/*
* 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
* 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.Alignment[] getAlignment() { uk.ac.vamsas.objects.core.Alignment[] array = new uk.ac.vamsas.objects.core.Alignment[0]; return (uk.ac.vamsas.objects.core.Alignment[]) this._alignmentList .toArray(array); } /** * Method getAlignmentAsReference.Returns a reference to '_alignmentList'. No * type checking is performed on any modifications to the Vector. * * @return a reference to the Vector backing this class */ public java.util.Vector getAlignmentAsReference() { return this._alignmentList; } /** * Method getAlignmentCount. * * @return the size of this collection */ public int getAlignmentCount() { return this._alignmentList.size(); } /** * Method getDataSetAnnotations. * * @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.DataSetAnnotations at * the given index */ public uk.ac.vamsas.objects.core.DataSetAnnotations getDataSetAnnotations( final int index) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._dataSetAnnotationsList.size()) { throw new IndexOutOfBoundsException( "getDataSetAnnotations: Index value '" + index + "' not in range [0.." + (this._dataSetAnnotationsList.size() - 1) + "]"); } return (uk.ac.vamsas.objects.core.DataSetAnnotations) _dataSetAnnotationsList .get(index); } /** * Method getDataSetAnnotations.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.DataSetAnnotations[] getDataSetAnnotations() { uk.ac.vamsas.objects.core.DataSetAnnotations[] array = new uk.ac.vamsas.objects.core.DataSetAnnotations[0]; return (uk.ac.vamsas.objects.core.DataSetAnnotations[]) this._dataSetAnnotationsList .toArray(array); } /** * Method getDataSetAnnotationsAsReference.Returns a reference to * '_dataSetAnnotationsList'. No type checking is performed on any * modifications to the Vector. * * @return a reference to the Vector backing this class */ public java.util.Vector getDataSetAnnotationsAsReference() { return this._dataSetAnnotationsList; } /** * Method getDataSetAnnotationsCount. * * @return the size of this collection */ public int getDataSetAnnotationsCount() { return this._dataSetAnnotationsList.size(); } /** * 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 'provenance'. * * @return the value of field 'Provenance'. */ public uk.ac.vamsas.objects.core.Provenance getProvenance() { return this._provenance; } /** * Method getSequence. * * @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.Sequence at the given * index */ public uk.ac.vamsas.objects.core.Sequence getSequence(final int index) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._sequenceList.size()) { throw new IndexOutOfBoundsException("getSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]"); } return (uk.ac.vamsas.objects.core.Sequence) _sequenceList.get(index); } /** * Method getSequence.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.Sequence[] getSequence() { uk.ac.vamsas.objects.core.Sequence[] array = new uk.ac.vamsas.objects.core.Sequence[0]; return (uk.ac.vamsas.objects.core.Sequence[]) this._sequenceList .toArray(array); } /** * Method getSequenceAsReference.Returns a reference to '_sequenceList'. No * type checking is performed on any modifications to the Vector. * * @return a reference to the Vector backing this class */ public java.util.Vector getSequenceAsReference() { return this._sequenceList; } /** * Method getSequenceCount. * * @return the size of this collection */ public int getSequenceCount() { return this._sequenceList.size(); } /** * Method getSequenceMapping. * * @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.SequenceMapping at the * given index */ public uk.ac.vamsas.objects.core.SequenceMapping getSequenceMapping( final int index) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._sequenceMappingList.size()) { throw new IndexOutOfBoundsException("getSequenceMapping: Index value '" + index + "' not in range [0.." + (this._sequenceMappingList.size() - 1) + "]"); } return (uk.ac.vamsas.objects.core.SequenceMapping) _sequenceMappingList .get(index); } /** * Method getSequenceMapping.