X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FSequence.java;h=461b7d13db806f869c6a6f0bc90b67501a2ecd8b;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hp=03ea13a9508d11e586d3dff73bcecc714942c654;hpb=eae55a9d436c058b8f03036faa0a4baa930c2cd5;p=vamsas.git diff --git a/src/uk/ac/vamsas/objects/core/Sequence.java b/src/uk/ac/vamsas/objects/core/Sequence.java index 03ea13a..461b7d1 100644 --- a/src/uk/ac/vamsas/objects/core/Sequence.java +++ b/src/uk/ac/vamsas/objects/core/Sequence.java @@ -1,14 +1,28 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * This file is part of the Vamsas Client version 0.1. + * Copyright 2009 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 . */ - package uk.ac.vamsas.objects.core; - //---------------------------------/ - //- Imported classes and packages -/ +//---------------------------------/ +//- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -17,639 +31,707 @@ import org.exolab.castor.xml.Unmarshaller; /** * Class Sequence. * - * @version $Revision$ $Date$ + * @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007) + * $ */ -public class Sequence extends uk.ac.vamsas.objects.core.SequenceType -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Primary Key for vamsas object referencing - * - */ - private java.lang.String _id; - - /** - * symbol class for sequence - * - */ - private java.lang.String _dictionary; - - /** - * Store a list of database references - * for this sequence record - with optional mapping - * from database sequence to the given sequence record - */ - private java.util.Vector _dbRefList; - - /** - * explicitly named cross reference to other objects in the - * document. - * - */ - private java.util.Vector _vxrefList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Sequence() { - super(); - this._dbRefList = new java.util.Vector(); - this._vxrefList = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vDbRef - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addDbRef( - final uk.ac.vamsas.objects.core.DbRef vDbRef) - throws java.lang.IndexOutOfBoundsException { - this._dbRefList.addElement(vDbRef); - } - - /** - * - * - * @param index - * @param vDbRef - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addDbRef( - final int index, - final uk.ac.vamsas.objects.core.DbRef vDbRef) - throws java.lang.IndexOutOfBoundsException { - this._dbRefList.add(index, vDbRef); - } - - /** - * - * - * @param vVxref - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addVxref( - final uk.ac.vamsas.objects.core.Vxref vVxref) - throws java.lang.IndexOutOfBoundsException { - this._vxrefList.addElement(vVxref); - } - - /** - * - * - * @param index - * @param vVxref - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addVxref( - final int index, - final uk.ac.vamsas.objects.core.Vxref vVxref) - throws java.lang.IndexOutOfBoundsException { - this._vxrefList.add(index, vVxref); - } - - /** - * Method enumerateDbRef. - * - * @return an Enumeration over all - * uk.ac.vamsas.objects.core.DbRef elements - */ - public java.util.Enumeration enumerateDbRef( - ) { - return this._dbRefList.elements(); - } - - /** - * Method enumerateVxref. - * - * @return an Enumeration over all - * uk.ac.vamsas.objects.core.Vxref elements - */ - public java.util.Enumeration enumerateVxref( - ) { - return this._vxrefList.elements(); - } - - /** - * Overrides the java.lang.Object.equals method. - * - * @param obj - * @return true if the objects are equal. - */ - public boolean equals( - final java.lang.Object obj) { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) +public class Sequence extends uk.ac.vamsas.objects.core.SequenceType implements + java.io.Serializable { + + // --------------------------/ + // - Class/Member Variables -/ + // --------------------------/ + + /** + * Primary Key for vamsas object referencing + * + */ + private java.lang.String _id; + + /** + * symbol class for sequence + * + */ + private java.lang.String _dictionary; + + /** + * Store a list of database references for this sequence record - with + * optional mapping from database sequence to the given sequence record + */ + private java.util.Vector _dbRefList; + + /** + * explicitly named cross reference to other objects in the document. + */ + private java.util.Vector _vxrefList; + + // ----------------/ + // - Constructors -/ + // ----------------/ + + public Sequence() { + super(); + this._dbRefList = new java.util.Vector(); + this._vxrefList = new java.util.Vector(); + } + + // -----------/ + // - Methods -/ + // -----------/ + + /** + * + * + * @param vDbRef + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addDbRef(final uk.ac.vamsas.objects.core.DbRef vDbRef) + throws java.lang.IndexOutOfBoundsException { + this._dbRefList.addElement(vDbRef); + } + + /** + * + * + * @param index + * @param vDbRef + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addDbRef(final int index, + final uk.ac.vamsas.objects.core.DbRef vDbRef) + throws java.lang.IndexOutOfBoundsException { + this._dbRefList.add(index, vDbRef); + } + + /** + * + * + * @param vVxref + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addVxref(final uk.ac.vamsas.objects.core.Vxref vVxref) + throws java.lang.IndexOutOfBoundsException { + this._vxrefList.addElement(vVxref); + } + + /** + * + * + * @param index + * @param vVxref + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addVxref(final int index, + final uk.ac.vamsas.objects.core.Vxref vVxref) + throws java.lang.IndexOutOfBoundsException { + this._vxrefList.add(index, vVxref); + } + + /** + * Method enumerateDbRef. + * + * @return an Enumeration over all uk.ac.vamsas.objects.core.DbRef elements + */ + public java.util.Enumeration enumerateDbRef() { + return this._dbRefList.elements(); + } + + /** + * Method enumerateVxref. + * + * @return an Enumeration over all uk.ac.vamsas.objects.core.Vxref elements + */ + public java.util.Enumeration enumerateVxref() { + return this._vxrefList.elements(); + } + + /** + * Overrides the java.lang.Object.equals method. + * + * @param obj + * @return true if the objects are equal. + */ + public boolean equals(final java.lang.Object obj) { + if (this == obj) + return true; + + if (super.equals(obj) == false) + return false; + + if (obj instanceof Sequence) { + + Sequence temp = (Sequence) obj; + boolean thcycle; + boolean tmcycle; + if (this._id != null) { + if (temp._id == null) + return false; + if (this._id != temp._id) { + thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id); + tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + } + ; return false; - - if (obj instanceof Sequence) { - - Sequence temp = (Sequence)obj; - if (this._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; + } + if (!thcycle) { + if (!this._id.equals(temp._id)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + return false; } - else if (temp._id != null) - return false; - if (this._dictionary != null) { - if (temp._dictionary == null) return false; - else if (!(this._dictionary.equals(temp._dictionary))) - return false; + org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + } + } + } else if (temp._id != null) + return false; + if (this._dictionary != null) { + if (temp._dictionary == null) + return false; + if (this._dictionary != temp._dictionary) { + thcycle = org.castor.util.CycleBreaker + .startingToCycle(this._dictionary); + tmcycle = org.castor.util.CycleBreaker + .startingToCycle(temp._dictionary); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._dictionary); } - else if (temp._dictionary != null) - return false; - if (this._dbRefList != null) { - if (temp._dbRefList == null) return false; - else if (!(this._dbRefList.equals(temp._dbRefList))) - return false; + ; + if (!tmcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(temp._dictionary); } - else if (temp._dbRefList != null) - return false; - if (this._vxrefList != null) { - if (temp._vxrefList == null) return false; - else if (!(this._vxrefList.equals(temp._vxrefList))) - return false; + ; + return false; + } + if (!thcycle) { + if (!this._dictionary.equals(temp._dictionary)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._dictionary); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._dictionary); + return false; } - else if (temp._vxrefList != null) - return false; - return true; + org.castor.util.CycleBreaker.releaseCycleHandle(this._dictionary); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._dictionary); + } } + } else if (temp._dictionary != null) return false; - } - - /** - * Method getDbRef. - * - * @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.DbRef at - * the given index - */ - public uk.ac.vamsas.objects.core.DbRef getDbRef( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._dbRefList.size()) { - throw new IndexOutOfBoundsException("getDbRef: Index value '" + index + "' not in range [0.." + (this._dbRefList.size() - 1) + "]"); - } - - return (uk.ac.vamsas.objects.core.DbRef) _dbRefList.get(index); - } - - /** - * Method getDbRef.