+ } else if (temp._propertyList != null)\r
+ return false;\r
+ return true;\r
+ }\r
+ return false;\r
+ }\r
+\r
+ /**\r
+ * Method getAnnotationElement.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the uk.ac.vamsas.objects.core.AnnotationElement at the\r
+ * given inde\r
+ */\r
+ public uk.ac.vamsas.objects.core.AnnotationElement getAnnotationElement(\r
+ final int index) throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._annotationElementList.size()) {\r
+ throw new IndexOutOfBoundsException("getAnnotationElement: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._annotationElementList.size() - 1) + "]");\r
+ }\r
+\r
+ return (uk.ac.vamsas.objects.core.AnnotationElement) _annotationElementList\r
+ .get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getAnnotationElement.Returns the contents of the collection in an\r
+ * Array.\r
+ * <p>\r
+ * Note: Just in case the collection contents are changing in another thread,\r
+ * we pass a 0-length Array of the correct type into the API call. This way we\r
+ * <i>know</i> that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public uk.ac.vamsas.objects.core.AnnotationElement[] getAnnotationElement() {\r
+ uk.ac.vamsas.objects.core.AnnotationElement[] array = new uk.ac.vamsas.objects.core.AnnotationElement[0];\r
+ return (uk.ac.vamsas.objects.core.AnnotationElement[]) this._annotationElementList\r
+ .toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getAnnotationElementAsReference.Returns a reference to\r
+ * '_annotationElementList'. No type checking is performed on any\r
+ * modifications to the Vector.\r
+ * \r
+ * @return a reference to the Vector backing this class\r
+ */\r
+ public java.util.Vector getAnnotationElementAsReference() {\r
+ return this._annotationElementList;\r
+ }\r
+\r
+ /**\r
+ * Method getAnnotationElementCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getAnnotationElementCount() {\r
+ return this._annotationElementList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'description'. The field 'description' has the\r
+ * following description: Human readable description of the annotation\r
+ * \r
+ * \r
+ * @return the value of field 'Description'.\r
+ */\r
+ public java.lang.String getDescription() {\r
+ return this._description;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'group'. The field 'group' has the following\r
+ * description: Annotation with the same non-empty group name are grouped\r
+ * together\r
+ * \r
+ * @return the value of field 'Group'.\r
+ */\r
+ public java.lang.String getGroup() {\r
+ return this._group;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'id'. The field 'id' has the following\r
+ * description: Primary Key for vamsas object referencing\r
+ * \r
+ * \r
+ * @return the value of field 'Id'.\r
+ */\r
+ public java.lang.String getId() {\r
+ return this._id;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'label'. The field 'label' has the following\r
+ * description: Short, meaningful name for the annotation - if this is absent,\r
+ * then the type string should be used in its place.\r
+ * \r
+ * \r
+ * @return the value of field 'Label'.\r
+ */\r
+ public java.lang.String getLabel() {\r
+ return this._label;\r
+ }\r
+\r
+ /**\r
+ * Method getLink.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the uk.ac.vamsas.objects.core.Link at the given index\r
+ */\r
+ public uk.ac.vamsas.objects.core.Link getLink(final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._linkList.size()) {\r
+ throw new IndexOutOfBoundsException("getLink: Index value '" + index\r
+ + "' not in range [0.." + (this._linkList.size() - 1) + "]");\r
+ }\r
+\r
+ return (uk.ac.vamsas.objects.core.Link) _linkList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getLink.Returns the contents of the collection in an Array.\r
+ * <p>\r
+ * Note: Just in case the collection contents are changing in another thread,\r
+ * we pass a 0-length Array of the correct type into the API call. This way we\r
+ * <i>know</i> that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public uk.ac.vamsas.objects.core.Link[] getLink() {\r
+ uk.ac.vamsas.objects.core.Link[] array = new uk.ac.vamsas.objects.core.Link[0];\r
+ return (uk.ac.vamsas.objects.core.Link[]) this._linkList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getLinkAsReference.Returns a reference to '_linkList'. No type\r
+ * checking is performed on any modifications to the Vector.\r
+ * \r
+ * @return a reference to the Vector backing this class\r
+ */\r
+ public java.util.Vector getLinkAsReference() {\r
+ return this._linkList;\r
+ }\r
+\r
+ /**\r
+ * Method getLinkCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getLinkCount() {\r
+ return this._linkList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'modifiable'.\r
+ * \r
