2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
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3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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18 package jalview.schemabinding.version2;
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20 //---------------------------------/
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21 //- Imported classes and packages -/
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22 //---------------------------------/
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24 import org.exolab.castor.xml.Marshaller;
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25 import org.exolab.castor.xml.Unmarshaller;
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28 * Class JalviewModelSequence.
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30 * @version $Revision$ $Date$
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32 public class JalviewModelSequence implements java.io.Serializable
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35 // --------------------------/
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36 // - Class/Member Variables -/
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37 // --------------------------/
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42 private java.util.Vector _JSeqList;
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45 * Field _JGroupList.
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47 private java.util.Vector _JGroupList;
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50 * Field _viewportList.
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52 private java.util.Vector _viewportList;
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55 * Field _userColoursList.
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57 private java.util.Vector _userColoursList;
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62 private java.util.Vector _treeList;
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65 * Field _featureSettings.
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67 private jalview.schemabinding.version2.FeatureSettings _featureSettings;
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69 // ----------------/
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70 // - Constructors -/
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71 // ----------------/
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73 public JalviewModelSequence()
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76 this._JSeqList = new java.util.Vector();
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77 this._JGroupList = new java.util.Vector();
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78 this._viewportList = new java.util.Vector();
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79 this._userColoursList = new java.util.Vector();
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80 this._treeList = new java.util.Vector();
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91 * @throws java.lang.IndexOutOfBoundsException
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92 * if the index given is outside the bounds of the collection
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94 public void addJGroup(final jalview.schemabinding.version2.JGroup vJGroup)
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95 throws java.lang.IndexOutOfBoundsException
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97 this._JGroupList.addElement(vJGroup);
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105 * @throws java.lang.IndexOutOfBoundsException
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106 * if the index given is outside the bounds of the collection
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108 public void addJGroup(final int index,
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109 final jalview.schemabinding.version2.JGroup vJGroup)
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110 throws java.lang.IndexOutOfBoundsException
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112 this._JGroupList.add(index, vJGroup);
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119 * @throws java.lang.IndexOutOfBoundsException
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120 * if the index given is outside the bounds of the collection
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122 public void addJSeq(final jalview.schemabinding.version2.JSeq vJSeq)
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123 throws java.lang.IndexOutOfBoundsException
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125 this._JSeqList.addElement(vJSeq);
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133 * @throws java.lang.IndexOutOfBoundsException
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134 * if the index given is outside the bounds of the collection
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136 public void addJSeq(final int index,
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137 final jalview.schemabinding.version2.JSeq vJSeq)
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138 throws java.lang.IndexOutOfBoundsException
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140 this._JSeqList.add(index, vJSeq);
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147 * @throws java.lang.IndexOutOfBoundsException
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148 * if the index given is outside the bounds of the collection
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150 public void addTree(final jalview.schemabinding.version2.Tree vTree)
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151 throws java.lang.IndexOutOfBoundsException
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153 this._treeList.addElement(vTree);
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161 * @throws java.lang.IndexOutOfBoundsException
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162 * if the index given is outside the bounds of the collection
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164 public void addTree(final int index,
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165 final jalview.schemabinding.version2.Tree vTree)
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166 throws java.lang.IndexOutOfBoundsException
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168 this._treeList.add(index, vTree);
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174 * @param vUserColours
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175 * @throws java.lang.IndexOutOfBoundsException
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176 * if the index given is outside the bounds of the collection
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178 public void addUserColours(
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179 final jalview.schemabinding.version2.UserColours vUserColours)
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180 throws java.lang.IndexOutOfBoundsException
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182 this._userColoursList.addElement(vUserColours);
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189 * @param vUserColours
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190 * @throws java.lang.IndexOutOfBoundsException
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191 * if the index given is outside the bounds of the collection
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193 public void addUserColours(final int index,
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194 final jalview.schemabinding.version2.UserColours vUserColours)
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195 throws java.lang.IndexOutOfBoundsException
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197 this._userColoursList.add(index, vUserColours);
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204 * @throws java.lang.IndexOutOfBoundsException
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205 * if the index given is outside the bounds of the collection
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207 public void addViewport(
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208 final jalview.schemabinding.version2.Viewport vViewport)
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209 throws java.lang.IndexOutOfBoundsException
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211 this._viewportList.addElement(vViewport);
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219 * @throws java.lang.IndexOutOfBoundsException
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220 * if the index given is outside the bounds of the collection
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222 public void addViewport(final int index,
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223 final jalview.schemabinding.version2.Viewport vViewport)
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224 throws java.lang.IndexOutOfBoundsException
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226 this._viewportList.add(index, vViewport);
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230 * Method enumerateJGroup.
