2 * This class was automatically generated with
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3 * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
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8 package jalview.schemabinding.version2;
\r
10 //---------------------------------/
\r
11 //- Imported classes and packages -/
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12 //---------------------------------/
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14 import java.io.IOException;
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15 import java.io.Reader;
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16 import java.io.Serializable;
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17 import java.io.Writer;
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18 import java.util.Enumeration;
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19 import java.util.Vector;
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20 import org.exolab.castor.xml.MarshalException;
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21 import org.exolab.castor.xml.Marshaller;
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22 import org.exolab.castor.xml.Unmarshaller;
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23 import org.exolab.castor.xml.ValidationException;
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24 import org.xml.sax.ContentHandler;
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29 * @version $Revision$ $Date$
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31 public class Viewport implements java.io.Serializable {
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34 //--------------------------/
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35 //- Class/Member Variables -/
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36 //--------------------------/
\r
39 * Field _conservationSelected
\r
41 private boolean _conservationSelected;
\r
44 * keeps track of state for field: _conservationSelected
\r
46 private boolean _has_conservationSelected;
\r
49 * Field _pidSelected
\r
51 private boolean _pidSelected;
\r
54 * keeps track of state for field: _pidSelected
\r
56 private boolean _has_pidSelected;
\r
61 private java.lang.String _bgColour;
\r
64 * Field _consThreshold
\r
66 private int _consThreshold;
\r
69 * keeps track of state for field: _consThreshold
\r
71 private boolean _has_consThreshold;
\r
74 * Field _pidThreshold
\r
76 private int _pidThreshold;
\r
79 * keeps track of state for field: _pidThreshold
\r
81 private boolean _has_pidThreshold;
\r
86 private java.lang.String _title;
\r
91 private boolean _showFullId;
\r
94 * keeps track of state for field: _showFullId
\r
96 private boolean _has_showFullId;
\r
101 private boolean _showText;
\r
104 * keeps track of state for field: _showText
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106 private boolean _has_showText;
\r
109 * Field _showColourText
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111 private boolean _showColourText;
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114 * keeps track of state for field: _showColourText
\r
116 private boolean _has_showColourText;
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121 private boolean _showBoxes;
\r
124 * keeps track of state for field: _showBoxes
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126 private boolean _has_showBoxes;
\r
129 * Field _wrapAlignment
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131 private boolean _wrapAlignment;
\r
134 * keeps track of state for field: _wrapAlignment
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136 private boolean _has_wrapAlignment;
\r
139 * Field _renderGaps
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141 private boolean _renderGaps;
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144 * keeps track of state for field: _renderGaps
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146 private boolean _has_renderGaps;
\r
149 * Field _showSequenceFeatures
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151 private boolean _showSequenceFeatures;
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154 * keeps track of state for field: _showSequenceFeatures
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156 private boolean _has_showSequenceFeatures;
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159 * Field _showAnnotation
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161 private boolean _showAnnotation;
\r
164 * keeps track of state for field: _showAnnotation
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166 private boolean _has_showAnnotation;
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169 * Field _showConservation
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171 private boolean _showConservation;
\r
174 * keeps track of state for field: _showConservation
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176 private boolean _has_showConservation;
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179 * Field _showQuality
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181 private boolean _showQuality;
\r
184 * keeps track of state for field: _showQuality
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186 private boolean _has_showQuality;
\r
189 * Field _showIdentity
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191 private boolean _showIdentity;
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194 * keeps track of state for field: _showIdentity
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196 private boolean _has_showIdentity;
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204 * keeps track of state for field: _xpos
\r
206 private boolean _has_xpos;
\r
214 * keeps track of state for field: _ypos
\r
216 private boolean _has_ypos;
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221 private int _width;
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224 * keeps track of state for field: _width
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226 private boolean _has_width;
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231 private int _height;
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234 * keeps track of state for field: _height
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236 private boolean _has_height;
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241 private int _startRes;
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244 * keeps track of state for field: _startRes
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246 private boolean _has_startRes;
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251 private int _startSeq;
\r
254 * keeps track of state for field: _startSeq
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256 private boolean _has_startSeq;
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261 private java.lang.String _fontName;
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266 private int _fontSize;
\r
269 * keeps track of state for field: _fontSize
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271 private boolean _has_fontSize;
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276 private int _fontStyle;
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279 * keeps track of state for field: _fontStyle
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281 private boolean _has_fontStyle;
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286 private java.lang.String _viewName;
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289 * Field _sequenceSetId
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291 private java.lang.String _sequenceSetId;
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294 * Field _gatheredViews
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296 private boolean _gatheredViews;
\r
299 * keeps track of state for field: _gatheredViews
\r
301 private boolean _has_gatheredViews;
\r
304 * Field _annotationColours
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306 private jalview.schemabinding.version2.AnnotationColours _annotationColours;
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309 * Field _hiddenColumnsList
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311 private java.util.Vector _hiddenColumnsList;
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314 //----------------/
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315 //- Constructors -/
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316 //----------------/
