2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
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3 * Copyright (C) 2009 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 _showUnconserved.
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133 private boolean _showUnconserved;
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136 * keeps track of state for field: _showUnconserved
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138 private boolean _has_showUnconserved;
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141 * Field _showBoxes.
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143 private boolean _showBoxes;
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146 * keeps track of state for field: _showBoxes
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148 private boolean _has_showBoxes;
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151 * Field _wrapAlignment.
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153 private boolean _wrapAlignment;
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156 * keeps track of state for field: _wrapAlignment
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158 private boolean _has_wrapAlignment;
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161 * Field _renderGaps.
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163 private boolean _renderGaps;
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166 * keeps track of state for field: _renderGaps
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168 private boolean _has_renderGaps;
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171 * Field _showSequenceFeatures.
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173 private boolean _showSequenceFeatures;
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176 * keeps track of state for field: _showSequenceFeatures
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178 private boolean _has_showSequenceFeatures;
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181 * Field _showAnnotation.
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183 private boolean _showAnnotation;
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186 * keeps track of state for field: _showAnnotation
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188 private boolean _has_showAnnotation;
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196 * keeps track of state for field: _xpos
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198 private boolean _has_xpos;
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206 * keeps track of state for field: _ypos
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208 private boolean _has_ypos;
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213 private int _width;
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216 * keeps track of state for field: _width
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218 private boolean _has_width;
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223 private int _height;
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226 * keeps track of state for field: _height
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228 private boolean _has_height;
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233 private int _startRes;
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236 * keeps track of state for field: _startRes
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238 private boolean _has_startRes;
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243 private int _startSeq;
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246 * keeps track of state for field: _startSeq
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248 private boolean _has_startSeq;
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253 private java.lang.String _fontName;
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258 private int _fontSize;
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261 * keeps track of state for field: _fontSize
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263 private boolean _has_fontSize;
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266 * Field _fontStyle.
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268 private int _fontStyle;
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271 * keeps track of state for field: _fontStyle
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273 private boolean _has_fontStyle;
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278 private java.lang.String _viewName;
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281 * Field _sequenceSetId.
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283 private java.lang.String _sequenceSetId;
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286 * Field _gatheredViews.
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288 private boolean _gatheredViews;
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291 * keeps track of state for field: _gatheredViews
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293 private boolean _has_gatheredViews;
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298 private int _textCol1;
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301 * keeps track of state for field: _textCol1
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303 private boolean _has_textCol1;
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308 private int _textCol2;
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311 * keeps track of state for field: _textCol2
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313 private boolean _has_textCol2;
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316 * Field _textColThreshold.
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318 private int _textColThreshold;
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321 * keeps track of state for field: _textColThreshold
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323 private boolean _has_textColThreshold;
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326 * unique id used by jalview to synchronize between stored and
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327 * instantiated views
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330 private java.lang.String _id;
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333 * Field _annotationColours.
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335 private jalview.schemabinding.version2.AnnotationColours _annotationColours;
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338 * Field _hiddenColumnsList.