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.SequenceMapping[] getSequenceMapping() { uk.ac.vamsas.objects.core.SequenceMapping[] array = new uk.ac.vamsas.objects.core.SequenceMapping[0]; return (uk.ac.vamsas.objects.core.SequenceMapping[]) this._sequenceMappingList .toArray(array); } /** * Method getSequenceMappingAsReference.Returns a reference to * '_sequenceMappingList'. No type checking is performed on any modifications * to the Vector. * * @return a reference to the Vector backing this class */ public java.util.Vector getSequenceMappingAsReference() { return this._sequenceMappingList; } /** * Method getSequenceMappingCount. * * @return the size of this collection */ public int getSequenceMappingCount() { return this._sequenceMappingList.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 uk.ac.vamsas.objects.core.Tree at the given index */ public uk.ac.vamsas.objects.core.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 (uk.ac.vamsas.objects.core.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 uk.ac.vamsas.objects.core.Tree[] getTree() { uk.ac.vamsas.objects.core.Tree[] array = new uk.ac.vamsas.objects.core.Tree[0]; return (uk.ac.vamsas.objects.core.Tree[]) this._treeList.toArray(array); } /** * Method getTreeAsReference.Returns a reference to '_treeList'. No type * checking is performed on any modifications to the Vector. * * @return a reference to the Vector backing this class */ public java.util.Vector getTreeAsReference() { return this._treeList; } /** * Method getTreeCount. * * @return the size of this collection */ public int getTreeCount() { return this._treeList.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 (_sequenceList != null && !org.castor.util.CycleBreaker.startingToCycle(_sequenceList)) { result = 37 * result + _sequenceList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_sequenceList); } if (_sequenceMappingList != null && !org.castor.util.CycleBreaker.startingToCycle(_sequenceMappingList)) { result = 37 * result + _sequenceMappingList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_sequenceMappingList); } if (_dataSetAnnotationsList != null && !org.castor.util.CycleBreaker .startingToCycle(_dataSetAnnotationsList)) { result = 37 * result + _dataSetAnnotationsList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_dataSetAnnotationsList); } if (_alignmentList != null && !org.castor.util.CycleBreaker.startingToCycle(_alignmentList)) { result = 37 * result + _alignmentList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentList); } if (_treeList != null && !org.castor.util.CycleBreaker.startingToCycle(_treeList)) { result = 37 * result + _treeList.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_treeList); } if (_provenance != null && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) { result = 37 * result + _provenance.hashCode(); org.castor.util.CycleBreaker.releaseCycleHandle(_provenance); } 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); } /** * Method removeAlignment. * * @param vAlignment * @return true if the object was removed from the collection. */ public boolean removeAlignment( final uk.ac.vamsas.objects.core.Alignment vAlignment) { boolean removed = _alignmentList.remove(vAlignment); return removed; } /** * Method removeAlignmentAt. * * @param index * @return the element removed from the collection */ public uk.ac.vamsas.objects.core.Alignment removeAlignmentAt(final int index) { java.lang.Object obj = this._alignmentList.remove(index); return (uk.ac.vamsas.objects.core.Alignment) obj; } /** */ public void removeAllAlignment() { this._alignmentList.clear(); } /** */ public void removeAllDataSetAnnotations() { this._dataSetAnnotationsList.clear(); } /** */ public void removeAllSequence() { this._sequenceList.clear(); } /** */ public void removeAllSequenceMapping() { this._sequenceMappingList.clear(); } /** */ public void removeAllTree() { this._treeList.clear(); } /** * Method removeDataSetAnnotations. * * @param vDataSetAnnotations * @return true if the object was removed from the collection. */ public boolean removeDataSetAnnotations( final uk.ac.