-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- * \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- * \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.schemabinding.version2;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-\r
-/**\r
- * Class JalviewModelSequence.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class JalviewModelSequence implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _JSeqList.\r
- */\r
- private java.util.Vector _JSeqList;\r
-\r
- /**\r
- * Field _JGroupList.\r
- */\r
- private java.util.Vector _JGroupList;\r
-\r
- /**\r
- * Field _viewportList.\r
- */\r
- private java.util.Vector _viewportList;\r
-\r
- /**\r
- * Field _userColoursList.\r
- */\r
- private java.util.Vector _userColoursList;\r
-\r
- /**\r
- * Field _treeList.\r
- */\r
- private java.util.Vector _treeList;\r
-\r
- /**\r
- * Field _featureSettings.\r
- */\r
- private jalview.schemabinding.version2.FeatureSettings _featureSettings;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public JalviewModelSequence() {\r
- super();\r
- this._JSeqList = new java.util.Vector();\r
- this._JGroupList = new java.util.Vector();\r
- this._viewportList = new java.util.Vector();\r
- this._userColoursList = new java.util.Vector();\r
- this._treeList = new java.util.Vector();\r
- }\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vJGroup\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addJGroup(\r
- final jalview.schemabinding.version2.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._JGroupList.addElement(vJGroup);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vJGroup\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addJGroup(\r
- final int index,\r
- final jalview.schemabinding.version2.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._JGroupList.add(index, vJGroup);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vJSeq\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addJSeq(\r
- final jalview.schemabinding.version2.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._JSeqList.addElement(vJSeq);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vJSeq\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addJSeq(\r
- final int index,\r
- final jalview.schemabinding.version2.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._JSeqList.add(index, vJSeq);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vTree\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addTree(\r
- final jalview.schemabinding.version2.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._treeList.addElement(vTree);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vTree\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addTree(\r
- final int index,\r
- final jalview.schemabinding.version2.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._treeList.add(index, vTree);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vUserColours\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addUserColours(\r
- final jalview.schemabinding.version2.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._userColoursList.addElement(vUserColours);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vUserColours\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addUserColours(\r
- final int index,\r
- final jalview.schemabinding.version2.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._userColoursList.add(index, vUserColours);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vViewport\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addViewport(\r
- final jalview.schemabinding.version2.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._viewportList.addElement(vViewport);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vViewport\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addViewport(\r
- final int index,\r
- final jalview.schemabinding.version2.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._viewportList.add(index, vViewport);\r
- }\r
-\r
- /**\r
- * Method enumerateJGroup.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.JGroup elements\r
- */\r
- public java.util.Enumeration enumerateJGroup(\r
- ) {\r
- return this._JGroupList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateJSeq.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.JSeq elements\r
- */\r
- public java.util.Enumeration enumerateJSeq(\r
- ) {\r
- return this._JSeqList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateTree.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.Tree elements\r
- */\r
- public java.util.Enumeration enumerateTree(\r
- ) {\r
- return this._treeList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateUserColours.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.UserColours elements\r
- */\r
- public java.util.Enumeration enumerateUserColours(\r
- ) {\r
- return this._userColoursList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateViewport.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.Viewport elements\r
- */\r
- public java.util.Enumeration enumerateViewport(\r
- ) {\r
- return this._viewportList.elements();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'featureSettings'.\r
- * \r
- * @return the value of field 'FeatureSettings'.\r
- */\r
