X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FSequenceSet.java;h=8be802288a6b32b5f13f3b8114716239e1bf346b;hb=2dcd2b8cfb1b38575c8b2246d59ba1c1a2fb59cd;hp=6f0342ba78ad6a546549c38720fe89bc4273ca50;hpb=48df59aa393e03aa7269b2df662ac1b8d58cbb25;p=jalview.git diff --git a/src/jalview/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java old mode 100755 new mode 100644 index 6f0342b..8be8022 --- a/src/jalview/schemabinding/version2/SequenceSet.java +++ b/src/jalview/schemabinding/version2/SequenceSet.java @@ -1,451 +1,872 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class SequenceSet. - * - * @version $Revision$ $Date$ - */ -public class SequenceSet implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _gapChar - */ - private java.lang.String _gapChar; - - /** - * Field _sequenceList - */ - private java.util.Vector _sequenceList; - - /** - * Field _annotationList - */ - private java.util.Vector _annotationList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public SequenceSet() { - super(); - _sequenceList = new Vector(); - _annotationList = new Vector(); - } //-- jalview.schemabinding.version2.SequenceSet() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addAnnotation - * - * - * - * @param vAnnotation - */ - public void addAnnotation(jalview.schemabinding.version2.Annotation vAnnotation) - throws java.lang.IndexOutOfBoundsException - { - _annotationList.addElement(vAnnotation); - } //-- void addAnnotation(jalview.schemabinding.version2.Annotation) - - /** - * Method addAnnotation - * - * - * - * @param index - * @param vAnnotation - */ - public void addAnnotation(int index, jalview.schemabinding.version2.Annotation vAnnotation) - throws java.lang.IndexOutOfBoundsException - { - _annotationList.insertElementAt(vAnnotation, index); - } //-- void addAnnotation(int, jalview.schemabinding.version2.Annotation) - - /** - * Method addSequence - * - * - * - * @param vSequence - */ - public void addSequence(jalview.schemabinding.version2.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - _sequenceList.addElement(vSequence); - } //-- void addSequence(jalview.schemabinding.version2.Sequence) - - /** - * Method addSequence - * - * - * - * @param index - * @param vSequence - */ - public void addSequence(int index, jalview.schemabinding.version2.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - _sequenceList.insertElementAt(vSequence, index); - } //-- void addSequence(int, jalview.schemabinding.version2.Sequence) - - /** - * Method enumerateAnnotation - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAnnotation() - { - return _annotationList.elements(); - } //-- java.util.Enumeration enumerateAnnotation() - - /** - * Method enumerateSequence - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateSequence() - { - return _sequenceList.elements(); - } //-- java.util.Enumeration enumerateSequence() - - /** - * Method getAnnotation - * - * - * - * @param index - * @return Annotation - */ - public jalview.schemabinding.version2.Annotation getAnnotation(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _annotationList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.schemabinding.version2.Annotation) _annotationList.elementAt(index); - } //-- jalview.schemabinding.version2.Annotation getAnnotation(int) - - /** - * Method getAnnotation - * - * - * - * @return Annotation - */ - public jalview.schemabinding.version2.Annotation[] getAnnotation() - { - int size = _annotationList.size(); - jalview.schemabinding.version2.Annotation[] mArray = new jalview.schemabinding.version2.Annotation[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.schemabinding.version2.Annotation) _annotationList.elementAt(index); - } - return mArray; - } //-- jalview.schemabinding.version2.Annotation[] getAnnotation() - - /** - * Method getAnnotationCount - * - * - * - * @return int - */ - public int getAnnotationCount() - { - return _annotationList.size(); - } //-- int getAnnotationCount() - - /** - * Returns the value of field 'gapChar'. - * - * @return String - * @return the value of field 'gapChar'. - */ - public java.lang.String getGapChar() - { - return this._gapChar; - } //-- java.lang.String getGapChar() - - /** - * Method getSequence - * - * - * - * @param index - * @return Sequence - */ - public jalview.schemabinding.version2.Sequence getSequence(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _sequenceList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.schemabinding.version2.Sequence) _sequenceList.elementAt(index); - } //-- jalview.schemabinding.version2.Sequence