X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJalviewModelSequence.java;h=cf699345bb8443057cec7fe1eb51700ccd5a002c;hb=09e3cf7d0e936a9b69fc8f6c7315195694c5127e;hp=790a1cabc37096c7fa616b39a257454ec626eb71;hpb=aced09c4feeaf3406269442c14e54abeeb4cad81;p=jalview.git
diff --git a/src/jalview/schemabinding/version2/JalviewModelSequence.java b/src/jalview/schemabinding/version2/JalviewModelSequence.java
index 790a1ca..cf69934 100644
--- a/src/jalview/schemabinding/version2/JalviewModelSequence.java
+++ b/src/jalview/schemabinding/version2/JalviewModelSequence.java
@@ -1,30 +1,15 @@
/*
- * 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
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(); } - return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index); - } - - /** - * Method getJGroup.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.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() - })); + /** + * 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); } - 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() - })); + /** + * 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); } - 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() - })); + /** + * Method getUserColoursCount. + * + * @return the size of this collection + */ + public int getUserColoursCount( + ) { + return this._userColoursList.size(); } - 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() - })); + /** + * 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); } - 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; + /** + * 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); } - 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() - })); + + /** + * Method getViewportCount. + * + * @return the size of this collection + */ + public int getViewportCount( + ) { + return this._viewportList.size(); } - 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]); + /** + * 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 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() - })); + + /** + * + * + * @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); } - 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 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); } - } - - /** - * - * - * @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() - })); + + /** + */ + public void removeAllJGroup( + ) { + this._JGroupList.clear(); } - 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]); + /** + */ + public void removeAllJSeq( + ) { + this._JSeqList.clear(); } - } - - /** - * - * - * @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() - })); + + /** + */ + public void removeAllTree( + ) { + this._treeList.clear(); } - 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]); + /** + */ + public void removeAllUserColours( + ) { + this._userColoursList.clear(); } - } - - /** - * - * - * @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() - })); + + /** + */ + 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; } - 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 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); } - } - - /** - * 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); - } }