2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
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3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.schemabinding.version2;
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21 //---------------------------------/
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22 //- Imported classes and packages -/
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23 //---------------------------------/
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25 import org.exolab.castor.xml.Marshaller;
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26 import org.exolab.castor.xml.Unmarshaller;
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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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75 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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93 * @throws java.lang.IndexOutOfBoundsException if the index
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94 * given is outside the bounds of the collection
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96 public void addJGroup(
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97 final jalview.schemabinding.version2.JGroup vJGroup)
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98 throws java.lang.IndexOutOfBoundsException {
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99 this._JGroupList.addElement(vJGroup);
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107 * @throws java.lang.IndexOutOfBoundsException if the index
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108 * given is outside the bounds of the collection
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110 public void addJGroup(
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112 final jalview.schemabinding.version2.JGroup vJGroup)
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113 throws java.lang.IndexOutOfBoundsException {
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114 this._JGroupList.add(index, vJGroup);
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121 * @throws java.lang.IndexOutOfBoundsException if the index
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122 * given is outside the bounds of the collection
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124 public void addJSeq(
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125 final jalview.schemabinding.version2.JSeq vJSeq)
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126 throws java.lang.IndexOutOfBoundsException {
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127 this._JSeqList.addElement(vJSeq);
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135 * @throws java.lang.IndexOutOfBoundsException if the index
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136 * given is outside the bounds of the collection
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138 public void addJSeq(
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140 final jalview.schemabinding.version2.JSeq vJSeq)
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141 throws java.lang.IndexOutOfBoundsException {
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142 this._JSeqList.add(index, vJSeq);
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149 * @throws java.lang.IndexOutOfBoundsException if the index
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150 * given is outside the bounds of the collection
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152 public void addTree(
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153 final jalview.schemabinding.version2.Tree vTree)
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154 throws java.lang.IndexOutOfBoundsException {
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155 this._treeList.addElement(vTree);
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163 * @throws java.lang.IndexOutOfBoundsException if the index
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164 * given is outside the bounds of the collection
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166 public void addTree(
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168 final jalview.schemabinding.version2.Tree vTree)
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169 throws java.lang.IndexOutOfBoundsException {
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170 this._treeList.add(index, vTree);
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176 * @param vUserColours
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177 * @throws java.lang.IndexOutOfBoundsException if the index
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178 * given is outside the bounds of the collection
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180 public void addUserColours(
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181 final jalview.schemabinding.version2.UserColours vUserColours)
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182 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 if the index
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192 * given is outside the bounds of the collection
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194 public void addUserColours(
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196 final jalview.schemabinding.version2.UserColours vUserColours)
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197 throws java.lang.IndexOutOfBoundsException {
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198 this._userColoursList.add(index, vUserColours);
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205 * @throws java.lang.IndexOutOfBoundsException if the index
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206 * 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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211 this._viewportList.addElement(vViewport);
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219 * @throws java.lang.IndexOutOfBoundsException if the index
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220 * given is outside the bounds of the collection
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222 public void addViewport(
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224 final jalview.schemabinding.version2.Viewport vViewport)
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225 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
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233 * jalview.schemabinding.version2.JGroup elements
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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
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244 * jalview.schemabinding.version2.JSeq elements
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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
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255 * jalview.schemabinding.version2.Tree elements
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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
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266 * jalview.schemabinding.version2.UserColours elements
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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
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277 * jalview.schemabinding.version2.Viewport elements
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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 if the index
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299 * given is outside the bounds of the collection
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300 * @return the value of the
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301 * jalview.schemabinding.version2.JGroup at the given index
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303 public jalview.schemabinding.version2.JGroup getJGroup(
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305 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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308 throw new IndexOutOfBoundsException("getJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
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311 return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);
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315 * Method getJGroup.Returns the contents of the collection in
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316 * an Array. <p>Note: Just in case the collection contents
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317 * are changing in another thread, we pass a 0-length Array of
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318 * the correct type into the API call. This way we <i>know</i>
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319 * that the Array returned is of exactly the correct length.
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321 * @return this collection as an Array
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323 public jalview.schemabinding.version2.JGroup[] getJGroup(
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325 jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0];
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326 return (jalview.schemabinding.version2.JGroup[]) this._JGroupList.toArray(array);
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330 * Method getJGroupCount.
