2 * This class was automatically generated with
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3 * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
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8 package jalview.binding;
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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 java.io.IOException;
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15 import java.io.Reader;
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16 import java.io.Serializable;
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17 import java.io.Writer;
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18 import org.exolab.castor.xml.MarshalException;
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19 import org.exolab.castor.xml.Marshaller;
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20 import org.exolab.castor.xml.Unmarshaller;
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21 import org.exolab.castor.xml.ValidationException;
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22 import org.xml.sax.ContentHandler;
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27 * @version $Revision$ $Date$
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29 public class Tree implements java.io.Serializable {
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32 //--------------------------/
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33 //- Class/Member Variables -/
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34 //--------------------------/
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42 * keeps track of state for field: _width
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44 private boolean _has_width;
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49 private int _height;
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52 * keeps track of state for field: _height
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54 private boolean _has_height;
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62 * keeps track of state for field: _xpos
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64 private boolean _has_xpos;
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72 * keeps track of state for field: _ypos
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74 private boolean _has_ypos;
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79 private int _fontSize;
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82 * keeps track of state for field: _fontSize
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84 private boolean _has_fontSize;
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89 private float _threshold;
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92 * keeps track of state for field: _threshold
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94 private boolean _has_threshold;
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97 * Field _showBootstrap
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99 private boolean _showBootstrap;
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102 * keeps track of state for field: _showBootstrap
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104 private boolean _has_showBootstrap;
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107 * Field _showDistances
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109 private boolean _showDistances;
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112 * keeps track of state for field: _showDistances
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114 private boolean _has_showDistances;
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117 * Field _markUnlinked
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119 private boolean _markUnlinked;
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122 * keeps track of state for field: _markUnlinked
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124 private boolean _has_markUnlinked;
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127 * Field _fitToWindow
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129 private boolean _fitToWindow;
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132 * keeps track of state for field: _fitToWindow
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134 private boolean _has_fitToWindow;
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137 * Field _currentTree
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139 private boolean _currentTree;
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142 * keeps track of state for field: _currentTree
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144 private boolean _has_currentTree;
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149 private java.lang.String _title;
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154 private java.lang.String _newick;
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157 //----------------/
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158 //- Constructors -/
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159 //----------------/
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163 } //-- jalview.binding.Tree()
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171 * Method deleteCurrentTree
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174 public void deleteCurrentTree()
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176 this._has_currentTree= false;
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177 } //-- void deleteCurrentTree()
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180 * Method deleteFitToWindow
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183 public void deleteFitToWindow()
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185 this._has_fitToWindow= false;
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186 } //-- void deleteFitToWindow()
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189 * Method deleteFontSize
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192 public void deleteFontSize()
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194 this._has_fontSize= false;
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195 } //-- void deleteFontSize()
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198 * Method deleteHeight
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201 public void deleteHeight()
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203 this._has_height= false;
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204 } //-- void deleteHeight()
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207 * Method deleteMarkUnlinked
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210 public void deleteMarkUnlinked()
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212 this._has_markUnlinked= false;
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213 } //-- void deleteMarkUnlinked()
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216 * Method deleteShowBootstrap
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219 public void deleteShowBootstrap()
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221 this._has_showBootstrap= false;
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222 } //-- void deleteShowBootstrap()
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225 * Method deleteShowDistances
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228 public void deleteShowDistances()
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230 this._has_showDistances= false;
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231 } //-- void deleteShowDistances()
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234 * Method deleteThreshold
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237 public void deleteThreshold()
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239 this._has_threshold= false;
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240 } //-- void deleteThreshold()
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243 * Method deleteWidth
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246 public void deleteWidth()
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248 this._has_width= false;
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249 } //-- void deleteWidth()
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252 * Method deleteXpos
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255 public void deleteXpos()
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257 this._has_xpos= false;
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258 } //-- void deleteXpos()
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261 * Method deleteYpos
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264 public void deleteYpos()
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266 this._has_ypos= false;
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267 } //-- void deleteYpos()
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270 * Returns the value of field 'currentTree'.
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273 * @return the value of field 'currentTree'.
