/*
* 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.AnnotationElement[] getAnnotationElement() { uk.ac.vamsas.objects.core.AnnotationElement[] array = new uk.ac.vamsas.objects.core.AnnotationElement[0]; return (uk.ac.vamsas.objects.core.AnnotationElement[]) this._annotationElementList .toArray(array); } /** * Method getAnnotationElementAsReference.Returns a reference to * '_annotationElementList'. No type checking is performed on any * modifications to the Vector. * * @return a reference to the Vector backing this class */ public java.util.Vector getAnnotationElementAsReference() { return this._annotationElementList; } /** * Method getAnnotationElementCount. * * @return the size of this collection */ public int getAnnotationElementCount() { return this._annotationElementList.size(); } /** * Returns the value of field 'description'. The field 'description' has the * following description: Human readable description of the annotation * * * @return the value of field 'Description'. */ public java.lang.String getDescription() { return this._description; } /** * Returns the value of field 'group'. The field 'group' has the following * description: Annotation with the same non-empty group name are grouped * together * * @return the value of field 'Group'. */ public java.lang.String getGroup() { return this._group; } /** * Returns the value of field 'id'. The field 'id' has the following * description: Primary Key for vamsas object referencing * * * @return the value of field 'Id'. */ public java.lang.String getId() { return this._id; } /** * Returns the value of field 'label'. The field 'label' has the following * description: Short, meaningful name for the annotation - if this is absent, * then the type string should be used in its place. * * * @return the value of field 'Label'. */ public java.lang.String getLabel() { return this._label; } /** * Method getLink. * * @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.Link at the given index */ public uk.ac.vamsas.objects.core.Link getLink(final int index) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._linkList.size()) { throw new IndexOutOfBoundsException("getLink: Index value '" + index + "' not in range [0.." + (this._linkList.size() - 1) + "]"); } return (uk.ac.vamsas.objects.core.Link) _linkList.get(index); } /** * Method getLink.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.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(); } /** * Returns the value of field 'modifiable'. * * @return the value of field 'Modifiable'. */ public java.lang.String getModifiable() { return this._modifiable; } /** * 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(); } /** * Method getScore. * * @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.Score at the given index */ public uk.ac.vamsas.objects.core.Score getScore(final int index) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._scoreList.size()) { throw new IndexOutOfBoundsException("getScore: Index value '" + index + "' not in range [0.." + (this._scoreList.size() - 1) + "]"); } return (uk.ac.vamsas.objects.core.Score) _scoreList.get(index); } /** * Method getScore.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.Score[] getScore() { uk.ac.vamsas.objects.core.Score[] array = new uk.ac.vamsas.objects.core.Score[0]; return (uk.ac.vamsas.objects.core.Score[]) this._scoreList.toArray(array); } /** * Method getScoreAsReference.Returns a reference to '_scoreList'. No type * checking is performed on any modifications to the Vector. * * @return a reference to the Vector backing this class */ public java.util.Vector getScoreAsReference() { return this._scoreList; } /** * Method getScoreCount. * * @return the size of this collection */ public int getScoreCount() { return this._scoreList.size(); } /** * Returns the value of field 'status'. The field 'status' has the following * description: TODO: specify this - we have considered taking the GO evidence * codes as a model for assessing a measure of quality to an annotation. * * @return the value of field 'Status'. */ public java.lang.String getStatus() { return this._status; } /** * Returns the value of field 'type'. The field 'type' has the following * description: A Das Feature has both a type and a Type ID. We go the route * of requiring the type string to be taken from a controlled vocabulary if an * application expects others to make sense of it. The type may qualified - so * uniprot:CHAIN is a valid type name, and considered distinct from * someotherDB:CHAIN * * @return the value of field 'Type'. */ public java.lang.String getType() { return this._type; } /** * 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 (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) { result = 37 * result + _id.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_id); } if (_modifiable != null && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) { result = 37 * result + _modifiable.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable); } if (_group != null && !org.castor.util.CycleBreaker.startingToCycle(_group)) { result = 37 * result + _group.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_group); } if (_type != null && !org.castor.util.CycleBreaker.startingToCycle(_type)) { result = 37 * result + _type.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_type); } if (_label != null && !org.castor.util.CycleBreaker.startingToCycle(_label)) { result = 37 * result + _label.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_label); } if (_description != null && !org.castor.util.CycleBreaker.startingToCycle(_description)) { result = 37 * result + _description.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_description); } if (_status != null && !org.castor.util.CycleBreaker.startingToCycle(_status)) { result = 37 * result + _status.