- * 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); - } - -}