getSequence(int) - - /** - * Method getSequence - * - * - * - * @return Sequence - */ - public jalview.schemabinding.version2.Sequence[] getSequence() - { - int size = _sequenceList.size(); - jalview.schemabinding.version2.Sequence[] mArray = new jalview.schemabinding.version2.Sequence[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.schemabinding.version2.Sequence) _sequenceList.elementAt(index); - } - return mArray; - } //-- jalview.schemabinding.version2.Sequence[] getSequence() - - /** - * Method getSequenceCount - * - * - * - * @return int - */ - public int getSequenceCount() - { - return _sequenceList.size(); - } //-- int getSequenceCount() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllAnnotation - * - */ - public void removeAllAnnotation() - { - _annotationList.removeAllElements(); - } //-- void removeAllAnnotation() - - /** - * Method removeAllSequence - * - */ - public void removeAllSequence() - { - _sequenceList.removeAllElements(); - } //-- void removeAllSequence() - - /** - * Method removeAnnotation - * - * - * - * @param index - * @return Annotation - */ - public jalview.schemabinding.version2.Annotation removeAnnotation(int index) - { - java.lang.Object obj = _annotationList.elementAt(index); - _annotationList.removeElementAt(index); - return (jalview.schemabinding.version2.Annotation) obj; - } //-- jalview.schemabinding.version2.Annotation removeAnnotation(int) - - /** - * Method removeSequence - * - * - * - * @param index - * @return Sequence - */ - public jalview.schemabinding.version2.Sequence removeSequence(int index) - { - java.lang.Object obj = _sequenceList.elementAt(index); - _sequenceList.removeElementAt(index); - return (jalview.schemabinding.version2.Sequence) obj; - } //-- jalview.schemabinding.version2.Sequence removeSequence(int) - - /** - * Method setAnnotation - * - * - * - * @param index - * @param vAnnotation - */ - public void setAnnotation(int index, jalview.schemabinding.version2.Annotation vAnnotation) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _annotationList.size())) { - throw new IndexOutOfBoundsException(); - } - _annotationList.setElementAt(vAnnotation, index); - } //-- void setAnnotation(int, jalview.schemabinding.version2.Annotation) - - /** - * Method setAnnotation - * - * - * - * @param annotationArray - */ - public void setAnnotation(jalview.schemabinding.version2.Annotation[] annotationArray) - { - //-- copy array - _annotationList.removeAllElements(); - for (int i = 0; i < annotationArray.length; i++) { - _annotationList.addElement(annotationArray[i]); - } - } //-- void setAnnotation(jalview.schemabinding.version2.Annotation) - - /** - * Sets the value of field 'gapChar'. - * - * @param gapChar the value of field 'gapChar'. - */ - public void setGapChar(java.lang.String gapChar) - { - this._gapChar = gapChar; - } //-- void setGapChar(java.lang.String) - - /** - * Method setSequence - * - * - * - * @param index - * @param vSequence - */ - public void setSequence(int index, jalview.schemabinding.version2.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _sequenceList.size())) { - throw new IndexOutOfBoundsException(); - } - _sequenceList.setElementAt(vSequence, index); - } //-- void setSequence(int, jalview.schemabinding.version2.Sequence) - - /** - * Method setSequence - * - * - * - * @param sequenceArray - */ - public void setSequence(jalview.schemabinding.version2.Sequence[] sequenceArray) - { - //-- copy array - _sequenceList.removeAllElements(); - for (int i = 0; i < sequenceArray.length; i++) { - _sequenceList.addElement(sequenceArray[i]); - } - } //-- void setSequence(jalview.schemabinding.version2.Sequence) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(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); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2; + +//---------------------------------/ +//- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class SequenceSet. + * + * @version $Revision$ $Date$ + */ +public class SequenceSet implements java.io.Serializable +{ + + // --------------------------/ + // - Class/Member Variables -/ + // --------------------------/ + + /** + * Field _gapChar. + */ + private java.lang.String _gapChar; + + /** + * reference to set where jalview will gather the dataset sequences for all + * sequences in the set. + * + */ + private java.lang.String _datasetId; + + /** + * Field _sequenceList. + */ + private java.util.Vector _sequenceList; + + /** + * Field _annotationList. + */ + private java.util.Vector _annotationList; + + /** + * Field _sequenceSetPropertiesList. + */ + private java.util.Vector _sequenceSetPropertiesList; + + /** + * Field _alcodonFrameList. + */ + private java.util.Vector _alcodonFrameList; + + // ----------------/ + // - Constructors -/ + // ----------------/ + + public SequenceSet() + { + super(); + this._sequenceList = new java.util.Vector(); + this._annotationList = new java.util.Vector(); + this._sequenceSetPropertiesList = new java.util.Vector(); + this._alcodonFrameList = new java.util.Vector(); + } + + // -----------/ + // - Methods -/ + // -----------/ + + /** + * + * + * @param vAlcodonFrame + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addAlcodonFrame( + final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) + throws java.lang.IndexOutOfBoundsException + { + this._alcodonFrameList.addElement(vAlcodonFrame); + } + + /** + * + * + * @param index + * @param vAlcodonFrame + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addAlcodonFrame(final int index, + final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) + throws java.lang.IndexOutOfBoundsException + { + this._alcodonFrameList.add(index, vAlcodonFrame); + } + + /** + * + * + * @param vAnnotation + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addAnnotation( + final jalview.schemabinding.version2.Annotation vAnnotation) + throws java.lang.IndexOutOfBoundsException + { + this._annotationList.addElement(vAnnotation); + } + + /** + * + * + * @param index + * @param vAnnotation + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addAnnotation(final int index, + final jalview.schemabinding.version2.Annotation vAnnotation) + throws java.lang.IndexOutOfBoundsException + { + this._annotationList.add(index, vAnnotation); + } + + /** + * + * + * @param vSequence + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addSequence( + final jalview.schemabinding.version2.Sequence vSequence) + throws java.lang.IndexOutOfBoundsException + { + this._sequenceList.addElement(vSequence); + } + + /** + * + * + * @param index + * @param vSequence + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addSequence(final int index, + final jalview.schemabinding.version2.Sequence vSequence) + throws java.lang.IndexOutOfBoundsException + { + this._sequenceList.add(index, vSequence); + } + + /** + * + * + * @param vSequenceSetProperties + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addSequenceSetProperties( + final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) + throws java.lang.IndexOutOfBoundsException + { + this._sequenceSetPropertiesList.addElement(vSequenceSetProperties); + } + + /** + * + * + * @param index + * @param vSequenceSetProperties + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addSequenceSetProperties( + final int index, + final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) + throws java.lang.IndexOutOfBoundsException + { + this._sequenceSetPropertiesList.add(index, vSequenceSetProperties); + } + + /** + * Method enumerateAlcodonFrame. + * + * @return an Enumeration over all jalview.schemabinding.version2.AlcodonFrame + * elements + */ + public java.util.Enumeration enumerateAlcodonFrame() + { + return this._alcodonFrameList.elements(); + } + + /** + * Method enumerateAnnotation. + * + * @return an Enumeration over all jalview.schemabinding.version2.Annotation + * elements + */ + public java.util.Enumeration enumerateAnnotation() + { + return this._annotationList.elements(); + } + + /** + * Method enumerateSequence. + * + * @return an Enumeration over all jalview.schemabinding.version2.Sequence + * elements + */ + public java.util.Enumeration enumerateSequence() + { + return this._sequenceList.elements(); + } + + /** + * Method enumerateSequenceSetProperties. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.SequenceSetProperties elements + */ + public java.util.Enumeration enumerateSequenceSetProperties() + { + return this._sequenceSetPropertiesList.elements(); + } + + /** + * Method getAlcodonFrame. + * + * @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.AlcodonFrame at the + * given inde + */ + public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame( + final int index) throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._alcodonFrameList.size()) + { + throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '" + + index + "' not in range [0.." + + (this._alcodonFrameList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList + .get(index); + } + + /** + * Method getAlcodonFrame.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.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); + } + +}