2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
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3 * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.schemabinding.version2;
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21 // ---------------------------------/
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22 // - Imported classes and packages -/
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23 // ---------------------------------/
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25 import org.exolab.castor.xml.Marshaller;
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26 import org.exolab.castor.xml.Unmarshaller;
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31 * @version $Revision$ $Date$
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33 public class Viewport implements java.io.Serializable
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36 // --------------------------/
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37 // - Class/Member Variables -/
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38 // --------------------------/
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41 * Field _conservationSelected.
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43 private boolean _conservationSelected;
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46 * keeps track of state for field: _conservationSelected
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48 private boolean _has_conservationSelected;
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51 * Field _pidSelected.
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53 private boolean _pidSelected;
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56 * keeps track of state for field: _pidSelected
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58 private boolean _has_pidSelected;
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63 private java.lang.String _bgColour;
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66 * Field _consThreshold.
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68 private int _consThreshold;
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71 * keeps track of state for field: _consThreshold
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73 private boolean _has_consThreshold;
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76 * Field _pidThreshold.
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78 private int _pidThreshold;
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81 * keeps track of state for field: _pidThreshold
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83 private boolean _has_pidThreshold;
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88 private java.lang.String _title;
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91 * Field _showFullId.
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93 private boolean _showFullId;
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96 * keeps track of state for field: _showFullId
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98 private boolean _has_showFullId;
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101 * Field _rightAlignIds.
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103 private boolean _rightAlignIds;
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106 * keeps track of state for field: _rightAlignIds
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108 private boolean _has_rightAlignIds;
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113 private boolean _showText;
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116 * keeps track of state for field: _showText
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118 private boolean _has_showText;
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121 * Field _showColourText.
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123 private boolean _showColourText;
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126 * keeps track of state for field: _showColourText
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128 private boolean _has_showColourText;
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131 * Field _showBoxes.
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133 private boolean _showBoxes;
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136 * keeps track of state for field: _showBoxes
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138 private boolean _has_showBoxes;
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141 * Field _wrapAlignment.
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143 private boolean _wrapAlignment;
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146 * keeps track of state for field: _wrapAlignment
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148 private boolean _has_wrapAlignment;
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151 * Field _renderGaps.
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153 private boolean _renderGaps;
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156 * keeps track of state for field: _renderGaps
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158 private boolean _has_renderGaps;
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161 * Field _showSequenceFeatures.
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163 private boolean _showSequenceFeatures;
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166 * keeps track of state for field: _showSequenceFeatures
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168 private boolean _has_showSequenceFeatures;
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171 * Field _showAnnotation.
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173 private boolean _showAnnotation;
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176 * keeps track of state for field: _showAnnotation
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178 private boolean _has_showAnnotation;
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186 * keeps track of state for field: _xpos
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188 private boolean _has_xpos;
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196 * keeps track of state for field: _ypos
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198 private boolean _has_ypos;
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203 private int _width;
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206 * keeps track of state for field: _width
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208 private boolean _has_width;
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213 private int _height;
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216 * keeps track of state for field: _height
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218 private boolean _has_height;
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223 private int _startRes;
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226 * keeps track of state for field: _startRes
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228 private boolean _has_startRes;
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233 private int _startSeq;
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236 * keeps track of state for field: _startSeq
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238 private boolean _has_startSeq;
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243 private java.lang.String _fontName;
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248 private int _fontSize;
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251 * keeps track of state for field: _fontSize
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253 private boolean _has_fontSize;
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256 * Field _fontStyle.
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258 private int _fontStyle;
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261 * keeps track of state for field: _fontStyle
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263 private boolean _has_fontStyle;
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268 private java.lang.String _viewName;
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271 * Field _sequenceSetId.
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273 private java.lang.String _sequenceSetId;
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276 * Field _gatheredViews.
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278 private boolean _gatheredViews;
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281 * keeps track of state for field: _gatheredViews
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283 private boolean _has_gatheredViews;
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288 private int _textCol1;
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291 * keeps track of state for field: _textCol1
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293 private boolean _has_textCol1;
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298 private int _textCol2;
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301 * keeps track of state for field: _textCol2
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303 private boolean _has_textCol2;
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306 * Field _textColThreshold.