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340 private java.util.Vector _hiddenColumnsList;
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343 //----------------/
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344 //- Constructors -/
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345 //----------------/
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347 public Viewport() {
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349 this._hiddenColumnsList = new java.util.Vector();
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360 * @param vHiddenColumns
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361 * @throws java.lang.IndexOutOfBoundsException if the index
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362 * given is outside the bounds of the collection
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364 public void addHiddenColumns(
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365 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
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366 throws java.lang.IndexOutOfBoundsException {
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367 this._hiddenColumnsList.addElement(vHiddenColumns);
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374 * @param vHiddenColumns
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375 * @throws java.lang.IndexOutOfBoundsException if the index
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376 * given is outside the bounds of the collection
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378 public void addHiddenColumns(
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380 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
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381 throws java.lang.IndexOutOfBoundsException {
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382 this._hiddenColumnsList.add(index, vHiddenColumns);
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387 public void deleteConsThreshold(
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389 this._has_consThreshold= false;
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394 public void deleteConservationSelected(
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396 this._has_conservationSelected= false;
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401 public void deleteFontSize(
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403 this._has_fontSize= false;
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408 public void deleteFontStyle(
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410 this._has_fontStyle= false;
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415 public void deleteGatheredViews(
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417 this._has_gatheredViews= false;
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422 public void deleteHeight(
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424 this._has_height= false;
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429 public void deletePidSelected(
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431 this._has_pidSelected= false;
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436 public void deletePidThreshold(
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438 this._has_pidThreshold= false;
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443 public void deleteRenderGaps(
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445 this._has_renderGaps= false;
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450 public void deleteRightAlignIds(
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452 this._has_rightAlignIds= false;
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457 public void deleteShowAnnotation(
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459 this._has_showAnnotation= false;
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464 public void deleteShowBoxes(
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466 this._has_showBoxes= false;
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471 public void deleteShowColourText(
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473 this._has_showColourText= false;
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478 public void deleteShowFullId(
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480 this._has_showFullId= false;
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485 public void deleteShowSequenceFeatures(
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487 this._has_showSequenceFeatures= false;
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492 public void deleteShowText(
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494 this._has_showText= false;
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499 public void deleteShowUnconserved(
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501 this._has_showUnconserved= false;
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506 public void deleteStartRes(
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508 this._has_startRes= false;
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513 public void deleteStartSeq(
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515 this._has_startSeq= false;
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520 public void deleteTextCol1(
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522 this._has_textCol1= false;
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527 public void deleteTextCol2(
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529 this._has_textCol2= false;
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534 public void deleteTextColThreshold(
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536 this._has_textColThreshold= false;
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541 public void deleteWidth(
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543 this._has_width= false;
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548 public void deleteWrapAlignment(
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550 this._has_wrapAlignment= false;
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555 public void deleteXpos(
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557 this._has_xpos= false;
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562 public void deleteYpos(
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564 this._has_ypos= false;
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568 * Method enumerateHiddenColumns.
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570 * @return an Enumeration over all
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571 * jalview.schemabinding.version2.HiddenColumns elements
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573 public java.util.Enumeration enumerateHiddenColumns(
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575 return this._hiddenColumnsList.elements();
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579 * Returns the value of field 'annotationColours'.
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581 * @return the value of field 'AnnotationColours'.
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583 public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(
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585 return this._annotationColours;
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589 * Returns the value of field 'bgColour'.
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591 * @return the value of field 'BgColour'.
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593 public java.lang.String getBgColour(
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595 return this._bgColour;
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599 * Returns the value of field 'consThreshold'.
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601 * @return the value of field 'ConsThreshold'.
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603 public int getConsThreshold(
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605 return this._consThreshold;
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609 * Returns the value of field 'conservationSelected'.
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611 * @return the value of field 'ConservationSelected'.
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613 public boolean getConservationSelected(
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615 return this._conservationSelected;
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619 * Returns the value of field 'fontName'.
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621 * @return the value of field 'FontName'.
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623 public java.lang.String getFontName(
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625 return this._fontName;
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629 * Returns the value of field 'fontSize'.
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631 * @return the value of field 'FontSize'.
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633 public int getFontSize(
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635 return this._fontSize;
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639 * Returns the value of field 'fontStyle'.
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641 * @return the value of field 'FontStyle'.
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643 public int getFontStyle(
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645 return this._fontStyle;
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649 * Returns the value of field 'gatheredViews'.
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651 * @return the value of field 'GatheredViews'.
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653 public boolean getGatheredViews(
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655 return this._gatheredViews;
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659 * Returns the value of field 'height'.
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661 * @return the value of field 'Height'.
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663 public int getHeight(
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665 return this._height;
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669 * Method getHiddenColumns.
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672 * @throws java.lang.IndexOutOfBoundsException if the index
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673 * given is outside the bounds of the collection
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674 * @return the value of the
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675 * jalview.schemabinding.version2.HiddenColumns at the given
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678 public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
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680 throws java.lang.IndexOutOfBoundsException {
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681 // check bounds for index
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682 if (index < 0 || index >= this._hiddenColumnsList.size()) {
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683 throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
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686 return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index);
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690 * Method getHiddenColumns.Returns the contents of the
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691 * collection in an Array. <p>Note: Just in case the
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692 * collection contents are changing in another thread, we pass
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693 * a 0-length Array of the correct type into the API call.