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232 * @return an Enumeration over all jalview.schemabinding.version2.JGroup
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235 public java.util.Enumeration enumerateJGroup()
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237 return this._JGroupList.elements();
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241 * Method enumerateJSeq.
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243 * @return an Enumeration over all jalview.schemabinding.version2.JSeq
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246 public java.util.Enumeration enumerateJSeq()
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248 return this._JSeqList.elements();
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252 * Method enumerateTree.
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254 * @return an Enumeration over all jalview.schemabinding.version2.Tree
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257 public java.util.Enumeration enumerateTree()
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259 return this._treeList.elements();
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263 * Method enumerateUserColours.
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265 * @return an Enumeration over all jalview.schemabinding.version2.UserColours
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268 public java.util.Enumeration enumerateUserColours()
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270 return this._userColoursList.elements();
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274 * Method enumerateViewport.
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276 * @return an Enumeration over all jalview.schemabinding.version2.Viewport
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279 public java.util.Enumeration enumerateViewport()
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281 return this._viewportList.elements();
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285 * Returns the value of field 'featureSettings'.
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287 * @return the value of field 'FeatureSettings'.
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289 public jalview.schemabinding.version2.FeatureSettings getFeatureSettings()
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291 return this._featureSettings;
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295 * Method getJGroup.
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298 * @throws java.lang.IndexOutOfBoundsException
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299 * if the index given is outside the bounds of the collection
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300 * @return the value of the jalview.schemabinding.version2.JGroup at the given
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303 public jalview.schemabinding.version2.JGroup getJGroup(final int index)
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304 throws java.lang.IndexOutOfBoundsException
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306 // check bounds for index
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307 if (index < 0 || index >= this._JGroupList.size())
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309 throw new IndexOutOfBoundsException("getJGroup: Index value '"
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310 + index + "' not in range [0.."
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311 + (this._JGroupList.size() - 1) + "]");
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314 return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);
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318 * Method getJGroup.Returns the contents of the collection in an Array.
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320 * Note: Just in case the collection contents are changing in another thread,
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321 * we pass a 0-length Array of the correct type into the API call. This way we
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322 * <i>know</i> that the Array returned is of exactly the correct length.
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324 * @return this collection as an Array
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326 public jalview.schemabinding.version2.JGroup[] getJGroup()
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328 jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0];
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329 return (jalview.schemabinding.version2.JGroup[]) this._JGroupList
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334 * Method getJGroupCount.
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336 * @return the size of this collection
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338 public int getJGroupCount()
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340 return this._JGroupList.size();
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347 * @throws java.lang.IndexOutOfBoundsException
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348 * if the index given is outside the bounds of the collection
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349 * @return the value of the jalview.schemabinding.version2.JSeq at the given
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352 public jalview.schemabinding.version2.JSeq getJSeq(final int index)
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353 throws java.lang.IndexOutOfBoundsException
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355 // check bounds for index
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356 if (index < 0 || index >= this._JSeqList.size())
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358 throw new IndexOutOfBoundsException("getJSeq: Index value '" + index
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359 + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
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362 return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index);
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366 * Method getJSeq.Returns the contents of the collection in an Array.
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368 * Note: Just in case the collection contents are changing in another thread,
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369 * we pass a 0-length Array of the correct type into the API call. This way we
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370 * <i>know</i> that the Array returned is of exactly the correct length.
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372 * @return this collection as an Array
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374 public jalview.schemabinding.version2.JSeq[] getJSeq()
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376 jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0];
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377 return (jalview.schemabinding.version2.JSeq[]) this._JSeqList
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382 * Method getJSeqCount.
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384 * @return the size of this collection
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386 public int getJSeqCount()
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388 return this._JSeqList.size();
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395 * @throws java.lang.IndexOutOfBoundsException
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396 * if the index given is outside the bounds of the collection
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397 * @return the value of the jalview.schemabinding.version2.Tree at the given
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400 public jalview.schemabinding.version2.Tree getTree(final int index)
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401 throws java.lang.IndexOutOfBoundsException
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403 // check bounds for index
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404 if (index < 0 || index >= this._treeList.size())
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406 throw new IndexOutOfBoundsException("getTree: Index value '" + index
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407 + "' not in range [0.." + (this._treeList.size() - 1) + "]");
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410 return (jalview.schemabinding.version2.Tree) _treeList.get(index);
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414 * Method getTree.Returns the contents of the collection in an Array.