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318 public Viewport() {
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320 _hiddenColumnsList = new Vector();
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321 } //-- jalview.schemabinding.version2.Viewport()
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329 * Method addHiddenColumns
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333 * @param vHiddenColumns
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335 public void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
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336 throws java.lang.IndexOutOfBoundsException
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338 _hiddenColumnsList.addElement(vHiddenColumns);
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339 } //-- void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns)
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342 * Method addHiddenColumns
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347 * @param vHiddenColumns
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349 public void addHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
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350 throws java.lang.IndexOutOfBoundsException
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352 _hiddenColumnsList.insertElementAt(vHiddenColumns, index);
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353 } //-- void addHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns)
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356 * Method deleteConsThreshold
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359 public void deleteConsThreshold()
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361 this._has_consThreshold= false;
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362 } //-- void deleteConsThreshold()
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365 * Method deleteConservationSelected
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368 public void deleteConservationSelected()
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370 this._has_conservationSelected= false;
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371 } //-- void deleteConservationSelected()
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374 * Method deleteFontSize
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377 public void deleteFontSize()
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379 this._has_fontSize= false;
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380 } //-- void deleteFontSize()
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383 * Method deleteFontStyle
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386 public void deleteFontStyle()
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388 this._has_fontStyle= false;
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389 } //-- void deleteFontStyle()
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392 * Method deleteGatheredViews
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395 public void deleteGatheredViews()
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397 this._has_gatheredViews= false;
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398 } //-- void deleteGatheredViews()
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401 * Method deleteHeight
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404 public void deleteHeight()
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406 this._has_height= false;
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407 } //-- void deleteHeight()
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410 * Method deletePidSelected
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413 public void deletePidSelected()
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415 this._has_pidSelected= false;
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416 } //-- void deletePidSelected()
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419 * Method deletePidThreshold
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422 public void deletePidThreshold()
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424 this._has_pidThreshold= false;
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425 } //-- void deletePidThreshold()
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428 * Method deleteRenderGaps
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431 public void deleteRenderGaps()
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433 this._has_renderGaps= false;
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434 } //-- void deleteRenderGaps()
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437 * Method deleteShowAnnotation
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440 public void deleteShowAnnotation()
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442 this._has_showAnnotation= false;
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443 } //-- void deleteShowAnnotation()
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446 * Method deleteShowBoxes
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449 public void deleteShowBoxes()
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451 this._has_showBoxes= false;
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452 } //-- void deleteShowBoxes()
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455 * Method deleteShowColourText
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458 public void deleteShowColourText()
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460 this._has_showColourText= false;
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461 } //-- void deleteShowColourText()
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464 * Method deleteShowConservation
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467 public void deleteShowConservation()
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469 this._has_showConservation= false;
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470 } //-- void deleteShowConservation()
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473 * Method deleteShowFullId
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476 public void deleteShowFullId()
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478 this._has_showFullId= false;
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479 } //-- void deleteShowFullId()
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482 * Method deleteShowIdentity
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485 public void deleteShowIdentity()
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487 this._has_showIdentity= false;
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488 } //-- void deleteShowIdentity()
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491 * Method deleteShowQuality
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494 public void deleteShowQuality()
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496 this._has_showQuality= false;
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497 } //-- void deleteShowQuality()
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500 * Method deleteShowSequenceFeatures
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503 public void deleteShowSequenceFeatures()
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505 this._has_showSequenceFeatures= false;
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506 } //-- void deleteShowSequenceFeatures()
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509 * Method deleteShowText
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512 public void deleteShowText()
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514 this._has_showText= false;
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515 } //-- void deleteShowText()
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518 * Method deleteStartRes
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521 public void deleteStartRes()
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523 this._has_startRes= false;
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524 } //-- void deleteStartRes()
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527 * Method deleteStartSeq
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530 public void deleteStartSeq()
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532 this._has_startSeq= false;
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533 } //-- void deleteStartSeq()