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694 * This way we <i>know</i> that the Array returned is of
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695 * exactly the correct length.
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697 * @return this collection as an Array
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699 public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns(
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701 jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
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702 return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array);
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706 * Method getHiddenColumnsCount.
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708 * @return the size of this collection
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710 public int getHiddenColumnsCount(
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712 return this._hiddenColumnsList.size();
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716 * Returns the value of field 'id'. The field 'id' has the
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717 * following description: unique id used by jalview to
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718 * synchronize between stored and instantiated views
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721 * @return the value of field 'Id'.
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723 public java.lang.String getId(
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729 * Returns the value of field 'pidSelected'.
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731 * @return the value of field 'PidSelected'.
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733 public boolean getPidSelected(
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735 return this._pidSelected;
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739 * Returns the value of field 'pidThreshold'.
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741 * @return the value of field 'PidThreshold'.
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743 public int getPidThreshold(
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745 return this._pidThreshold;
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749 * Returns the value of field 'renderGaps'.
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751 * @return the value of field 'RenderGaps'.
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753 public boolean getRenderGaps(
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755 return this._renderGaps;
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759 * Returns the value of field 'rightAlignIds'.
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761 * @return the value of field 'RightAlignIds'.
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763 public boolean getRightAlignIds(
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765 return this._rightAlignIds;
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769 * Returns the value of field 'sequenceSetId'.
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771 * @return the value of field 'SequenceSetId'.
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773 public java.lang.String getSequenceSetId(
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775 return this._sequenceSetId;
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779 * Returns the value of field 'showAnnotation'.
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781 * @return the value of field 'ShowAnnotation'.
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783 public boolean getShowAnnotation(
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785 return this._showAnnotation;
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789 * Returns the value of field 'showBoxes'.
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791 * @return the value of field 'ShowBoxes'.
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793 public boolean getShowBoxes(
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795 return this._showBoxes;
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799 * Returns the value of field 'showColourText'.
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801 * @return the value of field 'ShowColourText'.
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803 public boolean getShowColourText(
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805 return this._showColourText;
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809 * Returns the value of field 'showFullId'.
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811 * @return the value of field 'ShowFullId'.
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813 public boolean getShowFullId(
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815 return this._showFullId;
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819 * Returns the value of field 'showSequenceFeatures'.
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821 * @return the value of field 'ShowSequenceFeatures'.
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823 public boolean getShowSequenceFeatures(
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825 return this._showSequenceFeatures;
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829 * Returns the value of field 'showText'.
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831 * @return the value of field 'ShowText'.
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833 public boolean getShowText(
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835 return this._showText;
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839 * Returns the value of field 'showUnconserved'.
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841 * @return the value of field 'ShowUnconserved'.
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843 public boolean getShowUnconserved(
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845 return this._showUnconserved;
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849 * Returns the value of field 'startRes'.
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851 * @return the value of field 'StartRes'.
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853 public int getStartRes(
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855 return this._startRes;
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859 * Returns the value of field 'startSeq'.
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861 * @return the value of field 'StartSeq'.
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863 public int getStartSeq(
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865 return this._startSeq;
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869 * Returns the value of field 'textCol1'.
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871 * @return the value of field 'TextCol1'.
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873 public int getTextCol1(
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875 return this._textCol1;
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879 * Returns the value of field 'textCol2'.
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881 * @return the value of field 'TextCol2'.
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883 public int getTextCol2(
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885 return this._textCol2;
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889 * Returns the value of field 'textColThreshold'.
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891 * @return the value of field 'TextColThreshold'.
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893 public int getTextColThreshold(
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895 return this._textColThreshold;
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899 * Returns the value of field 'title'.
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901 * @return the value of field 'Title'.
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903 public java.lang.String getTitle(
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905 return this._title;
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909 * Returns the value of field 'viewName'.
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911 * @return the value of field 'ViewName'.
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913 public java.lang.String getViewName(
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915 return this._viewName;
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919 * Returns the value of field 'width'.
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921 * @return the value of field 'Width'.
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923 public int getWidth(
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925 return this._width;
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929 * Returns the value of field 'wrapAlignment'.
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931 * @return the value of field 'WrapAlignment'.
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933 public boolean getWrapAlignment(
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935 return this._wrapAlignment;
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939 * Returns the value of field 'xpos'.