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332 * @return the size of this collection
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334 public int getJGroupCount(
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336 return this._JGroupList.size();
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343 * @throws java.lang.IndexOutOfBoundsException if the index
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344 * given is outside the bounds of the collection
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345 * @return the value of the jalview.schemabinding.version2.JSeq
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346 * at the given index
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348 public jalview.schemabinding.version2.JSeq getJSeq(
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350 throws java.lang.IndexOutOfBoundsException {
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351 // check bounds for index
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352 if (index < 0 || index >= this._JSeqList.size()) {
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353 throw new IndexOutOfBoundsException("getJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
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356 return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index);
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360 * Method getJSeq.Returns the contents of the collection in an
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361 * Array. <p>Note: Just in case the collection contents are
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362 * changing in another thread, we pass a 0-length Array of the
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363 * correct type into the API call. This way we <i>know</i>
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364 * that the Array returned is of exactly the correct length.
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366 * @return this collection as an Array
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368 public jalview.schemabinding.version2.JSeq[] getJSeq(
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370 jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0];
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371 return (jalview.schemabinding.version2.JSeq[]) this._JSeqList.toArray(array);
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375 * Method getJSeqCount.
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377 * @return the size of this collection
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379 public int getJSeqCount(
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381 return this._JSeqList.size();
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388 * @throws java.lang.IndexOutOfBoundsException if the index
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389 * given is outside the bounds of the collection
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390 * @return the value of the jalview.schemabinding.version2.Tree
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391 * at the given index
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393 public jalview.schemabinding.version2.Tree getTree(
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395 throws java.lang.IndexOutOfBoundsException {
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396 // check bounds for index
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397 if (index < 0 || index >= this._treeList.size()) {
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398 throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
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401 return (jalview.schemabinding.version2.Tree) _treeList.get(index);
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405 * Method getTree.Returns the contents of the collection in an
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406 * Array. <p>Note: Just in case the collection contents are
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407 * changing in another thread, we pass a 0-length Array of the
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408 * correct type into the API call. This way we <i>know</i>
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409 * that the Array returned is of exactly the correct length.
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411 * @return this collection as an Array
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413 public jalview.schemabinding.version2.Tree[] getTree(
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415 jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0];
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416 return (jalview.schemabinding.version2.Tree[]) this._treeList.toArray(array);
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420 * Method getTreeCount.
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422 * @return the size of this collection
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424 public int getTreeCount(
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426 return this._treeList.size();
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430 * Method getUserColours.
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433 * @throws java.lang.IndexOutOfBoundsException if the index
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434 * given is outside the bounds of the collection
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435 * @return the value of the
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436 * jalview.schemabinding.version2.UserColours at the given index
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438 public jalview.schemabinding.version2.UserColours getUserColours(
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440 throws java.lang.IndexOutOfBoundsException {
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441 // check bounds for index
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442 if (index < 0 || index >= this._userColoursList.size()) {
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443 throw new IndexOutOfBoundsException("getUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
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446 return (jalview.schemabinding.version2.UserColours) _userColoursList.get(index);
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450 * Method getUserColours.Returns the contents of the collection
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451 * in an Array. <p>Note: Just in case the collection contents
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452 * are changing in another thread, we pass a 0-length Array of
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453 * the correct type into the API call. This way we <i>know</i>
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454 * that the Array returned is of exactly the correct length.
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456 * @return this collection as an Array
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458 public jalview.schemabinding.version2.UserColours[] getUserColours(
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460 jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0];
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461 return (jalview.schemabinding.version2.UserColours[]) this._userColoursList.toArray(array);
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465 * Method getUserColoursCount.
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467 * @return the size of this collection
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469 public int getUserColoursCount(
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471 return this._userColoursList.size();
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475 * Method getViewport.
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478 * @throws java.lang.IndexOutOfBoundsException if the index
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479 * given is outside the bounds of the collection
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480 * @return the value of the
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481 * jalview.schemabinding.version2.Viewport at the given index
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483 public jalview.schemabinding.version2.Viewport getViewport(
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485 throws java.lang.IndexOutOfBoundsException {
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486 // check bounds for index
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487 if (index < 0 || index >= this._viewportList.size()) {
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488 throw new IndexOutOfBoundsException("getViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
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491 return (jalview.schemabinding.version2.Viewport) _viewportList.get(index);
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495 * Method getViewport.Returns the contents of the collection in
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496 * an Array. <p>Note: Just in case the collection contents
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497 * are changing in another thread, we pass a 0-length Array of
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498 * the correct type into the API call. This way we <i>know</i>
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499 * that the Array returned is of exactly the correct length.
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501 * @return this collection as an Array
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503 public jalview.schemabinding.version2.Viewport[] getViewport(
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505 jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0];
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506 return (jalview.schemabinding.version2.Viewport[]) this._viewportList.toArray(array);
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510 * Method getViewportCount.
