2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
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3 * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.schemabinding.version2;
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21 // ---------------------------------/
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22 // - Imported classes and packages -/
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23 // ---------------------------------/
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25 import org.exolab.castor.xml.Marshaller;
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26 import org.exolab.castor.xml.Unmarshaller;
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29 * Class JalviewModelSequence.
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31 * @version $Revision$ $Date$
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33 public class JalviewModelSequence 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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43 private java.util.Vector _JSeqList;
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46 * Field _JGroupList.
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48 private java.util.Vector _JGroupList;
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51 * Field _viewportList.
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53 private java.util.Vector _viewportList;
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56 * Field _userColoursList.
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58 private java.util.Vector _userColoursList;
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63 private java.util.Vector _treeList;
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66 * Field _featureSettings.
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68 private jalview.schemabinding.version2.FeatureSettings _featureSettings;
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70 // ----------------/
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71 // - Constructors -/
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72 // ----------------/
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74 public JalviewModelSequence()
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77 this._JSeqList = new java.util.Vector();
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78 this._JGroupList = new java.util.Vector();
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79 this._viewportList = new java.util.Vector();
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80 this._userColoursList = new java.util.Vector();
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81 this._treeList = new java.util.Vector();
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92 * @throws java.lang.IndexOutOfBoundsException
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93 * if the index given is outside the bounds of the collection
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95 public void addJGroup(final jalview.schemabinding.version2.JGroup vJGroup)
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96 throws java.lang.IndexOutOfBoundsException
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98 this._JGroupList.addElement(vJGroup);
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106 * @throws java.lang.IndexOutOfBoundsException
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107 * if the index given is outside the bounds of the collection
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109 public void addJGroup(final int index,
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110 final jalview.schemabinding.version2.JGroup vJGroup)
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111 throws java.lang.IndexOutOfBoundsException
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113 this._JGroupList.add(index, vJGroup);
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120 * @throws java.lang.IndexOutOfBoundsException
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121 * if the index given is outside the bounds of the collection
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123 public void addJSeq(final jalview.schemabinding.version2.JSeq vJSeq)
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124 throws java.lang.IndexOutOfBoundsException
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126 this._JSeqList.addElement(vJSeq);
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134 * @throws java.lang.IndexOutOfBoundsException
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135 * if the index given is outside the bounds of the collection
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137 public void addJSeq(final int index,
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138 final jalview.schemabinding.version2.JSeq vJSeq)
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139 throws java.lang.IndexOutOfBoundsException
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141 this._JSeqList.add(index, vJSeq);
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148 * @throws java.lang.IndexOutOfBoundsException
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149 * if the index given is outside the bounds of the collection
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151 public void addTree(final jalview.schemabinding.version2.Tree vTree)
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152 throws java.lang.IndexOutOfBoundsException
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154 this._treeList.addElement(vTree);
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162 * @throws java.lang.IndexOutOfBoundsException
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163 * if the index given is outside the bounds of the collection
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165 public void addTree(final int index,
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166 final jalview.schemabinding.version2.Tree vTree)
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167 throws java.lang.IndexOutOfBoundsException
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169 this._treeList.add(index, vTree);
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175 * @param vUserColours
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176 * @throws java.lang.IndexOutOfBoundsException
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177 * if the index given is outside the bounds of the collection
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179 public void addUserColours(
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180 final jalview.schemabinding.version2.UserColours vUserColours)
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181 throws java.lang.IndexOutOfBoundsException
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183 this._userColoursList.addElement(vUserColours);
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190 * @param vUserColours
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191 * @throws java.lang.IndexOutOfBoundsException
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192 * if the index given is outside the bounds of the collection
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194 public void addUserColours(final int index,
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195 final jalview.schemabinding.version2.UserColours vUserColours)
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196 throws java.lang.IndexOutOfBoundsException
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198 this._userColoursList.add(index, vUserColours);
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205 * @throws java.lang.IndexOutOfBoundsException
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206 * if the index given is outside the bounds of the collection
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208 public void addViewport(
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209 final jalview.schemabinding.version2.Viewport vViewport)
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210 throws java.lang.IndexOutOfBoundsException
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212 this._viewportList.addElement(vViewport);
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220 * @throws java.lang.IndexOutOfBoundsException
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221 * if the index given is outside the bounds of the collection
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223 public void addViewport(final int index,
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224 final jalview.schemabinding.version2.Viewport vViewport)
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225 throws java.lang.IndexOutOfBoundsException
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227 this._viewportList.add(index, vViewport);
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231 * Method enumerateJGroup.