+ * @return the value of field 'Modifiable'.\r
+ */\r
+ public java.lang.String getModifiable() {\r
+ return this._modifiable;\r
+ }\r
+\r
+ /**\r
+ * Method getProperty.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the uk.ac.vamsas.objects.core.Property at the given\r
+ * index\r
+ */\r
+ public uk.ac.vamsas.objects.core.Property getProperty(final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._propertyList.size()) {\r
+ throw new IndexOutOfBoundsException("getProperty: Index value '" + index\r
+ + "' not in range [0.." + (this._propertyList.size() - 1) + "]");\r
+ }\r
+\r
+ return (uk.ac.vamsas.objects.core.Property) _propertyList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getProperty.Returns the contents of the collection in an Array.\r
+ * <p>\r
+ * Note: Just in case the collection contents are changing in another thread,\r
+ * we pass a 0-length Array of the correct type into the API call. This way we\r
+ * <i>know</i> that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public uk.ac.vamsas.objects.core.Property[] getProperty() {\r
+ uk.ac.vamsas.objects.core.Property[] array = new uk.ac.vamsas.objects.core.Property[0];\r
+ return (uk.ac.vamsas.objects.core.Property[]) this._propertyList\r
+ .toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getPropertyAsReference.Returns a reference to '_propertyList'. No\r
+ * type checking is performed on any modifications to the Vector.\r
+ * \r
+ * @return a reference to the Vector backing this class\r
+ */\r
+ public java.util.Vector getPropertyAsReference() {\r
+ return this._propertyList;\r
+ }\r
+\r
+ /**\r
+ * Method getPropertyCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getPropertyCount() {\r
+ return this._propertyList.size();\r
+ }\r
+\r
+ /**\r
+ * Method getScore.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the uk.ac.vamsas.objects.core.Score at the given index\r
+ */\r
+ public uk.ac.vamsas.objects.core.Score getScore(final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._scoreList.size()) {\r
+ throw new IndexOutOfBoundsException("getScore: Index value '" + index\r
+ + "' not in range [0.." + (this._scoreList.size() - 1) + "]");\r
+ }\r
+\r
+ return (uk.ac.vamsas.objects.core.Score) _scoreList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getScore.Returns the contents of the collection in an Array.\r
+ * <p>\r
+ * Note: Just in case the collection contents are changing in another thread,\r
+ * we pass a 0-length Array of the correct type into the API call. This way we\r
+ * <i>know</i> that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public uk.ac.vamsas.objects.core.Score[] getScore() {\r
+ uk.ac.vamsas.objects.core.Score[] array = new uk.ac.vamsas.objects.core.Score[0];\r
+ return (uk.ac.vamsas.objects.core.Score[]) this._scoreList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getScoreAsReference.Returns a reference to '_scoreList'. No type\r
+ * checking is performed on any modifications to the Vector.\r
+ * \r
+ * @return a reference to the Vector backing this class\r
+ */\r
+ public java.util.Vector getScoreAsReference() {\r
+ return this._scoreList;\r
+ }\r
+\r
+ /**\r
+ * Method getScoreCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getScoreCount() {\r
+ return this._scoreList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'status'. The field 'status' has the following\r
+ * description: TODO: specify this - we have considered taking the GO evidence\r
+ * codes as a model for assessing a measure of quality to an annotation.\r
+ * \r
+ * @return the value of field 'Status'.\r
+ */\r
+ public java.lang.String getStatus() {\r
+ return this._status;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'type'. The field 'type' has the following\r
+ * description: A Das Feature has both a type and a Type ID. We go the route\r
+ * of requiring the type string to be taken from a controlled vocabulary if an\r
+ * application expects others to make sense of it. The type may qualified - so\r
+ * uniprot:CHAIN is a valid type name, and considered distinct from\r
+ * someotherDB:CHAIN\r
+ * \r
+ * @return the value of field 'Type'.\r
+ */\r
+ public java.lang.String getType() {\r
+ return this._type;\r
+ }\r
+\r
+ /**\r
+ * Overrides the java.lang.Object.hashCode method.\r
+ * <p>\r
+ * The following steps came from <b>Effective Java Programming Language\r
+ * Guide</b> by Joshua Bloch, Chapter 3\r
+ * \r
+ * @return a hash code value for the object.\r
+ */\r
+ public int hashCode() {\r
+ int result = super.hashCode();\r
+\r
+ long tmp;\r
+ if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {\r
+ result = 37 * result + _id.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_id);\r
+ }\r
+ if (_modifiable != null\r
+ && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) {\r
+ result = 37 * result + _modifiable.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable);\r
+ }\r
+ if (_group != null && !org.castor.util.CycleBreaker.startingToCycle(_group)) {\r
+ result = 37 * result + _group.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_group);\r
+ }\r
+ if (_type != null && !org.castor.util.CycleBreaker.startingToCycle(_type)) {\r
+ result = 37 * result + _type.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_type);\r
+ }\r
+ if (_label != null && !org.castor.util.CycleBreaker.startingToCycle(_label)) {\r
+ result = 37 * result + _label.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_label);\r
+ }\r
+ if (_description != null\r
+ && !org.castor.util.CycleBreaker.startingToCycle(_description)) {\r
+ result = 37 * result + _description.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_description);\r
+ }\r
+ if (_status != null\r
+ && !org.castor.util.CycleBreaker.startingToCycle(_status)) {\r
+ result = 37 * result + _status.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_status);\r
+ }\r
+ if (_annotationElementList != null\r
+ && !org.castor.util.CycleBreaker\r
+ .startingToCycle(_annotationElementList)) {\r
+ result = 37 * result + _annotationElementList.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_annotationElementList);\r
+ }\r
+ if (_scoreList != null\r
+ && !org.castor.util.CycleBreaker.startingToCycle(_scoreList)) {\r
+ result = 37 * result + _scoreList.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_scoreList);\r
+ }\r
+ if (_linkList != null\r
+ && !org.castor.util.CycleBreaker.startingToCycle(_linkList)) {\r
+ result = 37 * result + _linkList.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_linkList);\r
+ }\r
+ if (_propertyList != null\r
+ && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {\r
+ result = 37 * result + _propertyList.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);\r
+ }\r
+\r
+ return result;\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
+ * \r
+ * @return true if this object is valid according to the schema\r
+ */\r
+ public boolean isValid() {\r
+ try {\r
+ validate();\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param out\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, out);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param handler\r
+ * @throws java.io.IOException\r
+ * if an IOException occurs during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ */\r
+ public void marshal(final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, handler);\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllAnnotationElement() {\r
+ this._annotationElementList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllLink() {\r
+ this._linkList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllProperty() {\r
+ this._propertyList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllScore() {\r
+ this._scoreList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeAnnotationElement.\r
+ * \r
+ * @param vAnnotationElement\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeAnnotationElement(\r
+ final uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement) {\r
+ boolean removed = _annotationElementList.remove(vAnnotationElement);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeAnnotationElementAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public uk.ac.vamsas.objects.core.AnnotationElement removeAnnotationElementAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._annotationElementList.remove(index);\r
+ return (uk.ac.vamsas.objects.core.AnnotationElement) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeLink.\r
+ * \r
+ * @param vLink\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeLink(final uk.ac.vamsas.objects.core.Link vLink) {\r
+ boolean removed = _linkList.remove(vLink);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeLinkAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public uk.ac.vamsas.objects.core.Link removeLinkAt(final int index) {\r
+ java.lang.Object obj = this._linkList.remove(index);\r
+ return (uk.ac.vamsas.objects.core.Link) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeProperty.\r
+ * \r
+ * @param vProperty\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeProperty(\r
+ final uk.ac.vamsas.objects.core.Property vProperty) {\r
+ boolean removed = _propertyList.remove(vProperty);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removePropertyAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public uk.ac.vamsas.objects.core.Property removePropertyAt(final int index) {\r
+ java.lang.Object obj = this._propertyList.remove(index);\r
+ return (uk.ac.vamsas.objects.core.Property) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeScore.\r
+ * \r
+ * @param vScore\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeScore(final uk.ac.vamsas.objects.core.Score vScore) {\r
+ boolean removed = _scoreList.remove(vScore);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeScoreAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public uk.ac.vamsas.objects.core.Score removeScoreAt(final int index) {\r
+ java.lang.Object obj = this._scoreList.remove(index);\r
+ return (uk.ac.vamsas.objects.core.Score) obj;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAnnotationElement\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setAnnotationElement(final int index,\r
+ final uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._annotationElementList.size()) {\r
+ throw new IndexOutOfBoundsException("setAnnotationElement: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._annotationElementList.size() - 1) + "]");\r
+ }\r
+\r
+ this._annotationElementList.set(index, vAnnotationElement);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAnnotationElementArray\r
+ */\r
+ public void setAnnotationElement(\r
+ final uk.ac.vamsas.objects.core.AnnotationElement[] vAnnotationElementArray) {\r
+ // -- copy array\r
+ _annotationElementList.clear();\r
+\r
+ for (int i = 0; i < vAnnotationElementArray.length; i++) {\r
+ this._annotationElementList.add(vAnnotationElementArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_annotationElementList' by copying the given Vector. All\r
+ * elements will be checked for type safety.\r
+ * \r
+ * @param vAnnotationElementList\r
+ * the Vector to copy.\r
+ */\r
+ public void setAnnotationElement(final java.util.Vector vAnnotationElementList) {\r
+ // copy vector\r
+ this._annotationElementList.clear();\r
+\r
+ this._annotationElementList.addAll(vAnnotationElementList);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_annotationElementList' by setting it to the given\r
+ * Vector. No type checking is performed.\r
+ * \r
+ * @deprecated\r
+ * \r
+ * @param annotationElementVector\r
+ * the Vector to set.\r
+ */\r
+ public void setAnnotationElementAsReference(\r
+ final java.util.Vector annotationElementVector) {\r
+ this._annotationElementList = annotationElementVector;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'description'. The field 'description' has the\r
+ * following description: Human readable description of the annotation\r
+ * \r
+ * \r
+ * @param description\r
+ * the value of field 'description'.\r
+ */\r
+ public void setDescription(final java.lang.String description) {\r
+ this._description = description;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'group'. The field 'group' has the following\r
+ * description: Annotation with the same non-empty group name are grouped\r
+ * together\r
+ * \r
+ * @param group\r
+ * the value of field 'group'.\r
+ */\r
+ public void setGroup(final java.lang.String group) {\r
+ this._group = group;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'id'. The field 'id' has the following description:\r
+ * Primary Key for vamsas object referencing\r
+ * \r
+ * \r
+ * @param id\r
+ * the value of field 'id'.\r
+ */\r
+ public void setId(final java.lang.String id) {\r
+ this._id = id;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'label'. The field 'label' has the following\r
+ * description: Short, meaningful name for the annotation - if this is absent,\r
+ * then the type string should be used in its place.\r
+ * \r
+ * \r
+ * @param label\r
+ * the value of field 'label'.\r
+ */\r
+ public void setLabel(final java.lang.String label) {\r
+ this._label = label;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vLink\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setLink(final int index,\r
+ final uk.ac.vamsas.objects.core.Link vLink)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._linkList.size()) {\r
+ throw new IndexOutOfBoundsException("setLink: Index value '" + index\r
+ + "' not in range [0.." + (this._linkList.size() - 1) + "]");\r
+ }\r
+\r
+ this._linkList.set(index, vLink);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vLinkArray\r
+ */\r
+ public void setLink(final uk.ac.vamsas.objects.core.Link[] vLinkArray) {\r
+ // -- copy array\r
+ _linkList.clear();\r
+\r
+ for (int i = 0; i < vLinkArray.length; i++) {\r
+ this._linkList.add(vLinkArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_linkList' by copying the given Vector. All elements\r
+ * will be checked for type safety.\r
+ * \r
+ * @param vLinkList\r
+ * the Vector to copy.\r
+ */\r
+ public void setLink(final java.util.Vector vLinkList) {\r
+ // copy vector\r
+ this._linkList.clear();\r
+\r
+ this._linkList.addAll(vLinkList);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_linkList' by setting it to the given Vector. No type\r
+ * checking is performed.\r
+ * \r
+ * @deprecated\r
+ * \r
+ * @param linkVector\r
+ * the Vector to set.\r
+ */\r
+ public void setLinkAsReference(final java.util.Vector linkVector) {\r
+ this._linkList = linkVector;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'modifiable'.\r
+ * \r
+ * @param modifiable\r
+ * the value of field 'modifiable'.\r
+ */\r
+ public void setModifiable(final java.lang.String modifiable) {\r
+ this._modifiable = modifiable;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vProperty\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setProperty(final int index,\r
+ final uk.ac.vamsas.objects.core.Property vProperty)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._propertyList.size()) {\r
+ throw new IndexOutOfBoundsException("setProperty: Index value '" + index\r
+ + "' not in range [0.." + (this._propertyList.size() - 1) + "]");\r
+ }\r
+\r
+ this._propertyList.set(index, vProperty);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vPropertyArray\r
+ */\r
+ public void setProperty(\r
+ final uk.ac.vamsas.objects.core.Property[] vPropertyArray) {\r
+ // -- copy array\r
+ _propertyList.clear();\r
+\r
+ for (int i = 0; i < vPropertyArray.length; i++) {\r
+ this._propertyList.add(vPropertyArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_propertyList' by copying the given Vector. All elements\r
+ * will be checked for type safety.\r
+ * \r
+ * @param vPropertyList\r
+ * the Vector to copy.\r
+ */\r
+ public void setProperty(final java.util.Vector vPropertyList) {\r
+ // copy vector\r
+ this._propertyList.clear();\r
+\r
+ this._propertyList.addAll(vPropertyList);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_propertyList' by setting it to the given Vector. No\r
+ * type checking is performed.\r
+ * \r
+ * @deprecated\r
+ * \r
+ * @param propertyVector\r
+ * the Vector to set.\r
+ */\r
+ public void setPropertyAsReference(final java.util.Vector propertyVector) {\r
+ this._propertyList = propertyVector;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vScore\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setScore(final int index,\r
+ final uk.ac.vamsas.objects.core.Score vScore)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._scoreList.size()) {\r
+ throw new IndexOutOfBoundsException("setScore: Index value '" + index\r
+ + "' not in range [0.." + (this._scoreList.size() - 1) + "]");\r
+ }\r
+\r
+ this._scoreList.set(index, vScore);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vScoreArray\r
+ */\r
+ public void setScore(final uk.ac.vamsas.objects.core.Score[] vScoreArray) {\r
+ // -- copy array\r
+ _scoreList.clear();\r
+\r
+ for (int i = 0; i < vScoreArray.length; i++) {\r
+ this._scoreList.add(vScoreArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_scoreList' by copying the given Vector. All elements\r
+ * will be checked for type safety.\r
+ * \r
+ * @param vScoreList\r
+ * the Vector to copy.\r
+ */\r
+ public void setScore(final java.util.Vector vScoreList) {\r
+ // copy vector\r
+ this._scoreList.clear();\r
+\r
+ this._scoreList.addAll(vScoreList);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_scoreList' by setting it to the given Vector. No type\r
+ * checking is performed.\r
+ * \r
+ * @deprecated\r
+ * \r
+ * @param scoreVector\r
+ * the Vector to set.\r
+ */\r
+ public void setScoreAsReference(final java.util.Vector scoreVector) {\r
+ this._scoreList = scoreVector;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'status'. The field 'status' has the following\r
+ * description: TODO: specify this - we have considered taking the GO evidence\r
+ * codes as a model for assessing a measure of quality to an annotation.\r
+ * \r
+ * @param status\r
+ * the value of field 'status'.\r
+ */\r
+ public void setStatus(final java.lang.String status) {\r
+ this._status = status;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'type'. The field 'type' has the following\r
+ * description: A Das Feature has both a type and a Type ID. We go the route\r
+ * of requiring the type string to be taken from a controlled vocabulary if an\r
+ * application expects others to make sense of it. The type may qualified - so\r
+ * uniprot:CHAIN is a valid type name, and considered distinct from\r
+ * someotherDB:CHAIN\r
+ * \r
+ * @param type\r
+ * the value of field 'type'.\r
+ */\r
+ public void setType(final java.lang.String type) {\r
+ this._type = type;\r
+ }\r
+\r
+ /**\r
+ * Method unmarshal.\r
+ * \r
+ * @param reader\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ * @return the unmarshaled uk.ac.vamsas.objects.core.RangeType\r
+ */\r
+ public static uk.ac.vamsas.objects.core.RangeType unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException {\r
+ return (uk.ac.vamsas.objects.core.RangeType) Unmarshaller.unmarshal(\r
+ uk.ac.vamsas.objects.core.RangeAnnotation.class, reader);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ */\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ }\r