/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ 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
* 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 * know 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ "getJSeq", Integer.valueOf(index).toString(), Integer.valueOf((this._JSeqList.size() - 1)).toString() })); } return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index); } /** * Method getJSeq.Returns the contents of the collection in an Array. *
* 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 * know 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ "getJgetTreeSeq", Integer.valueOf(index).toString(), Integer.valueOf((this._treeList.size() - 1)).toString() })); } return (jalview.schemabinding.version2.Tree) _treeList.get(index); } /** * Method getTree.Returns the contents of the collection in an Array. *
* 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 * know 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ "getUserColours", Integer.valueOf(index).toString(), Integer.valueOf((this._userColoursList.size() - 1)).toString() })); } return (jalview.schemabinding.version2.UserColours) _userColoursList .get(index); } /** * Method getUserColours.Returns the contents of the collection in an Array. *
* 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 * know 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ "getViewport", Integer.valueOf(index).toString(), Integer.valueOf((this._viewportList.size() - 1)).toString() })); } return (jalview.schemabinding.version2.Viewport) _viewportList .get(index); } /** * Method getViewport.Returns the contents of the collection in an Array. *
* 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 * know 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ "setJGroup", Integer.valueOf(index).toString(), Integer.valueOf((this._JGroupList.size() - 1)).toString() })); } 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ "setJSeq", Integer.valueOf(index).toString(), Integer.valueOf((this._JSeqList.size() - 1)).toString() })); } 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ "setTree", Integer.valueOf(index).toString(), Integer.valueOf((this._treeList.size() - 1)).toString() })); } 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ "setUserColours", Integer.valueOf(index).toString(), Integer.valueOf((this._userColoursList.size() - 1)).toString() })); } 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ "setViewport", Integer.valueOf(index).toString(), Integer.valueOf((this._viewportList.size() - 1)).toString() })); } 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); } }