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233 * @return an Enumeration over all jalview.schemabinding.version2.JGroup
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236 public java.util.Enumeration enumerateJGroup()
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238 return this._JGroupList.elements();
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242 * Method enumerateJSeq.
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244 * @return an Enumeration over all jalview.schemabinding.version2.JSeq
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247 public java.util.Enumeration enumerateJSeq()
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249 return this._JSeqList.elements();
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253 * Method enumerateTree.
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255 * @return an Enumeration over all jalview.schemabinding.version2.Tree
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258 public java.util.Enumeration enumerateTree()
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260 return this._treeList.elements();
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264 * Method enumerateUserColours.
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266 * @return an Enumeration over all jalview.schemabinding.version2.UserColours
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269 public java.util.Enumeration enumerateUserColours()
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271 return this._userColoursList.elements();
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275 * Method enumerateViewport.
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277 * @return an Enumeration over all jalview.schemabinding.version2.Viewport
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280 public java.util.Enumeration enumerateViewport()
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282 return this._viewportList.elements();
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286 * Returns the value of field 'featureSettings'.
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288 * @return the value of field 'FeatureSettings'.
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290 public jalview.schemabinding.version2.FeatureSettings getFeatureSettings()
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292 return this._featureSettings;
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296 * Method getJGroup.
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299 * @throws java.lang.IndexOutOfBoundsException
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300 * if the index given is outside the bounds of the collection
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301 * @return the value of the jalview.schemabinding.version2.JGroup at the given
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304 public jalview.schemabinding.version2.JGroup getJGroup(final int index)
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305 throws java.lang.IndexOutOfBoundsException
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307 // check bounds for index
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308 if (index < 0 || index >= this._JGroupList.size())
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310 throw new IndexOutOfBoundsException("getJGroup: Index value '"
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311 + index + "' not in range [0.."
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312 + (this._JGroupList.size() - 1) + "]");
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315 return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);
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319 * Method getJGroup.Returns the contents of the collection in an Array.
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321 * Note: Just in case the collection contents are changing in another thread,
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322 * we pass a 0-length Array of the correct type into the API call. This way we
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323 * <i>know</i> that the Array returned is of exactly the correct length.
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325 * @return this collection as an Array
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327 public jalview.schemabinding.version2.JGroup[] getJGroup()
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329 jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0];
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330 return (jalview.schemabinding.version2.JGroup[]) this._JGroupList
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335 * Method getJGroupCount.
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337 * @return the size of this collection
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339 public int getJGroupCount()
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341 return this._JGroupList.size();
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348 * @throws java.lang.IndexOutOfBoundsException
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349 * if the index given is outside the bounds of the collection
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350 * @return the value of the jalview.schemabinding.version2.JSeq at the given
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353 public jalview.schemabinding.version2.JSeq getJSeq(final int index)
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354 throws java.lang.IndexOutOfBoundsException
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356 // check bounds for index
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357 if (index < 0 || index >= this._JSeqList.size())
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359 throw new IndexOutOfBoundsException("getJSeq: Index value '" + index
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360 + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
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363 return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index);
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367 * Method getJSeq.Returns the contents of the collection in an Array.
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369 * Note: Just in case the collection contents are changing in another thread,
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370 * we pass a 0-length Array of the correct type into the API call. This way we
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371 * <i>know</i> that the Array returned is of exactly the correct length.
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373 * @return this collection as an Array
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375 public jalview.schemabinding.version2.JSeq[] getJSeq()
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377 jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0];
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378 return (jalview.schemabinding.version2.JSeq[]) this._JSeqList
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383 * Method getJSeqCount.
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385 * @return the size of this collection
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387 public int getJSeqCount()
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389 return this._JSeqList.size();
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396 * @throws java.lang.IndexOutOfBoundsException
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397 * if the index given is outside the bounds of the collection
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398 * @return the value of the jalview.schemabinding.version2.Tree at the given
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401 public jalview.schemabinding.version2.Tree getTree(final int index)
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402 throws java.lang.IndexOutOfBoundsException
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404 // check bounds for index
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405 if (index < 0 || index >= this._treeList.size())
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407 throw new IndexOutOfBoundsException("getTree: Index value '" + index
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408 + "' not in range [0.." + (this._treeList.size() - 1) + "]");
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411 return (jalview.schemabinding.version2.Tree) _treeList.get(index);
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415 * Method getTree.Returns the contents of the collection in an Array.