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275 public boolean getCurrentTree()
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277 return this._currentTree;
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278 } //-- boolean getCurrentTree()
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281 * Returns the value of field 'fitToWindow'.
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284 * @return the value of field 'fitToWindow'.
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286 public boolean getFitToWindow()
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288 return this._fitToWindow;
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289 } //-- boolean getFitToWindow()
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292 * Returns the value of field 'fontSize'.
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295 * @return the value of field 'fontSize'.
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297 public int getFontSize()
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299 return this._fontSize;
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300 } //-- int getFontSize()
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303 * Returns the value of field 'height'.
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306 * @return the value of field 'height'.
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308 public int getHeight()
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310 return this._height;
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311 } //-- int getHeight()
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314 * Returns the value of field 'markUnlinked'.
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317 * @return the value of field 'markUnlinked'.
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319 public boolean getMarkUnlinked()
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321 return this._markUnlinked;
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322 } //-- boolean getMarkUnlinked()
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325 * Returns the value of field 'newick'.
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328 * @return the value of field 'newick'.
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330 public java.lang.String getNewick()
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332 return this._newick;
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333 } //-- java.lang.String getNewick()
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336 * Returns the value of field 'showBootstrap'.
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339 * @return the value of field 'showBootstrap'.
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341 public boolean getShowBootstrap()
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343 return this._showBootstrap;
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344 } //-- boolean getShowBootstrap()
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347 * Returns the value of field 'showDistances'.
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350 * @return the value of field 'showDistances'.
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352 public boolean getShowDistances()
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354 return this._showDistances;
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355 } //-- boolean getShowDistances()
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358 * Returns the value of field 'threshold'.
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361 * @return the value of field 'threshold'.
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363 public float getThreshold()
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365 return this._threshold;
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366 } //-- float getThreshold()
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369 * Returns the value of field 'title'.
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372 * @return the value of field 'title'.
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374 public java.lang.String getTitle()
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376 return this._title;
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377 } //-- java.lang.String getTitle()
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380 * Returns the value of field 'width'.
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383 * @return the value of field 'width'.
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385 public int getWidth()
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387 return this._width;
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388 } //-- int getWidth()
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391 * Returns the value of field 'xpos'.
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394 * @return the value of field 'xpos'.
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396 public int getXpos()
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399 } //-- int getXpos()
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402 * Returns the value of field 'ypos'.
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405 * @return the value of field 'ypos'.
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407 public int getYpos()
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410 } //-- int getYpos()
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413 * Method hasCurrentTree
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419 public boolean hasCurrentTree()
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421 return this._has_currentTree;
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422 } //-- boolean hasCurrentTree()
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425 * Method hasFitToWindow
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431 public boolean hasFitToWindow()
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433 return this._has_fitToWindow;
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434 } //-- boolean hasFitToWindow()
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437 * Method hasFontSize
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443 public boolean hasFontSize()
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445 return this._has_fontSize;
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446 } //-- boolean hasFontSize()
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455 public boolean hasHeight()
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457 return this._has_height;
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458 } //-- boolean hasHeight()
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461 * Method hasMarkUnlinked
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467 public boolean hasMarkUnlinked()
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469 return this._has_markUnlinked;
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470 } //-- boolean hasMarkUnlinked()
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473 * Method hasShowBootstrap
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479 public boolean hasShowBootstrap()
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481 return this._has_showBootstrap;
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482 } //-- boolean hasShowBootstrap()
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485 * Method hasShowDistances
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491 public boolean hasShowDistances()
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493 return this._has_showDistances;
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494 } //-- boolean hasShowDistances()
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497 * Method hasThreshold
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503 public boolean hasThreshold()
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505 return this._has_threshold;
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506 } //-- boolean hasThreshold()
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515 public boolean hasWidth()
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517 return this._has_width;
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518 } //-- boolean hasWidth()
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527 public boolean hasXpos()
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529 return this._has_xpos;
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530 } //-- boolean hasXpos()
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539 public boolean hasYpos()
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541 return this._has_ypos;
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542 } //-- boolean hasYpos()
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551 public boolean isValid()
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556 catch (org.exolab.castor.xml.ValidationException vex) {
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560 } //-- boolean isValid()
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569 public void marshal(java.io.Writer out)
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570 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
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573 Marshaller.marshal(this, out);
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574 } //-- void marshal(java.io.Writer)
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583 public void marshal(org.xml.sax.ContentHandler handler)
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584 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
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587 Marshaller.marshal(this, handler);
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588 } //-- void marshal(org.xml.sax.ContentHandler)
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591 * Sets the value of field 'currentTree'.