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308 private int _textColThreshold;
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311 * keeps track of state for field: _textColThreshold
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313 private boolean _has_textColThreshold;
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316 * Field _annotationColours.
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318 private jalview.schemabinding.version2.AnnotationColours _annotationColours;
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321 * Field _hiddenColumnsList.
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323 private java.util.Vector _hiddenColumnsList;
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325 // ----------------/
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326 // - Constructors -/
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327 // ----------------/
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332 this._hiddenColumnsList = new java.util.Vector();
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342 * @param vHiddenColumns
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343 * @throws java.lang.IndexOutOfBoundsException
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344 * if the index given is outside the bounds of the collection
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346 public void addHiddenColumns(
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347 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
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348 throws java.lang.IndexOutOfBoundsException
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350 this._hiddenColumnsList.addElement(vHiddenColumns);
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357 * @param vHiddenColumns
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358 * @throws java.lang.IndexOutOfBoundsException
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359 * if the index given is outside the bounds of the collection
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361 public void addHiddenColumns(final int index,
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362 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
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363 throws java.lang.IndexOutOfBoundsException
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365 this._hiddenColumnsList.add(index, vHiddenColumns);
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370 public void deleteConsThreshold()
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372 this._has_consThreshold = false;
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377 public void deleteConservationSelected()
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379 this._has_conservationSelected = false;
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384 public void deleteFontSize()
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386 this._has_fontSize = false;
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391 public void deleteFontStyle()
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393 this._has_fontStyle = false;
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398 public void deleteGatheredViews()
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400 this._has_gatheredViews = false;
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405 public void deleteHeight()
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407 this._has_height = false;
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412 public void deletePidSelected()
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414 this._has_pidSelected = false;
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419 public void deletePidThreshold()
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421 this._has_pidThreshold = false;
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426 public void deleteRenderGaps()
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428 this._has_renderGaps = false;
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433 public void deleteRightAlignIds()
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435 this._has_rightAlignIds = false;
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440 public void deleteShowAnnotation()
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442 this._has_showAnnotation = false;
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447 public void deleteShowBoxes()
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449 this._has_showBoxes = false;
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454 public void deleteShowColourText()
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456 this._has_showColourText = false;
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461 public void deleteShowFullId()
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463 this._has_showFullId = false;
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468 public void deleteShowSequenceFeatures()
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470 this._has_showSequenceFeatures = false;
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475 public void deleteShowText()
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477 this._has_showText = false;
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482 public void deleteStartRes()
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484 this._has_startRes = false;
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489 public void deleteStartSeq()
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491 this._has_startSeq = false;
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496 public void deleteTextCol1()
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498 this._has_textCol1 = false;
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503 public void deleteTextCol2()
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505 this._has_textCol2 = false;
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510 public void deleteTextColThreshold()
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512 this._has_textColThreshold = false;
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517 public void deleteWidth()
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519 this._has_width = false;
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524 public void deleteWrapAlignment()
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526 this._has_wrapAlignment = false;
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531 public void deleteXpos()
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533 this._has_xpos = false;
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538 public void deleteYpos()
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540 this._has_ypos = false;
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544 * Method enumerateHiddenColumns.
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546 * @return an Enumeration over all
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547 * jalview.schemabinding.version2.HiddenColumns elements
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549 public java.util.Enumeration enumerateHiddenColumns()
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551 return this._hiddenColumnsList.elements();
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555 * Returns the value of field 'annotationColours'.
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557 * @return the value of field 'AnnotationColours'.
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559 public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
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561 return this._annotationColours;
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565 * Returns the value of field 'bgColour'.
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567 * @return the value of field 'BgColour'.
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569 public java.lang.String getBgColour()
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571 return this._bgColour;
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575 * Returns the value of field 'consThreshold'.
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577 * @return the value of field 'ConsThreshold'.
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579 public int getConsThreshold()
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581 return this._consThreshold;
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585 * Returns the value of field 'conservationSelected'.
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587 * @return the value of field 'ConservationSelected'.
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589 public boolean getConservationSelected()
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591 return this._conservationSelected;
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595 * Returns the value of field 'fontName'.
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597 * @return the value of field 'FontName'.
