X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJalviewModelSequence.java;h=eb0716db88533811f3e969fe06d1505d12e74d9c;hb=9876fdccf311378e690c1f9e18db52675d427b89;hp=4ac40d516600f7e75865249d5528b963f48fc175;hpb=c68ce4c63bd79f23b87aac3eb0afa7f6b42a3098;p=jalview.git diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java old mode 100755 new mode 100644 index 4ac40d5..eb0716d --- a/src/jalview/binding/JalviewModelSequence.java +++ b/src/jalview/binding/JalviewModelSequence.java @@ -1,878 +1,955 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * 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; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public JalviewModelSequence() { - super(); - _JSeqList = new Vector(); - _JGroupList = new Vector(); - _viewportList = new Vector(); - _userColoursList = new Vector(); - _treeList = new Vector(); - } //-- jalview.binding.JalviewModelSequence() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addJGroup - * - * - * - * @param vJGroup - */ - public void addJGroup(jalview.binding.JGroup vJGroup) - throws java.lang.IndexOutOfBoundsException - { - _JGroupList.addElement(vJGroup); - } //-- void addJGroup(jalview.binding.JGroup) - - /** - * Method addJGroup - * - * - * - * @param index - * @param vJGroup - */ - public void addJGroup(int index, jalview.binding.JGroup vJGroup) - throws java.lang.IndexOutOfBoundsException - { - _JGroupList.insertElementAt(vJGroup, index); - } //-- void addJGroup(int, jalview.binding.JGroup) - - /** - * Method addJSeq - * - * - * - * @param vJSeq - */ - public void addJSeq(jalview.binding.JSeq vJSeq) - throws java.lang.IndexOutOfBoundsException - { - _JSeqList.addElement(vJSeq); - } //-- void addJSeq(jalview.binding.JSeq) - - /** - * Method addJSeq - * - * - * - * @param index - * @param vJSeq - */ - public void addJSeq(int index, jalview.binding.JSeq vJSeq) - throws java.lang.IndexOutOfBoundsException - { - _JSeqList.insertElementAt(vJSeq, index); - } //-- void addJSeq(int, jalview.binding.JSeq) - - /** - * Method addTree - * - * - * - * @param vTree - */ - public void addTree(jalview.binding.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.addElement(vTree); - } //-- void addTree(jalview.binding.Tree) - - /** - * Method addTree - * - * - * - * @param index - * @param vTree - */ - public void addTree(int index, jalview.binding.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.insertElementAt(vTree, index); - } //-- void addTree(int, jalview.binding.Tree) - - /** - * Method addUserColours - * - * - * - * @param vUserColours - */ - public void addUserColours(jalview.binding.UserColours vUserColours) - throws java.lang.IndexOutOfBoundsException - { - _userColoursList.addElement(vUserColours); - } //-- void addUserColours(jalview.binding.UserColours) - - /** - * Method addUserColours - * - * - * - * @param index - * @param vUserColours - */ - public void addUserColours(int index, jalview.binding.UserColours vUserColours) - throws java.lang.IndexOutOfBoundsException - { - _userColoursList.insertElementAt(vUserColours, index); - } //-- void addUserColours(int, jalview.binding.UserColours) - - /** - * Method addViewport - * - * - * - * @param vViewport - */ - public void addViewport(jalview.binding.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException - { - _viewportList.addElement(vViewport); - } //-- void addViewport(jalview.binding.Viewport) - - /** - * Method addViewport - * - * - * - * @param index - * @param vViewport - */ - public void addViewport(int index, jalview.binding.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException - { - _viewportList.insertElementAt(vViewport, index); - } //-- void addViewport(int, jalview.binding.Viewport) - - /** - * Method enumerateJGroup - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateJGroup() - { - return _JGroupList.elements(); - } //-- java.util.Enumeration enumerateJGroup() - - /** - * Method enumerateJSeq - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateJSeq() - { - return _JSeqList.elements(); - } //-- java.util.Enumeration enumerateJSeq() - - /** - * Method enumerateTree - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateTree() - { - return _treeList.elements(); - } //-- java.util.Enumeration enumerateTree() - - /** - * Method enumerateUserColours - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateUserColours() - { - return _userColoursList.elements(); - } //-- java.util.Enumeration