forester/java/src/org/forester/archaeopteryx/Options.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2009 Christian M. Zmasek
   6 // Copyright (C) 2009 Burnham Institute for Medical Research
   7 // All rights reserved
   8 //
   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.
  13 //
  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.
  18 //
  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
  22 //
  23 // Contact: phylosoft @ gmail . com
  24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  25
  26 package org.forester.archaeopteryx;
  27
  28 import java.awt.Font;
  29
  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.NodeDataField;
  33 import org.forester.phylogeny.data.NodeVisualData;
  34 import org.forester.phylogeny.data.NodeVisualData.NodeFill;
  35 import org.forester.phylogeny.data.NodeVisualData.NodeShape;
  36 import org.forester.util.ForesterUtil;
  37
  38 /*
  39  * This is to hold changeable options.
  40  */
  41 final public class Options {
  42
  43     public static enum CLADOGRAM_TYPE {
  44         LINED_UP, NON_LINED_UP;
  45     }
  46
  47     public static enum NODE_LABEL_DIRECTION {
  48         HORIZONTAL, RADIAL;
  49     }
  50
  51     public static enum PHYLOGENY_GRAPHICS_TYPE {
  52         CIRCULAR, CONVEX, CURVED, EURO_STYLE, RECTANGULAR, ROUNDED, TRIANGULAR, UNROOTED;
  53     }
  54
  55     static enum OVERVIEW_PLACEMENT_TYPE {
  56         LOWER_LEFT( "lower left" ),
  57         LOWER_RIGHT( "lower right" ),
  58         UPPER_LEFT( "upper left" ),
  59         UPPER_RIGHT( "upper right" );
  60
  61         private final String _name;
  62
  63         private OVERVIEW_PLACEMENT_TYPE( final String name ) {
  64             _name = name;
  65         }
  66
  67         @Override
  68         public String toString() {
  69             return _name;
  70         }
  71
  72         public String toTag() {
  73             return toString().replaceAll( " ", "_" );
  74         }
  75     }
  76     static final double                       MIN_CONFIDENCE_DEFAULT = 0.0;
  77     private boolean                           _abbreviate_scientific_names;
  78     private boolean                           _allow_errors_in_distance_to_parent;
  79     private boolean                           _antialias_print;
  80     private boolean                           _antialias_screen;
  81     private boolean                           _background_color_gradient;
  82     private Font                              _base_font;
  83     private CLADOGRAM_TYPE                    _cladogram_type;
  84     private boolean                           _color_by_taxonomic_group;
  85     private boolean                           _color_labels_same_as_parent_branch;
  86     private NodeVisualData.NodeFill           _default_node_fill;
  87     private NodeVisualData.NodeShape          _default_node_shape;
  88     private short                             _default_node_shape_size;
  89     private boolean                           _editable;
  90     private NodeDataField                     _ext_desc_data_to_return;
  91     private final boolean                     _graphics_export_using_actual_size = true;
  92     private boolean                           _graphics_export_visible_only;
  93     private boolean                           _internal_number_are_confidence_for_nh_parsing;
  94     private boolean                           _inverse_search_result;
  95     private boolean                           _match_whole_terms_only;
  96     private boolean                           _search_with_regex;
  97     private double                            _min_confidence_value;
  98     private NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style;
  99     private boolean                           _nh_parsing_replace_underscores;
 100     private NODE_LABEL_DIRECTION              _node_label_direction;
 101     private short                             _number_of_digits_after_comma_for_branch_length_values;
 102     private short                             _number_of_digits_after_comma_for_confidence_values;
 103     private OVERVIEW_PLACEMENT_TYPE           _ov_placement;
 104     private PHYLOGENY_GRAPHICS_TYPE           _phylogeny_graphics_type;
 105     private boolean                           _print_black_and_white;
 106     private float                             _print_line_width;
 107     private final boolean                     _print_using_actual_size = true;