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599 public java.lang.String getFontName()
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601 return this._fontName;
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605 * Returns the value of field 'fontSize'.
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607 * @return the value of field 'FontSize'.
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609 public int getFontSize()
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611 return this._fontSize;
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615 * Returns the value of field 'fontStyle'.
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617 * @return the value of field 'FontStyle'.
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619 public int getFontStyle()
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621 return this._fontStyle;
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625 * Returns the value of field 'gatheredViews'.
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627 * @return the value of field 'GatheredViews'.
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629 public boolean getGatheredViews()
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631 return this._gatheredViews;
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635 * Returns the value of field 'height'.
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637 * @return the value of field 'Height'.
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639 public int getHeight()
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641 return this._height;
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645 * Method getHiddenColumns.
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648 * @throws java.lang.IndexOutOfBoundsException
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649 * if the index given is outside the bounds of the collection
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650 * @return the value of the jalview.schemabinding.version2.HiddenColumns at
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653 public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
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654 final int index) throws java.lang.IndexOutOfBoundsException
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656 // check bounds for index
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657 if (index < 0 || index >= this._hiddenColumnsList.size())
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659 throw new IndexOutOfBoundsException("getHiddenColumns: Index value '"
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660 + index + "' not in range [0.."
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661 + (this._hiddenColumnsList.size() - 1) + "]");
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664 return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList
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669 * Method getHiddenColumns.Returns the contents of the collection in an Array.
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671 * Note: Just in case the collection contents are changing in another thread,
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672 * we pass a 0-length Array of the correct type into the API call. This way we
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673 * <i>know</i> that the Array returned is of exactly the correct length.
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675 * @return this collection as an Array
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677 public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
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679 jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
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680 return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList
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685 * Method getHiddenColumnsCount.
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687 * @return the size of this collection
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689 public int getHiddenColumnsCount()
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691 return this._hiddenColumnsList.size();
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695 * Returns the value of field 'pidSelected'.
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697 * @return the value of field 'PidSelected'.
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699 public boolean getPidSelected()
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701 return this._pidSelected;
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705 * Returns the value of field 'pidThreshold'.
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707 * @return the value of field 'PidThreshold'.
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709 public int getPidThreshold()
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711 return this._pidThreshold;
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715 * Returns the value of field 'renderGaps'.
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717 * @return the value of field 'RenderGaps'.
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719 public boolean getRenderGaps()
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721 return this._renderGaps;
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725 * Returns the value of field 'rightAlignIds'.
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727 * @return the value of field 'RightAlignIds'.
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729 public boolean getRightAlignIds()
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731 return this._rightAlignIds;
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735 * Returns the value of field 'sequenceSetId'.
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737 * @return the value of field 'SequenceSetId'.
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739 public java.lang.String getSequenceSetId()
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741 return this._sequenceSetId;
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745 * Returns the value of field 'showAnnotation'.
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747 * @return the value of field 'ShowAnnotation'.
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749 public boolean getShowAnnotation()
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751 return this._showAnnotation;
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755 * Returns the value of field 'showBoxes'.
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757 * @return the value of field 'ShowBoxes'.
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759 public boolean getShowBoxes()
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761 return this._showBoxes;
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765 * Returns the value of field 'showColourText'.
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767 * @return the value of field 'ShowColourText'.
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769 public boolean getShowColourText()
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771 return this._showColourText;
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775 * Returns the value of field 'showFullId'.
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777 * @return the value of field 'ShowFullId'.
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779 public boolean getShowFullId()
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781 return this._showFullId;
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785 * Returns the value of field 'showSequenceFeatures'.
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787 * @return the value of field 'ShowSequenceFeatures'.
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789 public boolean getShowSequenceFeatures()
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791 return this._showSequenceFeatures;
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795 * Returns the value of field 'showText'.
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797 * @return the value of field 'ShowText'.
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799 public boolean getShowText()
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801 return this._showText;
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805 * Returns the value of field 'startRes'.
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807 * @return the value of field 'StartRes'.
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809 public int getStartRes()
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811 return this._startRes;
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815 * Returns the value of field 'startSeq'.
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817 * @return the value of field 'StartSeq'.