enumerateUserColours() - - /** - * Method enumerateViewport - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateViewport() - { - return _viewportList.elements(); - } //-- java.util.Enumeration enumerateViewport() - - /** - * Method getJGroup - * - * - * - * @param index - * @return JGroup - */ - public jalview.binding.JGroup getJGroup(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _JGroupList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.JGroup) _JGroupList.elementAt(index); - } //-- jalview.binding.JGroup getJGroup(int) - - /** - * Method getJGroup - * - * - * - * @return JGroup - */ - public jalview.binding.JGroup[] getJGroup() - { - int size = _JGroupList.size(); - jalview.binding.JGroup[] mArray = new jalview.binding.JGroup[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.JGroup) _JGroupList.elementAt(index); - } - return mArray; - } //-- jalview.binding.JGroup[] getJGroup() - - /** - * Method getJGroupCount - * - * - * - * @return int - */ - public int getJGroupCount() - { - return _JGroupList.size(); - } //-- int getJGroupCount() - - /** - * Method getJSeq - * - * - * - * @param index - * @return JSeq - */ - public jalview.binding.JSeq getJSeq(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _JSeqList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.JSeq) _JSeqList.elementAt(index); - } //-- jalview.binding.JSeq getJSeq(int) - - /** - * Method getJSeq - * - * - * - * @return JSeq - */ - public jalview.binding.JSeq[] getJSeq() - { - int size = _JSeqList.size(); - jalview.binding.JSeq[] mArray = new jalview.binding.JSeq[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.JSeq) _JSeqList.elementAt(index); - } - return mArray; - } //-- jalview.binding.JSeq[] getJSeq() - - /** - * Method getJSeqCount - * - * - * - * @return int - */ - public int getJSeqCount() - { - return _JSeqList.size(); - } //-- int getJSeqCount() - - /** - * Method getTree - * - * - * - * @param index - * @return Tree - */ - public jalview.binding.Tree getTree(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.Tree) _treeList.elementAt(index); - } //-- jalview.binding.Tree getTree(int) - - /** - * Method getTree - * - * - * - * @return Tree - */ - public jalview.binding.Tree[] getTree() - { - int size = _treeList.size(); - jalview.binding.Tree[] mArray = new jalview.binding.Tree[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.Tree) _treeList.elementAt(index); - } - return mArray; - } //-- jalview.binding.Tree[] getTree() - - /** - * Method getTreeCount - * - * - * - * @return int - */ - public int getTreeCount() - { - return _treeList.size(); - } //-- int getTreeCount() - - /** - * Method getUserColours - * - * - * - * @param index - * @return UserColours - */ - public jalview.binding.UserColours getUserColours(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _userColoursList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.UserColours) _userColoursList.elementAt(index); - } //-- jalview.binding.UserColours getUserColours(int) - - /** - * Method getUserColours - * - * - * - * @return UserColours - */ - public jalview.binding.UserColours[] getUserColours() - { - int size = _userColoursList.size(); - jalview.binding.UserColours[] mArray = new jalview.binding.UserColours[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.UserColours) _userColoursList.elementAt(index); - } - return mArray; - } //-- jalview.binding.UserColours[] getUserColours() - - /** - * Method getUserColoursCount - * - * - * - * @return int - */ - public int getUserColoursCount() - { - return _userColoursList.size(); - } //-- int getUserColoursCount() - - /** - * Method getViewport - * - * - * - * @param index - * @return Viewport - */ - public jalview.binding.Viewport getViewport(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _viewportList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.Viewport) _viewportList.elementAt(index); - } //-- jalview.binding.Viewport getViewport(int) - - /** - * Method getViewport - * - * - * - * @return Viewport - */ - public jalview.binding.Viewport[] getViewport() - { - int size = _viewportList.size(); - jalview.binding.Viewport[] mArray = new jalview.binding.Viewport[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.Viewport) _viewportList.elementAt(index); - } - return mArray; - } //-- jalview.binding.Viewport[] getViewport() - - /** - * Method getViewportCount - * - * - * - * @return int - */ - public int getViewportCount() - { - return _viewportList.size(); - } //-- int getViewportCount() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllJGroup - * - */ - public void removeAllJGroup() - { - _JGroupList.removeAllElements(); - } //-- void removeAllJGroup() - - /** - * Method removeAllJSeq - * - */ - public void removeAllJSeq() - { - _JSeqList.removeAllElements(); - } //-- void removeAllJSeq() - - /** - * Method removeAllTree - * - */ - public void removeAllTree() - { - _treeList.removeAllElements(); - } //-- void removeAllTree() - - /** - * Method removeAllUserColours - * - */ - public void removeAllUserColours() - { - _userColoursList.removeAllElements(); - } //-- void removeAllUserColours() - - /** - * Method removeAllViewport - * - */ - public void removeAllViewport() - { - _viewportList.removeAllElements(); - } //-- void removeAllViewport() - - /** - * Method removeJGroup - * - * - * - * @param index - * @return JGroup - */ - public jalview.binding.JGroup removeJGroup(int index) - { - java.lang.Object obj = _JGroupList.elementAt(index); - _JGroupList.removeElementAt(index); - return (jalview.binding.JGroup) obj; - } //-- jalview.binding.JGroup removeJGroup(int) - - /** - * Method removeJSeq - * - * - * - * @param index - * @return JSeq - */ - public jalview.binding.JSeq removeJSeq(int index) - { - java.lang.Object obj = _JSeqList.elementAt(index); - _JSeqList.removeElementAt(index); - return (jalview.binding.JSeq) obj; - } //-- jalview.binding.JSeq removeJSeq(int) - - /** - * Method removeTree - * - * - * - * @param index - * @return Tree - */ - public jalview.binding.Tree removeTree(int index) - { - java.lang.Object obj = _treeList.elementAt(index); - _treeList.removeElementAt(index); - return (jalview.binding.Tree) obj; - } //-- jalview.binding.Tree removeTree(int) - - /** - * Method removeUserColours - * - * - * - * @param index - * @return UserColours - */ - public jalview.binding.UserColours removeUserColours(int index) - { - java.lang.Object obj = _userColoursList.elementAt(index); - _userColoursList.removeElementAt(index); - return (jalview.binding.UserColours) obj; - } //-- jalview.binding.UserColours removeUserColours(int) - - /** - * Method removeViewport - * - * - * - * @param index - * @return Viewport - */ - public jalview.binding.Viewport removeViewport(int index) - { - java.lang.Object obj = _viewportList.elementAt(index); - _viewportList.removeElementAt(index); - return (jalview.binding.Viewport) obj; - } //-- jalview.binding.Viewport removeViewport(int) - - /** - * Method setJGroup - * - * - * - * @param index - * @param vJGroup - */ - public void setJGroup(int index, jalview.binding.JGroup vJGroup) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _JGroupList.size())) { - throw new IndexOutOfBoundsException(); - } - _JGroupList.setElementAt(vJGroup, index); - } //-- void setJGroup(int, jalview.binding.JGroup) - - /** - * Method setJGroup - * - * - * - * @param JGroupArray - */ - public void setJGroup(jalview.binding.JGroup[] JGroupArray) - { - //-- copy array - _JGroupList.removeAllElements(); - for (int i = 0; i < JGroupArray.length; i++) { - _JGroupList.addElement(JGroupArray[i]); - } - } //-- void setJGroup(jalview.binding.JGroup) - - /** - * Method setJSeq - * - * - * - * @param index - * @param vJSeq - */ - public void setJSeq(int index, jalview.binding.JSeq vJSeq) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _JSeqList.size())) { - throw new IndexOutOfBoundsException(); - } - _JSeqList.setElementAt(vJSeq, index); - } //-- void setJSeq(int, jalview.binding.JSeq) - - /** - * Method setJSeq - * - * - * - * @param JSeqArray - */ - public void setJSeq(jalview.binding.JSeq[] JSeqArray) - { - //-- copy array - _JSeqList.removeAllElements(); - for (int i = 0; i < JSeqArray.length; i++) { - _JSeqList.addElement(JSeqArray[i]); - } - } //-- void setJSeq(jalview.binding.JSeq) - - /** - * Method setTree - * - * - * - * @param index - * @param vTree - */ - public void setTree(int index, jalview.binding.