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536 * Method deleteWidth
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539 public void deleteWidth()
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541 this._has_width= false;
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542 } //-- void deleteWidth()
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545 * Method deleteWrapAlignment
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548 public void deleteWrapAlignment()
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550 this._has_wrapAlignment= false;
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551 } //-- void deleteWrapAlignment()
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554 * Method deleteXpos
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557 public void deleteXpos()
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559 this._has_xpos= false;
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560 } //-- void deleteXpos()
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563 * Method deleteYpos
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566 public void deleteYpos()
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568 this._has_ypos= false;
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569 } //-- void deleteYpos()
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572 * Method enumerateHiddenColumns
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576 * @return Enumeration
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578 public java.util.Enumeration enumerateHiddenColumns()
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580 return _hiddenColumnsList.elements();
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581 } //-- java.util.Enumeration enumerateHiddenColumns()
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584 * Returns the value of field 'annotationColours'.
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586 * @return AnnotationColours
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587 * @return the value of field 'annotationColours'.
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589 public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
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591 return this._annotationColours;
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592 } //-- jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
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595 * Returns the value of field 'bgColour'.
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598 * @return the value of field 'bgColour'.
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600 public java.lang.String getBgColour()
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602 return this._bgColour;
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603 } //-- java.lang.String getBgColour()
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606 * Returns the value of field 'consThreshold'.
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609 * @return the value of field 'consThreshold'.
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611 public int getConsThreshold()
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613 return this._consThreshold;
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614 } //-- int getConsThreshold()
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617 * Returns the value of field 'conservationSelected'.
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620 * @return the value of field 'conservationSelected'.
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622 public boolean getConservationSelected()
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624 return this._conservationSelected;
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625 } //-- boolean getConservationSelected()
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628 * Returns the value of field 'fontName'.
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631 * @return the value of field 'fontName'.
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633 public java.lang.String getFontName()
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635 return this._fontName;
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636 } //-- java.lang.String getFontName()
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639 * Returns the value of field 'fontSize'.
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642 * @return the value of field 'fontSize'.
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644 public int getFontSize()
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646 return this._fontSize;
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647 } //-- int getFontSize()
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650 * Returns the value of field 'fontStyle'.
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653 * @return the value of field 'fontStyle'.
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655 public int getFontStyle()
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657 return this._fontStyle;
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658 } //-- int getFontStyle()
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661 * Returns the value of field 'gatheredViews'.
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664 * @return the value of field 'gatheredViews'.
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666 public boolean getGatheredViews()
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668 return this._gatheredViews;
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669 } //-- boolean getGatheredViews()
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672 * Returns the value of field 'height'.
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675 * @return the value of field 'height'.
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677 public int getHeight()
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679 return this._height;
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680 } //-- int getHeight()
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683 * Method getHiddenColumns
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688 * @return HiddenColumns
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690 public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int index)
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691 throws java.lang.IndexOutOfBoundsException
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693 //-- check bounds for index
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694 if ((index < 0) || (index > _hiddenColumnsList.size())) {
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695 throw new IndexOutOfBoundsException();
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698 return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);
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699 } //-- jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int)
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702 * Method getHiddenColumns
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706 * @return HiddenColumns
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708 public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
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710 int size = _hiddenColumnsList.size();
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711 jalview.schemabinding.version2.HiddenColumns[] mArray = new jalview.schemabinding.version2.HiddenColumns[size];
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712 for (int index = 0; index < size; index++) {
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713 mArray[index] = (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);
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716 } //-- jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
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719 * Method getHiddenColumnsCount
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725 public int getHiddenColumnsCount()
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727 return _hiddenColumnsList.size();
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728 } //-- int getHiddenColumnsCount()
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731 * Returns the value of field 'pidSelected'.
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734 * @return the value of field 'pidSelected'.