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819 public int getStartSeq()
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821 return this._startSeq;
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825 * Returns the value of field 'textCol1'.
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827 * @return the value of field 'TextCol1'.
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829 public int getTextCol1()
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831 return this._textCol1;
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835 * Returns the value of field 'textCol2'.
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837 * @return the value of field 'TextCol2'.
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839 public int getTextCol2()
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841 return this._textCol2;
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845 * Returns the value of field 'textColThreshold'.
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847 * @return the value of field 'TextColThreshold'.
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849 public int getTextColThreshold()
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851 return this._textColThreshold;
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855 * Returns the value of field 'title'.
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857 * @return the value of field 'Title'.
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859 public java.lang.String getTitle()
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861 return this._title;
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865 * Returns the value of field 'viewName'.
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867 * @return the value of field 'ViewName'.
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869 public java.lang.String getViewName()
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871 return this._viewName;
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875 * Returns the value of field 'width'.
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877 * @return the value of field 'Width'.
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879 public int getWidth()
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881 return this._width;
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885 * Returns the value of field 'wrapAlignment'.
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887 * @return the value of field 'WrapAlignment'.
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889 public boolean getWrapAlignment()
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891 return this._wrapAlignment;
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895 * Returns the value of field 'xpos'.
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897 * @return the value of field 'Xpos'.
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899 public int getXpos()
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905 * Returns the value of field 'ypos'.
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907 * @return the value of field 'Ypos'.
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909 public int getYpos()
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915 * Method hasConsThreshold.
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917 * @return true if at least one ConsThreshold has been added
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919 public boolean hasConsThreshold()
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921 return this._has_consThreshold;
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925 * Method hasConservationSelected.
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927 * @return true if at least one ConservationSelected has been added
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929 public boolean hasConservationSelected()
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931 return this._has_conservationSelected;
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935 * Method hasFontSize.
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937 * @return true if at least one FontSize has been added
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939 public boolean hasFontSize()
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941 return this._has_fontSize;
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945 * Method hasFontStyle.
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947 * @return true if at least one FontStyle has been added
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949 public boolean hasFontStyle()
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951 return this._has_fontStyle;
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955 * Method hasGatheredViews.
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957 * @return true if at least one GatheredViews has been added
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959 public boolean hasGatheredViews()
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961 return this._has_gatheredViews;
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965 * Method hasHeight.
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967 * @return true if at least one Height has been added
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969 public boolean hasHeight()
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971 return this._has_height;
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975 * Method hasPidSelected.
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977 * @return true if at least one PidSelected has been added
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979 public boolean hasPidSelected()
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981 return this._has_pidSelected;
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985 * Method hasPidThreshold.
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987 * @return true if at least one PidThreshold has been added
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989 public boolean hasPidThreshold()
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991 return this._has_pidThreshold;
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995 * Method hasRenderGaps.
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997 * @return true if at least one RenderGaps has been added
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999 public boolean hasRenderGaps()
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1001 return this._has_renderGaps;
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1005 * Method hasRightAlignIds.
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1007 * @return true if at least one RightAlignIds has been added
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1009 public boolean hasRightAlignIds()
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1011 return this._has_rightAlignIds;
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1015 * Method hasShowAnnotation.
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1017 * @return true if at least one ShowAnnotation has been added
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1019 public boolean hasShowAnnotation()
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1021 return this._has_showAnnotation;
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1025 * Method hasShowBoxes.
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1027 * @return true if at least one ShowBoxes has been added
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1029 public boolean hasShowBoxes()
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1031 return this._has_showBoxes;
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1035 * Method hasShowColourText.
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1037 * @return true if at least one ShowColourText has been added
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1039 public boolean hasShowColourText()
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1041 return this._has_showColourText;
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1045 * Method hasShowFullId.
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1047 * @return true if at least one ShowFullId has been added
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1049 public boolean hasShowFullId()
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1051 return this._has_showFullId;
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1055 * Method hasShowSequenceFeatures.
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1057 * @return true if at least one ShowSequenceFeatures has been added
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1059 public boolean hasShowSequenceFeatures()
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1061 return this._has_showSequenceFeatures;
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1065 * Method hasShowText.
