/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
* Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* Jalview 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. 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 jalview.schemabinding.version2.AlcodonFrame[] getAlcodonFrame() { jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0]; return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList .toArray(array); } /** * Method getAlcodonFrameCount. * * @return the size of this collection */ public int getAlcodonFrameCount() { return this._alcodonFrameList.size(); } /** * Method getAnnotation. * * @param index * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection * @return the value of the jalview.schemabinding.version2.Annotation at the * given index */ public jalview.schemabinding.version2.Annotation getAnnotation( final int index) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._annotationList.size()) { throw new IndexOutOfBoundsException("getAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]"); } return (jalview.schemabinding.version2.Annotation) _annotationList .get(index); } /** * Method getAnnotation.Returns the contents of the collection in an Array. *
* Note: Just in case the collection contents are changing in another thread, * we pass a 0-length Array of the correct type into the API call. This way we * know that the Array returned is of exactly the correct length. * * @return this collection as an Array */ public jalview.schemabinding.version2.Annotation[] getAnnotation() { jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0]; return (jalview.schemabinding.version2.Annotation[]) this._annotationList .toArray(array); } /** * Method getAnnotationCount. * * @return the size of this collection */ public int getAnnotationCount() { return this._annotationList.size(); } /** * Returns the value of field 'datasetId'. The field 'datasetId' has the * following description: reference to set where jalview will gather the * dataset sequences for all sequences in the set. * * * @return the value of field 'DatasetId'. */ public java.lang.String getDatasetId() { return this._datasetId; } /** * Returns the value of field 'gapChar'. * * @return the value of field 'GapChar'. */ public java.lang.String getGapChar() { return this._gapChar; } /** * Method getSequence. * * @param index * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection * @return the value of the jalview.schemabinding.version2.Sequence at the * given index */ public jalview.schemabinding.version2.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 (jalview.schemabinding.version2.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 jalview.schemabinding.version2.Sequence[] getSequence() { jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0]; return (jalview.schemabinding.version2.Sequence[]) this._sequenceList .toArray(array); } /** * Method getSequenceCount. * * @return the size of this collection */ public int getSequenceCount() { return this._sequenceList.size(); } /** * Method getSequenceSetProperties. * * @param index * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection * @return the value of the * jalview.schemabinding.version2.SequenceSetProperties at the given * index */ public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties( final int index) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._sequenceSetPropertiesList.size()) { throw new IndexOutOfBoundsException( "getSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]"); } return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList .get(index); } /** * Method getSequenceSetProperties.Returns the contents of the collection in * an Array. *
* Note: Just in case the collection contents are changing in another thread, * we pass a 0-length Array of the correct type into the API call. This way we * know that the Array returned is of exactly the correct length. * * @return this collection as an Array */ public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties() { jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0]; return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList .toArray(array); } /** * Method getSequenceSetPropertiesCount. * * @return the size of this collection */ public int getSequenceSetPropertiesCount() { return this._sequenceSetPropertiesList.size(); } /** * Method isValid. * * @return true if this object is valid according to the schema */ public boolean isValid() { try { validate(); } catch (org.exolab.castor.xml.ValidationException vex) { return false; } return true; } /** * * * @param out * @throws org.exolab.castor.xml.MarshalException * if object is null or if any SAXException is thrown during * marshaling * @throws org.exolab.castor.xml.ValidationException * if this object is an invalid instance according to the schema */ public void marshal(final java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { Marshaller.marshal(this, out); } /** * * * @param handler * @throws java.io.IOException * if an IOException occurs during marshaling * @throws org.exolab.castor.xml.ValidationException * if this object is an invalid instance according to the schema * @throws org.exolab.castor.xml.MarshalException * if object is null or if any SAXException is thrown during * marshaling */ public void marshal(final org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { Marshaller.marshal(this, handler); } /** * Method removeAlcodonFrame. * * @param vAlcodonFrame * @return true if the object was removed from the collection. */ public boolean removeAlcodonFrame( final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) { boolean removed = _alcodonFrameList.remove(vAlcodonFrame); return removed; } /** * Method removeAlcodonFrameAt. * * @param index * @return the element removed from the collection */ public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt( final int