 108     private double                            _scale_bar_length;
 109     private boolean                           _search_case_sensitive;
 110     private boolean                           _show_annotation_ref_source;
 111     private boolean                           _show_confidence_stddev;
 112     private boolean                           _show_default_node_shapes_for_marked_nodes;
 113     private boolean                           _show_default_node_shapes_external;
 114     private boolean                           _show_default_node_shapes_internal;
 115     private boolean                           _show_domain_labels;
 116     private boolean                           _show_overview;
 117     private boolean                           _show_scale;
 118     private TAXONOMY_EXTRACTION               _taxonomy_extraction;
 119     private boolean                           _line_up_renderable_node_data;
 120     private boolean                           _right_align_domains;
 121     private boolean                           _color_all_found_nodes_when_coloring_subtree;
 122     private boolean                           _parse_beast_style_extended_nexus_tags;
 123     private boolean                           _collapsed_with_average_height;
 124     private boolean                           _show_abbreviated_labels_for_collapsed_nodes;
 125     private boolean                           _align_ext_labels_in_phylogram;
 126
 127     private Options() {
 128         init();
 129     }
 130
 131     public NodeDataField getExtDescNodeDataToReturn() {
 132         return _ext_desc_data_to_return;
 133     }
 134
 135     public boolean isAllowErrorsInDistanceToParent() {
 136         return _allow_errors_in_distance_to_parent;
 137     }
 138
 139     final public boolean isLineUpRendarableNodeData() {
 140         return _line_up_renderable_node_data;
 141     }
 142
 143     final public boolean isRightLineUpDomains() {
 144         return _right_align_domains;
 145     }
 146
 147     public final boolean isShowAnnotationRefSource() {
 148         return _show_annotation_ref_source;
 149     }
 150
 151     public final boolean isShowDomainLabels() {
 152         return _show_domain_labels;
 153     }
 154
 155     public final void setAllowErrorsInDistanceToParent( final boolean allow_errors_in_distance_to_parent ) {
 156         _allow_errors_in_distance_to_parent = allow_errors_in_distance_to_parent;
 157     }
 158
 159     public void setBackgroundColorGradient( final boolean background_color_gradient ) {
 160         _background_color_gradient = background_color_gradient;
 161     }
 162
 163     public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
 164         _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
 165     }
 166
 167     public void setExtDescNodeDataToReturn( final NodeDataField ext_desc_data_to_return ) {
 168         _ext_desc_data_to_return = ext_desc_data_to_return;
 169     }
 170
 171     final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) {
 172         _line_up_renderable_node_data = line_up_renderable_node_data;
 173     }
 174
 175     final public void setRightLineUpDomains( final boolean right_align_domains ) {
 176         _right_align_domains = right_align_domains;
 177     }
 178
 179     public final void setShowAnnotationRefSource( final boolean show_annotation_ref_source ) {
 180         _show_annotation_ref_source = show_annotation_ref_source;
 181     }
 182
 183     public void setShowDomainLabels( final boolean show_domain_labels ) {
 184         _show_domain_labels = show_domain_labels;
 185     }
 186
 187     final private void init() {
 188         _default_node_shape = NodeShape.CIRCLE;
 189         _default_node_fill = NodeFill.GRADIENT;
 190         _default_node_shape_size = AptxConstants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
 191         _internal_number_are_confidence_for_nh_parsing = false;
 192         _show_scale = false;
 193         _antialias_screen = true;
 194         _antialias_print = true;
 195         _graphics_export_visible_only = false;
 196         _editable = true;
 197         _background_color_gradient = false;
 198         _show_default_node_shapes_internal = false;
 199         _show_default_node_shapes_external = false;
 200         _show_default_node_shapes_for_marked_nodes = false;
 201         _color_all_found_nodes_when_coloring_subtree = false;
 202         _parse_beast_style_extended_nexus_tags= true;