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1067 * @return true if at least one ShowText has been added
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1069 public boolean hasShowText()
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1071 return this._has_showText;
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1075 * Method hasStartRes.
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1077 * @return true if at least one StartRes has been added
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1079 public boolean hasStartRes()
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1081 return this._has_startRes;
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1085 * Method hasStartSeq.
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1087 * @return true if at least one StartSeq has been added
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1089 public boolean hasStartSeq()
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1091 return this._has_startSeq;
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1095 * Method hasTextCol1.
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1097 * @return true if at least one TextCol1 has been added
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1099 public boolean hasTextCol1()
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1101 return this._has_textCol1;
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1105 * Method hasTextCol2.
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1107 * @return true if at least one TextCol2 has been added
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1109 public boolean hasTextCol2()
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1111 return this._has_textCol2;
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1115 * Method hasTextColThreshold.
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1117 * @return true if at least one TextColThreshold has been added
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1119 public boolean hasTextColThreshold()
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1121 return this._has_textColThreshold;
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1125 * Method hasWidth.
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1127 * @return true if at least one Width has been added
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1129 public boolean hasWidth()
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1131 return this._has_width;
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1135 * Method hasWrapAlignment.
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1137 * @return true if at least one WrapAlignment has been added
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1139 public boolean hasWrapAlignment()
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1141 return this._has_wrapAlignment;
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1147 * @return true if at least one Xpos has been added
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1149 public boolean hasXpos()
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1151 return this._has_xpos;
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1157 * @return true if at least one Ypos has been added
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1159 public boolean hasYpos()
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1161 return this._has_ypos;
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1165 * Returns the value of field 'conservationSelected'.
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1167 * @return the value of field 'ConservationSelected'.
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1169 public boolean isConservationSelected()
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1171 return this._conservationSelected;
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1175 * Returns the value of field 'gatheredViews'.
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1177 * @return the value of field 'GatheredViews'.
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1179 public boolean isGatheredViews()
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1181 return this._gatheredViews;
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1185 * Returns the value of field 'pidSelected'.
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1187 * @return the value of field 'PidSelected'.
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1189 public boolean isPidSelected()
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1191 return this._pidSelected;
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1195 * Returns the value of field 'renderGaps'.
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1197 * @return the value of field 'RenderGaps'.
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1199 public boolean isRenderGaps()
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1201 return this._renderGaps;
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1205 * Returns the value of field 'rightAlignIds'.
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1207 * @return the value of field 'RightAlignIds'.
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1209 public boolean isRightAlignIds()
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1211 return this._rightAlignIds;
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1215 * Returns the value of field 'showAnnotation'.
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1217 * @return the value of field 'ShowAnnotation'.
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1219 public boolean isShowAnnotation()
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1221 return this._showAnnotation;
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1225 * Returns the value of field 'showBoxes'.
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1227 * @return the value of field 'ShowBoxes'.
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1229 public boolean isShowBoxes()
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1231 return this._showBoxes;
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1235 * Returns the value of field 'showColourText'.
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1237 * @return the value of field 'ShowColourText'.
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1239 public boolean isShowColourText()
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1241 return this._showColourText;
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1245 * Returns the value of field 'showFullId'.
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1247 * @return the value of field 'ShowFullId'.
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1249 public boolean isShowFullId()
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1251 return this._showFullId;
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1255 * Returns the value of field 'showSequenceFeatures'.
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1257 * @return the value of field 'ShowSequenceFeatures'.
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1259 public boolean isShowSequenceFeatures()
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1261 return this._showSequenceFeatures;
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1265 * Returns the value of field 'showText'.
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1267 * @return the value of field 'ShowText'.
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1269 public boolean isShowText()
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1271 return this._showText;
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1277 * @return true if this object is valid according to the schema
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1279 public boolean isValid()
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1284 } catch (org.exolab.castor.xml.ValidationException vex)
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1292 * Returns the value of field 'wrapAlignment'.
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1294 * @return the value of field 'WrapAlignment'.