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417 * Note: Just in case the collection contents are changing in another thread,
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418 * we pass a 0-length Array of the correct type into the API call. This way we
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419 * <i>know</i> that the Array returned is of exactly the correct length.
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421 * @return this collection as an Array
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423 public jalview.schemabinding.version2.Tree[] getTree()
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425 jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0];
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426 return (jalview.schemabinding.version2.Tree[]) this._treeList
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431 * Method getTreeCount.
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433 * @return the size of this collection
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435 public int getTreeCount()
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437 return this._treeList.size();
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441 * Method getUserColours.
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444 * @throws java.lang.IndexOutOfBoundsException
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445 * if the index given is outside the bounds of the collection
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446 * @return the value of the jalview.schemabinding.version2.UserColours at the
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449 public jalview.schemabinding.version2.UserColours getUserColours(
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450 final int index) throws java.lang.IndexOutOfBoundsException
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452 // check bounds for index
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453 if (index < 0 || index >= this._userColoursList.size())
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455 throw new IndexOutOfBoundsException("getUserColours: Index value '"
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456 + index + "' not in range [0.."
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457 + (this._userColoursList.size() - 1) + "]");
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460 return (jalview.schemabinding.version2.UserColours) _userColoursList
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465 * Method getUserColours.Returns the contents of the collection in an Array.
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467 * Note: Just in case the collection contents are changing in another thread,
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468 * we pass a 0-length Array of the correct type into the API call. This way we
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469 * <i>know</i> that the Array returned is of exactly the correct length.
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471 * @return this collection as an Array
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473 public jalview.schemabinding.version2.UserColours[] getUserColours()
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475 jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0];
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476 return (jalview.schemabinding.version2.UserColours[]) this._userColoursList
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481 * Method getUserColoursCount.
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483 * @return the size of this collection
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485 public int getUserColoursCount()
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487 return this._userColoursList.size();
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491 * Method getViewport.
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494 * @throws java.lang.IndexOutOfBoundsException
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495 * if the index given is outside the bounds of the collection
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496 * @return the value of the jalview.schemabinding.version2.Viewport at the
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499 public jalview.schemabinding.version2.Viewport getViewport(final int index)
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500 throws java.lang.IndexOutOfBoundsException
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502 // check bounds for index
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503 if (index < 0 || index >= this._viewportList.size())
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505 throw new IndexOutOfBoundsException("getViewport: Index value '"
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506 + index + "' not in range [0.."
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507 + (this._viewportList.size() - 1) + "]");
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510 return (jalview.schemabinding.version2.Viewport) _viewportList
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515 * Method getViewport.Returns the contents of the collection in an Array.
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517 * Note: Just in case the collection contents are changing in another thread,
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518 * we pass a 0-length Array of the correct type into the API call. This way we
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519 * <i>know</i> that the Array returned is of exactly the correct length.
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521 * @return this collection as an Array
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523 public jalview.schemabinding.version2.Viewport[] getViewport()
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525 jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0];
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526 return (jalview.schemabinding.version2.Viewport[]) this._viewportList
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531 * Method getViewportCount.
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533 * @return the size of this collection
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535 public int getViewportCount()
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537 return this._viewportList.size();
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543 * @return true if this object is valid according to the schema
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545 public boolean isValid()
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550 } catch (org.exolab.castor.xml.ValidationException vex)
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561 * @throws org.exolab.castor.xml.MarshalException
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562 * if object is null or if any SAXException is thrown during
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564 * @throws org.exolab.castor.xml.ValidationException
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565 * if this object is an invalid instance according to the
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568 public void marshal(final java.io.Writer out)
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569 throws org.exolab.castor.xml.MarshalException,
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570 org.exolab.castor.xml.ValidationException
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572 Marshaller.marshal(this, out);
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579 * @throws java.io.IOException
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580 * if an IOException occurs during marshaling
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581 * @throws org.exolab.castor.xml.ValidationException
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582 * if this object is an invalid instance according to the
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584 * @throws org.exolab.castor.xml.MarshalException
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585 * if object is null or if any SAXException is thrown during
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588 public void marshal(final org.xml.sax.ContentHandler handler)
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589 throws java.io.IOException,
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590 org.exolab.castor.xml.MarshalException,
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591 org.exolab.castor.xml.ValidationException
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593 Marshaller.marshal(this, handler);
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598 public void removeAllJGroup()
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600 this._JGroupList.clear();
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605 public void removeAllJSeq()
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607 this._JSeqList.clear();
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612 public void removeAllTree()
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614 this._treeList.clear();
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619 public void removeAllUserColours()
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621 this._userColoursList.clear();
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626 public void removeAllViewport()
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628 this._viewportList.clear();
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632 * Method removeJGroup.