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416 * Note: Just in case the collection contents are changing in another thread,
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417 * we pass a 0-length Array of the correct type into the API call. This way we
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418 * <i>know</i> that the Array returned is of exactly the correct length.
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420 * @return this collection as an Array
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422 public jalview.schemabinding.version2.Tree[] getTree()
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424 jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0];
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425 return (jalview.schemabinding.version2.Tree[]) this._treeList
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430 * Method getTreeCount.
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432 * @return the size of this collection
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434 public int getTreeCount()
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436 return this._treeList.size();
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440 * Method getUserColours.
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443 * @throws java.lang.IndexOutOfBoundsException
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444 * if the index given is outside the bounds of the collection
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445 * @return the value of the jalview.schemabinding.version2.UserColours at the
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448 public jalview.schemabinding.version2.UserColours getUserColours(
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449 final int index) throws java.lang.IndexOutOfBoundsException
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451 // check bounds for index
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452 if (index < 0 || index >= this._userColoursList.size())
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454 throw new IndexOutOfBoundsException("getUserColours: Index value '"
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455 + index + "' not in range [0.."
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456 + (this._userColoursList.size() - 1) + "]");
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459 return (jalview.schemabinding.version2.UserColours) _userColoursList
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464 * Method getUserColours.Returns the contents of the collection in an Array.
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466 * Note: Just in case the collection contents are changing in another thread,
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467 * we pass a 0-length Array of the correct type into the API call. This way we
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468 * <i>know</i> that the Array returned is of exactly the correct length.
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470 * @return this collection as an Array
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472 public jalview.schemabinding.version2.UserColours[] getUserColours()
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474 jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0];
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475 return (jalview.schemabinding.version2.UserColours[]) this._userColoursList
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480 * Method getUserColoursCount.
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482 * @return the size of this collection
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484 public int getUserColoursCount()
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486 return this._userColoursList.size();
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490 * Method getViewport.
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493 * @throws java.lang.IndexOutOfBoundsException
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494 * if the index given is outside the bounds of the collection
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495 * @return the value of the jalview.schemabinding.version2.Viewport at the
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498 public jalview.schemabinding.version2.Viewport getViewport(final int index)
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499 throws java.lang.IndexOutOfBoundsException
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501 // check bounds for index
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502 if (index < 0 || index >= this._viewportList.size())
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504 throw new IndexOutOfBoundsException("getViewport: Index value '"
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505 + index + "' not in range [0.."
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506 + (this._viewportList.size() - 1) + "]");
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509 return (jalview.schemabinding.version2.Viewport) _viewportList
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514 * Method getViewport.Returns the contents of the collection in an Array.
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516 * Note: Just in case the collection contents are changing in another thread,
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517 * we pass a 0-length Array of the correct type into the API call. This way we
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518 * <i>know</i> that the Array returned is of exactly the correct length.
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520 * @return this collection as an Array
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522 public jalview.schemabinding.version2.Viewport[] getViewport()
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524 jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0];
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525 return (jalview.schemabinding.version2.Viewport[]) this._viewportList
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530 * Method getViewportCount.
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532 * @return the size of this collection
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534 public int getViewportCount()
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536 return this._viewportList.size();
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542 * @return true if this object is valid according to the schema
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544 public boolean isValid()
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549 } catch (org.exolab.castor.xml.ValidationException vex)
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560 * @throws org.exolab.castor.xml.MarshalException
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561 * if object is null or if any SAXException is thrown during
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563 * @throws org.exolab.castor.xml.ValidationException
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564 * if this object is an invalid instance according to the schema
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566 public void marshal(final java.io.Writer out)
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567 throws org.exolab.castor.xml.MarshalException,
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568 org.exolab.castor.xml.ValidationException
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570 Marshaller.marshal(this, out);
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577 * @throws java.io.IOException
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578 * if an IOException occurs during marshaling
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579 * @throws org.exolab.castor.xml.ValidationException
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580 * if this object is an invalid instance according to the schema
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581 * @throws org.exolab.castor.xml.MarshalException
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582 * if object is null or if any SAXException is thrown during
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585 public void marshal(final org.xml.sax.ContentHandler handler)
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586 throws java.io.IOException,
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587 org.exolab.castor.xml.MarshalException,
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588 org.exolab.castor.xml.ValidationException
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590 Marshaller.marshal(this, handler);
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595 public void removeAllJGroup()
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597 this._JGroupList.clear();
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602 public void removeAllJSeq()
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604 this._JSeqList.clear();
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609 public void removeAllTree()
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611 this._treeList.clear();
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616 public void removeAllUserColours()
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618 this._userColoursList.clear();
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623 public void removeAllViewport()
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625 this._viewportList.clear();
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629 * Method removeJGroup.