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1296 public boolean isWrapAlignment()
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1298 return this._wrapAlignment;
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1305 * @throws org.exolab.castor.xml.MarshalException
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1306 * if object is null or if any SAXException is thrown during
\r
1308 * @throws org.exolab.castor.xml.ValidationException
\r
1309 * if this object is an invalid instance according to the
\r
1312 public void marshal(final java.io.Writer out)
\r
1313 throws org.exolab.castor.xml.MarshalException,
\r
1314 org.exolab.castor.xml.ValidationException
\r
1316 Marshaller.marshal(this, out);
\r
1323 * @throws java.io.IOException
\r
1324 * if an IOException occurs during marshaling
\r
1325 * @throws org.exolab.castor.xml.ValidationException
\r
1326 * if this object is an invalid instance according to the
\r
1328 * @throws org.exolab.castor.xml.MarshalException
\r
1329 * if object is null or if any SAXException is thrown during
\r
1332 public void marshal(final org.xml.sax.ContentHandler handler)
\r
1333 throws java.io.IOException,
\r
1334 org.exolab.castor.xml.MarshalException,
\r
1335 org.exolab.castor.xml.ValidationException
\r
1337 Marshaller.marshal(this, handler);
\r
1342 public void removeAllHiddenColumns()
\r
1344 this._hiddenColumnsList.clear();
\r
1348 * Method removeHiddenColumns.
\r
1350 * @param vHiddenColumns
\r
1351 * @return true if the object was removed from the collection.
\r
1353 public boolean removeHiddenColumns(
\r
1354 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
\r
1356 boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
\r
1361 * Method removeHiddenColumnsAt.
\r
1364 * @return the element removed from the collection
\r
1366 public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
\r
1369 java.lang.Object obj = this._hiddenColumnsList.remove(index);
\r
1370 return (jalview.schemabinding.version2.HiddenColumns) obj;
\r
1374 * Sets the value of field 'annotationColours'.
\r
1376 * @param annotationColours
\r
1377 * the value of field 'annotationColours'.
\r
1379 public void setAnnotationColours(
\r
1380 final jalview.schemabinding.version2.AnnotationColours annotationColours)
\r
1382 this._annotationColours = annotationColours;
\r
1386 * Sets the value of field 'bgColour'.
\r
1389 * the value of field 'bgColour'.
\r
1391 public void setBgColour(final java.lang.String bgColour)
\r
1393 this._bgColour = bgColour;
\r
1397 * Sets the value of field 'consThreshold'.
\r
1399 * @param consThreshold
\r
1400 * the value of field 'consThreshold'.
\r
1402 public void setConsThreshold(final int consThreshold)
\r
1404 this._consThreshold = consThreshold;
\r
1405 this._has_consThreshold = true;
\r
1409 * Sets the value of field 'conservationSelected'.
\r
1411 * @param conservationSelected
\r
1412 * the value of field 'conservationSelected'.
\r
1414 public void setConservationSelected(final boolean conservationSelected)
\r
1416 this._conservationSelected = conservationSelected;
\r
1417 this._has_conservationSelected = true;
\r
1421 * Sets the value of field 'fontName'.
\r
1424 * the value of field 'fontName'.
\r
1426 public void setFontName(final java.lang.String fontName)
\r
1428 this._fontName = fontName;
\r
1432 * Sets the value of field 'fontSize'.
\r
1435 * the value of field 'fontSize'.
\r
1437 public void setFontSize(final int fontSize)
\r
1439 this._fontSize = fontSize;
\r
1440 this._has_fontSize = true;
\r
1444 * Sets the value of field 'fontStyle'.
\r
1446 * @param fontStyle
\r
1447 * the value of field 'fontStyle'.
\r
1449 public void setFontStyle(final int fontStyle)
\r
1451 this._fontStyle = fontStyle;
\r
1452 this._has_fontStyle = true;
\r
1456 * Sets the value of field 'gatheredViews'.
\r
1458 * @param gatheredViews
\r
1459 * the value of field 'gatheredViews'.
\r
1461 public void setGatheredViews(final boolean gatheredViews)
\r
1463 this._gatheredViews = gatheredViews;
\r
1464 this._has_gatheredViews = true;
\r
1468 * Sets the value of field 'height'.
\r
1471 * the value of field 'height'.
