- * 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);
- }
-
-}
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * 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); + } + +}