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632 * @return true if the object was removed from the collection.
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634 public boolean removeJGroup(
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635 final jalview.schemabinding.version2.JGroup vJGroup)
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637 boolean removed = _JGroupList.remove(vJGroup);
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642 * Method removeJGroupAt.
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645 * @return the element removed from the collection
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647 public jalview.schemabinding.version2.JGroup removeJGroupAt(
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650 java.lang.Object obj = this._JGroupList.remove(index);
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651 return (jalview.schemabinding.version2.JGroup) obj;
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655 * Method removeJSeq.
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658 * @return true if the object was removed from the collection.
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660 public boolean removeJSeq(final jalview.schemabinding.version2.JSeq vJSeq)
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662 boolean removed = _JSeqList.remove(vJSeq);
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667 * Method removeJSeqAt.
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670 * @return the element removed from the collection
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672 public jalview.schemabinding.version2.JSeq removeJSeqAt(final int index)
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674 java.lang.Object obj = this._JSeqList.remove(index);
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675 return (jalview.schemabinding.version2.JSeq) obj;
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679 * Method removeTree.
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682 * @return true if the object was removed from the collection.
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684 public boolean removeTree(final jalview.schemabinding.version2.Tree vTree)
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686 boolean removed = _treeList.remove(vTree);
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691 * Method removeTreeAt.
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694 * @return the element removed from the collection
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696 public jalview.schemabinding.version2.Tree removeTreeAt(final int index)
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698 java.lang.Object obj = this._treeList.remove(index);
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699 return (jalview.schemabinding.version2.Tree) obj;
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703 * Method removeUserColours.
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705 * @param vUserColours
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706 * @return true if the object was removed from the collection.
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708 public boolean removeUserColours(
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709 final jalview.schemabinding.version2.UserColours vUserColours)
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711 boolean removed = _userColoursList.remove(vUserColours);
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716 * Method removeUserColoursAt.
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719 * @return the element removed from the collection
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721 public jalview.schemabinding.version2.UserColours removeUserColoursAt(
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724 java.lang.Object obj = this._userColoursList.remove(index);
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725 return (jalview.schemabinding.version2.UserColours) obj;
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729 * Method removeViewport.
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732 * @return true if the object was removed from the collection.
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734 public boolean removeViewport(
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735 final jalview.schemabinding.version2.Viewport vViewport)
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737 boolean removed = _viewportList.remove(vViewport);
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742 * Method removeViewportAt.
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745 * @return the element removed from the collection
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747 public jalview.schemabinding.version2.Viewport removeViewportAt(
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750 java.lang.Object obj = this._viewportList.remove(index);
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751 return (jalview.schemabinding.version2.Viewport) obj;
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755 * Sets the value of field 'featureSettings'.
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757 * @param featureSettings
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758 * the value of field 'featureSettings'.
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760 public void setFeatureSettings(
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761 final jalview.schemabinding.version2.FeatureSettings featureSettings)
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763 this._featureSettings = featureSettings;
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771 * @throws java.lang.IndexOutOfBoundsException
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772 * if the index given is outside the bounds of the collection
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774 public void setJGroup(final int index,
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775 final jalview.schemabinding.version2.JGroup vJGroup)
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776 throws java.lang.IndexOutOfBoundsException
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778 // check bounds for index
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779 if (index < 0 || index >= this._JGroupList.size())
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781 throw new IndexOutOfBoundsException("setJGroup: Index value '"
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782 + index + "' not in range [0.."