\r
1473 public void setHeight(final int height)
\r
1475 this._height = height;
\r
1476 this._has_height = true;
\r
1483 * @param vHiddenColumns
\r
1484 * @throws java.lang.IndexOutOfBoundsException
\r
1485 * if the index given is outside the bounds of the collection
\r
1487 public void setHiddenColumns(final int index,
\r
1488 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
\r
1489 throws java.lang.IndexOutOfBoundsException
\r
1491 // check bounds for index
\r
1492 if (index < 0 || index >= this._hiddenColumnsList.size())
\r
1494 throw new IndexOutOfBoundsException("setHiddenColumns: Index value '"
\r
1495 + index + "' not in range [0.."
\r
1496 + (this._hiddenColumnsList.size() - 1) + "]");
\r
1499 this._hiddenColumnsList.set(index, vHiddenColumns);
\r
1505 * @param vHiddenColumnsArray
\r
1507 public void setHiddenColumns(
\r
1508 final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray)
\r
1511 _hiddenColumnsList.clear();
\r
1513 for (int i = 0; i < vHiddenColumnsArray.length; i++)
\r
1515 this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
\r
1520 * Sets the value of field 'pidSelected'.
\r
1522 * @param pidSelected
\r
1523 * the value of field 'pidSelected'.
\r
1525 public void setPidSelected(final boolean pidSelected)
\r
1527 this._pidSelected = pidSelected;
\r
1528 this._has_pidSelected = true;
\r
1532 * Sets the value of field 'pidThreshold'.
\r
1534 * @param pidThreshold
\r
1535 * the value of field 'pidThreshold'.
\r
1537 public void setPidThreshold(final int pidThreshold)
\r
1539 this._pidThreshold = pidThreshold;
\r
1540 this._has_pidThreshold = true;
\r
1544 * Sets the value of field 'renderGaps'.
\r
1546 * @param renderGaps
\r
1547 * the value of field 'renderGaps'.
\r
1549 public void setRenderGaps(final boolean renderGaps)
\r
1551 this._renderGaps = renderGaps;
\r
1552 this._has_renderGaps = true;
\r
1556 * Sets the value of field 'rightAlignIds'.
\r
1558 * @param rightAlignIds
\r
1559 * the value of field 'rightAlignIds'.
\r
1561 public void setRightAlignIds(final boolean rightAlignIds)
\r
1563 this._rightAlignIds = rightAlignIds;
\r
1564 this._has_rightAlignIds = true;
\r
1568 * Sets the value of field 'sequenceSetId'.
\r
1570 * @param sequenceSetId
\r
1571 * the value of field 'sequenceSetId'.
\r
1573 public void setSequenceSetId(final java.lang.String sequenceSetId)
\r
1575 this._sequenceSetId = sequenceSetId;
\r
1579 * Sets the value of field 'showAnnotation'.
\r
1581 * @param showAnnotation
\r
1582 * the value of field 'showAnnotation'.
\r
1584 public void setShowAnnotation(final boolean showAnnotation)
\r
1586 this._showAnnotation = showAnnotation;
\r
1587 this._has_showAnnotation = true;
\r
1591 * Sets the value of field 'showBoxes'.
\r
1593 * @param showBoxes
\r
1594 * the value of field 'showBoxes'.
\r
1596 public void setShowBoxes(final boolean showBoxes)
\r
1598 this._showBoxes = showBoxes;
\r
1599 this._has_showBoxes = true;
\r
1603 * Sets the value of field 'showColourText'.
\r
1605 * @param showColourText
\r
1606 * the value of field 'showColourText'.
\r
1608 public void setShowColourText(final boolean showColourText)
\r
1610 this._showColourText = showColourText;
\r
1611 this._has_showColourText = true;
\r
1615 * Sets the value of field 'showFullId'.
\r
1617 * @param showFullId
\r
1618 * the value of field 'showFullId'.
\r
1620 public void setShowFullId(final boolean showFullId)
\r
1622 this._showFullId = showFullId;
\r
1623 this._has_showFullId = true;
\r
1627 * Sets the value of field 'showSequenceFeatures'.
\r
1629 * @param showSequenceFeatures
\r
1630 * the value of field 'showSequenceFeatures'.
