2 * This class was automatically generated with
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3 * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
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8 package jalview.schemabinding.version2;
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10 //---------------------------------/
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11 //- Imported classes and packages -/
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12 //---------------------------------/
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14 import org.exolab.castor.xml.Marshaller;
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15 import org.exolab.castor.xml.Unmarshaller;
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20 * @version $Revision$ $Date$
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22 public class Tree implements java.io.Serializable {
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25 //--------------------------/
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26 //- Class/Member Variables -/
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27 //--------------------------/
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35 * keeps track of state for field: _width
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37 private boolean _has_width;
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42 private int _height;
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45 * keeps track of state for field: _height
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47 private boolean _has_height;
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55 * keeps track of state for field: _xpos
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57 private boolean _has_xpos;
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65 * keeps track of state for field: _ypos
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67 private boolean _has_ypos;
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72 private java.lang.String _fontName;
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77 private int _fontSize;
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80 * keeps track of state for field: _fontSize
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82 private boolean _has_fontSize;
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87 private int _fontStyle;
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90 * keeps track of state for field: _fontStyle
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92 private boolean _has_fontStyle;
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97 private float _threshold;
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100 * keeps track of state for field: _threshold
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102 private boolean _has_threshold;
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105 * Field _showBootstrap.
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107 private boolean _showBootstrap;
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110 * keeps track of state for field: _showBootstrap
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112 private boolean _has_showBootstrap;
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115 * Field _showDistances.
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117 private boolean _showDistances;
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120 * keeps track of state for field: _showDistances
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122 private boolean _has_showDistances;
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125 * Field _markUnlinked.
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127 private boolean _markUnlinked;
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130 * keeps track of state for field: _markUnlinked
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132 private boolean _has_markUnlinked;
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135 * Field _fitToWindow.
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137 private boolean _fitToWindow;
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140 * keeps track of state for field: _fitToWindow
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142 private boolean _has_fitToWindow;
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145 * Field _currentTree.
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147 private boolean _currentTree;
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150 * keeps track of state for field: _currentTree
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152 private boolean _has_currentTree;
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155 * Tree ID added for binding tree visualization settings to
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156 * vamsas document trees in jalview 2.4.1
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158 private java.lang.String _id;
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163 private java.lang.String _title;
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168 private java.lang.String _newick;
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171 //----------------/
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172 //- Constructors -/
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173 //----------------/
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186 public void deleteCurrentTree(
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188 this._has_currentTree= false;
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193 public void deleteFitToWindow(
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195 this._has_fitToWindow= false;
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200 public void deleteFontSize(
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202 this._has_fontSize= false;
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207 public void deleteFontStyle(
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209 this._has_fontStyle= false;
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214 public void deleteHeight(
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216 this._has_height= false;
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221 public void deleteMarkUnlinked(
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223 this._has_markUnlinked= false;
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228 public void deleteShowBootstrap(
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230 this._has_showBootstrap= false;
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235 public void deleteShowDistances(
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237 this._has_showDistances= false;
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242 public void deleteThreshold(
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244 this._has_threshold= false;
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249 public void deleteWidth(
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251 this._has_width= false;
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256 public void deleteXpos(
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258 this._has_xpos= false;
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263 public void deleteYpos(
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265 this._has_ypos= false;
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269 * Returns the value of field 'currentTree'.
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271 * @return the value of field 'CurrentTree'.
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273 public boolean getCurrentTree(
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275 return this._currentTree;
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279 * Returns the value of field 'fitToWindow'.
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281 * @return the value of field 'FitToWindow'.
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283 public boolean getFitToWindow(
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285 return this._fitToWindow;
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289 * Returns the value of field 'fontName'.
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291 * @return the value of field 'FontName'.
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293 public java.lang.String getFontName(
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295 return this._fontName;
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299 * Returns the value of field 'fontSize'.
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301 * @return the value of field 'FontSize'.
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303 public int getFontSize(
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305 return this._fontSize;
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309 * Returns the value of field 'fontStyle'.
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311 * @return the value of field 'FontStyle'.
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313 public int getFontStyle(
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315 return this._fontStyle;
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319 * Returns the value of field 'height'.
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321 * @return the value of field 'Height'.
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323 public int getHeight(
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325 return this._height;
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329 * Returns the value of field 'id'. The field 'id' has the
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330 * following description: Tree ID added for binding tree
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331 * visualization settings to vamsas document trees in jalview
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334 * @return the value of field 'Id'.
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336 public java.lang.String getId(
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342 * Returns the value of field 'markUnlinked'.
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344 * @return the value of field 'MarkUnlinked'.
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346 public boolean getMarkUnlinked(
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348 return this._markUnlinked;
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352 * Returns the value of field 'newick'.