- public jalview.schemabinding.version2.FeatureSettings getFeatureSettings(\r
- ) {\r
- return this._featureSettings;\r
- }\r
-\r
- /**\r
- * Method getJGroup.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- * @return the value of the\r
- * jalview.schemabinding.version2.JGroup at the given index\r
- */\r
- public jalview.schemabinding.version2.JGroup getJGroup(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._JGroupList.size()) {\r
- throw new IndexOutOfBoundsException("getJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");\r
- }\r
- \r
- return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);\r
- }\r
-\r
- /**\r
- * Method getJGroup.Returns the contents of the collection in\r
- * an Array. <p>Note: Just in case the collection contents\r
- * are changing in another thread, we pass a 0-length Array of\r
- * the correct type into the API call. This way we <i>know</i>\r
- * that the Array returned is of exactly the correct length.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public jalview.schemabinding.version2.JGroup[] getJGroup(\r
- ) {\r
- jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0];\r
- return (jalview.schemabinding.version2.JGroup[]) this._JGroupList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getJGroupCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getJGroupCount(\r
- ) {\r
- return this._JGroupList.size();\r
- }\r
-\r
- /**\r
- * Method getJSeq.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- * @return the value of the jalview.schemabinding.version2.JSeq\r
- * at the given index\r
- */\r
- public jalview.schemabinding.version2.JSeq getJSeq(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._JSeqList.size()) {\r
- throw new IndexOutOfBoundsException("getJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");\r
- }\r
- \r
- return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index);\r
- }\r
-\r
- /**\r
- * Method getJSeq.Returns the contents of the collection in an\r
- * Array. <p>Note: Just in case the collection contents are\r
- * changing in another thread, we pass a 0-length Array of the\r
- * correct type into the API call. This way we <i>know</i>\r
- * that the Array returned is of exactly the correct length.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public jalview.schemabinding.version2.JSeq[] getJSeq(\r
- ) {\r
- jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0];\r
- return (jalview.schemabinding.version2.JSeq[]) this._JSeqList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getJSeqCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getJSeqCount(\r
- ) {\r
- return this._JSeqList.size();\r
- }\r
-\r
- /**\r
- * Method getTree.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- * @return the value of the jalview.schemabinding.version2.Tree\r
- * at the given index\r
- */\r
- public jalview.schemabinding.version2.Tree getTree(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._treeList.size()) {\r
- throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
- }\r
- \r
- return (jalview.schemabinding.version2.Tree) _treeList.get(index);\r
- }\r
-\r
- /**\r
- * Method getTree.Returns the contents of the collection in an\r
- * Array. <p>Note: Just in case the collection contents are\r
- * changing in another thread, we pass a 0-length Array of the\r
- * correct type into the API call. This way we <i>know</i>\r
- * that the Array returned is of exactly the correct length.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public jalview.schemabinding.version2.Tree[] getTree(\r
- ) {\r
- jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0];\r
- return (jalview.schemabinding.version2.Tree[]) this._treeList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getTreeCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getTreeCount(\r
- ) {\r
- return this._treeList.size();\r
- }\r
-\r
- /**\r
- * Method getUserColours.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- * @return the value of the\r
- * jalview.schemabinding.version2.UserColours at the given index\r
- */\r
- public jalview.schemabinding.version2.UserColours getUserColours(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._userColoursList.size()) {\r
- throw new IndexOutOfBoundsException("getUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");\r
- }\r
- \r
- return (jalview.schemabinding.version2.UserColours) _userColoursList.get(index);\r
- }\r
-\r
- /**\r
- * Method getUserColours.Returns the contents of the collection\r
- * in an Array. <p>Note: Just in case the collection contents\r
- * are changing in another thread, we pass a 0-length Array of\r
- * the correct type into the API call. This way we <i>know</i>\r
- * that the Array returned is of exactly the correct length.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public jalview.schemabinding.version2.UserColours[] getUserColours(\r
- ) {\r
- jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0];\r
- return (jalview.schemabinding.version2.UserColours[]) this._userColoursList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getUserColoursCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getUserColoursCount(\r
- ) {\r
- return this._userColoursList.size();\r
- }\r
-\r
- /**\r