\r
736 public boolean getPidSelected()
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738 return this._pidSelected;
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739 } //-- boolean getPidSelected()
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742 * Returns the value of field 'pidThreshold'.
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745 * @return the value of field 'pidThreshold'.
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747 public int getPidThreshold()
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749 return this._pidThreshold;
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750 } //-- int getPidThreshold()
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753 * Returns the value of field 'renderGaps'.
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756 * @return the value of field 'renderGaps'.
\r
758 public boolean getRenderGaps()
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760 return this._renderGaps;
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761 } //-- boolean getRenderGaps()
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764 * Returns the value of field 'sequenceSetId'.
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767 * @return the value of field 'sequenceSetId'.
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769 public java.lang.String getSequenceSetId()
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771 return this._sequenceSetId;
\r
772 } //-- java.lang.String getSequenceSetId()
\r
775 * Returns the value of field 'showAnnotation'.
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778 * @return the value of field 'showAnnotation'.
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780 public boolean getShowAnnotation()
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782 return this._showAnnotation;
\r
783 } //-- boolean getShowAnnotation()
\r
786 * Returns the value of field 'showBoxes'.
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789 * @return the value of field 'showBoxes'.
\r
791 public boolean getShowBoxes()
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793 return this._showBoxes;
\r
794 } //-- boolean getShowBoxes()
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797 * Returns the value of field 'showColourText'.
\r
800 * @return the value of field 'showColourText'.
\r
802 public boolean getShowColourText()
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804 return this._showColourText;
\r
805 } //-- boolean getShowColourText()
\r
808 * Returns the value of field 'showConservation'.
\r
811 * @return the value of field 'showConservation'.
\r
813 public boolean getShowConservation()
\r
815 return this._showConservation;
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816 } //-- boolean getShowConservation()
\r
819 * Returns the value of field 'showFullId'.
\r
822 * @return the value of field 'showFullId'.
\r
824 public boolean getShowFullId()
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826 return this._showFullId;
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827 } //-- boolean getShowFullId()
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830 * Returns the value of field 'showIdentity'.
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833 * @return the value of field 'showIdentity'.
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835 public boolean getShowIdentity()
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837 return this._showIdentity;
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838 } //-- boolean getShowIdentity()
\r
841 * Returns the value of field 'showQuality'.
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844 * @return the value of field 'showQuality'.
\r
846 public boolean getShowQuality()
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848 return this._showQuality;
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849 } //-- boolean getShowQuality()
\r
852 * Returns the value of field 'showSequenceFeatures'.
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855 * @return the value of field 'showSequenceFeatures'.
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857 public boolean getShowSequenceFeatures()
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859 return this._showSequenceFeatures;
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860 } //-- boolean getShowSequenceFeatures()
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863 * Returns the value of field 'showText'.
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866 * @return the value of field 'showText'.
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868 public boolean getShowText()
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870 return this._showText;
\r
871 } //-- boolean getShowText()
\r
874 * Returns the value of field 'startRes'.
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877 * @return the value of field 'startRes'.
\r
879 public int getStartRes()
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881 return this._startRes;
\r
882 } //-- int getStartRes()
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885 * Returns the value of field 'startSeq'.
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888 * @return the value of field 'startSeq'.
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890 public int getStartSeq()
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892 return this._startSeq;
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893 } //-- int getStartSeq()
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896 * Returns the value of field 'title'.
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899 * @return the value of field 'title'.
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901 public java.lang.String getTitle()
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903 return this._title;
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904 } //-- java.lang.String getTitle()
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907 * Returns the value of field 'viewName'.
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910 * @return the value of field 'viewName'.
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912 public java.lang.String getViewName()
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914 return this._viewName;
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915 } //-- java.lang.String getViewName()
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918 * 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;
\r
926 } //-- int getWidth()
\r
929 * Returns the value of field 'wrapAlignment'.
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932 * @return the value of field 'wrapAlignment'.
\r
934 public boolean getWrapAlignment()
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936 return this._wrapAlignment;
\r
937 } //-- boolean getWrapAlignment()
\r
940 * Returns the value of field 'xpos'.
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943 * @return the value of field 'xpos'.
\r
945 public int getXpos()
\r
948 } //-- int getXpos()
\r
951 * Returns the value of field 'ypos'.
\r
954 * @return the value of field 'ypos'.