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941 * @return the value of field 'Xpos'.
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943 public int getXpos(
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949 * Returns the value of field 'ypos'.
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951 * @return the value of field 'Ypos'.
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953 public int getYpos(
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959 * Method hasConsThreshold.
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961 * @return true if at least one ConsThreshold has been added
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963 public boolean hasConsThreshold(
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965 return this._has_consThreshold;
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969 * Method hasConservationSelected.
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971 * @return true if at least one ConservationSelected has been
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974 public boolean hasConservationSelected(
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976 return this._has_conservationSelected;
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980 * Method hasFontSize.
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982 * @return true if at least one FontSize has been added
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984 public boolean hasFontSize(
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986 return this._has_fontSize;
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990 * Method hasFontStyle.
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992 * @return true if at least one FontStyle has been added
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994 public boolean hasFontStyle(
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996 return this._has_fontStyle;
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1000 * Method hasGatheredViews.
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1002 * @return true if at least one GatheredViews has been added
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1004 public boolean hasGatheredViews(
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1006 return this._has_gatheredViews;
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1010 * Method hasHeight.
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1012 * @return true if at least one Height has been added
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1014 public boolean hasHeight(
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1016 return this._has_height;
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1020 * Method hasPidSelected.
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1022 * @return true if at least one PidSelected has been added
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1024 public boolean hasPidSelected(
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1026 return this._has_pidSelected;
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1030 * Method hasPidThreshold.
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1032 * @return true if at least one PidThreshold has been added
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1034 public boolean hasPidThreshold(
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1036 return this._has_pidThreshold;
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1040 * Method hasRenderGaps.
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1042 * @return true if at least one RenderGaps has been added
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1044 public boolean hasRenderGaps(
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1046 return this._has_renderGaps;
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1050 * Method hasRightAlignIds.
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1052 * @return true if at least one RightAlignIds has been added
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1054 public boolean hasRightAlignIds(
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1056 return this._has_rightAlignIds;
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1060 * Method hasShowAnnotation.
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1062 * @return true if at least one ShowAnnotation has been added
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1064 public boolean hasShowAnnotation(
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1066 return this._has_showAnnotation;
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1070 * Method hasShowBoxes.
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1072 * @return true if at least one ShowBoxes has been added
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1074 public boolean hasShowBoxes(
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1076 return this._has_showBoxes;
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1080 * Method hasShowColourText.
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1082 * @return true if at least one ShowColourText has been added
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1084 public boolean hasShowColourText(
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1086 return this._has_showColourText;
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1090 * Method hasShowFullId.
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1092 * @return true if at least one ShowFullId has been added
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1094 public boolean hasShowFullId(
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1096 return this._has_showFullId;
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1100 * Method hasShowSequenceFeatures.
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1102 * @return true if at least one ShowSequenceFeatures has been
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1105 public boolean hasShowSequenceFeatures(
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1107 return this._has_showSequenceFeatures;
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1111 * Method hasShowText.
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1113 * @return true if at least one ShowText has been added
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1115 public boolean hasShowText(
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1117 return this._has_showText;
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1121 * Method hasShowUnconserved.
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1123 * @return true if at least one ShowUnconserved has been added
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1125 public boolean hasShowUnconserved(
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1127 return this._has_showUnconserved;
\r
1131 * Method hasStartRes.
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1133 * @return true if at least one StartRes has been added
\r
1135 public boolean hasStartRes(
\r
1137 return this._has_startRes;
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1141 * Method hasStartSeq.
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1143 * @return true if at least one StartSeq has been added
\r
1145 public boolean hasStartSeq(
\r
1147 return this._has_startSeq;
\r
1151 * Method hasTextCol1.
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1153 * @return true if at least one TextCol1 has been added
\r
1155 public boolean hasTextCol1(
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1157 return this._has_textCol1;
\r
1161 * Method hasTextCol2.
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1163 * @return true if at least one TextCol2 has been added
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1165 public boolean hasTextCol2(
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1167 return this._has_textCol2;
\r
1171 * Method hasTextColThreshold.
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1173 * @return true if at least one TextColThreshold has been added
\r
1175 public boolean hasTextColThreshold(
\r
1177 return this._has_textColThreshold;
\r
1181 * Method hasWidth.