- * Method getViewport.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- * @return the value of the\r
- * jalview.schemabinding.version2.Viewport at the given index\r
- */\r
- public jalview.schemabinding.version2.Viewport getViewport(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._viewportList.size()) {\r
- throw new IndexOutOfBoundsException("getViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");\r
- }\r
- \r
- return (jalview.schemabinding.version2.Viewport) _viewportList.get(index);\r
- }\r
-\r
- /**\r
- * Method getViewport.Returns the contents of the collection in\r
- * an Array. <p>Note: Just in case the collection contents\r
- * are changing in another thread, we pass a 0-length Array of\r
- * the correct type into the API call. This way we <i>know</i>\r
- * that the Array returned is of exactly the correct length.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public jalview.schemabinding.version2.Viewport[] getViewport(\r
- ) {\r
- jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0];\r
- return (jalview.schemabinding.version2.Viewport[]) this._viewportList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getViewportCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getViewportCount(\r
- ) {\r
- return this._viewportList.size();\r
- }\r
-\r
- /**\r
- * Method isValid.\r
- * \r
- * @return true if this object is valid according to the schema\r
- */\r
- public boolean isValid(\r
- ) {\r
- try {\r
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param out\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- */\r
- public void marshal(\r
- final java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- Marshaller.marshal(this, out);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param handler\r
- * @throws java.io.IOException if an IOException occurs during\r
- * marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- */\r
- public void marshal(\r
- final org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- Marshaller.marshal(this, handler);\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllJGroup(\r
- ) {\r
- this._JGroupList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllJSeq(\r
- ) {\r
- this._JSeqList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllTree(\r
- ) {\r
- this._treeList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllUserColours(\r
- ) {\r
- this._userColoursList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllViewport(\r
- ) {\r
- this._viewportList.clear();\r
- }\r
-\r
- /**\r
- * Method removeJGroup.\r
- * \r
- * @param vJGroup\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeJGroup(\r
- final jalview.schemabinding.version2.JGroup vJGroup) {\r
- boolean removed = _JGroupList.remove(vJGroup);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeJGroupAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.JGroup removeJGroupAt(\r
- final int index) {\r
- java.lang.Object obj = this._JGroupList.remove(index);\r
- return (jalview.schemabinding.version2.JGroup) obj;\r
- }\r
-\r
- /**\r
- * Method removeJSeq.\r
- * \r
- * @param vJSeq\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeJSeq(\r
- final jalview.schemabinding.version2.JSeq vJSeq) {\r
- boolean removed = _JSeqList.remove(vJSeq);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeJSeqAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.JSeq removeJSeqAt(\r
- final int index) {\r
- java.lang.Object obj = this._JSeqList.remove(index);\r
- return (jalview.schemabinding.version2.JSeq) obj;\r
- }\r
-\r
- /**\r
- * Method removeTree.\r
- * \r
- * @param vTree\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeTree(\r
- final jalview.schemabinding.version2.Tree vTree) {\r
- boolean removed = _treeList.remove(vTree);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeTreeAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.Tree removeTreeAt(\r
- final int index) {\r
- java.lang.Object obj = this._treeList.remove(index);\r
- return (jalview.schemabinding.version2.Tree) obj;\r
- }\r
-\r
- /**\r
- * Method removeUserColours.\r
- * \r
- * @param vUserColours\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeUserColours(\r
- final jalview.schemabinding.version2.UserColours vUserColours) {\r
- boolean removed = _userColoursList.remove(vUserColours);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeUserColoursAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.UserColours removeUserColoursAt(\r
- final int index) {\r
- java.lang.Object obj = this._userColoursList.remove(index);\r
- return (jalview.schemabinding.version2.UserColours) obj;\r
- }\r
-\r
- /**\r
- * Method removeViewport.\r
- * \r
- * @param vViewport\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeViewport(\r
- final jalview.schemabinding.version2.Viewport vViewport) {\r
- boolean removed = _viewportList.remove(vViewport);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeViewportAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.Viewport removeViewportAt(\r
- final int index) {\r
- java.lang.Object obj = this._viewportList.remove(index);\r
- return (jalview.schemabinding.version2.Viewport) obj;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'featureSettings'.\r
- * \r