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_status); } if (_annotationElementList != null && !org.castor.util.CycleBreaker .startingToCycle(_annotationElementList)) { result = 37 * result + _annotationElementList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_annotationElementList); } if (_scoreList != null && !org.castor.util.CycleBreaker.startingToCycle(_scoreList)) { result = 37 * result + _scoreList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_scoreList); } 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 removeAllAnnotationElement() { this._annotationElementList.clear(); } /** */ public void removeAllLink() { this._linkList.clear(); } /** */ public void removeAllProperty() { this._propertyList.clear(); } /** */ public void removeAllScore() { this._scoreList.clear(); } /** * Method removeAnnotationElement. * * @param vAnnotationElement * @return true if the object was removed from the collection. */ public boolean removeAnnotationElement( final uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement) { boolean removed = _annotationElementList.remove(vAnnotationElement); return removed; } /** * Method removeAnnotationElementAt. * * @param index * @return the element removed from the collection */ public uk.ac.vamsas.objects.core.AnnotationElement removeAnnotationElementAt( final int index) { java.lang.Object obj = this._annotationElementList.remove(index); return (uk.ac.vamsas.objects.core.AnnotationElement) obj; } /** * 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 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; } /** * Method removeScore. * * @param vScore * @return true if the object was removed from the collection. */ public boolean removeScore(final uk.ac.vamsas.objects.core.Score vScore) { boolean removed = _scoreList.remove(vScore); return removed; } /** * Method removeScoreAt. * * @param index * @return the element removed from the collection */ public uk.ac.vamsas.objects.core.Score removeScoreAt(final int index) { java.lang.Object obj = this._scoreList.remove(index); return (uk.ac.vamsas.objects.core.Score) obj; } /** * * * @param index * @param vAnnotationElement * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setAnnotationElement(final int index, final uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._annotationElementList.size()) { throw new IndexOutOfBoundsException("setAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]"); } this._annotationElementList.set(index, vAnnotationElement); } /** * * * @param vAnnotationElementArray */ public void setAnnotationElement( final uk.ac.vamsas.objects.core.AnnotationElement[] vAnnotationElementArray) { // -- copy array _annotationElementList.clear(); for (int i = 0; i < vAnnotationElementArray.length; i++) { this._annotationElementList.add(vAnnotationElementArray[i]); } } /** * Sets the value of '_annotationElementList' by copying the given Vector. All * elements will be checked for type safety. * * @param vAnnotationElementList * the Vector to copy. */ public void setAnnotationElement(final java.util.Vector vAnnotationElementList) { // copy vector this._annotationElementList.clear(); this._annotationElementList.addAll(vAnnotationElementList); } /** * Sets the value of '_annotationElementList' by setting it to the given * Vector. No type checking is performed. * * @deprecated * * @param annotationElementVector * the Vector to set. */ public void setAnnotationElementAsReference( final java.util.Vector annotationElementVector) { this._annotationElementList = annotationElementVector; } /** * Sets the value of field 'description'. The field 'description' has the * following description: Human readable description of the annotation * * * @param description * the value of field 'description'. */ public void setDescription(final java.lang.String description) { this._description = description; } /** * Sets the value of field 'group'. The field 'group' has the following * description: Annotation with the same non-empty group name are grouped * together * * @param group * the value of field 'group'. */ public void setGroup(final java.lang.String group) { this._group = group; } /** * 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; } /** * Sets the value of field 'label'. The field 'label' has the following * description: Short, meaningful name for the annotation - if this is absent, * then the type string should be used in its place. * * * @param label * the value of field 'label'. */ public void setLabel(final java.lang.String label) { this._label = label; } /** * * * @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; } /** * Sets the value of field 'modifiable'. * * @param modifiable * the value of field 'modifiable'. */ public void setModifiable(final java.lang.String modifiable) { this._modifiable = modifiable; } /** * * * @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; } /** * * * @param index * @param vScore * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setScore(final int index, final uk.ac.vamsas.objects.core.Score vScore) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._scoreList.size()) { throw new IndexOutOfBoundsException("setScore: Index value '" + index + "' not in range [0.." + (this._scoreList.size() - 1) + "]"); } this._scoreList.set(index, vScore); } /** * * * @param vScoreArray */ public void setScore(final uk.ac.vamsas.objects.core.Score[] vScoreArray) { // -- copy array _scoreList.clear(); for (int i = 0; i < vScoreArray.length; i++) { this._scoreList.add(vScoreArray[i]); } } /** * Sets the value of '_scoreList' by copying the given Vector. All elements * will be checked for type safety. * * @param vScoreList * the Vector to copy. */ public void setScore(final java.util.Vector vScoreList) { // copy vector this._scoreList.clear(); this._scoreList.addAll(vScoreList); } /** * Sets the value of '_scoreList' by setting it to the given Vector. No type * checking is performed. * * @deprecated * * @param scoreVector * the Vector to set. */ public void setScoreAsReference(final java.util.Vector scoreVector) { this._scoreList = scoreVector; } /** * Sets the value of field 'status'. The field 'status' has the following * description: TODO: specify this - we have considered taking the GO evidence * codes as a model for assessing a measure of quality to an annotation. * * @param status * the value of field 'status'. */ public void setStatus(final java.lang.String status) { this._status = status; } /** * Sets the value of field 'type'. The field 'type' has the following * description: A Das Feature has both a type and a Type ID. We go the route * of requiring the type string to be taken from a controlled vocabulary if an * application expects others to make sense of it. The type may qualified - so * uniprot:CHAIN is a valid type name, and considered distinct from * someotherDB:CHAIN * * @param type * the value of field 'type'. */ public void setType(final java.lang.String type) { this._type = type; } /** * 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.RangeType */ public static uk.ac.vamsas.objects.core.RangeType unmarshal( final java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (uk.ac.vamsas.objects.core.RangeType) Unmarshaller.unmarshal( uk.ac.vamsas.objects.core.RangeAnnotation.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); } }