nh_parsing_extract_pfam_taxonomy_codes = false;
189 _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
190 _show_domain_labels = true;
191 setAbbreviateScientificTaxonNames( false );
192 _color_labels_same_as_parent_branch = false;
193 _show_confidence_stddev = true;
194 _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
195 _ext_desc_data_to_return = NODE_DATA.NODE_NAME;
198 boolean isShowConfidenceStddev() {
199 return _show_confidence_stddev;
202 void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
203 _show_confidence_stddev = show_confidence_stddev;
206 NH_CONVERSION_SUPPORT_VALUE_STYLE getNhConversionSupportValueStyle() {
207 return _nh_conversion_support_value_style;
210 void setNhConversionSupportValueStyle( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_value_style ) {
211 _nh_conversion_support_value_style = nh_conversion_support_value_style;
214 final boolean isAbbreviateScientificTaxonNames() {
215 return _abbreviate_scientific_names;
218 boolean isAllowMagnificationOfTaxonomyImages() {
222 final boolean isAntialiasPrint() {
223 return _antialias_print;
226 final boolean isAntialiasScreen() {
227 return _antialias_screen;
230 final boolean isBackgroundColorGradient() {
231 return _background_color_gradient;
234 final boolean isColorLabelsSameAsParentBranch() {
235 return _color_labels_same_as_parent_branch;
238 final boolean isEditable() {
242 final boolean isExtractPfamTaxonomyCodesInNhParsing() {
243 return _nh_parsing_extract_pfam_taxonomy_codes;
246 final boolean isGraphicsExportUsingActualSize() {
247 return _graphics_export_using_actual_size;
250 final boolean isGraphicsExportVisibleOnly() {
251 return _graphics_export_visible_only;
254 final boolean isInternalNumberAreConfidenceForNhParsing() {
255 return _internal_number_are_confidence_for_nh_parsing;
258 final boolean isInverseSearchResult() {
259 return _inverse_search_result;
262 final boolean isMatchWholeTermsOnly() {
263 return _match_whole_terms_only;
266 final boolean isPrintBlackAndWhite() {
267 return _print_black_and_white;
270 final boolean isPrintUsingActualSize() {
271 return _print_using_actual_size;
274 final boolean isReplaceUnderscoresInNhParsing() {
275 return _nh_parsing_replace_underscores;
278 final boolean isSearchCaseSensitive() {
279 return _search_case_sensitive;
282 final boolean isShowBranchLengthValues() {
283 return _show_branch_length_values;
286 public final boolean isShowDomainLabels() {
287 return _show_domain_labels;
290 final boolean isShowOverview() {
291 return _show_overview;
294 final boolean isShowScale() {
298 boolean isTaxonomyColorizeNodeShapes() {
299 return _taxonomy_colorize_node_shapes;
302 final void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
303 _abbreviate_scientific_names = abbreviate_scientific_names;
306 final void setAntialiasPrint( final boolean antialias_print ) {
307 _antialias_print = antialias_print;
310 final void setAntialiasScreen( final boolean antialias_screen ) {
311 _antialias_screen = antialias_screen;
314 public void setBackgroundColorGradient( final boolean background_color_gradient ) {
315 _background_color_gradient = background_color_gradient;
318 final void setBaseFont( final Font base_font ) {
319 _base_font = base_font;
322 final void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
323 _cladogram_type = cladogram_type;
326 public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
327 _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
330 final void setDefaultNodeFill( final NodeFill default_node_fill ) {
331 _default_node_fill = default_node_fill;
334 final void setDefaultNodeShape( final NodeShape default_node_shape ) {
335 _default_node_shape = default_node_shape;
338 final void setDefaultNodeShapeSize( final short default_node_shape_size ) {
339 _default_node_shape_size = default_node_shape_size;
342 final void setEditable( final boolean editable ) {
343 _editable = editable;