 203         _min_confidence_value = MIN_CONFIDENCE_DEFAULT;
 204         _print_black_and_white = false;
 205         _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
 206         _base_font = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 10 );
 207         _match_whole_terms_only = false;
 208         _search_with_regex = false;
 209         _search_case_sensitive = false;
 210         _print_line_width = AptxConstants.PDF_LINE_WIDTH_DEFAULT;
 211         _show_overview = true;
 212         _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
 213         _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
 214         _inverse_search_result = false;
 215         _scale_bar_length = 0.0;
 216         _number_of_digits_after_comma_for_branch_length_values = AptxConstants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
 217         _number_of_digits_after_comma_for_confidence_values = AptxConstants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
 218         _nh_parsing_replace_underscores = false;
 219         _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
 220         _cladogram_type = AptxConstants.CLADOGRAM_TYPE_DEFAULT;
 221         _show_domain_labels = true;
 222         _show_annotation_ref_source = true;
 223         setAbbreviateScientificTaxonNames( false );
 224         _color_labels_same_as_parent_branch = false;
 225         _show_confidence_stddev = false;
 226         _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
 227         _ext_desc_data_to_return = NodeDataField.UNKNOWN;
 228         _line_up_renderable_node_data = true;
 229         _right_align_domains = false;
 230         _collapsed_with_average_height = true;
 231         _show_abbreviated_labels_for_collapsed_nodes = true;
 232         _align_ext_labels_in_phylogram = true;
 233     }
 234
 235     final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) {
 236         _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
 237     }
 238
 239     final private void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
 240         _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
 241     }
 242
 243     final Font getBaseFont() {
 244         return _base_font;
 245     }
 246
 247     final CLADOGRAM_TYPE getCladogramType() {
 248         return _cladogram_type;
 249     }
 250
 251     final NodeFill getDefaultNodeFill() {
 252         return _default_node_fill;
 253     }
 254
 255     final NodeShape getDefaultNodeShape() {
 256         return _default_node_shape;
 257     }
 258
 259     final short getDefaultNodeShapeSize() {
 260         return _default_node_shape_size;
 261     }
 262
 263     final double getMinConfidenceValue() {
 264         return _min_confidence_value;
 265     }
 266
 267     NH_CONVERSION_SUPPORT_VALUE_STYLE getNhConversionSupportValueStyle() {
 268         return _nh_conversion_support_value_style;
 269     }
 270
 271     final NODE_LABEL_DIRECTION getNodeLabelDirection() {
 272         return _node_label_direction;
 273     }
 274
 275     final short getNumberOfDigitsAfterCommaForBranchLengthValues() {
 276         return _number_of_digits_after_comma_for_branch_length_values;
 277     }
 278
 279     final short getNumberOfDigitsAfterCommaForConfidenceValues() {
 280         return _number_of_digits_after_comma_for_confidence_values;
 281     }
 282
 283     final OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
 284         return _ov_placement;
 285     }
 286
 287     final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
 288         return _phylogeny_graphics_type;
 289     }
 290
 291     final float getPrintLineWidth() {
 292         return _print_line_width;
 293     }
 294
 295     final double getScaleBarLength() {
 296         return _scale_bar_length;
 297     }
 298
 299     final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
 300         return _taxonomy_extraction;
 301     }
 302
 303     final boolean isAbbreviateScientificTaxonNames() {
 304         return _abbreviate_scientific_names;
 305     }
 306
 307     boolean isAllowMagnificationOfTaxonomyImages() {
 308         return true;
 309     }
 310
 311     final boolean isAntialiasPrint() {
 312         return _antialias_print;
 313     }
 314
 315     final boolean isAntialiasScreen() {
 316         return _antialias_screen;
 317     }
 318
 319     final boolean isBackgroundColorGradient() {
 320         return _background_color_gradient;
 321     }
 322
 323     final boolean isColorByTaxonomicGroup() {
 324         return _color_by_taxonomic_group;
 325     }
 326
 327     final boolean isColorLabelsSameAsParentBranch() {
 328         return _color_labels_same_as_parent_branch;
 329     }
 330
 331     final boolean isEditable() {
 332         return _editable;
 333     }
 334
 335     final boolean isGraphicsExportUsingActualSize() {
 336         return _graphics_export_using_actual_size;
 337     }
 338
 339     final boolean isGraphicsExportVisibleOnly() {
 340         return _graphics_export_visible_only;
 341     }
 342
 343     final boolean isInternalNumberAreConfidenceForNhParsing() {
 344         return _internal_number_are_confidence_for_nh_parsing;
 345     }
 346
 347     final boolean isInverseSearchResult() {
 348         return _inverse_search_result;
 349     }
 350
 351     final boolean isMatchWholeTermsOnly() {
 352         return _match_whole_terms_only;
 353     }
 354
 355     final boolean isPrintBlackAndWhite() {
 356         return _print_black_and_white;
 357     }
 358
 359     final boolean isPrintUsingActualSize() {
 360         return _print_using_actual_size;
 361     }
 362
 363     final boolean isReplaceUnderscoresInNhParsing() {
 364         return _nh_parsing_replace_underscores;
 365     }
 366
 367     final boolean isSearchCaseSensitive() {
 368         return _search_case_sensitive;
 369     }
 370
 371     final boolean isSearchWithRegex() {
 372         return _search_with_regex;
 373     }
 374
 375     boolean isShowConfidenceStddev() {
 376         return _show_confidence_stddev;
 377     }
 378
 379     boolean isShowDefaultNodeShapesExternal() {
 380         return _show_default_node_shapes_external;
 381     }
 382
 383     boolean isShowDefaultNodeShapesForMarkedNodes() {
 384         return _show_default_node_shapes_for_marked_nodes;
 385     }
 386
 387     boolean isShowDefaultNodeShapesInternal() {
 388         return _show_default_node_shapes_internal;
 389     }
 390
 391     final boolean isShowOverview() {
 392         return _show_overview;
 393     }
 394
 395     final boolean isShowScale() {
 396         return _show_scale;
 397     }
 398
 399     final void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
 400         _abbreviate_scientific_names = abbreviate_scientific_names;
 401     }
 402
 403     final void setAntialiasPrint( final boolean antialias_print ) {
 404         _antialias_print = antialias_print;
 405     }
 406
 407     final void setAntialiasScreen( final boolean antialias_screen ) {
 408         _antialias_screen = antialias_screen;
 409     }
 410
 411     final void setBaseFont( final Font base_font ) {
 412         _base_font = base_font;
 413     }
 414
 415     final void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
 416         _cladogram_type = cladogram_type;
 417     }
 418
 419     final void setColorByTaxonomicGroup( final boolean color_by_taxonomic_group ) {
 420         _color_by_taxonomic_group = color_by_taxonomic_group;
 421     }
 422
 423     final void setDefaultNodeFill( final NodeFill default_node_fill ) {
 424         _default_node_fill = default_node_fill;
 425     }
 426
 427     final void setDefaultNodeShape( final NodeShape default_node_shape ) {
 428         _default_node_shape = default_node_shape;
 429     }
 430
 431     final void setDefaultNodeShapeSize( final short default_node_shape_size ) {
 432         _default_node_shape_size = default_node_shape_size;
 433     }
 434
 435     final void setEditable( final boolean editable ) {
 436         _editable = editable;
 437     }
 438
 439     final void setGraphicsExportVisibleOnly( final boolean graphics_export_visible_only ) {
 440         _graphics_export_visible_only = graphics_export_visible_only;
 441     }
 442
 443     final void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
 444         _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
 445     }
 446
 447     final void setInverseSearchResult( final boolean inverse_search_result ) {
 448         _inverse_search_result = inverse_search_result;
 449     }
 450
 451     final void setMatchWholeTermsOnly( final boolean search_whole_words_only ) {
 452         _match_whole_terms_only = search_whole_words_only;
 453     }
 454
 455     final void setMinConfidenceValue( final double min_confidence_value ) {
 456         _min_confidence_value = min_confidence_value;
 457     }
 458
 459     void setNhConversionSupportValueStyle( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_value_style ) {