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512 * @return the size of this collection
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514 public int getViewportCount(
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516 return this._viewportList.size();
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522 * @return true if this object is valid according to the schema
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524 public boolean isValid(
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528 } catch (org.exolab.castor.xml.ValidationException vex) {
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538 * @throws org.exolab.castor.xml.MarshalException if object is
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539 * null or if any SAXException is thrown during marshaling
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540 * @throws org.exolab.castor.xml.ValidationException if this
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541 * object is an invalid instance according to the schema
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543 public void marshal(
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544 final java.io.Writer out)
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545 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
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546 Marshaller.marshal(this, out);
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553 * @throws java.io.IOException if an IOException occurs during
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555 * @throws org.exolab.castor.xml.ValidationException if this
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556 * object is an invalid instance according to the schema
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557 * @throws org.exolab.castor.xml.MarshalException if object is
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558 * null or if any SAXException is thrown during marshaling
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560 public void marshal(
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561 final org.xml.sax.ContentHandler handler)
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562 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
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563 Marshaller.marshal(this, handler);
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568 public void removeAllJGroup(
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570 this._JGroupList.clear();
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575 public void removeAllJSeq(
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577 this._JSeqList.clear();
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582 public void removeAllTree(
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584 this._treeList.clear();
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589 public void removeAllUserColours(
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591 this._userColoursList.clear();
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596 public void removeAllViewport(
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598 this._viewportList.clear();
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602 * Method removeJGroup.
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605 * @return true if the object was removed from the collection.
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607 public boolean removeJGroup(
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608 final jalview.schemabinding.version2.JGroup vJGroup) {
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609 boolean removed = _JGroupList.remove(vJGroup);
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614 * Method removeJGroupAt.
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617 * @return the element removed from the collection
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619 public jalview.schemabinding.version2.JGroup removeJGroupAt(
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621 java.lang.Object obj = this._JGroupList.remove(index);
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622 return (jalview.schemabinding.version2.JGroup) obj;
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626 * Method removeJSeq.
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629 * @return true if the object was removed from the collection.
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631 public boolean removeJSeq(
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632 final jalview.schemabinding.version2.JSeq vJSeq) {
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633 boolean removed = _JSeqList.remove(vJSeq);
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638 * Method removeJSeqAt.
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641 * @return the element removed from the collection
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643 public jalview.schemabinding.version2.JSeq removeJSeqAt(
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645 java.lang.Object obj = this._JSeqList.remove(index);
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646 return (jalview.schemabinding.version2.JSeq) obj;
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650 * Method removeTree.
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653 * @return true if the object was removed from the collection.
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655 public boolean removeTree(
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656 final jalview.schemabinding.version2.Tree vTree) {
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657 boolean removed = _treeList.remove(vTree);
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662 * Method removeTreeAt.
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665 * @return the element removed from the collection
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667 public jalview.schemabinding.version2.Tree removeTreeAt(
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669 java.lang.Object obj = this._treeList.remove(index);
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670 return (jalview.schemabinding.version2.Tree) obj;
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674 * Method removeUserColours.
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676 * @param vUserColours
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677 * @return true if the object was removed from the collection.
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679 public boolean removeUserColours(
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680 final jalview.schemabinding.version2.UserColours vUserColours) {
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681 boolean removed = _userColoursList.remove(vUserColours);
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686 * Method removeUserColoursAt.
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689 * @return the element removed from the collection
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691 public jalview.schemabinding.version2.UserColours removeUserColoursAt(
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693 java.lang.Object obj = this._userColoursList.remove(index);
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694 return (jalview.schemabinding.version2.UserColours) obj;
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698 * Method removeViewport.
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701 * @return true if the object was removed from the collection.
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703 public boolean removeViewport(
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704 final jalview.schemabinding.version2.Viewport vViewport) {
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705 boolean removed = _viewportList.remove(vViewport);
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710 * Method removeViewportAt.
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713 * @return the element removed from the collection
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715 public jalview.schemabinding.version2.Viewport removeViewportAt(
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717 java.lang.Object obj = this._viewportList.remove(index);
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718 return (jalview.schemabinding.version2.Viewport) obj;
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722 * Sets the value of field 'featureSettings'.
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724 * @param featureSettings the value of field 'featureSettings'.