\r
1183 * @return true if at least one Width has been added
\r
1185 public boolean hasWidth(
\r
1187 return this._has_width;
\r
1191 * Method hasWrapAlignment.
\r
1193 * @return true if at least one WrapAlignment has been added
\r
1195 public boolean hasWrapAlignment(
\r
1197 return this._has_wrapAlignment;
\r
1203 * @return true if at least one Xpos has been added
\r
1205 public boolean hasXpos(
\r
1207 return this._has_xpos;
\r
1213 * @return true if at least one Ypos has been added
\r
1215 public boolean hasYpos(
\r
1217 return this._has_ypos;
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1221 * Returns the value of field 'conservationSelected'.
\r
1223 * @return the value of field 'ConservationSelected'.
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1225 public boolean isConservationSelected(
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1227 return this._conservationSelected;
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1231 * Returns the value of field 'gatheredViews'.
\r
1233 * @return the value of field 'GatheredViews'.
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1235 public boolean isGatheredViews(
\r
1237 return this._gatheredViews;
\r
1241 * Returns the value of field 'pidSelected'.
\r
1243 * @return the value of field 'PidSelected'.
\r
1245 public boolean isPidSelected(
\r
1247 return this._pidSelected;
\r
1251 * Returns the value of field 'renderGaps'.
\r
1253 * @return the value of field 'RenderGaps'.
\r
1255 public boolean isRenderGaps(
\r
1257 return this._renderGaps;
\r
1261 * Returns the value of field 'rightAlignIds'.
\r
1263 * @return the value of field 'RightAlignIds'.
\r
1265 public boolean isRightAlignIds(
\r
1267 return this._rightAlignIds;
\r
1271 * Returns the value of field 'showAnnotation'.
\r
1273 * @return the value of field 'ShowAnnotation'.
\r
1275 public boolean isShowAnnotation(
\r
1277 return this._showAnnotation;
\r
1281 * Returns the value of field 'showBoxes'.
\r
1283 * @return the value of field 'ShowBoxes'.
\r
1285 public boolean isShowBoxes(
\r
1287 return this._showBoxes;
\r
1291 * Returns the value of field 'showColourText'.
\r
1293 * @return the value of field 'ShowColourText'.
\r
1295 public boolean isShowColourText(
\r
1297 return this._showColourText;
\r
1301 * Returns the value of field 'showFullId'.
\r
1303 * @return the value of field 'ShowFullId'.
\r
1305 public boolean isShowFullId(
\r
1307 return this._showFullId;
\r
1311 * Returns the value of field 'showSequenceFeatures'.
\r
1313 * @return the value of field 'ShowSequenceFeatures'.
\r
1315 public boolean isShowSequenceFeatures(
\r
1317 return this._showSequenceFeatures;
\r
1321 * Returns the value of field 'showText'.
\r
1323 * @return the value of field 'ShowText'.
\r
1325 public boolean isShowText(
\r
1327 return this._showText;
\r
1331 * Returns the value of field 'showUnconserved'.
\r
1333 * @return the value of field 'ShowUnconserved'.
\r
1335 public boolean isShowUnconserved(
\r
1337 return this._showUnconserved;
\r
1343 * @return true if this object is valid according to the schema
\r
1345 public boolean isValid(
\r
1349 } catch (org.exolab.castor.xml.ValidationException vex) {
\r
1356 * Returns the value of field 'wrapAlignment'.
\r
1358 * @return the value of field 'WrapAlignment'.
\r
1360 public boolean isWrapAlignment(
\r
1362 return this._wrapAlignment;
\r
1369 * @throws org.exolab.castor.xml.MarshalException if object is
\r
1370 * null or if any SAXException is thrown during marshaling
\r
1371 * @throws org.exolab.castor.xml.ValidationException if this
\r
1372 * object is an invalid instance according to the schema
\r
1374 public void marshal(
\r
1375 final java.io.Writer out)
\r
1376 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
\r
1377 Marshaller.marshal(this, out);
\r
1384 * @throws java.io.IOException if an IOException occurs during
\r
1386 * @throws org.exolab.castor.xml.ValidationException if this
\r
1387 * object is an invalid instance according to the schema
\r
1388 * @throws org.exolab.castor.xml.MarshalException if object is
\r
1389 * null or if any SAXException is thrown during marshaling
\r
1391 public void marshal(
\r
1392 final org.xml.sax.ContentHandler handler)
\r
1393 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
\r
1394 Marshaller.marshal(this, handler);
\r
1399 public void removeAllHiddenColumns(
\r
1401 this._hiddenColumnsList.clear();
\r
1405 * Method removeHiddenColumns.