- * @param featureSettings the value of field 'featureSettings'.\r
- */\r
- public void setFeatureSettings(\r
- final jalview.schemabinding.version2.FeatureSettings featureSettings) {\r
- this._featureSettings = featureSettings;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vJGroup\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setJGroup(\r
- final int index,\r
- final jalview.schemabinding.version2.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._JGroupList.size()) {\r
- throw new IndexOutOfBoundsException("setJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");\r
- }\r
- \r
- this._JGroupList.set(index, vJGroup);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vJGroupArray\r
- */\r
- public void setJGroup(\r
- final jalview.schemabinding.version2.JGroup[] vJGroupArray) {\r
- //-- copy array\r
- _JGroupList.clear();\r
- \r
- for (int i = 0; i < vJGroupArray.length; i++) {\r
- this._JGroupList.add(vJGroupArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vJSeq\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setJSeq(\r
- final int index,\r
- final jalview.schemabinding.version2.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._JSeqList.size()) {\r
- throw new IndexOutOfBoundsException("setJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");\r
- }\r
- \r
- this._JSeqList.set(index, vJSeq);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vJSeqArray\r
- */\r
- public void setJSeq(\r
- final jalview.schemabinding.version2.JSeq[] vJSeqArray) {\r
- //-- copy array\r
- _JSeqList.clear();\r
- \r
- for (int i = 0; i < vJSeqArray.length; i++) {\r
- this._JSeqList.add(vJSeqArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vTree\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setTree(\r
- final int index,\r
- final jalview.schemabinding.version2.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._treeList.size()) {\r
- throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
- }\r
- \r
- this._treeList.set(index, vTree);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vTreeArray\r
- */\r
- public void setTree(\r
- final jalview.schemabinding.version2.Tree[] vTreeArray) {\r
- //-- copy array\r
- _treeList.clear();\r
- \r
- for (int i = 0; i < vTreeArray.length; i++) {\r
- this._treeList.add(vTreeArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vUserColours\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setUserColours(\r
- final int index,\r
- final jalview.schemabinding.version2.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._userColoursList.size()) {\r
- throw new IndexOutOfBoundsException("setUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");\r
- }\r
- \r
- this._userColoursList.set(index, vUserColours);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vUserColoursArray\r
- */\r
- public void setUserColours(\r
- final jalview.schemabinding.version2.UserColours[] vUserColoursArray) {\r
- //-- copy array\r
- _userColoursList.clear();\r
- \r
- for (int i = 0; i < vUserColoursArray.length; i++) {\r
- this._userColoursList.add(vUserColoursArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vViewport\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setViewport(\r
- final int index,\r
- final jalview.schemabinding.version2.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._viewportList.size()) {\r
- throw new IndexOutOfBoundsException("setViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");\r
- }\r
- \r
- this._viewportList.set(index, vViewport);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vViewportArray\r
- */\r
- public void setViewport(\r
- final jalview.schemabinding.version2.Viewport[] vViewportArray) {\r
- //-- copy array\r
- _viewportList.clear();\r
- \r
- for (int i = 0; i < vViewportArray.length; i++) {\r
- this._viewportList.add(vViewportArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * Method unmarshal.\r
- * \r
- * @param reader\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- * @return the unmarshaled\r
- * jalview.schemabinding.version2.JalviewModelSequence\r
- */\r
- public static jalview.schemabinding.version2.JalviewModelSequence unmarshal(\r
- final java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModelSequence.class, reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- */\r
- public void validate(\r
- )\r
- throws org.exolab.castor.xml.ValidationException {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- }\r
-\r
-}\r
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview.
+ * If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ ******************************************************************************/
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class JalviewModelSequence.
+ *
+ * @version $Revision$ $Date$
+ */
+public class JalviewModelSequence implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _JSeqList.
+ */
+ private java.util.Vector _JSeqList;
+
+ /**
+ * Field _JGroupList.
+ */
+ private java.util.Vector _JGroupList;
+
+ /**
+ * Field _viewportList.
+ */
+ private java.util.Vector _viewportList;
+
+ /**
+ * Field _userColoursList.
+ */
+ private java.util.Vector _userColoursList;
+
+ /**
+ * Field _treeList.
+ */
+ private java.util.Vector _treeList;
+
+ /**
+ * Field _featureSettings.