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.DbRef[] getDbRef( - ) { - uk.ac.vamsas.objects.core.DbRef[] array = new uk.ac.vamsas.objects.core.DbRef[0]; - return (uk.ac.vamsas.objects.core.DbRef[]) this._dbRefList.toArray(array); - } - - /** - * Method getDbRefAsReference.Returns a reference to - * '_dbRefList'. No type checking is performed on any - * modifications to the Vector. - * - * @return a reference to the Vector backing this class - */ - public java.util.Vector getDbRefAsReference( - ) { - return this._dbRefList; - } - - /** - * Method getDbRefCount. - * - * @return the size of this collection - */ - public int getDbRefCount( - ) { - return this._dbRefList.size(); - } - - /** - * Returns the value of field 'dictionary'. The field - * 'dictionary' has the following description: symbol class for - * sequence - * - * - * @return the value of field 'Dictionary'. - */ - public java.lang.String getDictionary( - ) { - return this._dictionary; - } - - /** - * 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; - } - - /** - * Method getVxref. - * - * @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.Vxref at - * the given index - */ - public uk.ac.vamsas.objects.core.Vxref getVxref( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._vxrefList.size()) { - throw new IndexOutOfBoundsException("getVxref: Index value '" + index + "' not in range [0.." + (this._vxrefList.size() - 1) + "]"); - } - - return (uk.ac.vamsas.objects.core.Vxref) _vxrefList.get(index); - } - - /** - * Method getVxref.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.Vxref[] getVxref( - ) { - uk.ac.vamsas.objects.core.Vxref[] array = new uk.ac.vamsas.objects.core.Vxref[0]; - return (uk.ac.vamsas.objects.core.Vxref[]) this._vxrefList.toArray(array); - } - - /** - * Method getVxrefAsReference.Returns a reference to - * '_vxrefList'. No type checking is performed on any - * modifications to the Vector. - * - * @return a reference to the Vector backing this class - */ - public java.util.Vector getVxrefAsReference( - ) { - return this._vxrefList; - } - - /** - * Method getVxrefCount. - * - * @return the size of this collection - */ - public int getVxrefCount( - ) { - return this._vxrefList.size(); - } - - /** - * 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) { - result = 37 * result + _id.hashCode(); - } - if (_dictionary != null) { - result = 37 * result + _dictionary.hashCode(); - } - if (_dbRefList != null) { - result = 37 * result + _dbRefList.hashCode(); - } - if (_vxrefList != null) { - result = 37 * result + _vxrefList.hashCode(); - } - - 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) { + if (this._dbRefList != null) { + if (temp._dbRefList == null) + return false; + if (this._dbRefList != temp._dbRefList) { + thcycle = org.castor.util.CycleBreaker + .startingToCycle(this._dbRefList); + tmcycle = org.castor.util.CycleBreaker + .startingToCycle(temp._dbRefList); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._dbRefList); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(temp._dbRefList); + } + ; return false; + } + if (!thcycle) { + if (!this._dbRefList.equals(temp._dbRefList)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._dbRefList); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._dbRefList); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._dbRefList); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._dbRefList); + } } - 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 removeAllDbRef( - ) { - this._dbRefList.clear(); - } - - /** - */ - public void removeAllVxref( - ) { - this._vxrefList.clear(); - } - - /** - * Method removeDbRef. - * - * @param vDbRef - * @return true if the object was removed from the collection. - */ - public boolean removeDbRef( - final uk.ac.vamsas.objects.core.DbRef vDbRef) { - boolean removed = _dbRefList.remove(vDbRef); - return removed; - } - - /** - * Method removeDbRefAt. - * - * @param index - * @return the element removed from the collection - */ - public