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783 + (this._JGroupList.size() - 1) + "]");
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786 this._JGroupList.set(index, vJGroup);
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792 * @param vJGroupArray
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794 public void setJGroup(
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795 final jalview.schemabinding.version2.JGroup[] vJGroupArray)
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798 _JGroupList.clear();
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800 for (int i = 0; i < vJGroupArray.length; i++)
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802 this._JGroupList.add(vJGroupArray[i]);
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811 * @throws java.lang.IndexOutOfBoundsException
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812 * if the index given is outside the bounds of the collection
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814 public void setJSeq(final int index,
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815 final jalview.schemabinding.version2.JSeq vJSeq)
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816 throws java.lang.IndexOutOfBoundsException
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818 // check bounds for index
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819 if (index < 0 || index >= this._JSeqList.size())
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821 throw new IndexOutOfBoundsException("setJSeq: Index value '" + index
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822 + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
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825 this._JSeqList.set(index, vJSeq);
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831 * @param vJSeqArray
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833 public void setJSeq(final jalview.schemabinding.version2.JSeq[] vJSeqArray)
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838 for (int i = 0; i < vJSeqArray.length; i++)
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840 this._JSeqList.add(vJSeqArray[i]);
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849 * @throws java.lang.IndexOutOfBoundsException
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850 * if the index given is outside the bounds of the collection
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852 public void setTree(final int index,
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853 final jalview.schemabinding.version2.Tree vTree)
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854 throws java.lang.IndexOutOfBoundsException
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856 // check bounds for index
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857 if (index < 0 || index >= this._treeList.size())
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859 throw new IndexOutOfBoundsException("setTree: Index value '" + index
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860 + "' not in range [0.." + (this._treeList.size() - 1) + "]");
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863 this._treeList.set(index, vTree);
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869 * @param vTreeArray
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871 public void setTree(final jalview.schemabinding.version2.Tree[] vTreeArray)
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876 for (int i = 0; i < vTreeArray.length; i++)
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878 this._treeList.add(vTreeArray[i]);
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886 * @param vUserColours
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887 * @throws java.lang.IndexOutOfBoundsException
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888 * if the index given is outside the bounds of the collection
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890 public void setUserColours(final int index,
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891 final jalview.schemabinding.version2.UserColours vUserColours)
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892 throws java.lang.IndexOutOfBoundsException
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894 // check bounds for index
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895 if (index < 0 || index >= this._userColoursList.size())
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897 throw new IndexOutOfBoundsException("setUserColours: Index value '"
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898 + index + "' not in range [0.."
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899 + (this._userColoursList.size() - 1) + "]");
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902 this._userColoursList.set(index, vUserColours);
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908 * @param vUserColoursArray
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910 public void setUserColours(
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911 final jalview.schemabinding.version2.UserColours[] vUserColoursArray)
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914 _userColoursList.clear();
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916 for (int i = 0; i < vUserColoursArray.length; i++)
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918 this._userColoursList.add(vUserColoursArray[i]);
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927 * @throws java.lang.IndexOutOfBoundsException
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928 * if the index given is outside the bounds of the collection
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930 public void setViewport(final int index,
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931 final jalview.schemabinding.version2.Viewport vViewport)
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932 throws java.lang.IndexOutOfBoundsException
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934 // check bounds for index
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935 if (index < 0 || index >= this._viewportList.size())
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937 throw new IndexOutOfBoundsException("setViewport: Index value '"
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938 + index + "' not in range [0.."
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939 + (this._viewportList.size() - 1) + "]");
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942 this._viewportList.set(index, vViewport);
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948 * @param vViewportArray
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950 public void setViewport(
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951 final jalview.schemabinding.version2.Viewport[] vViewportArray)
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954 _viewportList.clear();
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956 for (int i = 0; i < vViewportArray.length; i++)
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958 this._viewportList.add(vViewportArray[i]);
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963 * Method unmarshal.
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966 * @throws org.exolab.castor.xml.MarshalException
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967 * if object is null or if any SAXException is thrown during
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969 * @throws org.exolab.castor.xml.ValidationException
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970 * if this object is an invalid instance according to the schema
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971 * @return the unmarshaled jalview.schemabinding.version2.JalviewModelSequence
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973 public static jalview.schemabinding.version2.JalviewModelSequence unmarshal(
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974 final java.io.Reader reader)
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975 throws org.exolab.castor.xml.MarshalException,
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976 org.exolab.castor.xml.ValidationException
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978 return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller
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980 jalview.schemabinding.version2.JalviewModelSequence.class,
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987 * @throws org.exolab.castor.xml.ValidationException
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988 * if this object is an invalid instance according to the schema
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990 public void validate() throws org.exolab.castor.xml.ValidationException
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992 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
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993 validator.validate(this);
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