\r
1407 * @param vHiddenColumns
\r
1408 * @return true if the object was removed from the collection.
\r
1410 public boolean removeHiddenColumns(
\r
1411 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) {
\r
1412 boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
\r
1417 * Method removeHiddenColumnsAt.
\r
1420 * @return the element removed from the collection
\r
1422 public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
\r
1423 final int index) {
\r
1424 java.lang.Object obj = this._hiddenColumnsList.remove(index);
\r
1425 return (jalview.schemabinding.version2.HiddenColumns) obj;
\r
1429 * Sets the value of field 'annotationColours'.
\r
1431 * @param annotationColours the value of field
\r
1432 * 'annotationColours'.
\r
1434 public void setAnnotationColours(
\r
1435 final jalview.schemabinding.version2.AnnotationColours annotationColours) {
\r
1436 this._annotationColours = annotationColours;
\r
1440 * Sets the value of field 'bgColour'.
\r
1442 * @param bgColour the value of field 'bgColour'.
\r
1444 public void setBgColour(
\r
1445 final java.lang.String bgColour) {
\r
1446 this._bgColour = bgColour;
\r
1450 * Sets the value of field 'consThreshold'.
\r
1452 * @param consThreshold the value of field 'consThreshold'.
\r
1454 public void setConsThreshold(
\r
1455 final int consThreshold) {
\r
1456 this._consThreshold = consThreshold;
\r
1457 this._has_consThreshold = true;
\r
1461 * Sets the value of field 'conservationSelected'.
\r
1463 * @param conservationSelected the value of field
\r
1464 * 'conservationSelected'.
\r
1466 public void setConservationSelected(
\r
1467 final boolean conservationSelected) {
\r
1468 this._conservationSelected = conservationSelected;
\r
1469 this._has_conservationSelected = true;
\r
1473 * Sets the value of field 'fontName'.
\r
1475 * @param fontName the value of field 'fontName'.
\r
1477 public void setFontName(
\r
1478 final java.lang.String fontName) {
\r
1479 this._fontName = fontName;
\r
1483 * Sets the value of field 'fontSize'.
\r
1485 * @param fontSize the value of field 'fontSize'.
\r
1487 public void setFontSize(
\r
1488 final int fontSize) {
\r
1489 this._fontSize = fontSize;
\r
1490 this._has_fontSize = true;
\r
1494 * Sets the value of field 'fontStyle'.
\r
1496 * @param fontStyle the value of field 'fontStyle'.
\r
1498 public void setFontStyle(
\r
1499 final int fontStyle) {
\r
1500 this._fontStyle = fontStyle;
\r
1501 this._has_fontStyle = true;
\r
1505 * Sets the value of field 'gatheredViews'.
\r
1507 * @param gatheredViews the value of field 'gatheredViews'.
\r
1509 public void setGatheredViews(
\r
1510 final boolean gatheredViews) {
\r
1511 this._gatheredViews = gatheredViews;
\r
1512 this._has_gatheredViews = true;
\r
1516 * Sets the value of field 'height'.
\r
1518 * @param height the value of field 'height'.
\r
1520 public void setHeight(
\r
1521 final int height) {
\r
1522 this._height = height;
\r
1523 this._has_height = true;
\r
1530 * @param vHiddenColumns
\r
1531 * @throws java.lang.IndexOutOfBoundsException if the index
\r
1532 * given is outside the bounds of the collection
\r
1534 public void setHiddenColumns(
\r
1536 final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
\r
1537 throws java.lang.IndexOutOfBoundsException {
\r
1538 // check bounds for index
\r
1539 if (index < 0 || index >= this._hiddenColumnsList.size()) {
\r
1540 throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
\r
1543 this._hiddenColumnsList.set(index, vHiddenColumns);
\r
1549 * @param vHiddenColumnsArray
\r
1551 public void setHiddenColumns(
\r
1552 final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) {
\r
1554 _hiddenColumnsList.clear();
\r
1556 for (int i = 0; i < vHiddenColumnsArray.length; i++) {
\r
1557 this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
\r
1562 * Sets the value of field 'id'. The field 'id' has the
\r
1563 * following description: unique id used by jalview to
\r
1564 * synchronize between stored and instantiated views
\r
1567 * @param id the value of field 'id'.