\r
1632 public void setShowSequenceFeatures(final boolean showSequenceFeatures)
\r
1634 this._showSequenceFeatures = showSequenceFeatures;
\r
1635 this._has_showSequenceFeatures = true;
\r
1639 * Sets the value of field 'showText'.
\r
1642 * the value of field 'showText'.
\r
1644 public void setShowText(final boolean showText)
\r
1646 this._showText = showText;
\r
1647 this._has_showText = true;
\r
1651 * Sets the value of field 'startRes'.
\r
1654 * the value of field 'startRes'.
\r
1656 public void setStartRes(final int startRes)
\r
1658 this._startRes = startRes;
\r
1659 this._has_startRes = true;
\r
1663 * Sets the value of field 'startSeq'.
\r
1666 * the value of field 'startSeq'.
\r
1668 public void setStartSeq(final int startSeq)
\r
1670 this._startSeq = startSeq;
\r
1671 this._has_startSeq = true;
\r
1675 * Sets the value of field 'textCol1'.
\r
1678 * the value of field 'textCol1'.
\r
1680 public void setTextCol1(final int textCol1)
\r
1682 this._textCol1 = textCol1;
\r
1683 this._has_textCol1 = true;
\r
1687 * Sets the value of field 'textCol2'.
\r
1690 * the value of field 'textCol2'.
\r
1692 public void setTextCol2(final int textCol2)
\r
1694 this._textCol2 = textCol2;
\r
1695 this._has_textCol2 = true;
\r
1699 * Sets the value of field 'textColThreshold'.
\r
1701 * @param textColThreshold
\r
1702 * the value of field 'textColThreshold'
\r
1704 public void setTextColThreshold(final int textColThreshold)
\r
1706 this._textColThreshold = textColThreshold;
\r
1707 this._has_textColThreshold = true;
\r
1711 * Sets the value of field 'title'.
\r
1714 * the value of field 'title'.
\r
1716 public void setTitle(final java.lang.String title)
\r
1718 this._title = title;
\r
1722 * Sets the value of field 'viewName'.
\r
1725 * the value of field 'viewName'.
\r
1727 public void setViewName(final java.lang.String viewName)
\r
1729 this._viewName = viewName;
\r
1733 * Sets the value of field 'width'.
\r
1736 * the value of field 'width'.
\r
1738 public void setWidth(final int width)
\r
1740 this._width = width;
\r
1741 this._has_width = true;
\r
1745 * Sets the value of field 'wrapAlignment'.
\r
1747 * @param wrapAlignment
\r
1748 * the value of field 'wrapAlignment'.
\r
1750 public void setWrapAlignment(final boolean wrapAlignment)
\r
1752 this._wrapAlignment = wrapAlignment;
\r
1753 this._has_wrapAlignment = true;
\r
1757 * Sets the value of field 'xpos'.
\r
1760 * the value of field 'xpos'.
\r
1762 public void setXpos(final int xpos)
\r
1764 this._xpos = xpos;
\r
1765 this._has_xpos = true;
\r
1769 * Sets the value of field 'ypos'.
\r
1772 * the value of field 'ypos'.
\r
1774 public void setYpos(final int ypos)
\r
1776 this._ypos = ypos;
\r
1777 this._has_ypos = true;
\r
1781 * Method unmarshal.
\r
1784 * @throws org.exolab.castor.xml.MarshalException
\r
1785 * if object is null or if any SAXException is thrown during
\r
1787 * @throws org.exolab.castor.xml.ValidationException
\r
1788 * if this object is an invalid instance according to the
\r
1790 * @return the unmarshaled jalview.schemabinding.version2.Viewport
\r
1792 public static jalview.schemabinding.version2.Viewport unmarshal(
\r
1793 final java.io.Reader reader)
\r
1794 throws org.exolab.castor.xml.MarshalException,
\r
1795 org.exolab.castor.xml.ValidationException
\r
1797 return (jalview.schemabinding.version2.Viewport) Unmarshaller
\r
1798 .unmarshal(jalview.schemabinding.version2.Viewport.class,
\r
1805 * @throws org.exolab.castor.xml.ValidationException
\r
1806 * if this object is an invalid instance according to the
\r
1809 public void validate() throws org.exolab.castor.xml.ValidationException
\r
1811 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
\r
1812 validator.validate(this);
\r