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635 * @return true if the object was removed from the collection.
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637 public boolean removeJGroup(
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638 final jalview.schemabinding.version2.JGroup vJGroup)
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640 boolean removed = _JGroupList.remove(vJGroup);
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645 * Method removeJGroupAt.
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648 * @return the element removed from the collection
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650 public jalview.schemabinding.version2.JGroup removeJGroupAt(
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653 java.lang.Object obj = this._JGroupList.remove(index);
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654 return (jalview.schemabinding.version2.JGroup) obj;
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658 * Method removeJSeq.
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661 * @return true if the object was removed from the collection.
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663 public boolean removeJSeq(final jalview.schemabinding.version2.JSeq vJSeq)
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665 boolean removed = _JSeqList.remove(vJSeq);
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670 * Method removeJSeqAt.
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673 * @return the element removed from the collection
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675 public jalview.schemabinding.version2.JSeq removeJSeqAt(final int index)
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677 java.lang.Object obj = this._JSeqList.remove(index);
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678 return (jalview.schemabinding.version2.JSeq) obj;
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682 * Method removeTree.
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685 * @return true if the object was removed from the collection.
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687 public boolean removeTree(final jalview.schemabinding.version2.Tree vTree)
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689 boolean removed = _treeList.remove(vTree);
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694 * Method removeTreeAt.
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697 * @return the element removed from the collection
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699 public jalview.schemabinding.version2.Tree removeTreeAt(final int index)
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701 java.lang.Object obj = this._treeList.remove(index);
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702 return (jalview.schemabinding.version2.Tree) obj;
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706 * Method removeUserColours.
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708 * @param vUserColours
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709 * @return true if the object was removed from the collection.
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711 public boolean removeUserColours(
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712 final jalview.schemabinding.version2.UserColours vUserColours)
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714 boolean removed = _userColoursList.remove(vUserColours);
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719 * Method removeUserColoursAt.
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722 * @return the element removed from the collection
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724 public jalview.schemabinding.version2.UserColours removeUserColoursAt(
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727 java.lang.Object obj = this._userColoursList.remove(index);
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728 return (jalview.schemabinding.version2.UserColours) obj;
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732 * Method removeViewport.
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735 * @return true if the object was removed from the collection.
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737 public boolean removeViewport(
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738 final jalview.schemabinding.version2.Viewport vViewport)
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740 boolean removed = _viewportList.remove(vViewport);
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745 * Method removeViewportAt.
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748 * @return the element removed from the collection
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750 public jalview.schemabinding.version2.Viewport removeViewportAt(
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753 java.lang.Object obj = this._viewportList.remove(index);
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754 return (jalview.schemabinding.version2.Viewport) obj;
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758 * Sets the value of field 'featureSettings'.
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760 * @param featureSettings
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761 * the value of field 'featureSettings'.
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763 public void setFeatureSettings(
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764 final jalview.schemabinding.version2.FeatureSettings featureSettings)
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766 this._featureSettings = featureSettings;
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774 * @throws java.lang.IndexOutOfBoundsException
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775 * if the index given is outside the bounds of the collection
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777 public void setJGroup(final int index,
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778 final jalview.schemabinding.version2.JGroup vJGroup)
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779 throws java.lang.IndexOutOfBoundsException
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781 // check bounds for index
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782 if (index < 0 || index >= this._JGroupList.size())
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784 throw new IndexOutOfBoundsException("setJGroup: Index value '"
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785 + index + "' not in range [0.."