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException(); - } - _treeList.setElementAt(vTree, index); - } //-- void setTree(int, jalview.binding.Tree) - - /** - * Method setTree - * - * - * - * @param treeArray - */ - public void setTree(jalview.binding.Tree[] treeArray) - { - //-- copy array - _treeList.removeAllElements(); - for (int i = 0; i < treeArray.length; i++) { - _treeList.addElement(treeArray[i]); - } - } //-- void setTree(jalview.binding.Tree) - - /** - * Method setUserColours - * - * - * - * @param index - * @param vUserColours - */ - public void setUserColours(int index, jalview.binding.UserColours vUserColours) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _userColoursList.size())) { - throw new IndexOutOfBoundsException(); - } - _userColoursList.setElementAt(vUserColours, index); - } //-- void setUserColours(int, jalview.binding.UserColours) - - /** - * Method setUserColours - * - * - * - * @param userColoursArray - */ - public void setUserColours(jalview.binding.UserColours[] userColoursArray) - { - //-- copy array - _userColoursList.removeAllElements(); - for (int i = 0; i < userColoursArray.length; i++) { - _userColoursList.addElement(userColoursArray[i]); - } - } //-- void setUserColours(jalview.binding.UserColours) - - /** - * Method setViewport - * - * - * - * @param index - * @param vViewport - */ - public void setViewport(int index, jalview.binding.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _viewportList.size())) { - throw new IndexOutOfBoundsException(); - } - _viewportList.setElementAt(vViewport, index); - } //-- void setViewport(int, jalview.binding.Viewport) - - /** - * Method setViewport - * - * - * - * @param viewportArray - */ - public void setViewport(jalview.binding.Viewport[] viewportArray) - { - //-- copy array - _viewportList.removeAllElements(); - for (int i = 0; i < viewportArray.length; i++) { - _viewportList.addElement(viewportArray[i]); - } - } //-- void setViewport(jalview.binding.Viewport) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + +//---------------------------------/ +//- 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.binding.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.binding.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.binding.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.binding.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.binding.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.binding.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.binding.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.binding.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.binding.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.binding.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.binding.Viewport vViewport) + throws java.lang.IndexOutOfBoundsException + { + this._viewportList.add(index, vViewport); + } + + /** + * Method enumerateJGroup. + * + * @return an Enumeration over all jalview.binding.JGroup elements + */ + public java.util.Enumeration enumerateJGroup() + { + return this._JGroupList.elements(); + } + + /** + * Method enumerateJSeq. + * + * @return an Enumeration over all jalview.binding.JSeq elements + */ + public java.util.Enumeration enumerateJSeq() + { + return this._JSeqList.elements(); + } + + /** + * Method enumerateTree. + * + * @return an Enumeration over all jalview.binding.Tree elements + */ + public java.util.Enumeration enumerateTree() + { + return this._treeList.elements(); + } + + /** + * Method enumerateUserColours. + * + * @return an Enumeration over all jalview.binding.UserColours elements + */ + public java.util.Enumeration enumerateUserColours() + { + return this._userColoursList.elements(); + } + + /** + * Method enumerateViewport. + * + * @return an Enumeration over all jalview.binding.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.binding.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.binding.JGroup at the given index + */ + public jalview.binding.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.binding.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.binding.JGroup[] getJGroup() + { + jalview.binding.JGroup[] array = new jalview.binding.JGroup[0]; + return (jalview.binding.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.binding.JSeq at the given index + */ + public jalview.binding.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.binding.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.binding.JSeq[] getJSeq() + { + jalview.binding.JSeq[] array = new jalview.binding.JSeq[0]; + return (jalview.binding.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.binding.Tree at the given index + */ + public jalview.binding.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.binding.