uk.ac.vamsas.objects.core.DbRef removeDbRefAt( - final int index) { - java.lang.Object obj = this._dbRefList.remove(index); - return (uk.ac.vamsas.objects.core.DbRef) obj; - } - - /** - * Method removeVxref. - * - * @param vVxref - * @return true if the object was removed from the collection. - */ - public boolean removeVxref( - final uk.ac.vamsas.objects.core.Vxref vVxref) { - boolean removed = _vxrefList.remove(vVxref); - return removed; - } - - /** - * Method removeVxrefAt. - * - * @param index - * @return the element removed from the collection - */ - public uk.ac.vamsas.objects.core.Vxref removeVxrefAt( - final int index) { - java.lang.Object obj = this._vxrefList.remove(index); - return (uk.ac.vamsas.objects.core.Vxref) obj; - } - - /** - * - * - * @param index - * @param vDbRef - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setDbRef( - final int index, - final uk.ac.vamsas.objects.core.DbRef vDbRef) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._dbRefList.size()) { - throw new IndexOutOfBoundsException("setDbRef: Index value '" + index + "' not in range [0.." + (this._dbRefList.size() - 1) + "]"); - } - - this._dbRefList.set(index, vDbRef); - } - - /** - * - * - * @param vDbRefArray - */ - public void setDbRef( - final uk.ac.vamsas.objects.core.DbRef[] vDbRefArray) { - //-- copy array - _dbRefList.clear(); - - for (int i = 0; i < vDbRefArray.length; i++) { - this._dbRefList.add(vDbRefArray[i]); - } - } - - /** - * Sets the value of '_dbRefList' by copying the given Vector. - * All elements will be checked for type safety. - * - * @param vDbRefList the Vector to copy. - */ - public void setDbRef( - final java.util.Vector vDbRefList) { - // copy vector - this._dbRefList.clear(); - - this._dbRefList.addAll(vDbRefList); - } - - /** - * Sets the value of '_dbRefList' by setting it to the given - * Vector. No type checking is performed. - * @deprecated - * - * @param dbRefVector the Vector to set. - */ - public void setDbRefAsReference( - final java.util.Vector dbRefVector) { - this._dbRefList = dbRefVector; - } - - /** - * Sets the value of field 'dictionary'. The field 'dictionary' - * has the following description: symbol class for sequence - * - * - * @param dictionary the value of field 'dictionary'. - */ - public void setDictionary( - final java.lang.String dictionary) { - this._dictionary = dictionary; - } - - /** - * 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 vVxref - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setVxref( - final int index, - final uk.ac.vamsas.objects.core.Vxref vVxref) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._vxrefList.size()) { - throw new IndexOutOfBoundsException("setVxref: Index value '" + index + "' not in range [0.." + (this._vxrefList.size() - 1) + "]"); - } - - this._vxrefList.set(index, vVxref); - } - - /** - * - * - * @param vVxrefArray - */ - public void setVxref( - final uk.ac.vamsas.objects.core.Vxref[] vVxrefArray) { - //-- copy array - _vxrefList.clear(); - - for (int i = 0; i < vVxrefArray.length; i++) { - this._vxrefList.add(vVxrefArray[i]); + } else if (temp._dbRefList != null) + return false; + if (this._vxrefList != null) { + if (temp._vxrefList == null) + return false; + if (this._vxrefList != temp._vxrefList) { + thcycle = org.castor.util.CycleBreaker + .startingToCycle(this._vxrefList); + tmcycle = org.castor.util.CycleBreaker + .startingToCycle(temp._vxrefList); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._vxrefList); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(temp._vxrefList); + } + ; + return false; + } + if (!thcycle) { + if (!this._vxrefList.equals(temp._vxrefList)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._vxrefList); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._vxrefList); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._vxrefList); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._vxrefList); + } } - } - - /** - * Sets the value of '_vxrefList' by copying the given Vector. - * All elements will be checked for type safety. - * - * @param vVxrefList the Vector to copy. - */ - public void setVxref( - final java.util.Vector vVxrefList) { - // copy vector - this._vxrefList.clear(); - - this._vxrefList.addAll(vVxrefList); - } - - /** - * Sets the value of '_vxrefList' by setting it to the given - * Vector. No type checking is performed. - * @deprecated - * - * @param vxrefVector the Vector to set. - */ - public void setVxrefAsReference( - final java.util.Vector vxrefVector) { - this._vxrefList = vxrefVector; - } - - /** - * 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.SequenceTyp - */ - public static uk.ac.vamsas.objects.core.SequenceType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (uk.ac.vamsas.objects.core.SequenceType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Sequence.