\r
956 public int getYpos()
\r
959 } //-- int getYpos()
\r
962 * Method hasConsThreshold
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968 public boolean hasConsThreshold()
\r
970 return this._has_consThreshold;
\r
971 } //-- boolean hasConsThreshold()
\r
974 * Method hasConservationSelected
\r
980 public boolean hasConservationSelected()
\r
982 return this._has_conservationSelected;
\r
983 } //-- boolean hasConservationSelected()
\r
986 * Method hasFontSize
\r
992 public boolean hasFontSize()
\r
994 return this._has_fontSize;
\r
995 } //-- boolean hasFontSize()
\r
998 * Method hasFontStyle
\r
1004 public boolean hasFontStyle()
\r
1006 return this._has_fontStyle;
\r
1007 } //-- boolean hasFontStyle()
\r
1010 * Method hasGatheredViews
\r
1016 public boolean hasGatheredViews()
\r
1018 return this._has_gatheredViews;
\r
1019 } //-- boolean hasGatheredViews()
\r
1022 * Method hasHeight
\r
1028 public boolean hasHeight()
\r
1030 return this._has_height;
\r
1031 } //-- boolean hasHeight()
\r
1034 * Method hasPidSelected
\r
1040 public boolean hasPidSelected()
\r
1042 return this._has_pidSelected;
\r
1043 } //-- boolean hasPidSelected()
\r
1046 * Method hasPidThreshold
\r
1052 public boolean hasPidThreshold()
\r
1054 return this._has_pidThreshold;
\r
1055 } //-- boolean hasPidThreshold()
\r
1058 * Method hasRenderGaps
\r
1064 public boolean hasRenderGaps()
\r
1066 return this._has_renderGaps;
\r
1067 } //-- boolean hasRenderGaps()
\r
1070 * Method hasShowAnnotation
\r
1076 public boolean hasShowAnnotation()
\r
1078 return this._has_showAnnotation;
\r
1079 } //-- boolean hasShowAnnotation()
\r
1082 * Method hasShowBoxes
\r
1088 public boolean hasShowBoxes()
\r
1090 return this._has_showBoxes;
\r
1091 } //-- boolean hasShowBoxes()
\r
1094 * Method hasShowColourText
\r
1100 public boolean hasShowColourText()
\r
1102 return this._has_showColourText;
\r
1103 } //-- boolean hasShowColourText()
\r
1106 * Method hasShowConservation
\r
1112 public boolean hasShowConservation()
\r
1114 return this._has_showConservation;
\r
1115 } //-- boolean hasShowConservation()
\r
1118 * Method hasShowFullId
\r
1124 public boolean hasShowFullId()
\r
1126 return this._has_showFullId;
\r
1127 } //-- boolean hasShowFullId()
\r
1130 * Method hasShowIdentity
\r
1136 public boolean hasShowIdentity()
\r
1138 return this._has_showIdentity;
\r
1139 } //-- boolean hasShowIdentity()
\r
1142 * Method hasShowQuality
\r
1148 public boolean hasShowQuality()
\r
1150 return this._has_showQuality;
\r
1151 } //-- boolean hasShowQuality()
\r
1154 * Method hasShowSequenceFeatures
\r
1160 public boolean hasShowSequenceFeatures()
\r
1162 return this._has_showSequenceFeatures;
\r
1163 } //-- boolean hasShowSequenceFeatures()
\r
1166 * Method hasShowText
\r
1172 public boolean hasShowText()
\r
1174 return this._has_showText;
\r
1175 } //-- boolean hasShowText()
\r
1178 * Method hasStartRes
\r
1184 public boolean hasStartRes()
\r
1186 return this._has_startRes;
\r
1187 } //-- boolean hasStartRes()
\r
1190 * Method hasStartSeq
\r
1196 public boolean hasStartSeq()
\r
1198 return this._has_startSeq;
\r
1199 } //-- boolean hasStartSeq()
\r
1208 public boolean hasWidth()
\r
1210 return this._has_width;
\r
1211 } //-- boolean hasWidth()
\r
1214 * Method hasWrapAlignment
\r
1220 public boolean hasWrapAlignment()
\r
1222 return this._has_wrapAlignment;
\r
1223 } //-- boolean hasWrapAlignment()
\r
1232 public boolean hasXpos()
\r
1234 return this._has_xpos;
\r
1235 } //-- boolean hasXpos()
\r
1244 public boolean hasYpos()
\r
1246 return this._has_ypos;
\r
1247 } //-- boolean hasYpos()
\r
1256 public boolean isValid()
\r
1261 catch (org.exolab.castor.xml.ValidationException vex) {
\r
1265 } //-- boolean isValid()
\r
1274 public void marshal(java.io.Writer out)