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.binding.Tree[] getTree() + { + jalview.binding.Tree[] array = new jalview.binding.Tree[0]; + return (jalview.binding.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.binding.UserColours at the given index + */ + public jalview.binding.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.binding.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.binding.UserColours[] getUserColours() + { + jalview.binding.UserColours[] array = new jalview.binding.UserColours[0]; + return (jalview.binding.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.binding.Viewport at the given index + */ + public jalview.binding.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.binding.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.binding.Viewport[] getViewport() + { + jalview.binding.Viewport[] array = new jalview.binding.Viewport[0]; + return (jalview.binding.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.binding.JGroup vJGroup) + { + boolean removed = _JGroupList.remove(vJGroup); + return removed; + } + + /** + * Method removeJGroupAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.JGroup removeJGroupAt(final int index) + { + java.lang.Object obj = this._JGroupList.remove(index); + return (jalview.binding.JGroup) obj; + } + + /** + * Method removeJSeq. + * + * @param vJSeq + * @return true if the object was removed from the collection. + */ + public boolean removeJSeq(final jalview.binding.JSeq vJSeq) + { + boolean removed = _JSeqList.remove(vJSeq); + return removed; + } + + /** + * Method removeJSeqAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.JSeq removeJSeqAt(final int index) + { + java.lang.Object obj = this._JSeqList.remove(index); + return (jalview.binding.JSeq) obj; + } + + /** + * Method removeTree. + * + * @param vTree + * @return true if the object was removed from the collection. + */ + public boolean removeTree(final jalview.binding.Tree vTree) + { + boolean removed = _treeList.remove(vTree); + return removed; + } + + /** + * Method removeTreeAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.Tree removeTreeAt(final int index) + { + java.lang.Object obj = this._treeList.remove(index); + return (jalview.binding.Tree) obj; + } + + /** + * Method removeUserColours. + * + * @param vUserColours + * @return true if the object was removed from the collection. + */ + public boolean removeUserColours( + final jalview.binding.UserColours vUserColours) + { + boolean removed = _userColoursList.remove(vUserColours); + return removed; + } + + /** + * Method removeUserColoursAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.UserColours removeUserColoursAt(final int index) + { + java.lang.Object obj = this._userColoursList.remove(index); + return (jalview.binding.UserColours) obj; + } + + /** + * Method removeViewport. + * + * @param vViewport + * @return true if the object was removed from the collection. + */ + public boolean removeViewport(final jalview.binding.Viewport vViewport) + { + boolean removed = _viewportList.remove(vViewport); + return removed; + } + + /** + * Method removeViewportAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.Viewport removeViewportAt(final int index) + { + java.lang.Object obj = this._viewportList.remove(index); + return (jalview.binding.Viewport) obj; + } + + /** + * Sets the value of field 'featureSettings'. + * + * @param featureSettings + * the value of field 'featureSettings'. + */ + public void setFeatureSettings( + final jalview.binding.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.binding.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.binding.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.binding.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.binding.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.binding.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.binding.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.binding.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.binding.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.binding.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.binding.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.binding.JalviewModelSequence + */ + public static jalview.binding.JalviewModelSequence unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException + { + return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal( + jalview.binding.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); + } + +}