+ */
+ private jalview.schemabinding.version2.FeatureSettings _featureSettings;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public JalviewModelSequence()
+ {
+ super();
+ this._JSeqList = new java.util.Vector();
+ this._JGroupList = new java.util.Vector();
+ this._viewportList = new java.util.Vector();
+ this._userColoursList = new java.util.Vector();
+ this._treeList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vJGroup
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addJGroup(final jalview.schemabinding.version2.JGroup vJGroup)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._JGroupList.addElement(vJGroup);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJGroup
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addJGroup(final int index,
+ final jalview.schemabinding.version2.JGroup vJGroup)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._JGroupList.add(index, vJGroup);
+ }
+
+ /**
+ *
+ *
+ * @param vJSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addJSeq(final jalview.schemabinding.version2.JSeq vJSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._JSeqList.addElement(vJSeq);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addJSeq(final int index,
+ final jalview.schemabinding.version2.JSeq vJSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._JSeqList.add(index, vJSeq);
+ }
+
+ /**
+ *
+ *
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addTree(final jalview.schemabinding.version2.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._treeList.addElement(vTree);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addTree(final int index,
+ final jalview.schemabinding.version2.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._treeList.add(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vUserColours
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addUserColours(
+ final jalview.schemabinding.version2.UserColours vUserColours)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._userColoursList.addElement(vUserColours);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vUserColours
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addUserColours(final int index,
+ final jalview.schemabinding.version2.UserColours vUserColours)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._userColoursList.add(index, vUserColours);
+ }
+
+ /**
+ *
+ *
+ * @param vViewport
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addViewport(
+ final jalview.schemabinding.version2.Viewport vViewport)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._viewportList.addElement(vViewport);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vViewport
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addViewport(final int index,
+ final jalview.schemabinding.version2.Viewport vViewport)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._viewportList.add(index, vViewport);
+ }
+
+ /**
+ * Method enumerateJGroup.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.JGroup
+ * elements
+ */
+ public java.util.Enumeration enumerateJGroup()
+ {
+ return this._JGroupList.elements();
+ }
+
+ /**
+ * Method enumerateJSeq.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.JSeq
+ * elements
+ */
+ public java.util.Enumeration enumerateJSeq()
+ {
+ return this._JSeqList.elements();
+ }
+
+ /**
+ * Method enumerateTree.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.Tree
+ * elements
+ */
+ public java.util.Enumeration enumerateTree()
+ {
+ return this._treeList.elements();
+ }
+
+ /**
+ * Method enumerateUserColours.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.UserColours
+ * elements
+ */
+ public java.util.Enumeration enumerateUserColours()
+ {
+ return this._userColoursList.elements();
+ }
+
+ /**
+ * Method enumerateViewport.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.Viewport
+ * elements
+ */
+ public java.util.Enumeration enumerateViewport()
+ {
+ return this._viewportList.elements();
+ }
+
+ /**
+ * Returns the value of field 'featureSettings'.
+ *
+ * @return the value of field 'FeatureSettings'.
+ */
+ public jalview.schemabinding.version2.FeatureSettings getFeatureSettings()
+ {
+ return this._featureSettings;
+ }
+
+ /**
+ * Method getJGroup.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.JGroup at the given
+ * index
+ */
+ public jalview.schemabinding.version2.JGroup getJGroup(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._JGroupList.size())
+ {
+ throw new IndexOutOfBoundsException("getJGroup: Index value '"
+ + index + "' not in range [0.."
+ + (this._JGroupList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);
+ }
+
+ /**
+ * Method getJGroup.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.JGroup[] getJGroup()
+ {
+ jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0];
+ return (jalview.schemabinding.version2.JGroup[]) this._JGroupList
+ .toArray(array);
+ }
+
+ /**
+ * Method getJGroupCount.
+ *
+ * @return the size of this collection
+ */
+ public int getJGroupCount()
+ {
+ return this._JGroupList.size();
+ }
+
+ /**
+ * Method getJSeq.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.JSeq at the given
+ * index
+ */
+ public jalview.schemabinding.version2.JSeq getJSeq(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._JSeqList.size())
+ {
+ throw new IndexOutOfBoundsException("getJSeq: Index value '" + index
+ + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index);
+ }
+
+ /**
+ * Method getJSeq.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.JSeq[] getJSeq()
+ {
+ jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0];
+ return (jalview.schemabinding.version2.JSeq[]) this._JSeqList
+ .toArray(array);
+ }
+
+ /**
+ * Method getJSeqCount.
+ *
+ * @return the size of this collection
+ */
+ public int getJSeqCount()
+ {
+ return this._JSeqList.size();
+ }
+
+ /**
+ * Method getTree.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.Tree at the given
+ * index
+ */
+ public jalview.schemabinding.version2.Tree getTree(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size())
+ {
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.Tree) _treeList.get(index);
+ }
+
+ /**
+ * Method getTree.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.Tree[] getTree()
+ {
+ jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0];
+ return (jalview.schemabinding.version2.Tree[]) this._treeList
+ .toArray(array);
+ }
+
+ /**
+ * Method getTreeCount.