\r
1275 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
\r
1278 Marshaller.marshal(this, out);
\r
1279 } //-- void marshal(java.io.Writer)
\r
1288 public void marshal(org.xml.sax.ContentHandler handler)
\r
1289 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
\r
1292 Marshaller.marshal(this, handler);
\r
1293 } //-- void marshal(org.xml.sax.ContentHandler)
\r
1296 * Method removeAllHiddenColumns
\r
1299 public void removeAllHiddenColumns()
\r
1301 _hiddenColumnsList.removeAllElements();
\r
1302 } //-- void removeAllHiddenColumns()
\r
1305 * Method removeHiddenColumns
\r
1310 * @return HiddenColumns
\r
1312 public jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int index)
\r
1314 java.lang.Object obj = _hiddenColumnsList.elementAt(index);
\r
1315 _hiddenColumnsList.removeElementAt(index);
\r
1316 return (jalview.schemabinding.version2.HiddenColumns) obj;
\r
1317 } //-- jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int)
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1320 * Sets the value of field 'annotationColours'.
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1322 * @param annotationColours the value of field
\r
1323 * 'annotationColours'.
\r
1325 public void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours annotationColours)
\r
1327 this._annotationColours = annotationColours;
\r
1328 } //-- void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours)
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1331 * Sets the value of field 'bgColour'.
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1333 * @param bgColour the value of field 'bgColour'.
\r
1335 public void setBgColour(java.lang.String bgColour)
\r
1337 this._bgColour = bgColour;
\r
1338 } //-- void setBgColour(java.lang.String)
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1341 * Sets the value of field 'consThreshold'.
\r
1343 * @param consThreshold the value of field 'consThreshold'.
\r
1345 public void setConsThreshold(int consThreshold)
\r
1347 this._consThreshold = consThreshold;
\r
1348 this._has_consThreshold = true;
\r
1349 } //-- void setConsThreshold(int)
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1352 * Sets the value of field 'conservationSelected'.
\r
1354 * @param conservationSelected the value of field
\r
1355 * 'conservationSelected'.
\r
1357 public void setConservationSelected(boolean conservationSelected)
\r
1359 this._conservationSelected = conservationSelected;
\r
1360 this._has_conservationSelected = true;
\r
1361 } //-- void setConservationSelected(boolean)
\r
1364 * Sets the value of field 'fontName'.
\r
1366 * @param fontName the value of field 'fontName'.
\r
1368 public void setFontName(java.lang.String fontName)
\r
1370 this._fontName = fontName;
\r
1371 } //-- void setFontName(java.lang.String)
\r
1374 * Sets the value of field 'fontSize'.
\r
1376 * @param fontSize the value of field 'fontSize'.
\r
1378 public void setFontSize(int fontSize)
\r
1380 this._fontSize = fontSize;
\r
1381 this._has_fontSize = true;
\r
1382 } //-- void setFontSize(int)
\r
1385 * Sets the value of field 'fontStyle'.
\r
1387 * @param fontStyle the value of field 'fontStyle'.
\r
1389 public void setFontStyle(int fontStyle)
\r
1391 this._fontStyle = fontStyle;
\r
1392 this._has_fontStyle = true;
\r
1393 } //-- void setFontStyle(int)
\r
1396 * Sets the value of field 'gatheredViews'.
\r
1398 * @param gatheredViews the value of field 'gatheredViews'.
\r
1400 public void setGatheredViews(boolean gatheredViews)
\r
1402 this._gatheredViews = gatheredViews;
\r
1403 this._has_gatheredViews = true;
\r
1404 } //-- void setGatheredViews(boolean)
\r
1407 * Sets the value of field 'height'.
\r
1409 * @param height the value of field 'height'.
