/*
* This file is part of the Vamsas Client version 0.2.
* Copyright 2010 by Jim Procter, Iain Milne, Pierre Marguerite,
* Andrew Waterhouse and Dominik Lindner.
*
* Earlier versions have also been incorporated into Jalview version 2.4
* since 2008, and TOPALi version 2 since 2007.
*
* The Vamsas Client is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* The Vamsas Client 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 Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with the Vamsas Client. 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 uk.ac.vamsas.objects.core.Link[] getLink() { uk.ac.vamsas.objects.core.Link[] array = new uk.ac.vamsas.objects.core.Link[0]; return (uk.ac.vamsas.objects.core.Link[]) this._linkList.toArray(array); } /** * Method getLinkAsReference.Returns a reference to '_linkList'. No type * checking is performed on any modifications to the Vector. * * @return a reference to the Vector backing this class */ public java.util.Vector getLinkAsReference() { return this._linkList; } /** * Method getLinkCount. * * @return the size of this collection */ public int getLinkCount() { return this._linkList.size(); } /** * Method getMap. * * @param index * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection * @return the value of the uk.ac.vamsas.objects.core.Map at the given index */ public uk.ac.vamsas.objects.core.Map getMap(final int index) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._mapList.size()) { throw new IndexOutOfBoundsException("getMap: Index value '" + index + "' not in range [0.." + (this._mapList.size() - 1) + "]"); } return (uk.ac.vamsas.objects.core.Map) _mapList.get(index); } /** * Method getMap.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 uk.ac.vamsas.objects.core.Map[] getMap() { uk.ac.vamsas.objects.core.Map[] array = new uk.ac.vamsas.objects.core.Map[0]; return (uk.ac.vamsas.objects.core.Map[]) this._mapList.toArray(array); } /** * Method getMapAsReference.Returns a reference to '_mapList'. No type * checking is performed on any modifications to the Vector. * * @return a reference to the Vector backing this class */ public java.util.Vector getMapAsReference() { return this._mapList; } /** * Method getMapCount. * * @return the size of this collection */ public int getMapCount() { return this._mapList.size(); } /** * Method getProperty. * * @param index * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection * @return the value of the uk.ac.vamsas.objects.core.Property at the given * index */ public uk.ac.vamsas.objects.core.Property getProperty(final int index) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._propertyList.size()) { throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]"); } return (uk.ac.vamsas.objects.core.Property) _propertyList.get(index); } /** * Method getProperty.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 uk.ac.vamsas.objects.core.Property[] getProperty() { uk.ac.vamsas.objects.core.Property[] array = new uk.ac.vamsas.objects.core.Property[0]; return (uk.ac.vamsas.objects.core.Property[]) this._propertyList .toArray(array); } /** * Method getPropertyAsReference.Returns a reference to '_propertyList'. No * type checking is performed on any modifications to the Vector. * * @return a reference to the Vector backing this class */ public java.util.Vector getPropertyAsReference() { return this._propertyList; } /** * Method getPropertyCount. * * @return the size of this collection */ public int getPropertyCount() { return this._propertyList.size(); } /** * Returns the value of field 'source'. The field 'source' has the following * description: TODO Database Naming Convention: either start using LSID (so * change type to URI) or leave this as an uncontrolled/unspecified string ID * * * @return the value of field 'Source'. */ public java.lang.String getSource() { return this._source; } /** * Returns the value of field 'version'. The field 'version' has the following * description: Version must be specified - * * * @return the value of field 'Version'. */ public java.lang.String getVersion() { return this._version; } /** * Overrides the java.lang.Object.hashCode method. *
* The following steps came from Effective Java Programming Language * Guide by Joshua Bloch, Chapter 3 * * @return a hash code value for the object. */ public int hashCode() { int result = super.hashCode(); long tmp; if (_source != null && !org.castor.util.CycleBreaker.startingToCycle(_source)) { result = 37 * result + _source.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_source); } if (_version != null && !org.castor.util.CycleBreaker.startingToCycle(_version)) { result = 37 * result + _version.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_version); } if (_accessionId != null && !org.castor.util.CycleBreaker.startingToCycle(_accessionId)) { result = 37 * result + _accessionId.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_accessionId); } if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) { result = 37 * result + _id.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_id); } if (_mapList != null && !org.castor.util.CycleBreaker.startingToCycle(_mapList)) { result = 37 * result + _mapList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_mapList); } if (_linkList != null && !org.castor.util.CycleBreaker.startingToCycle(_linkList)) { result = 37 * result + _linkList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_linkList); } if (_propertyList != null && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) { result = 37 * result + _propertyList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList); } return result; } /** * 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 removeAllLink() { this._linkList.clear(); } /** */ public void removeAllMap() { this._mapList.clear(); } /** */ public void removeAllProperty() { this._propertyList.clear(); } /** * Method removeLink. * * @param vLink * @return true if the object was removed from the collection. */ public boolean removeLink(final uk.ac.vamsas.objects.core.Link vLink) { boolean removed = _linkList.remove(vLink); return removed; } /** * Method removeLinkAt. * * @param index * @return the element removed from the collection */ public uk.ac.vamsas.objects.core.Link removeLinkAt(final int index) { java.lang.Object obj = this._linkList.remove(index); return (uk.ac.vamsas.objects.core.Link) obj; } /** * Method removeMap. * * @param vMap * @return true if the object was removed from the collection. */ public boolean removeMap(final uk.ac.vamsas.objects.core.Map vMap) { boolean removed = _mapList.remove(vMap); return removed; } /** * Method removeMapAt. * * @param index * @return the element removed from the collection */ public uk.ac.vamsas.objects.core.Map removeMapAt(final int index) { java.lang.Object obj = this._mapList.remove(index); return (uk.ac.vamsas.objects.core.Map) obj; } /** * Method removeProperty. * * @param vProperty * @return true if the object was removed from the collection. */ public boolean removeProperty( final uk.ac.vamsas.objects.core.Property vProperty) { boolean removed = _propertyList.remove(vProperty); return removed; } /** * Method removePropertyAt. * * @param index * @return the element removed from the collection */ public uk.ac.vamsas.objects.core.Property removePropertyAt(final int index) { java.lang.Object obj = this._propertyList.remove(index); return (uk.ac.vamsas.objects.core.Property) obj; } /** * Sets the value of field 'accessionId'. The field 'accessionId' has the * following description: TODO: make some specification of the database field * from which this accessionId is taken from - should that be a special * property of the dbRef object ? * * * @param accessionId * the value of field 'accessionId'. */ public void setAccessionId(final java.lang.String accessionId) { this._accessionId = accessionId; } /** * Sets the value of field 'id'. The field 'id' has the following description: * Primary Key for vamsas object referencing * * @param id * the value of field 'id'. */ public void setId(final java.lang.String id) { this._id = id; } /** * * * @param index * @param vLink * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setLink(final int index, final uk.ac.vamsas.objects.core.Link vLink) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._linkList.size()) { throw new IndexOutOfBoundsException("setLink: Index value '" + index + "' not in range [0.." + (this._linkList.size() - 1) + "]"); } this._linkList.set(index, vLink); } /** * * * @param vLinkArray */ public void setLink(final uk.ac.vamsas.objects.core.Link[] vLinkArray) { // -- copy array _linkList.clear(); for (int i = 0; i < vLinkArray.length; i++) { this._linkList.add(vLinkArray[i]); } } /** * Sets the value of '_linkList' by copying the given Vector. All elements * will be checked for type safety. * * @param vLinkList * the Vector to copy. */ public void setLink(final java.util.Vector vLinkList) { // copy vector this._linkList.clear(); this._linkList.addAll(vLinkList); } /** * Sets the value of '_linkList' by setting it to the given Vector. No type * checking is performed. * * @deprecated * * @param linkVector * the Vector to set. */ public void setLinkAsReference(final java.util.Vector linkVector) { this._linkList = linkVector; } /** * * * @param index * @param vMap * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setMap(final int index, final uk.ac.vamsas.objects.core.Map vMap) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._mapList.size()) { throw new IndexOutOfBoundsException("setMap: Index value '" + index + "' not in range [0.." + (this._mapList.size() - 1) + "]"); } this._mapList.set(index, vMap); } /** * * * @param vMapArray */ public void setMap(final uk.ac.vamsas.objects.core.Map[] vMapArray) { // -- copy array _mapList.clear(); for (int i = 0; i < vMapArray.length; i++) { this._mapList.add(vMapArray[i]); } } /** * Sets the value of '_mapList' by copying the given Vector. All elements will * be checked for type safety. * * @param vMapList * the Vector to copy. */ public void setMap(final java.util.Vector vMapList) { // copy vector this._mapList.clear(); this._mapList.addAll(vMapList); } /** * Sets the value of '_mapList' by setting it to the given Vector. No type * checking is performed. * * @deprecated * * @param mapVector * the Vector to set. */ public void setMapAsReference(final java.util.Vector mapVector) { this._mapList = mapVector; } /** * * * @param index * @param vProperty * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setProperty(final int index, final uk.ac.vamsas.objects.core.Property vProperty) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._propertyList.size()) { throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]"); } this._propertyList.set(index, vProperty); } /** * * * @param vPropertyArray */ public void setProperty( final uk.ac.vamsas.objects.core.Property[] vPropertyArray) { // -- copy array _propertyList.clear(); for (int i = 0; i < vPropertyArray.length; i++) { this._propertyList.add(vPropertyArray[i]); } } /** * Sets the value of '_propertyList' by copying the given Vector. All elements * will be checked for type safety. * * @param vPropertyList * the Vector to copy. */ public void setProperty(final java.util.Vector vPropertyList) { // copy vector this._propertyList.clear(); this._propertyList.addAll(vPropertyList); } /** * Sets the value of '_propertyList' by setting it to the given Vector. No * type checking is performed. * * @deprecated * * @param propertyVector * the Vector to set. */ public void setPropertyAsReference(final java.util.Vector propertyVector) { this._propertyList = propertyVector; } /** * Sets the value of field 'source'. The field 'source' has the following * description: TODO Database Naming Convention: either start using LSID (so * change type to URI) or leave this as an uncontrolled/unspecified string ID * * * @param source * the value of field 'source'. */ public void setSource(final java.lang.String source) { this._source = source; } /** * Sets the value of field 'version'. The field 'version' has the following * description: Version must be specified - * * * @param version * the value of field 'version'. */ public void setVersion(final java.lang.String version) { this._version = version; } /** * 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 uk.ac.vamsas.objects.core.DbRef */ public static uk.ac.vamsas.objects.core.DbRef unmarshal( final java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (uk.ac.vamsas.objects.core.DbRef) Unmarshaller.unmarshal( uk.ac.vamsas.objects.core.DbRef.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); } }