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations) { boolean removed = _dataSetAnnotationsList.remove(vDataSetAnnotations); return removed; } /** * Method removeDataSetAnnotationsAt. * * @param index * @return the element removed from the collection */ public uk.ac.vamsas.objects.core.DataSetAnnotations removeDataSetAnnotationsAt( final int index) { java.lang.Object obj = this._dataSetAnnotationsList.remove(index); return (uk.ac.vamsas.objects.core.DataSetAnnotations) obj; } /** * Method removeSequence. * * @param vSequence * @return true if the object was removed from the collection. */ public boolean removeSequence( final uk.ac.vamsas.objects.core.Sequence vSequence) { boolean removed = _sequenceList.remove(vSequence); return removed; } /** * Method removeSequenceAt. * * @param index * @return the element removed from the collection */ public uk.ac.vamsas.objects.core.Sequence removeSequenceAt(final int index) { java.lang.Object obj = this._sequenceList.remove(index); return (uk.ac.vamsas.objects.core.Sequence) obj; } /** * Method removeSequenceMapping. * * @param vSequenceMapping * @return true if the object was removed from the collection. */ public boolean removeSequenceMapping( final uk.ac.vamsas.objects.core.SequenceMapping vSequenceMapping) { boolean removed = _sequenceMappingList.remove(vSequenceMapping); return removed; } /** * Method removeSequenceMappingAt. * * @param index * @return the element removed from the collection */ public uk.ac.vamsas.objects.core.SequenceMapping removeSequenceMappingAt( final int index) { java.lang.Object obj = this._sequenceMappingList.remove(index); return (uk.ac.vamsas.objects.core.SequenceMapping) obj; } /** * Method removeTree. * * @param vTree * @return true if the object was removed from the collection. */ public boolean removeTree(final uk.ac.vamsas.objects.core.Tree vTree) { boolean removed = _treeList.remove(vTree); return removed; } /** * Method removeTreeAt. * * @param index * @return the element removed from the collection */ public uk.ac.vamsas.objects.core.Tree removeTreeAt(final int index) { java.lang.Object obj = this._treeList.remove(index); return (uk.ac.vamsas.objects.core.Tree) obj; } /** * * * @param index * @param vAlignment * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setAlignment(final int index, final uk.ac.vamsas.objects.core.Alignment vAlignment) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._alignmentList.size()) { throw new IndexOutOfBoundsException("setAlignment: Index value '" + index + "' not in range [0.." + (this._alignmentList.size() - 1) + "]"); } this._alignmentList.set(index, vAlignment); } /** * * * @param vAlignmentArray */ public void setAlignment( final uk.ac.vamsas.objects.core.Alignment[] vAlignmentArray) { // -- copy array _alignmentList.clear(); for (int i = 0; i < vAlignmentArray.length; i++) { this._alignmentList.add(vAlignmentArray[i]); } } /** * Sets the value of '_alignmentList' by copying the given Vector. All * elements will be checked for type safety. * * @param vAlignmentList * the Vector to copy. */ public void setAlignment(final java.util.Vector vAlignmentList) { // copy vector this._alignmentList.clear(); this._alignmentList.addAll(vAlignmentList); } /** * Sets the value of '_alignmentList' by setting it to the given Vector. No * type checking is performed. * * @deprecated * * @param alignmentVector * the Vector to set. */ public void setAlignmentAsReference(final java.util.Vector alignmentVector) { this._alignmentList = alignmentVector; } /** * * * @param index * @param vDataSetAnnotations * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setDataSetAnnotations(final int index, final uk.ac.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._dataSetAnnotationsList.size()) { throw new IndexOutOfBoundsException( "setDataSetAnnotations: Index value '" + index + "' not in range [0.." + (this._dataSetAnnotationsList.size() - 1) + "]"); } this._dataSetAnnotationsList.set(index, vDataSetAnnotations); } /** * * * @param vDataSetAnnotationsArray */ public void setDataSetAnnotations( final uk.ac.vamsas.objects.core.DataSetAnnotations[] vDataSetAnnotationsArray) { // -- copy array _dataSetAnnotationsList.clear(); for (int i = 0; i < vDataSetAnnotationsArray.length; i++) { this._dataSetAnnotationsList.add(vDataSetAnnotationsArray[i]); } } /** * Sets the value of '_dataSetAnnotationsList' by copying the given Vector. * All elements will be checked for type safety. * * @param vDataSetAnnotationsList * the Vector to copy. */ public void setDataSetAnnotations( final java.util.Vector vDataSetAnnotationsList) { // copy vector this._dataSetAnnotationsList.clear(); this._dataSetAnnotationsList.addAll(vDataSetAnnotationsList); } /** * Sets the value of '_dataSetAnnotationsList' by setting it to the given * Vector. No type checking is performed. * * @deprecated * * @param dataSetAnnotationsVector * the Vector to set. */ public void