\r
1411 public void setHeight(int height)
\r
1413 this._height = height;
\r
1414 this._has_height = true;
\r
1415 } //-- void setHeight(int)
\r
1418 * Method setHiddenColumns
\r
1423 * @param vHiddenColumns
\r
1425 public void setHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
\r
1426 throws java.lang.IndexOutOfBoundsException
\r
1428 //-- check bounds for index
\r
1429 if ((index < 0) || (index > _hiddenColumnsList.size())) {
\r
1430 throw new IndexOutOfBoundsException();
\r
1432 _hiddenColumnsList.setElementAt(vHiddenColumns, index);
\r
1433 } //-- void setHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns)
\r
1436 * Method setHiddenColumns
\r
1440 * @param hiddenColumnsArray
\r
1442 public void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns[] hiddenColumnsArray)
\r
1445 _hiddenColumnsList.removeAllElements();
\r
1446 for (int i = 0; i < hiddenColumnsArray.length; i++) {
\r
1447 _hiddenColumnsList.addElement(hiddenColumnsArray[i]);
\r
1449 } //-- void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns)
\r
1452 * Sets the value of field 'pidSelected'.
\r
1454 * @param pidSelected the value of field 'pidSelected'.
\r
1456 public void setPidSelected(boolean pidSelected)
\r
1458 this._pidSelected = pidSelected;
\r
1459 this._has_pidSelected = true;
\r
1460 } //-- void setPidSelected(boolean)
\r
1463 * Sets the value of field 'pidThreshold'.
\r
1465 * @param pidThreshold the value of field 'pidThreshold'.
\r
1467 public void setPidThreshold(int pidThreshold)
\r
1469 this._pidThreshold = pidThreshold;
\r
1470 this._has_pidThreshold = true;
\r
1471 } //-- void setPidThreshold(int)
\r
1474 * Sets the value of field 'renderGaps'.
\r
1476 * @param renderGaps the value of field 'renderGaps'.
\r
1478 public void setRenderGaps(boolean renderGaps)
\r
1480 this._renderGaps = renderGaps;
\r
1481 this._has_renderGaps = true;
\r
1482 } //-- void setRenderGaps(boolean)
\r
1485 * Sets the value of field 'sequenceSetId'.
\r
1487 * @param sequenceSetId the value of field 'sequenceSetId'.
\r
1489 public void setSequenceSetId(java.lang.String sequenceSetId)
\r
1491 this._sequenceSetId = sequenceSetId;
\r
1492 } //-- void setSequenceSetId(java.lang.String)
\r
1495 * Sets the value of field 'showAnnotation'.
\r
1497 * @param showAnnotation the value of field 'showAnnotation'.
\r
1499 public void setShowAnnotation(boolean showAnnotation)
\r
1501 this._showAnnotation = showAnnotation;
\r
1502 this._has_showAnnotation = true;
\r
1503 } //-- void setShowAnnotation(boolean)
\r
1506 * Sets the value of field 'showBoxes'.
\r
1508 * @param showBoxes the value of field 'showBoxes'.
\r
1510 public void setShowBoxes(boolean showBoxes)
\r
1512 this._showBoxes = showBoxes;
\r
1513 this._has_showBoxes = true;
\r
1514 } //-- void setShowBoxes(boolean)
\r
1517 * Sets the value of field 'showColourText'.
\r
1519 * @param showColourText the value of field 'showColourText'.
\r
1521 public void setShowColourText(boolean showColourText)
\r
1523 this._showColourText = showColourText;
\r
1524 this._has_showColourText = true;
\r
1525 } //-- void setShowColourText(boolean)
\r
1528 * Sets the value of field 'showConservation'.
\r
1530 * @param showConservation the value of field 'showConservation'
\r
1532 public void setShowConservation(boolean showConservation)
\r
1534 this._showConservation = showConservation;
\r
1535 this._has_showConservation = true;
\r
1536 } //-- void setShowConservation(boolean)
\r
1539 * Sets the value of field 'showFullId'.
\r
1541 * @param showFullId the value of field 'showFullId'.
\r
1543 public void setShowFullId(boolean showFullId)
\r
1545 this._showFullId = showFullId;
\r
1546 this._has_showFullId = true;
\r
1547 } //-- void setShowFullId(boolean)
\r
1550 * Sets the value of field 'showIdentity'.