346 final void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) {
347 _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes;
350 final void setGraphicsExportUsingActualSize( final boolean graphics_export_using_actual_size ) {
351 _graphics_export_using_actual_size = graphics_export_using_actual_size;
352 if ( !graphics_export_using_actual_size ) {
353 setGraphicsExportVisibleOnly( false );
357 final void setGraphicsExportVisibleOnly( final boolean graphics_export_visible_only ) {
358 _graphics_export_visible_only = graphics_export_visible_only;
359 if ( graphics_export_visible_only ) {
360 setGraphicsExportUsingActualSize( true );
364 final void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
365 _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
368 final void setInverseSearchResult( final boolean inverse_search_result ) {
369 _inverse_search_result = inverse_search_result;
372 final void setMatchWholeTermsOnly( final boolean search_whole_words_only ) {
373 _match_whole_terms_only = search_whole_words_only;
376 final void setMinConfidenceValue( final double min_confidence_value ) {
377 _min_confidence_value = min_confidence_value;
380 final void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
381 _node_label_direction = node_label_direction;
384 final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) {
385 _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
388 final private void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
389 _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
392 final void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
393 _ov_placement = ov_placement;
396 final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
397 _phylogeny_graphics_type = phylogeny_graphics_type;
400 final void setPrintBlackAndWhite( final boolean print_black_and_white ) {
401 _print_black_and_white = print_black_and_white;
404 final void setPrintLineWidth( final float print_line_width ) {
405 _print_line_width = print_line_width;
408 final void setPrintSizeX( final int print_size_x ) {
409 _print_size_x = print_size_x;
412 final void setPrintSizeY( final int print_size_y ) {
413 _print_size_y = print_size_y;
416 final void setPrintUsingActualSize( final boolean print_using_actual_size ) {
417 _print_using_actual_size = print_using_actual_size;
420 final void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
421 _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
424 final void setScaleBarLength( final double scale_bar_length ) {
425 _scale_bar_length = scale_bar_length;
428 final void setSearchCaseSensitive( final boolean search_case_sensitive ) {
429 _search_case_sensitive = search_case_sensitive;
432 final void setShowBranchLengthValues( final boolean show_branch_length_values ) {
433 _show_branch_length_values = show_branch_length_values;
436 public void setShowDomainLabels( final boolean show_domain_labels ) {
437 _show_domain_labels = show_domain_labels;
440 final void setShowOverview( final boolean show_overview ) {
441 _show_overview = show_overview;
444 final void setShowScale( final boolean show_scale ) {
445 _show_scale = show_scale;
448 void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
449 _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
452 final static Options createDefaultInstance() {
453 return new Options();
456 boolean isShowDefaultNodeShapes() {
457 return _show_default_node_shapes;
460 void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
461 _show_default_node_shapes = show_default_node_shapes;
464 public final static Options createInstance( final Configuration configuration ) {
465 final Options instance = createDefaultInstance();
466 if ( configuration != null ) {
467 instance.setAntialiasScreen( configuration.isAntialiasScreen() );
468 instance.setShowScale( configuration.isShowScale() );
469 instance.setShowBranchLengthValues( configuration.isShowBranchLengthValues() );
