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("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.
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("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.
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("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.
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("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.
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("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);
- }
-
-}
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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("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.
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("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.
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("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.
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("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.
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("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); + } + +}