+ *
+ * @return the size of this collection
+ */
+ public int getTreeCount()
+ {
+ return this._treeList.size();
+ }
+
+ /**
+ * Method getUserColours.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.UserColours at the
+ * given index
+ */
+ public jalview.schemabinding.version2.UserColours getUserColours(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._userColoursList.size())
+ {
+ throw new IndexOutOfBoundsException("getUserColours: Index value '"
+ + index + "' not in range [0.."
+ + (this._userColoursList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.UserColours) _userColoursList
+ .get(index);
+ }
+
+ /**
+ * Method getUserColours.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.UserColours[] getUserColours()
+ {
+ jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0];
+ return (jalview.schemabinding.version2.UserColours[]) this._userColoursList
+ .toArray(array);
+ }
+
+ /**
+ * Method getUserColoursCount.
+ *
+ * @return the size of this collection
+ */
+ public int getUserColoursCount()
+ {
+ return this._userColoursList.size();
+ }
+
+ /**
+ * Method getViewport.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.Viewport at the
+ * given index
+ */
+ public jalview.schemabinding.version2.Viewport getViewport(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._viewportList.size())
+ {
+ throw new IndexOutOfBoundsException("getViewport: Index value '"
+ + index + "' not in range [0.."
+ + (this._viewportList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.Viewport) _viewportList
+ .get(index);
+ }
+
+ /**
+ * Method getViewport.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.Viewport[] getViewport()
+ {
+ jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0];
+ return (jalview.schemabinding.version2.Viewport[]) this._viewportList
+ .toArray(array);
+ }
+
+ /**
+ * Method getViewportCount.
+ *
+ * @return the size of this collection
+ */
+ public int getViewportCount()
+ {
+ return this._viewportList.size();
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllJGroup()
+ {
+ this._JGroupList.clear();
+ }
+
+ /**
+ */
+ public void removeAllJSeq()
+ {
+ this._JSeqList.clear();
+ }
+
+ /**
+ */
+ public void removeAllTree()
+ {
+ this._treeList.clear();
+ }
+
+ /**
+ */
+ public void removeAllUserColours()
+ {
+ this._userColoursList.clear();
+ }
+
+ /**
+ */
+ public void removeAllViewport()
+ {
+ this._viewportList.clear();
+ }
+
+ /**
+ * Method removeJGroup.
+ *
+ * @param vJGroup
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeJGroup(
+ final jalview.schemabinding.version2.JGroup vJGroup)
+ {
+ boolean removed = _JGroupList.remove(vJGroup);
+ return removed;
+ }
+
+ /**
+ * Method removeJGroupAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.JGroup removeJGroupAt(
+ final int index)
+ {
+ java.lang.Object obj = this._JGroupList.remove(index);
+ return (jalview.schemabinding.version2.JGroup) obj;
+ }
+
+ /**
+ * Method removeJSeq.
+ *
+ * @param vJSeq
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeJSeq(final jalview.schemabinding.version2.JSeq vJSeq)
+ {
+ boolean removed = _JSeqList.remove(vJSeq);
+ return removed;
+ }
+
+ /**
+ * Method removeJSeqAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.JSeq removeJSeqAt(final int index)
+ {
+ java.lang.Object obj = this._JSeqList.remove(index);
+ return (jalview.schemabinding.version2.JSeq) obj;
+ }
+
+ /**
+ * Method removeTree.
+ *
+ * @param vTree
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeTree(final jalview.schemabinding.version2.Tree vTree)
+ {
+ boolean removed = _treeList.remove(vTree);
+ return removed;
+ }
+
+ /**
+ * Method removeTreeAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Tree removeTreeAt(final int index)
+ {
+ java.lang.Object obj = this._treeList.remove(index);
+ return (jalview.schemabinding.version2.Tree) obj;
+ }
+
+ /**
+ * Method removeUserColours.
+ *
+ * @param vUserColours
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeUserColours(
+ final jalview.schemabinding.version2.UserColours vUserColours)
+ {
+ boolean removed = _userColoursList.remove(vUserColours);
+ return removed;
+ }
+
+ /**
+ * Method removeUserColoursAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.UserColours removeUserColoursAt(
+ final int index)
+ {
+ java.lang.Object obj = this._userColoursList.remove(index);
+ return (jalview.schemabinding.version2.UserColours) obj;
+ }
+
+ /**
+ * Method removeViewport.