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354 * @return the value of field 'Newick'.
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356 public java.lang.String getNewick(
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358 return this._newick;
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362 * Returns the value of field 'showBootstrap'.
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364 * @return the value of field 'ShowBootstrap'.
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366 public boolean getShowBootstrap(
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368 return this._showBootstrap;
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372 * Returns the value of field 'showDistances'.
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374 * @return the value of field 'ShowDistances'.
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376 public boolean getShowDistances(
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378 return this._showDistances;
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382 * Returns the value of field 'threshold'.
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384 * @return the value of field 'Threshold'.
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386 public float getThreshold(
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388 return this._threshold;
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392 * Returns the value of field 'title'.
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394 * @return the value of field 'Title'.
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396 public java.lang.String getTitle(
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398 return this._title;
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402 * Returns the value of field 'width'.
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404 * @return the value of field 'Width'.
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406 public int getWidth(
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408 return this._width;
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412 * Returns the value of field 'xpos'.
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414 * @return the value of field 'Xpos'.
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416 public int getXpos(
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422 * Returns the value of field 'ypos'.
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424 * @return the value of field 'Ypos'.
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426 public int getYpos(
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432 * Method hasCurrentTree.
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434 * @return true if at least one CurrentTree has been added
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436 public boolean hasCurrentTree(
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438 return this._has_currentTree;
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442 * Method hasFitToWindow.
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444 * @return true if at least one FitToWindow has been added
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446 public boolean hasFitToWindow(
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448 return this._has_fitToWindow;
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452 * Method hasFontSize.
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454 * @return true if at least one FontSize has been added
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456 public boolean hasFontSize(
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458 return this._has_fontSize;
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462 * Method hasFontStyle.
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464 * @return true if at least one FontStyle has been added
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466 public boolean hasFontStyle(
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468 return this._has_fontStyle;
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472 * Method hasHeight.
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474 * @return true if at least one Height has been added
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476 public boolean hasHeight(
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478 return this._has_height;
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482 * Method hasMarkUnlinked.
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484 * @return true if at least one MarkUnlinked has been added
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486 public boolean hasMarkUnlinked(
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488 return this._has_markUnlinked;
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492 * Method hasShowBootstrap.
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494 * @return true if at least one ShowBootstrap has been added
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496 public boolean hasShowBootstrap(
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498 return this._has_showBootstrap;
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502 * Method hasShowDistances.
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504 * @return true if at least one ShowDistances has been added
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506 public boolean hasShowDistances(
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508 return this._has_showDistances;
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512 * Method hasThreshold.
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514 * @return true if at least one Threshold has been added
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516 public boolean hasThreshold(
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518 return this._has_threshold;
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524 * @return true if at least one Width has been added
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526 public boolean hasWidth(
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528 return this._has_width;
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534 * @return true if at least one Xpos has been added
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536 public boolean hasXpos(
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538 return this._has_xpos;
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544 * @return true if at least one Ypos has been added
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546 public boolean hasYpos(
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548 return this._has_ypos;
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552 * Returns the value of field 'currentTree'.
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554 * @return the value of field 'CurrentTree'.
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556 public boolean isCurrentTree(
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558 return this._currentTree;
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562 * Returns the value of field 'fitToWindow'.
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564 * @return the value of field 'FitToWindow'.
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566 public boolean isFitToWindow(
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568 return this._fitToWindow;
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572 * Returns the value of field 'markUnlinked'.
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574 * @return the value of field 'MarkUnlinked'.
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576 public boolean isMarkUnlinked(
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578 return this._markUnlinked;
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582 * Returns the value of field 'showBootstrap'.
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584 * @return the value of field 'ShowBootstrap'.
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586 public boolean isShowBootstrap(
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588 return this._showBootstrap;
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592 * Returns the value of field 'showDistances'.
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594 * @return the value of field 'ShowDistances'.
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596 public boolean isShowDistances(
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598 return this._showDistances;
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604 * @return true if this object is valid according to the schema
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606 public boolean isValid(
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610 } catch (org.exolab.castor.xml.ValidationException vex) {
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620 * @throws org.exolab.castor.xml.MarshalException if object is
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621 * null or if any SAXException is thrown during marshaling
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622 * @throws org.exolab.castor.xml.ValidationException if this
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623 * object is an invalid instance according to the schema
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625 public void marshal(
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626 final java.io.Writer out)
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627 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
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628 Marshaller.marshal(this, out);
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635 * @throws java.io.IOException if an IOException occurs during
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637 * @throws org.exolab.castor.xml.ValidationException if this
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638 * object is an invalid instance according to the schema
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639 * @throws org.exolab.castor.xml.MarshalException if object is
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640 * null or if any SAXException is thrown during marshaling
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642 public void marshal(
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643 final org.xml.sax.ContentHandler handler)
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644 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
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645 Marshaller.marshal(this, handler);
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649 * Sets the value of field 'currentTree'.