 460         _nh_conversion_support_value_style = nh_conversion_support_value_style;
 461     }
 462
 463     final void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
 464         _node_label_direction = node_label_direction;
 465     }
 466
 467     final void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
 468         _ov_placement = ov_placement;
 469     }
 470
 471     final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
 472         _phylogeny_graphics_type = phylogeny_graphics_type;
 473     }
 474
 475     final void setPrintBlackAndWhite( final boolean print_black_and_white ) {
 476         _print_black_and_white = print_black_and_white;
 477     }
 478
 479     final void setPrintLineWidth( final float print_line_width ) {
 480         _print_line_width = print_line_width;
 481     }
 482
 483     final void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
 484         _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
 485     }
 486
 487     final void setScaleBarLength( final double scale_bar_length ) {
 488         _scale_bar_length = scale_bar_length;
 489     }
 490
 491     final void setSearchCaseSensitive( final boolean search_case_sensitive ) {
 492         _search_case_sensitive = search_case_sensitive;
 493     }
 494
 495     final void setSearchWithRegex( final boolean search_with_regex ) {
 496         _search_with_regex = search_with_regex;
 497     }
 498
 499     void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
 500         _show_confidence_stddev = show_confidence_stddev;
 501     }
 502
 503     void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
 504         _show_default_node_shapes_external = show_default_node_shapes_external;
 505     }
 506
 507     void setShowDefaultNodeShapesForMarkedNodes( final boolean show_default_node_shapes_for_marked_nodes ) {
 508         _show_default_node_shapes_for_marked_nodes = show_default_node_shapes_for_marked_nodes;
 509     }
 510
 511     void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
 512         _show_default_node_shapes_internal = show_default_node_shapes_internal;
 513     }
 514
 515     final void setShowOverview( final boolean show_overview ) {
 516         _show_overview = show_overview;
 517     }
 518
 519     final void setShowScale( final boolean show_scale ) {
 520         _show_scale = show_scale;
 521     }
 522
 523     final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
 524         _taxonomy_extraction = taxonomy_extraction;
 525     }
 526
 527     public final static Options createInstance( final Configuration configuration ) {
 528         final Options instance = createDefaultInstance();
 529         if ( configuration != null ) {
 530             instance.setAntialiasScreen( configuration.isAntialiasScreen() );
 531             instance.setShowScale( configuration.isShowScale() );
 532             instance.setShowOverview( configuration.isShowOverview() );
 533             instance.setColorByTaxonomicGroup( configuration.isColorByTaxonomicGroup() );
 534             instance.setCladogramType( configuration.getCladogramType() );
 535             instance.setOvPlacement( configuration.getOvPlacement() );
 536             instance.setPrintLineWidth( configuration.getPrintLineWidth() );
 537             instance.setNodeLabelDirection( configuration.getNodeLabelDirection() );
 538             instance.setBackgroundColorGradient( configuration.isBackgroundColorGradient() );
 539             if ( configuration.getNumberOfDigitsAfterCommaForBranchLengthValues() >= 0 ) {
 540                 instance.setNumberOfDigitsAfterCommaForBranchLength( configuration
 541                         .getNumberOfDigitsAfterCommaForBranchLengthValues() );
 542             }
 543             if ( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() >= 0 ) {
 544                 instance.setNumberOfDigitsAfterCommaForConfidenceValues( configuration
 545                         .getNumberOfDigitsAfterCommaForConfidenceValues() );
 546             }
 547             instance.setTaxonomyExtraction( configuration.getTaxonomyExtraction() );
 548             instance.setReplaceUnderscoresInNhParsing( configuration.isReplaceUnderscoresInNhParsing() );
 549             instance.setInternalNumberAreConfidenceForNhParsing( configuration
 550                     .isInternalNumberAreConfidenceForNhParsing() );
 551             instance.setEditable( configuration.isEditable() );
 552             instance.setColorLabelsSameAsParentBranch( configuration.isColorLabelsSameAsParentBranch() );
 553             instance.setShowDomainLabels( configuration.isShowDomainLabels() );
 554             instance.setShowAnnotationRefSource( configuration.isShowAnnotationRefSource() );
 555             instance.setAbbreviateScientificTaxonNames( configuration.isAbbreviateScientificTaxonNames() );
 556             if ( configuration.getMinConfidenceValue() != MIN_CONFIDENCE_DEFAULT ) {
 557                 instance.setMinConfidenceValue( configuration.getMinConfidenceValue() );
 558             }
 559             if ( configuration.getBaseFontSize() > 0 ) {
 560                 instance.setBaseFont( instance.getBaseFont().deriveFont( ( float ) configuration.getBaseFontSize() ) );
 561             }
 562             if ( !ForesterUtil.isEmpty( configuration.getBaseFontFamilyName() ) ) {
 563                 instance.setBaseFont( new Font( configuration.getBaseFontFamilyName(), Font.PLAIN, instance
 564                         .getBaseFont().getSize() ) );
 565             }
 566             if ( configuration.getPhylogenyGraphicsType() != null ) {
 567                 instance.setPhylogenyGraphicsType( configuration.getPhylogenyGraphicsType() );
 568             }
 569             if ( configuration.getDefaultNodeFill() != null ) {
 570                 instance.setDefaultNodeFill( configuration.getDefaultNodeFill() );
 571             }
 572             if ( configuration.getDefaultNodeShape() != null ) {
 573                 instance.setDefaultNodeShape( configuration.getDefaultNodeShape() );
 574             }
 575             if ( configuration.getDefaultNodeShapeSize() >= 0 ) {
 576                 instance.setDefaultNodeShapeSize( configuration.getDefaultNodeShapeSize() );
 577             }
 578             instance.setShowDefaultNodeShapesInternal( configuration.isShowDefaultNodeShapesInternal() );
 579             instance.setShowDefaultNodeShapesExternal( configuration.isShowDefaultNodeShapesExternal() );
 580             instance.setShowDefaultNodeShapesForMarkedNodes( configuration.isShowDefaultNodeShapesForMarkedNodes() );
 581             if ( configuration.getExtDescNodeDataToReturn() != null ) {
 582                 instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() );
 583             }
 584             instance.setRightLineUpDomains( configuration.isRightLineUpDomains() );
 585             instance.setLineUpRendarableNodeData( configuration.isLineUpRendarableNodeData() );
 586             instance.setAllowErrorsInDistanceToParent( false );
 587         }
 588         return instance;
 589     }
 590
 591     final static Options createDefaultInstance() {
 592         return new Options();
 593     }
 594
 595     final boolean isColorAllFoundNodesWhenColoringSubtree() {
 596         return _color_all_found_nodes_when_coloring_subtree;
 597     }
 598
 599     final void setColorAllFoundNodesWhenColoringSubtree( final boolean color_all_found_nodes_when_coloring_subtree ) {
 600         _color_all_found_nodes_when_coloring_subtree = color_all_found_nodes_when_coloring_subtree;
 601     }
 602
 603     final boolean isParseBeastStyleExtendedNexusTags() {
 604         return _parse_beast_style_extended_nexus_tags;
 605     }
 606
 607     final void setParseBeastStyleExtendedNexusTags( final boolean parse_beast_style_extended_nexus_tags ) {
 608         _parse_beast_style_extended_nexus_tags = parse_beast_style_extended_nexus_tags;
 609     }
 610
 611     final boolean isCollapsedWithAverageHeigh() {
 612         return _collapsed_with_average_height;
 613     }
 614
 615     final void setCollapsedWithAverageHeigh( final boolean collapsed_with_average_height ) {
 616         _collapsed_with_average_height = collapsed_with_average_height;
 617     }
 618
 619     final boolean isShowAbbreviatedLabelsForCollapsedNodes() {
 620         return _show_abbreviated_labels_for_collapsed_nodes;
 621     }
 622
 623     final void setShowAbbreviatedLabelsForCollapsedNodes(final boolean show_abbreviated_labels_for_collapsed_nodes) {
 624         _show_abbreviated_labels_for_collapsed_nodes =  show_abbreviated_labels_for_collapsed_nodes;
 625     }
 626
 627     final boolean isAlignExtLabelsInPhylogram() {
 628         return _align_ext_labels_in_phylogram;
 629     }
 630
 631     final void setAlignExtLabelsInPhylogram( final boolean align_ext_labels_in_phylogram ) {
 632         _align_ext_labels_in_phylogram = align_ext_labels_in_phylogram;
 633     }
 634
 635
 636 }