470 instance.setShowOverview( configuration.isShowOverview() );
471 instance.setCladogramType( configuration.getCladogramType() );
472 instance.setOvPlacement( configuration.getOvPlacement() );
473 instance.setPrintLineWidth( configuration.getPrintLineWidth() );
474 instance.setNodeLabelDirection( configuration.getNodeLabelDirection() );
475 instance.setBackgroundColorGradient( configuration.isBackgroundColorGradient() );
476 if ( configuration.getNumberOfDigitsAfterCommaForBranchLengthValues() >= 0 ) {
477 instance.setNumberOfDigitsAfterCommaForBranchLength( configuration
478 .getNumberOfDigitsAfterCommaForBranchLengthValues() );
480 if ( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() >= 0 ) {
481 instance.setNumberOfDigitsAfterCommaForConfidenceValues( configuration
482 .getNumberOfDigitsAfterCommaForConfidenceValues() );
484 instance.setExtractPfamTaxonomyCodesInNhParsing( configuration.isExtractPfamTaxonomyCodesInNhParsing() );
485 instance.setReplaceUnderscoresInNhParsing( configuration.isReplaceUnderscoresInNhParsing() );
486 instance.setInternalNumberAreConfidenceForNhParsing( configuration
487 .isInternalNumberAreConfidenceForNhParsing() );
488 instance.setEditable( configuration.isEditable() );
489 instance.setColorLabelsSameAsParentBranch( configuration.isColorLabelsSameAsParentBranch() );
490 instance.setShowDomainLabels( configuration.isShowDomainLabels() );
491 instance.setAbbreviateScientificTaxonNames( configuration.isAbbreviateScientificTaxonNames() );
492 if ( configuration.getMinConfidenceValue() != MIN_CONFIDENCE_DEFAULT ) {
493 instance.setMinConfidenceValue( configuration.getMinConfidenceValue() );
495 if ( configuration.getGraphicsExportX() > 0 ) {
496 instance.setPrintSizeX( configuration.getGraphicsExportX() );
498 if ( configuration.getGraphicsExportY() > 0 ) {
499 instance.setPrintSizeY( configuration.getGraphicsExportY() );
501 if ( configuration.getBaseFontSize() > 0 ) {
502 instance.setBaseFont( instance.getBaseFont().deriveFont( ( float ) configuration.getBaseFontSize() ) );
504 if ( !ForesterUtil.isEmpty( configuration.getBaseFontFamilyName() ) ) {
505 instance.setBaseFont( new Font( configuration.getBaseFontFamilyName(), Font.PLAIN, instance
506 .getBaseFont().getSize() ) );
508 if ( configuration.getPhylogenyGraphicsType() != null ) {
509 instance.setPhylogenyGraphicsType( configuration.getPhylogenyGraphicsType() );
511 if ( configuration.getDefaultNodeFill() != null ) {
512 instance.setDefaultNodeFill( configuration.getDefaultNodeFill() );
514 if ( configuration.getDefaultNodeShape() != null ) {
515 instance.setDefaultNodeShape( configuration.getDefaultNodeShape() );
517 if ( configuration.getDefaultNodeShapeSize() >= 0 ) {
518 instance.setDefaultNodeShapeSize( configuration.getDefaultNodeShapeSize() );
520 instance.setTaxonomyColorizeNodeShapes( configuration.isTaxonomyColorizeNodeShapes() );
521 instance.setShowDefaultNodeShapes( configuration.isShowDefaultNodeShapes() );
522 if ( configuration.getExtDescNodeDataToReturn() != null ) {
523 instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() );
529 public static enum CLADOGRAM_TYPE {
530 NON_LINED_UP, EXT_NODE_SUM_DEP, TOTAL_NODE_SUM_DEP;
533 public static enum NODE_LABEL_DIRECTION {
537 static enum OVERVIEW_PLACEMENT_TYPE {
538 UPPER_LEFT( "upper left" ),
539 UPPER_RIGHT( "upper right" ),
540 LOWER_LEFT( "lower left" ),
541 LOWER_RIGHT( "lower right" );
543 private final String _name;
545 private OVERVIEW_PLACEMENT_TYPE( final String name ) {
550 public String toString() {
554 public String toTag() {
555 return toString().replaceAll( " ", "_" );
559 public static enum PHYLOGENY_GRAPHICS_TYPE {
560 RECTANGULAR, TRIANGULAR, EURO_STYLE, ROUNDED, CONVEX, CURVED, UNROOTED, CIRCULAR;
563 public NodeData.NODE_DATA getExtDescNodeDataToReturn() {
564 return _ext_desc_data_to_return;
567 public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
568 _ext_desc_data_to_return = ext_desc_data_to_return;