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726 public void setFeatureSettings(
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727 final jalview.schemabinding.version2.FeatureSettings featureSettings) {
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728 this._featureSettings = featureSettings;
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736 * @throws java.lang.IndexOutOfBoundsException if the index
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737 * given is outside the bounds of the collection
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739 public void setJGroup(
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741 final jalview.schemabinding.version2.JGroup vJGroup)
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742 throws java.lang.IndexOutOfBoundsException {
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743 // check bounds for index
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744 if (index < 0 || index >= this._JGroupList.size()) {
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745 throw new IndexOutOfBoundsException("setJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
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748 this._JGroupList.set(index, vJGroup);
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754 * @param vJGroupArray
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756 public void setJGroup(
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757 final jalview.schemabinding.version2.JGroup[] vJGroupArray) {
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759 _JGroupList.clear();
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761 for (int i = 0; i < vJGroupArray.length; i++) {
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762 this._JGroupList.add(vJGroupArray[i]);
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771 * @throws java.lang.IndexOutOfBoundsException if the index
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772 * given is outside the bounds of the collection
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774 public void setJSeq(
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776 final jalview.schemabinding.version2.JSeq vJSeq)
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777 throws java.lang.IndexOutOfBoundsException {
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778 // check bounds for index
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779 if (index < 0 || index >= this._JSeqList.size()) {
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780 throw new IndexOutOfBoundsException("setJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
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783 this._JSeqList.set(index, vJSeq);
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789 * @param vJSeqArray
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791 public void setJSeq(
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792 final jalview.schemabinding.version2.JSeq[] vJSeqArray) {
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796 for (int i = 0; i < vJSeqArray.length; i++) {
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797 this._JSeqList.add(vJSeqArray[i]);
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806 * @throws java.lang.IndexOutOfBoundsException if the index
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807 * given is outside the bounds of the collection
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809 public void setTree(
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811 final jalview.schemabinding.version2.Tree vTree)
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812 throws java.lang.IndexOutOfBoundsException {
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813 // check bounds for index
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814 if (index < 0 || index >= this._treeList.size()) {
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815 throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
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818 this._treeList.set(index, vTree);
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824 * @param vTreeArray
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826 public void setTree(
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827 final jalview.schemabinding.version2.Tree[] vTreeArray) {
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831 for (int i = 0; i < vTreeArray.length; i++) {
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832 this._treeList.add(vTreeArray[i]);
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840 * @param vUserColours
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841 * @throws java.lang.IndexOutOfBoundsException if the index
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842 * given is outside the bounds of the collection
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844 public void setUserColours(
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846 final jalview.schemabinding.version2.UserColours vUserColours)
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847 throws java.lang.IndexOutOfBoundsException {
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848 // check bounds for index
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849 if (index < 0 || index >= this._userColoursList.size()) {
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850 throw new IndexOutOfBoundsException("setUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
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853 this._userColoursList.set(index, vUserColours);
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859 * @param vUserColoursArray
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861 public void setUserColours(
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862 final jalview.schemabinding.version2.UserColours[] vUserColoursArray) {
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864 _userColoursList.clear();
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866 for (int i = 0; i < vUserColoursArray.length; i++) {
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867 this._userColoursList.add(vUserColoursArray[i]);
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876 * @throws java.lang.IndexOutOfBoundsException if the index
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877 * given is outside the bounds of the collection
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879 public void setViewport(
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881 final jalview.schemabinding.version2.Viewport vViewport)
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882 throws java.lang.IndexOutOfBoundsException {
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883 // check bounds for index
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884 if (index < 0 || index >= this._viewportList.size()) {
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885 throw new IndexOutOfBoundsException("setViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
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888 this._viewportList.set(index, vViewport);
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894 * @param vViewportArray
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896 public void setViewport(
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897 final jalview.schemabinding.version2.Viewport[] vViewportArray) {
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899 _viewportList.clear();
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901 for (int i = 0; i < vViewportArray.length; i++) {
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902 this._viewportList.add(vViewportArray[i]);
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907 * Method unmarshal.
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910 * @throws org.exolab.castor.xml.MarshalException if object is
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911 * null or if any SAXException is thrown during marshaling
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912 * @throws org.exolab.castor.xml.ValidationException if this
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913 * object is an invalid instance according to the schema
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914 * @return the unmarshaled
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915 * jalview.schemabinding.version2.JalviewModelSequence
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917 public static jalview.schemabinding.version2.JalviewModelSequence unmarshal(
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918 final java.io.Reader reader)
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919 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
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920 return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModelSequence.class, reader);
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926 * @throws org.exolab.castor.xml.ValidationException if this
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927 * object is an invalid instance according to the schema
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929 public void validate(
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931 throws org.exolab.castor.xml.ValidationException {
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932 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
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933 validator.validate(this);
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