index) { java.lang.Object obj = this._alcodonFrameList.remove(index); return (jalview.schemabinding.version2.AlcodonFrame) obj; } /** */ public void removeAllAlcodonFrame() { this._alcodonFrameList.clear(); } /** */ public void removeAllAnnotation() { this._annotationList.clear(); } /** */ public void removeAllSequence() { this._sequenceList.clear(); } /** */ public void removeAllSequenceSetProperties() { this._sequenceSetPropertiesList.clear(); } /** * Method removeAnnotation. * * @param vAnnotation * @return true if the object was removed from the collection. */ public boolean removeAnnotation( final jalview.schemabinding.version2.Annotation vAnnotation) { boolean removed = _annotationList.remove(vAnnotation); return removed; } /** * Method removeAnnotationAt. * * @param index * @return the element removed from the collection */ public jalview.schemabinding.version2.Annotation removeAnnotationAt( final int index) { java.lang.Object obj = this._annotationList.remove(index); return (jalview.schemabinding.version2.Annotation) obj; } /** * Method removeSequence. * * @param vSequence * @return true if the object was removed from the collection. */ public boolean removeSequence( final jalview.schemabinding.version2.Sequence vSequence) { boolean removed = _sequenceList.remove(vSequence); return removed; } /** * Method removeSequenceAt. * * @param index * @return the element removed from the collection */ public jalview.schemabinding.version2.Sequence removeSequenceAt( final int index) { java.lang.Object obj = this._sequenceList.remove(index); return (jalview.schemabinding.version2.Sequence) obj; } /** * Method removeSequenceSetProperties. * * @param vSequenceSetProperties * @return true if the object was removed from the collection. */ public boolean removeSequenceSetProperties( final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) { boolean removed = _sequenceSetPropertiesList .remove(vSequenceSetProperties); return removed; } /** * Method removeSequenceSetPropertiesAt. * * @param index * @return the element removed from the collection */ public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt( final int index) { java.lang.Object obj = this._sequenceSetPropertiesList.remove(index); return (jalview.schemabinding.version2.SequenceSetProperties) obj; } /** * * * @param index * @param vAlcodonFrame * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setAlcodonFrame(final int index, final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._alcodonFrameList.size()) { throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]"); } this._alcodonFrameList.set(index, vAlcodonFrame); } /** * * * @param vAlcodonFrameArray */ public void setAlcodonFrame( final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray) { // -- copy array _alcodonFrameList.clear(); for (int i = 0; i < vAlcodonFrameArray.length; i++) { this._alcodonFrameList.add(vAlcodonFrameArray[i]); } } /** * * * @param index * @param vAnnotation * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setAnnotation(final int index, final jalview.schemabinding.version2.Annotation vAnnotation) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._annotationList.size()) { throw new IndexOutOfBoundsException("setAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]"); } this._annotationList.set(index, vAnnotation); } /** * * * @param vAnnotationArray */ public void setAnnotation( final jalview.schemabinding.version2.Annotation[] vAnnotationArray) { // -- copy array _annotationList.clear(); for (int i = 0; i < vAnnotationArray.length; i++) { this._annotationList.add(vAnnotationArray[i]); } } /** * Sets the value of field 'datasetId'. The field 'datasetId' has the * following description: reference to set where jalview will gather the * dataset sequences for all sequences in the set. * * * @param datasetId * the value of field 'datasetId'. */ public void setDatasetId(final java.lang.String datasetId) { this._datasetId = datasetId; } /** * Sets the value of field 'gapChar'. * * @param gapChar * the value of field 'gapChar'. */ public void setGapChar(final java.lang.String gapChar) { this._gapChar = gapChar; } /** * * * @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 jalview.schemabinding.version2.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 jalview.schemabinding.version2.Sequence[] vSequenceArray) { // -- copy array _sequenceList.clear(); for (int i = 0; i < vSequenceArray.length; i++) { this._sequenceList.add(vSequenceArray[i]); } } /** * * * @param index * @param vSequenceSetProperties * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection */ public void setSequenceSetProperties( final int index, final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._sequenceSetPropertiesList.size()) { throw new IndexOutOfBoundsException( "setSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]"); } this._sequenceSetPropertiesList.set(index, vSequenceSetProperties); } /** * * * @param vSequenceSetPropertiesArray */ public void setSequenceSetProperties( final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray) { // -- copy array _sequenceSetPropertiesList.clear(); for (int i = 0; i < vSequenceSetPropertiesArray.length; i++) { this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[i]); } } /** * Method unmarshal. * * @param reader * @throws org.exolab.castor.xml.MarshalException * if object is null or if any SAXException is thrown during * marshaling * @throws org.exolab.castor.xml.ValidationException * if this object is an invalid instance according to the schema * @return the unmarshaled jalview.schemabinding.version2.SequenceSet */ public static jalview.schemabinding.version2.SequenceSet unmarshal( final java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.schemabinding.version2.SequenceSet) Unmarshaller .unmarshal(jalview.schemabinding.version2.SequenceSet.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); } }