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651 * @param currentTree the value of field 'currentTree'.
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653 public void setCurrentTree(
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654 final boolean currentTree) {
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655 this._currentTree = currentTree;
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656 this._has_currentTree = true;
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660 * Sets the value of field 'fitToWindow'.
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662 * @param fitToWindow the value of field 'fitToWindow'.
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664 public void setFitToWindow(
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665 final boolean fitToWindow) {
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666 this._fitToWindow = fitToWindow;
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667 this._has_fitToWindow = true;
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671 * Sets the value of field 'fontName'.
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673 * @param fontName the value of field 'fontName'.
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675 public void setFontName(
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676 final java.lang.String fontName) {
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677 this._fontName = fontName;
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681 * Sets the value of field 'fontSize'.
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683 * @param fontSize the value of field 'fontSize'.
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685 public void setFontSize(
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686 final int fontSize) {
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687 this._fontSize = fontSize;
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688 this._has_fontSize = true;
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692 * Sets the value of field 'fontStyle'.
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694 * @param fontStyle the value of field 'fontStyle'.
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696 public void setFontStyle(
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697 final int fontStyle) {
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698 this._fontStyle = fontStyle;
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699 this._has_fontStyle = true;
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703 * Sets the value of field 'height'.
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705 * @param height the value of field 'height'.
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707 public void setHeight(
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708 final int height) {
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709 this._height = height;
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710 this._has_height = true;
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714 * Sets the value of field 'id'. The field 'id' has the
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715 * following description: Tree ID added for binding tree
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716 * visualization settings to vamsas document trees in jalview
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719 * @param id the value of field 'id'.
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722 final java.lang.String id) {
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727 * Sets the value of field 'markUnlinked'.
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729 * @param markUnlinked the value of field 'markUnlinked'.
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731 public void setMarkUnlinked(
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732 final boolean markUnlinked) {
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733 this._markUnlinked = markUnlinked;
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734 this._has_markUnlinked = true;
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738 * Sets the value of field 'newick'.
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740 * @param newick the value of field 'newick'.
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742 public void setNewick(
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743 final java.lang.String newick) {
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744 this._newick = newick;
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748 * Sets the value of field 'showBootstrap'.
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750 * @param showBootstrap the value of field 'showBootstrap'.
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752 public void setShowBootstrap(
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753 final boolean showBootstrap) {
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754 this._showBootstrap = showBootstrap;
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755 this._has_showBootstrap = true;
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759 * Sets the value of field 'showDistances'.
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761 * @param showDistances the value of field 'showDistances'.
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763 public void setShowDistances(
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764 final boolean showDistances) {
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765 this._showDistances = showDistances;
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766 this._has_showDistances = true;
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770 * Sets the value of field 'threshold'.
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772 * @param threshold the value of field 'threshold'.
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774 public void setThreshold(
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775 final float threshold) {
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776 this._threshold = threshold;
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777 this._has_threshold = true;
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781 * Sets the value of field 'title'.
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783 * @param title the value of field 'title'.
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785 public void setTitle(
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786 final java.lang.String title) {
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787 this._title = title;
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791 * Sets the value of field 'width'.
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793 * @param width the value of field 'width'.
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795 public void setWidth(
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797 this._width = width;
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798 this._has_width = true;
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802 * Sets the value of field 'xpos'.
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804 * @param xpos the value of field 'xpos'.
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806 public void setXpos(
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809 this._has_xpos = true;
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813 * Sets the value of field 'ypos'.
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815 * @param ypos the value of field 'ypos'.
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817 public void setYpos(
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820 this._has_ypos = true;
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824 * Method unmarshal.
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827 * @throws org.exolab.castor.xml.MarshalException if object is
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828 * null or if any SAXException is thrown during marshaling
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829 * @throws org.exolab.castor.xml.ValidationException if this
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830 * object is an invalid instance according to the schema
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831 * @return the unmarshaled jalview.schemabinding.version2.Tree
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833 public static jalview.schemabinding.version2.Tree unmarshal(
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834 final java.io.Reader reader)
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835 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
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836 return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(jalview.schemabinding.version2.Tree.class, reader);
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842 * @throws org.exolab.castor.xml.ValidationException if this
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843 * object is an invalid instance according to the schema
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845 public void validate(
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847 throws org.exolab.castor.xml.ValidationException {
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848 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
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849 validator.validate(this);
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