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593 * @param currentTree the value of field 'currentTree'.
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595 public void setCurrentTree(boolean currentTree)
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597 this._currentTree = currentTree;
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598 this._has_currentTree = true;
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599 } //-- void setCurrentTree(boolean)
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602 * Sets the value of field 'fitToWindow'.
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604 * @param fitToWindow the value of field 'fitToWindow'.
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606 public void setFitToWindow(boolean fitToWindow)
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608 this._fitToWindow = fitToWindow;
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609 this._has_fitToWindow = true;
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610 } //-- void setFitToWindow(boolean)
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613 * Sets the value of field 'fontSize'.
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615 * @param fontSize the value of field 'fontSize'.
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617 public void setFontSize(int fontSize)
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619 this._fontSize = fontSize;
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620 this._has_fontSize = true;
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621 } //-- void setFontSize(int)
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624 * Sets the value of field 'height'.
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626 * @param height the value of field 'height'.
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628 public void setHeight(int height)
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630 this._height = height;
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631 this._has_height = true;
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632 } //-- void setHeight(int)
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635 * Sets the value of field 'markUnlinked'.
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637 * @param markUnlinked the value of field 'markUnlinked'.
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639 public void setMarkUnlinked(boolean markUnlinked)
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641 this._markUnlinked = markUnlinked;
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642 this._has_markUnlinked = true;
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643 } //-- void setMarkUnlinked(boolean)
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646 * Sets the value of field 'newick'.
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648 * @param newick the value of field 'newick'.
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650 public void setNewick(java.lang.String newick)
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652 this._newick = newick;
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653 } //-- void setNewick(java.lang.String)
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656 * Sets the value of field 'showBootstrap'.
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658 * @param showBootstrap the value of field 'showBootstrap'.
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660 public void setShowBootstrap(boolean showBootstrap)
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662 this._showBootstrap = showBootstrap;
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663 this._has_showBootstrap = true;
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664 } //-- void setShowBootstrap(boolean)
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667 * Sets the value of field 'showDistances'.
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669 * @param showDistances the value of field 'showDistances'.
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671 public void setShowDistances(boolean showDistances)
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673 this._showDistances = showDistances;
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674 this._has_showDistances = true;
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675 } //-- void setShowDistances(boolean)
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678 * Sets the value of field 'threshold'.
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680 * @param threshold the value of field 'threshold'.
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682 public void setThreshold(float threshold)
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684 this._threshold = threshold;
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685 this._has_threshold = true;
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686 } //-- void setThreshold(float)
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689 * Sets the value of field 'title'.
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691 * @param title the value of field 'title'.
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693 public void setTitle(java.lang.String title)
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695 this._title = title;
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696 } //-- void setTitle(java.lang.String)
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699 * Sets the value of field 'width'.
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701 * @param width the value of field 'width'.
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703 public void setWidth(int width)
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705 this._width = width;
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706 this._has_width = true;
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707 } //-- void setWidth(int)
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710 * Sets the value of field 'xpos'.
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712 * @param xpos the value of field 'xpos'.
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714 public void setXpos(int xpos)
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717 this._has_xpos = true;
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718 } //-- void setXpos(int)
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721 * Sets the value of field 'ypos'.
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723 * @param ypos the value of field 'ypos'.
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725 public void setYpos(int ypos)
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728 this._has_ypos = true;
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729 } //-- void setYpos(int)
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739 public static java.lang.Object unmarshal(java.io.Reader reader)
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740 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
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742 return (jalview.binding.Tree) Unmarshaller.unmarshal(jalview.binding.Tree.class, reader);
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743 } //-- java.lang.Object unmarshal(java.io.Reader)
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749 public void validate()
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750 throws org.exolab.castor.xml.ValidationException
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752 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
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753 validator.validate(this);
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754 } //-- void validate()
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