setDataSetAnnotationsAsReference( final java.util.Vector dataSetAnnotationsVector) { this._dataSetAnnotationsList = dataSetAnnotationsVector; } /** * 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 'provenance'. * * @param provenance * the value of field 'provenance'. */ public void setProvenance( final uk.ac.vamsas.objects.core.Provenance provenance) { this._provenance = provenance; } /** * * * @param index * @param vSequence * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setSequence(final int index, final uk.ac.vamsas.objects.core.Sequence vSequence) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._sequenceList.size()) { throw new IndexOutOfBoundsException("setSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]"); } this._sequenceList.set(index, vSequence); } /** * * * @param vSequenceArray */ public void setSequence( final uk.ac.vamsas.objects.core.Sequence[] vSequenceArray) { // -- copy array _sequenceList.clear(); for (int i = 0; i < vSequenceArray.length; i++) { this._sequenceList.add(vSequenceArray[i]); } } /** * Sets the value of '_sequenceList' by copying the given Vector. All elements * will be checked for type safety. * * @param vSequenceList * the Vector to copy. */ public void setSequence(final java.util.Vector vSequenceList) { // copy vector this._sequenceList.clear(); this._sequenceList.addAll(vSequenceList); } /** * Sets the value of '_sequenceList' by setting it to the given Vector. No * type checking is performed. * * @deprecated * * @param sequenceVector * the Vector to set. */ public void setSequenceAsReference(final java.util.Vector sequenceVector) { this._sequenceList = sequenceVector; } /** * * * @param index * @param vSequenceMapping * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setSequenceMapping(final int index, final uk.ac.vamsas.objects.core.SequenceMapping vSequenceMapping) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._sequenceMappingList.size()) { throw new IndexOutOfBoundsException("setSequenceMapping: Index value '" + index + "' not in range [0.." + (this._sequenceMappingList.size() - 1) + "]"); } this._sequenceMappingList.set(index, vSequenceMapping); } /** * * * @param vSequenceMappingArray */ public void setSequenceMapping( final uk.ac.vamsas.objects.core.SequenceMapping[] vSequenceMappingArray) { // -- copy array _sequenceMappingList.clear(); for (int i = 0; i < vSequenceMappingArray.length; i++) { this._sequenceMappingList.add(vSequenceMappingArray[i]); } } /** * Sets the value of '_sequenceMappingList' by copying the given Vector. All * elements will be checked for type safety. * * @param vSequenceMappingList * the Vector to copy. */ public void setSequenceMapping(final java.util.Vector vSequenceMappingList) { // copy vector this._sequenceMappingList.clear(); this._sequenceMappingList.addAll(vSequenceMappingList); } /** * Sets the value of '_sequenceMappingList' by setting it to the given Vector. * No type checking is performed. * * @deprecated * * @param sequenceMappingVector * the Vector to set. */ public void setSequenceMappingAsReference( final java.util.Vector sequenceMappingVector) { this._sequenceMappingList = sequenceMappingVector; } /** * * * @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 uk.ac.vamsas.objects.core.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 uk.ac.vamsas.objects.core.Tree[] vTreeArray) { // -- copy array _treeList.clear(); for (int i = 0; i < vTreeArray.length; i++) { this._treeList.add(vTreeArray[i]); } } /** * Sets the value of '_treeList' by copying the given Vector. All elements * will be checked for type safety. * * @param vTreeList * the Vector to copy. */ public void setTree(final java.util.Vector vTreeList) { // copy vector this._treeList.clear(); this._treeList.addAll(vTreeList); } /** * Sets the value of '_treeList' by setting it to the given Vector. No type * checking is performed. * * @deprecated * * @param treeVector * the Vector to set. */ public void setTreeAsReference(final java.util.Vector treeVector) { this._treeList = treeVector; } /** * 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.DataSet */ public static uk.ac.vamsas.objects.core.DataSet unmarshal( final java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (uk.ac.vamsas.objects.core.DataSet) Unmarshaller.unmarshal( uk.ac.vamsas.objects.core.DataSet.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); } }