\r
1552 * @param showIdentity the value of field 'showIdentity'.
\r
1554 public void setShowIdentity(boolean showIdentity)
\r
1556 this._showIdentity = showIdentity;
\r
1557 this._has_showIdentity = true;
\r
1558 } //-- void setShowIdentity(boolean)
\r
1561 * Sets the value of field 'showQuality'.
\r
1563 * @param showQuality the value of field 'showQuality'.
\r
1565 public void setShowQuality(boolean showQuality)
\r
1567 this._showQuality = showQuality;
\r
1568 this._has_showQuality = true;
\r
1569 } //-- void setShowQuality(boolean)
\r
1572 * Sets the value of field 'showSequenceFeatures'.
\r
1574 * @param showSequenceFeatures the value of field
\r
1575 * 'showSequenceFeatures'.
\r
1577 public void setShowSequenceFeatures(boolean showSequenceFeatures)
\r
1579 this._showSequenceFeatures = showSequenceFeatures;
\r
1580 this._has_showSequenceFeatures = true;
\r
1581 } //-- void setShowSequenceFeatures(boolean)
\r
1584 * Sets the value of field 'showText'.
\r
1586 * @param showText the value of field 'showText'.
\r
1588 public void setShowText(boolean showText)
\r
1590 this._showText = showText;
\r
1591 this._has_showText = true;
\r
1592 } //-- void setShowText(boolean)
\r
1595 * Sets the value of field 'startRes'.
\r
1597 * @param startRes the value of field 'startRes'.
\r
1599 public void setStartRes(int startRes)
\r
1601 this._startRes = startRes;
\r
1602 this._has_startRes = true;
\r
1603 } //-- void setStartRes(int)
\r
1606 * Sets the value of field 'startSeq'.
\r
1608 * @param startSeq the value of field 'startSeq'.
\r
1610 public void setStartSeq(int startSeq)
\r
1612 this._startSeq = startSeq;
\r
1613 this._has_startSeq = true;
\r
1614 } //-- void setStartSeq(int)
\r
1617 * Sets the value of field 'title'.
\r
1619 * @param title the value of field 'title'.
\r
1621 public void setTitle(java.lang.String title)
\r
1623 this._title = title;
\r
1624 } //-- void setTitle(java.lang.String)
\r
1627 * Sets the value of field 'viewName'.
\r
1629 * @param viewName the value of field 'viewName'.
\r
1631 public void setViewName(java.lang.String viewName)
\r
1633 this._viewName = viewName;
\r
1634 } //-- void setViewName(java.lang.String)
\r
1637 * Sets the value of field 'width'.
\r
1639 * @param width the value of field 'width'.
\r
1641 public void setWidth(int width)
\r
1643 this._width = width;
\r
1644 this._has_width = true;
\r
1645 } //-- void setWidth(int)
\r
1648 * Sets the value of field 'wrapAlignment'.
\r
1650 * @param wrapAlignment the value of field 'wrapAlignment'.
\r
1652 public void setWrapAlignment(boolean wrapAlignment)
\r
1654 this._wrapAlignment = wrapAlignment;
\r
1655 this._has_wrapAlignment = true;
\r
1656 } //-- void setWrapAlignment(boolean)
\r
1659 * Sets the value of field 'xpos'.
\r
1661 * @param xpos the value of field 'xpos'.
\r
1663 public void setXpos(int xpos)
\r
1665 this._xpos = xpos;
\r
1666 this._has_xpos = true;
\r
1667 } //-- void setXpos(int)
\r
1670 * Sets the value of field 'ypos'.
\r
1672 * @param ypos the value of field 'ypos'.
\r
1674 public void setYpos(int ypos)
\r
1676 this._ypos = ypos;
\r
1677 this._has_ypos = true;
\r
1678 } //-- void setYpos(int)
\r
1681 * Method unmarshal
\r
1688 public static java.lang.Object unmarshal(java.io.Reader reader)
\r
1689 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
\r
1691 return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);
\r
1692 } //-- java.lang.Object unmarshal(java.io.Reader)
\r
1698 public void validate()
\r
1699 throws org.exolab.castor.xml.ValidationException
\r
1701 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
\r
1702 validator.validate(this);
\r
1703 } //-- void validate()
\r