+ *
+ * @param vViewport
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeViewport(
+ final jalview.schemabinding.version2.Viewport vViewport)
+ {
+ boolean removed = _viewportList.remove(vViewport);
+ return removed;
+ }
+
+ /**
+ * Method removeViewportAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Viewport removeViewportAt(
+ final int index)
+ {
+ java.lang.Object obj = this._viewportList.remove(index);
+ return (jalview.schemabinding.version2.Viewport) obj;
+ }
+
+ /**
+ * Sets the value of field 'featureSettings'.
+ *
+ * @param featureSettings
+ * the value of field 'featureSettings'.
+ */
+ public void setFeatureSettings(
+ final jalview.schemabinding.version2.FeatureSettings featureSettings)
+ {
+ this._featureSettings = featureSettings;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJGroup
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setJGroup(final int index,
+ final jalview.schemabinding.version2.JGroup vJGroup)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._JGroupList.size())
+ {
+ throw new IndexOutOfBoundsException("setJGroup: Index value '"
+ + index + "' not in range [0.."
+ + (this._JGroupList.size() - 1) + "]");
+ }
+
+ this._JGroupList.set(index, vJGroup);
+ }
+
+ /**
+ *
+ *
+ * @param vJGroupArray
+ */
+ public void setJGroup(
+ final jalview.schemabinding.version2.JGroup[] vJGroupArray)
+ {
+ // -- copy array
+ _JGroupList.clear();
+
+ for (int i = 0; i < vJGroupArray.length; i++)
+ {
+ this._JGroupList.add(vJGroupArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setJSeq(final int index,
+ final jalview.schemabinding.version2.JSeq vJSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._JSeqList.size())
+ {
+ throw new IndexOutOfBoundsException("setJSeq: Index value '" + index
+ + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+ }
+
+ this._JSeqList.set(index, vJSeq);
+ }
+
+ /**
+ *
+ *
+ * @param vJSeqArray
+ */
+ public void setJSeq(final jalview.schemabinding.version2.JSeq[] vJSeqArray)
+ {
+ // -- copy array
+ _JSeqList.clear();
+
+ for (int i = 0; i < vJSeqArray.length; i++)
+ {
+ this._JSeqList.add(vJSeqArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setTree(final int index,
+ final jalview.schemabinding.version2.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size())
+ {
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ this._treeList.set(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vTreeArray
+ */
+ public void setTree(final jalview.schemabinding.version2.Tree[] vTreeArray)
+ {
+ // -- copy array
+ _treeList.clear();
+
+ for (int i = 0; i < vTreeArray.length; i++)
+ {
+ this._treeList.add(vTreeArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vUserColours
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setUserColours(final int index,
+ final jalview.schemabinding.version2.UserColours vUserColours)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._userColoursList.size())
+ {
+ throw new IndexOutOfBoundsException("setUserColours: Index value '"
+ + index + "' not in range [0.."
+ + (this._userColoursList.size() - 1) + "]");
+ }
+
+ this._userColoursList.set(index, vUserColours);
+ }
+
+ /**
+ *
+ *
+ * @param vUserColoursArray
+ */
+ public void setUserColours(
+ final jalview.schemabinding.version2.UserColours[] vUserColoursArray)
+ {
+ // -- copy array
+ _userColoursList.clear();
+
+ for (int i = 0; i < vUserColoursArray.length; i++)
+ {
+ this._userColoursList.add(vUserColoursArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vViewport
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setViewport(final int index,
+ final jalview.schemabinding.version2.Viewport vViewport)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._viewportList.size())
+ {
+ throw new IndexOutOfBoundsException("setViewport: Index value '"
+ + index + "' not in range [0.."
+ + (this._viewportList.size() - 1) + "]");
+ }
+
+ this._viewportList.set(index, vViewport);
+ }
+
+ /**
+ *
+ *
+ * @param vViewportArray
+ */
+ public void setViewport(
+ final jalview.schemabinding.version2.Viewport[] vViewportArray)
+ {
+ // -- copy array
+ _viewportList.clear();
+
+ for (int i = 0; i < vViewportArray.length; i++)
+ {
+ this._viewportList.add(vViewportArray[i]);
+ }
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.JalviewModelSequence
+ */
+ public static jalview.schemabinding.version2.JalviewModelSequence unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller
+ .unmarshal(
+ jalview.schemabinding.version2.JalviewModelSequence.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff