Note: Just in case the + * collection contents are changing in another thread, we pass + * a 0-length Array of the correct type into the API call. + * This way we know that the Array returned is of + * exactly the correct length. + * + * @return this collection as an Array */ - public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation() - { - int size = _alignmentSequenceAnnotationList.size(); - uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] mArray = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index); - } - return mArray; - } //-- uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation() + public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation( + ) { + uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] array = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[0]; + return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[]) this._alignmentSequenceAnnotationList.toArray(array); + } /** - * Method getAlignmentSequenceAnnotationCount - * + * Method getAlignmentSequenceAnnotationAsReference.Returns a + * reference to '_alignmentSequenceAnnotationList'. No type + * checking is performed on any modifications to the Vector. * + * @return a reference to the Vector backing this class + */ + public java.util.Vector getAlignmentSequenceAnnotationAsReference( + ) { + return this._alignmentSequenceAnnotationList; + } + + /** + * Method getAlignmentSequenceAnnotationCount. * - * @return int + * @return the size of this collection */ - public int getAlignmentSequenceAnnotationCount() - { - return _alignmentSequenceAnnotationList.size(); - } //-- int getAlignmentSequenceAnnotationCount() + public int getAlignmentSequenceAnnotationCount( + ) { + return this._alignmentSequenceAnnotationList.size(); + } /** * Returns the value of field 'id'. The field 'id' has the * following description: Primary Key for vamsas object * referencing * - * @return String - * @return the value of field 'id'. + * @return the value of field 'Id'. */ - public java.lang.String getId() - { + public java.lang.String getId( + ) { return this._id; - } //-- java.lang.String getId() + } /** * Returns the value of field 'refid'. The field 'refid' has @@ -220,117 +267,185 @@ implements java.io.Serializable * this alignment sequence is taken from * * - * @return Object - * @return the value of field 'refid'. + * @return the value of field 'Refid'. */ - public java.lang.Object getRefid() - { + public java.lang.Object getRefid( + ) { return this._refid; - } //-- java.lang.Object getRefid() + } /** - * Method isValid - * + * Overrides the java.lang.Object.hashCode method. + *
+ * The following steps came from Effective Java Programming + * Language Guide by Joshua Bloch, Chapter 3 * + * @return a hash code value for the object. + */ + public int hashCode( + ) { + int result = super.hashCode(); + + long tmp; + if (_id != null + && !org.castor.util.CycleBreaker.startingToCycle(_id)) { + result = 37 * result + _id.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_id); + } + if (_refid != null + && !org.castor.util.CycleBreaker.startingToCycle(_refid)) { + result = 37 * result + _refid.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_refid); + } + if (_alignmentSequenceAnnotationList != null + && !org.castor.util.CycleBreaker.startingToCycle(_alignmentSequenceAnnotationList)) { + result = 37 * result + _alignmentSequenceAnnotationList.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentSequenceAnnotationList); + } + + return result; + } + + /** + * Method isValid. * - * @return boolean + * @return true if this object is valid according to the schema */ - public boolean isValid() - { + public boolean isValid( + ) { try { validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { + } catch (org.exolab.castor.xml.ValidationException vex) { return false; } return true; - } //-- boolean isValid() + } /** - * Method marshal - * * * * @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(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - + public void marshal( + final 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 + * @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(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - + 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); - } //-- void marshal(org.xml.sax.ContentHandler) + } /** - * Method removeAlignmentSequenceAnnotation - * + * Method removeAlignmentSequenceAnnotation. * + * @param vAlignmentSequenceAnnotation + * @return true if the object was removed from the collection. + */ + public boolean removeAlignmentSequenceAnnotation( + final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation) { + boolean removed = _alignmentSequenceAnnotationList.remove(vAlignmentSequenceAnnotation); + return removed; + } + + /** + * Method removeAlignmentSequenceAnnotationAt. * * @param index - * @return AlignmentSequenceAnnotation + * @return the element removed from the collection */ - public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int index) - { - java.lang.Object obj = _alignmentSequenceAnnotationList.elementAt(index); - _alignmentSequenceAnnotationList.removeElementAt(index); + public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotationAt( + final int index) { + java.lang.Object obj = this._alignmentSequenceAnnotationList.remove(index); return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) obj; - } //-- uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int) + } /** - * Method removeAllAlignmentSequenceAnnotation - * */ - public void removeAllAlignmentSequenceAnnotation() - { - _alignmentSequenceAnnotationList.removeAllElements(); - } //-- void removeAllAlignmentSequenceAnnotation() + public void removeAllAlignmentSequenceAnnotation( + ) { + this._alignmentSequenceAnnotationList.clear(); + } /** - * Method setAlignmentSequenceAnnotation - * * * * @param index * @param vAlignmentSequenceAnnotation + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection */ - public void setAlignmentSequenceAnnotation(int index, uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentSequenceAnnotationList.size())) { - throw new IndexOutOfBoundsException("setAlignmentSequenceAnnotation: Index value '"+index+"' not in range [0.."+_alignmentSequenceAnnotationList.size()+ "]"); + public void setAlignmentSequenceAnnotation( + final int index, + final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._alignmentSequenceAnnotationList.size()) { + throw new IndexOutOfBoundsException("setAlignmentSequenceAnnotation: Index value '" + index + "' not in range [0.." + (this._alignmentSequenceAnnotationList.size() - 1) + "]"); } - _alignmentSequenceAnnotationList.setElementAt(vAlignmentSequenceAnnotation, index); - } //-- void setAlignmentSequenceAnnotation(int, uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) + + this._alignmentSequenceAnnotationList.set(index, vAlignmentSequenceAnnotation); + } /** - * Method setAlignmentSequenceAnnotation - * * * - * @param alignmentSequenceAnnotationArray + * @param vAlignmentSequenceAnnotationArray */ - public void setAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] alignmentSequenceAnnotationArray) - { + public void setAlignmentSequenceAnnotation( + final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] vAlignmentSequenceAnnotationArray) { //-- copy array - _alignmentSequenceAnnotationList.removeAllElements(); - for (int i = 0; i < alignmentSequenceAnnotationArray.length; i++) { - _alignmentSequenceAnnotationList.addElement(alignmentSequenceAnnotationArray[i]); + _alignmentSequenceAnnotationList.clear(); + + for (int i = 0; i < vAlignmentSequenceAnnotationArray.length; i++) { + this._alignmentSequenceAnnotationList.add(vAlignmentSequenceAnnotationArray[i]); } - } //-- void setAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) + } + + /** + * Sets the value of '_alignmentSequenceAnnotationList' by + * copying the given Vector. All elements will be checked for + * type safety. + * + * @param vAlignmentSequenceAnnotationList the Vector to copy. + */ + public void setAlignmentSequenceAnnotation( + final java.util.Vector vAlignmentSequenceAnnotationList) { + // copy vector + this._alignmentSequenceAnnotationList.clear(); + + this._alignmentSequenceAnnotationList.addAll(vAlignmentSequenceAnnotationList); + } + + /** + * Sets the value of '_alignmentSequenceAnnotationList' by + * setting it to the given Vector. No type checking is + * performed. + * @deprecated + * + * @param alignmentSequenceAnnotationVector the Vector to set. + */ + public void setAlignmentSequenceAnnotationAsReference( + final java.util.Vector alignmentSequenceAnnotationVector) { + this._alignmentSequenceAnnotationList = alignmentSequenceAnnotationVector; + } /** * Sets the value of field 'id'. The field 'id' has the @@ -339,10 +454,10 @@ implements java.io.Serializable * * @param id the value of field 'id'. */ - public void setId(java.lang.String id) - { + public void setId( + final java.lang.String id) { this._id = id; - } //-- void setId(java.lang.String) + } /** * Sets the value of field 'refid'. The field 'refid' has the @@ -352,34 +467,38 @@ implements java.io.Serializable * * @param refid the value of field 'refid'. */ - public void setRefid(java.lang.Object refid) - { + public void setRefid( + final java.lang.Object refid) { this._refid = refid; - } //-- void setRefid(java.lang.Object) + } /** - * Method unmarshal - * - * + * Method unmarshal. * * @param reader - * @return SequenceType + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled uk.ac.vamsas.objects.core.SequenceTyp */ - public static uk.ac.vamsas.objects.core.SequenceType unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (uk.ac.vamsas.objects.core.AlignmentSequence) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.AlignmentSequence.class, reader); - } //-- uk.ac.vamsas.objects.core.SequenceType unmarshal(java.io.Reader) + public static uk.ac.vamsas.objects.core.SequenceType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (uk.ac.vamsas.objects.core.SequenceType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.AlignmentSequence.class, reader); + } /** - * Method validate * + * + * @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 - { + 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() + } }