\r
1569 public void setId(
\r
1570 final java.lang.String id) {
\r
1575 * Sets the value of field 'pidSelected'.
\r
1577 * @param pidSelected the value of field 'pidSelected'.
\r
1579 public void setPidSelected(
\r
1580 final boolean pidSelected) {
\r
1581 this._pidSelected = pidSelected;
\r
1582 this._has_pidSelected = true;
\r
1586 * Sets the value of field 'pidThreshold'.
\r
1588 * @param pidThreshold the value of field 'pidThreshold'.
\r
1590 public void setPidThreshold(
\r
1591 final int pidThreshold) {
\r
1592 this._pidThreshold = pidThreshold;
\r
1593 this._has_pidThreshold = true;
\r
1597 * Sets the value of field 'renderGaps'.
\r
1599 * @param renderGaps the value of field 'renderGaps'.
\r
1601 public void setRenderGaps(
\r
1602 final boolean renderGaps) {
\r
1603 this._renderGaps = renderGaps;
\r
1604 this._has_renderGaps = true;
\r
1608 * Sets the value of field 'rightAlignIds'.
\r
1610 * @param rightAlignIds the value of field 'rightAlignIds'.
\r
1612 public void setRightAlignIds(
\r
1613 final boolean rightAlignIds) {
\r
1614 this._rightAlignIds = rightAlignIds;
\r
1615 this._has_rightAlignIds = true;
\r
1619 * Sets the value of field 'sequenceSetId'.
\r
1621 * @param sequenceSetId the value of field 'sequenceSetId'.
\r
1623 public void setSequenceSetId(
\r
1624 final java.lang.String sequenceSetId) {
\r
1625 this._sequenceSetId = sequenceSetId;
\r
1629 * Sets the value of field 'showAnnotation'.
\r
1631 * @param showAnnotation the value of field 'showAnnotation'.
\r
1633 public void setShowAnnotation(
\r
1634 final boolean showAnnotation) {
\r
1635 this._showAnnotation = showAnnotation;
\r
1636 this._has_showAnnotation = true;
\r
1640 * Sets the value of field 'showBoxes'.
\r
1642 * @param showBoxes the value of field 'showBoxes'.
\r
1644 public void setShowBoxes(
\r
1645 final boolean showBoxes) {
\r
1646 this._showBoxes = showBoxes;
\r
1647 this._has_showBoxes = true;
\r
1651 * Sets the value of field 'showColourText'.
\r
1653 * @param showColourText the value of field 'showColourText'.
\r
1655 public void setShowColourText(
\r
1656 final boolean showColourText) {
\r
1657 this._showColourText = showColourText;
\r
1658 this._has_showColourText = true;
\r
1662 * Sets the value of field 'showFullId'.
\r
1664 * @param showFullId the value of field 'showFullId'.
\r
1666 public void setShowFullId(
\r
1667 final boolean showFullId) {
\r
1668 this._showFullId = showFullId;
\r
1669 this._has_showFullId = true;
\r
1673 * Sets the value of field 'showSequenceFeatures'.
\r
1675 * @param showSequenceFeatures the value of field
\r
1676 * 'showSequenceFeatures'.
\r
1678 public void setShowSequenceFeatures(
\r
1679 final boolean showSequenceFeatures) {
\r
1680 this._showSequenceFeatures = showSequenceFeatures;
\r
1681 this._has_showSequenceFeatures = true;
\r
1685 * Sets the value of field 'showText'.
\r
1687 * @param showText the value of field 'showText'.
\r
1689 public void setShowText(
\r
1690 final boolean showText) {
\r
1691 this._showText = showText;
\r
1692 this._has_showText = true;
\r
1696 * Sets the value of field 'showUnconserved'.