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786 + (this._JGroupList.size() - 1) + "]");
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789 this._JGroupList.set(index, vJGroup);
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795 * @param vJGroupArray
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797 public void setJGroup(
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798 final jalview.schemabinding.version2.JGroup[] vJGroupArray)
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801 _JGroupList.clear();
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803 for (int i = 0; i < vJGroupArray.length; i++)
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805 this._JGroupList.add(vJGroupArray[i]);
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814 * @throws java.lang.IndexOutOfBoundsException
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815 * if the index given is outside the bounds of the collection
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817 public void setJSeq(final int index,
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818 final jalview.schemabinding.version2.JSeq vJSeq)
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819 throws java.lang.IndexOutOfBoundsException
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821 // check bounds for index
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822 if (index < 0 || index >= this._JSeqList.size())
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824 throw new IndexOutOfBoundsException("setJSeq: Index value '" + index
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825 + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
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828 this._JSeqList.set(index, vJSeq);
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834 * @param vJSeqArray
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836 public void setJSeq(final jalview.schemabinding.version2.JSeq[] vJSeqArray)
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841 for (int i = 0; i < vJSeqArray.length; i++)
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843 this._JSeqList.add(vJSeqArray[i]);
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852 * @throws java.lang.IndexOutOfBoundsException
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853 * if the index given is outside the bounds of the collection
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855 public void setTree(final int index,
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856 final jalview.schemabinding.version2.Tree vTree)
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857 throws java.lang.IndexOutOfBoundsException
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859 // check bounds for index
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860 if (index < 0 || index >= this._treeList.size())
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862 throw new IndexOutOfBoundsException("setTree: Index value '" + index
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863 + "' not in range [0.." + (this._treeList.size() - 1) + "]");
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866 this._treeList.set(index, vTree);
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872 * @param vTreeArray
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874 public void setTree(final jalview.schemabinding.version2.Tree[] vTreeArray)
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879 for (int i = 0; i < vTreeArray.length; i++)
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881 this._treeList.add(vTreeArray[i]);
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889 * @param vUserColours
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890 * @throws java.lang.IndexOutOfBoundsException
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891 * if the index given is outside the bounds of the collection
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893 public void setUserColours(final int index,
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894 final jalview.schemabinding.version2.UserColours vUserColours)
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895 throws java.lang.IndexOutOfBoundsException
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897 // check bounds for index
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898 if (index < 0 || index >= this._userColoursList.size())
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900 throw new IndexOutOfBoundsException("setUserColours: Index value '"
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901 + index + "' not in range [0.."
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902 + (this._userColoursList.size() - 1) + "]");
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905 this._userColoursList.set(index, vUserColours);
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911 * @param vUserColoursArray
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913 public void setUserColours(
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914 final jalview.schemabinding.version2.UserColours[] vUserColoursArray)
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917 _userColoursList.clear();
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919 for (int i = 0; i < vUserColoursArray.length; i++)
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921 this._userColoursList.add(vUserColoursArray[i]);
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930 * @throws java.lang.IndexOutOfBoundsException
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931 * if the index given is outside the bounds of the collection
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933 public void setViewport(final int index,
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934 final jalview.schemabinding.version2.Viewport vViewport)
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935 throws java.lang.IndexOutOfBoundsException
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937 // check bounds for index
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938 if (index < 0 || index >= this._viewportList.size())
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940 throw new IndexOutOfBoundsException("setViewport: Index value '"
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941 + index + "' not in range [0.."
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942 + (this._viewportList.size() - 1) + "]");
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945 this._viewportList.set(index, vViewport);
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951 * @param vViewportArray
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953 public void setViewport(
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954 final jalview.schemabinding.version2.Viewport[] vViewportArray)
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957 _viewportList.clear();
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959 for (int i = 0; i < vViewportArray.length; i++)
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961 this._viewportList.add(vViewportArray[i]);
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966 * Method unmarshal.
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969 * @throws org.exolab.castor.xml.MarshalException
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970 * if object is null or if any SAXException is thrown during
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972 * @throws org.exolab.castor.xml.ValidationException
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973 * if this object is an invalid instance according to the
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975 * @return the unmarshaled jalview.schemabinding.version2.JalviewModelSequence
\r
977 public static jalview.schemabinding.version2.JalviewModelSequence unmarshal(
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978 final java.io.Reader reader)
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979 throws org.exolab.castor.xml.MarshalException,
\r
980 org.exolab.castor.xml.ValidationException
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982 return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller
\r
984 jalview.schemabinding.version2.JalviewModelSequence.class,
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991 * @throws org.exolab.castor.xml.ValidationException
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992 * if this object is an invalid instance according to the
\r
995 public void validate() throws org.exolab.castor.xml.ValidationException
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997 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
\r
998 validator.validate(this);
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