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); - } + } else if (temp._vxrefList != null) + return false; + return true; + } + return false; + } + + /** + * Method getDbRef. + * + * @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.DbRef at the given index + */ + public uk.ac.vamsas.objects.core.DbRef getDbRef(final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._dbRefList.size()) { + throw new IndexOutOfBoundsException("getDbRef: Index value '" + index + + "' not in range [0.." + (this._dbRefList.size() - 1) + "]"); + } + + return (uk.ac.vamsas.objects.core.DbRef) _dbRefList.get(index); + } + + /** + * Method getDbRef.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.DbRef[] getDbRef() { + uk.ac.vamsas.objects.core.DbRef[] array = new uk.ac.vamsas.objects.core.DbRef[0]; + return (uk.ac.vamsas.objects.core.DbRef[]) this._dbRefList.toArray(array); + } + + /** + * Method getDbRefAsReference.Returns a reference to '_dbRefList'. No type + * checking is performed on any modifications to the Vector. + * + * @return a reference to the Vector backing this class + */ + public java.util.Vector getDbRefAsReference() { + return this._dbRefList; + } + + /** + * Method getDbRefCount. + * + * @return the size of this collection + */ + public int getDbRefCount() { + return this._dbRefList.size(); + } + + /** + * Returns the value of field 'dictionary'. The field 'dictionary' has the + * following description: symbol class for sequence + * + * + * @return the value of field 'Dictionary'. + */ + public java.lang.String getDictionary() { + return this._dictionary; + } + + /** + * 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; + } + + /** + * Method getVxref. + * + * @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.Vxref at the given index + */ + public uk.ac.vamsas.objects.core.Vxref getVxref(final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._vxrefList.size()) { + throw new IndexOutOfBoundsException("getVxref: Index value '" + index + + "' not in range [0.." + (this._vxrefList.size() - 1) + "]"); + } + + return (uk.ac.vamsas.objects.core.Vxref) _vxrefList.get(index); + } + + /** + * Method getVxref.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.Vxref[] getVxref() { + uk.ac.vamsas.objects.core.Vxref[] array = new uk.ac.vamsas.objects.core.Vxref[0]; + return (uk.ac.vamsas.objects.core.Vxref[]) this._vxrefList.toArray(array); + } + + /** + * Method getVxrefAsReference.Returns a reference to '_vxrefList'. No type + * checking is performed on any modifications to the Vector. + * + * @return a reference to the Vector backing this class + */ + public java.util.Vector getVxrefAsReference() { + return this._vxrefList; + } + + /** + * Method getVxrefCount. + * + * @return the size of this collection + */ + public int getVxrefCount() { + return this._vxrefList.size(); + } + + /** + * 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 (_dictionary != null + && !org.castor.util.CycleBreaker.startingToCycle(_dictionary)) { + result = 37 * result + _dictionary.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_dictionary); + } + if (_dbRefList != null + && !org.castor.util.CycleBreaker.startingToCycle(_dbRefList)) { + result = 37 * result + _dbRefList.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_dbRefList); + } + if (_vxrefList != null + && !org.castor.util.CycleBreaker.startingToCycle(_vxrefList)) { + result = 37 * result + _vxrefList.