\r
1698 * @param showUnconserved the value of field 'showUnconserved'.
\r
1700 public void setShowUnconserved(
\r
1701 final boolean showUnconserved) {
\r
1702 this._showUnconserved = showUnconserved;
\r
1703 this._has_showUnconserved = true;
\r
1707 * Sets the value of field 'startRes'.
\r
1709 * @param startRes the value of field 'startRes'.
\r
1711 public void setStartRes(
\r
1712 final int startRes) {
\r
1713 this._startRes = startRes;
\r
1714 this._has_startRes = true;
\r
1718 * Sets the value of field 'startSeq'.
\r
1720 * @param startSeq the value of field 'startSeq'.
\r
1722 public void setStartSeq(
\r
1723 final int startSeq) {
\r
1724 this._startSeq = startSeq;
\r
1725 this._has_startSeq = true;
\r
1729 * Sets the value of field 'textCol1'.
\r
1731 * @param textCol1 the value of field 'textCol1'.
\r
1733 public void setTextCol1(
\r
1734 final int textCol1) {
\r
1735 this._textCol1 = textCol1;
\r
1736 this._has_textCol1 = true;
\r
1740 * Sets the value of field 'textCol2'.
\r
1742 * @param textCol2 the value of field 'textCol2'.
\r
1744 public void setTextCol2(
\r
1745 final int textCol2) {
\r
1746 this._textCol2 = textCol2;
\r
1747 this._has_textCol2 = true;
\r
1751 * Sets the value of field 'textColThreshold'.
\r
1753 * @param textColThreshold the value of field 'textColThreshold'
\r
1755 public void setTextColThreshold(
\r
1756 final int textColThreshold) {
\r
1757 this._textColThreshold = textColThreshold;
\r
1758 this._has_textColThreshold = true;
\r
1762 * Sets the value of field 'title'.
\r
1764 * @param title the value of field 'title'.
\r
1766 public void setTitle(
\r
1767 final java.lang.String title) {
\r
1768 this._title = title;
\r
1772 * Sets the value of field 'viewName'.
\r
1774 * @param viewName the value of field 'viewName'.
\r
1776 public void setViewName(
\r
1777 final java.lang.String viewName) {
\r
1778 this._viewName = viewName;
\r
1782 * Sets the value of field 'width'.
\r
1784 * @param width the value of field 'width'.
\r
1786 public void setWidth(
\r
1787 final int width) {
\r
1788 this._width = width;
\r
1789 this._has_width = true;
\r
1793 * Sets the value of field 'wrapAlignment'.
\r
1795 * @param wrapAlignment the value of field 'wrapAlignment'.
\r
1797 public void setWrapAlignment(
\r
1798 final boolean wrapAlignment) {
\r
1799 this._wrapAlignment = wrapAlignment;
\r
1800 this._has_wrapAlignment = true;
\r
1804 * Sets the value of field 'xpos'.
\r
1806 * @param xpos the value of field 'xpos'.
\r
1808 public void setXpos(
\r
1810 this._xpos = xpos;
\r
1811 this._has_xpos = true;
\r
1815 * Sets the value of field 'ypos'.
\r
1817 * @param ypos the value of field 'ypos'.
\r
1819 public void setYpos(
\r
1821 this._ypos = ypos;
\r
1822 this._has_ypos = true;
\r
1826 * Method unmarshal.
\r
1829 * @throws org.exolab.castor.xml.MarshalException if object is
\r
1830 * null or if any SAXException is thrown during marshaling
\r
1831 * @throws org.exolab.castor.xml.ValidationException if this
\r
1832 * object is an invalid instance according to the schema
\r
1833 * @return the unmarshaled
\r
1834 * jalview.schemabinding.version2.Viewport
\r
1836 public static jalview.schemabinding.version2.Viewport unmarshal(
\r
1837 final java.io.Reader reader)
\r
1838 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
\r
1839 return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);
\r
1845 * @throws org.exolab.castor.xml.ValidationException if this
\r
1846 * object is an invalid instance according to the schema
\r
1848 public void validate(
\r
1850 throws org.exolab.castor.xml.ValidationException {
\r
1851 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
\r
1852 validator.validate(this);
\r