X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJalviewModelSequence.java;h=eb0716db88533811f3e969fe06d1505d12e74d9c;hb=9876fdccf311378e690c1f9e18db52675d427b89;hp=5ebcee6497257f7c581264eeaf9f21813dd882a9;hpb=cd07a161a10680208029f76aa46710c1032aae46;p=jalview.git diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java old mode 100755 new mode 100644 index 5ebcee6..eb0716d --- a/src/jalview/binding/JalviewModelSequence.java +++ b/src/jalview/binding/JalviewModelSequence.java @@ -7,8 +7,8 @@ package jalview.binding; - //---------------------------------/ - //- Imported classes and packages -/ +//---------------------------------/ +//- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -19,904 +19,937 @@ import org.exolab.castor.xml.Unmarshaller; * * @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); - } +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); + } }