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_vxrefList); + } + + 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 removeAllDbRef() { + this._dbRefList.clear(); + } + + /** + */ + public void removeAllVxref() { + this._vxrefList.clear(); + } + + /** + * Method removeDbRef. + * + * @param vDbRef + * @return true if the object was removed from the collection. + */ + public boolean removeDbRef(final uk.ac.vamsas.objects.core.DbRef vDbRef) { + boolean removed = _dbRefList.remove(vDbRef); + return removed; + } + + /** + * Method removeDbRefAt. + * + * @param index + * @return the element removed from the collection + */ + public uk.ac.vamsas.objects.core.DbRef removeDbRefAt(final int index) { + java.lang.Object obj = this._dbRefList.remove(index); + return (uk.ac.vamsas.objects.core.DbRef) obj; + } + + /** + * Method removeVxref. + * + * @param vVxref + * @return true if the object was removed from the collection. + */ + public boolean removeVxref(final uk.ac.vamsas.objects.core.Vxref vVxref) { + boolean removed = _vxrefList.remove(vVxref); + return removed; + } + + /** + * Method removeVxrefAt. + * + * @param index + * @return the element removed from the collection + */ + public uk.ac.vamsas.objects.core.Vxref removeVxrefAt(final int index) { + java.lang.Object obj = this._vxrefList.remove(index); + return (uk.ac.vamsas.objects.core.Vxref) obj; + } + + /** + * + * + * @param index + * @param vDbRef + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setDbRef(final int index, + final uk.ac.vamsas.objects.core.DbRef vDbRef) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._dbRefList.size()) { + throw new IndexOutOfBoundsException("setDbRef: Index value '" + index + + "' not in range [0.." + (this._dbRefList.size() - 1) + "]"); + } + + this._dbRefList.set(index, vDbRef); + } + + /** + * + * + * @param vDbRefArray + */ + public void setDbRef(final uk.ac.vamsas.objects.core.DbRef[] vDbRefArray) { + // -- copy array + _dbRefList.clear(); + + for (int i = 0; i < vDbRefArray.length; i++) { + this._dbRefList.add(vDbRefArray[i]); + } + } + + /** + * Sets the value of '_dbRefList' by copying the given Vector. All elements + * will be checked for type safety. + * + * @param vDbRefList + * the Vector to copy. + */ + public void setDbRef(final java.util.Vector vDbRefList) { + // copy vector + this._dbRefList.clear(); + + this._dbRefList.addAll(vDbRefList); + } + + /** + * Sets the value of '_dbRefList' by setting it to the given Vector. No type + * checking is performed. + * + * @deprecated + * + * @param dbRefVector + * the Vector to set. + */ + public void setDbRefAsReference(final java.util.Vector dbRefVector) { + this._dbRefList = dbRefVector; + } + + /** + * Sets the value of field 'dictionary'. The field 'dictionary' has the + * following description: symbol class for sequence + * + * + * @param dictionary + * the value of field 'dictionary'. + */ + public void setDictionary(final java.lang.String dictionary) { + this._dictionary = dictionary; + } + + /** + * 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 vVxref + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setVxref(final int index, + final uk.ac.vamsas.objects.core.Vxref vVxref) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._vxrefList.size()) { + throw new IndexOutOfBoundsException("setVxref: Index value '" + index + + "' not in range [0.." + (this._vxrefList.size() - 1) + "]"); + } + + this._vxrefList.set(index, vVxref); + } + + /** + * + * + * @param vVxrefArray + */ + public void setVxref(final uk.ac.vamsas.objects.core.Vxref[] vVxrefArray) { + // -- copy array + _vxrefList.clear(); + + for (int i = 0; i < vVxrefArray.length; i++) { + this._vxrefList.add(vVxrefArray[i]); + } + } + + /** + * Sets the value of '_vxrefList' by copying the given Vector. All elements + * will be checked for type safety. + * + * @param vVxrefList + * the Vector to copy. + */ + public void setVxref(final java.util.Vector vVxrefList) { + // copy vector + this._vxrefList.clear(); + + this._vxrefList.addAll(vVxrefList); + } + + /** + * Sets the value of '_vxrefList' by setting it to the given Vector. No type + * checking is performed. + * + * @deprecated + * + * @param vxrefVector + * the Vector to set. + */ + public void setVxrefAsReference(final java.util.Vector vxrefVector) { + this._vxrefList = vxrefVector; + } + + /** + * 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.SequenceTyp + */ + public static uk.ac.vamsas.objects.core.SequenceType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException { + return (uk.ac.vamsas.objects.core.SequenceType) Unmarshaller.unmarshal( + uk.ac.vamsas.objects.core.Sequence.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); + } }