--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- 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;
+
+/**
+ * Annotation for a rangeSpec - values can be attached for the
+ * whole specification, and to each position within the spec.
+ * following the orientation specified by the ordered set of
+ * rangeSpec (pos, seg) elements.
+ *
+ *
+ * @version $Revision$ $Date$
+ */
+public class RangeAnnotation extends org.vamsas.objects.core.RangeType
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Primary Key for vamsas object referencing
+ *
+ */
+ private java.lang.String _id;
+
+ /**
+ * objects with modifiable=false will not be
+ * modified by a vamsas client update
+ *
+ */
+ private boolean _modifiable = true;
+
+ /**
+ * keeps track of state for field: _modifiable
+ */
+ private boolean _has_modifiable;
+
+ /**
+ * Annotation with the same non-empty group
+ * name are grouped together
+ *
+ */
+ private java.lang.String _group = "";
+
+ /**
+ * A Das Feature has both a type and a Type ID.
+ * We go the route of requiring the type string
+ * to be taken from a controlled vocabulary if
+ * an application expects others to make sense
+ * of it.
+ * The type may qualified - so uniprot:CHAIN is a valid type
+ * name,
+ * and considered distinct from someotherDB:CHAIN
+ *
+ */
+ private java.lang.String _type;
+
+ /**
+ * Short, meaningful name for the annotation - if this is
+ * absent, then the type string should be used in its place.
+ *
+ */
+ private java.lang.String _label;
+
+ /**
+ * Human readable description of the annotation
+ *
+ */
+ private java.lang.String _description;
+
+ /**
+ * TODO: specify this - we have considered taking the GO
+ * evidence codes as a model for assessing a measure of quality
+ * to an annotation.
+ *
+ */
+ private java.lang.String _status;
+
+ /**
+ * Annotation Element position maps to
+ * ordered positions defined by the
+ * sequence of rangeType pos positions or
+ * concatenated seg start/end segments.
+ *
+ */
+ private java.util.Vector _annotationElementList;
+
+ /**
+ * Ordered set of optionally named float
+ * values for the whole annotation
+ *
+ */
+ private java.util.Vector _scoreList;
+
+ /**
+ * Field _urlList
+ */
+ private java.util.Vector _urlList;
+
+ /**
+ * Note:These are mutable so an application
+ * should check them each time.
+ *
+ */
+ private java.util.Vector _propertyList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public RangeAnnotation()
+ {
+ super();
+ setGroup("");
+ _annotationElementList = new Vector();
+ _scoreList = new Vector();
+ _urlList = new Vector();
+ _propertyList = new Vector();
+ } //-- org.vamsas.objects.core.RangeAnnotation()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addAnnotationElement
+ *
+ *
+ *
+ * @param vAnnotationElement
+ */
+ public void addAnnotationElement(org.vamsas.objects.core.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _annotationElementList.addElement(vAnnotationElement);
+ } //-- void addAnnotationElement(org.vamsas.objects.core.AnnotationElement)
+
+ /**
+ * Method addAnnotationElement
+ *
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ */
+ public void addAnnotationElement(int index, org.vamsas.objects.core.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _annotationElementList.insertElementAt(vAnnotationElement, index);
+ } //-- void addAnnotationElement(int, org.vamsas.objects.core.AnnotationElement)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param vProperty
+ */
+ public void addProperty(org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.addElement(vProperty);
+ } //-- void addProperty(org.vamsas.objects.core.Property)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void addProperty(int index, org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.insertElementAt(vProperty, index);
+ } //-- void addProperty(int, org.vamsas.objects.core.Property)
+
+ /**
+ * Method addScore
+ *
+ *
+ *
+ * @param vScore
+ */
+ public void addScore(org.vamsas.objects.core.Score vScore)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _scoreList.addElement(vScore);
+ } //-- void addScore(org.vamsas.objects.core.Score)
+
+ /**
+ * Method addScore
+ *
+ *
+ *
+ * @param index
+ * @param vScore
+ */
+ public void addScore(int index, org.vamsas.objects.core.Score vScore)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _scoreList.insertElementAt(vScore, index);
+ } //-- void addScore(int, org.vamsas.objects.core.Score)
+
+ /**
+ * Method addUrl
+ *
+ *
+ *
+ * @param vUrl
+ */
+ public void addUrl(org.vamsas.objects.core.Url vUrl)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _urlList.addElement(vUrl);
+ } //-- void addUrl(org.vamsas.objects.core.Url)
+
+ /**
+ * Method addUrl
+ *
+ *
+ *
+ * @param index
+ * @param vUrl
+ */
+ public void addUrl(int index, org.vamsas.objects.core.Url vUrl)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _urlList.insertElementAt(vUrl, index);
+ } //-- void addUrl(int, org.vamsas.objects.core.Url)
+
+ /**
+ * Method deleteModifiable
+ *
+ */
+ public void deleteModifiable()
+ {
+ this._has_modifiable= false;
+ } //-- void deleteModifiable()
+
+ /**
+ * Method enumerateAnnotationElement
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateAnnotationElement()
+ {
+ return _annotationElementList.elements();
+ } //-- java.util.Enumeration enumerateAnnotationElement()
+
+ /**
+ * Method enumerateProperty
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateProperty()
+ {
+ return _propertyList.elements();
+ } //-- java.util.Enumeration enumerateProperty()
+
+ /**
+ * Method enumerateScore
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateScore()
+ {
+ return _scoreList.elements();
+ } //-- java.util.Enumeration enumerateScore()
+
+ /**
+ * Method enumerateUrl
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateUrl()
+ {
+ return _urlList.elements();
+ } //-- java.util.Enumeration enumerateUrl()
+
+ /**
+ * Note: hashCode() has not been overriden
+ *
+ * @param obj
+ * @return boolean
+ */
+ public boolean equals(java.lang.Object obj)
+ {
+ if ( this == obj )
+ return true;
+
+ if (super.equals(obj)==false)
+ return false;
+
+ if (obj instanceof RangeAnnotation) {
+
+ RangeAnnotation temp = (RangeAnnotation)obj;
+ if (this._id != null) {
+ if (temp._id == null) return false;
+ else if (!(this._id.equals(temp._id)))
+ return false;
+ }
+ else if (temp._id != null)
+ return false;
+ if (this._modifiable != temp._modifiable)
+ return false;
+ if (this._has_modifiable != temp._has_modifiable)
+ return false;
+ if (this._group != null) {
+ if (temp._group == null) return false;
+ else if (!(this._group.equals(temp._group)))
+ return false;
+ }
+ else if (temp._group != null)
+ return false;
+ if (this._type != null) {
+ if (temp._type == null) return false;
+ else if (!(this._type.equals(temp._type)))
+ return false;
+ }
+ else if (temp._type != null)
+ return false;
+ if (this._label != null) {
+ if (temp._label == null) return false;
+ else if (!(this._label.equals(temp._label)))
+ return false;
+ }
+ else if (temp._label != null)
+ return false;
+ if (this._description != null) {
+ if (temp._description == null) return false;
+ else if (!(this._description.equals(temp._description)))
+ return false;
+ }
+ else if (temp._description != null)
+ return false;
+ if (this._status != null) {
+ if (temp._status == null) return false;
+ else if (!(this._status.equals(temp._status)))
+ return false;
+ }
+ else if (temp._status != null)
+ return false;
+ if (this._annotationElementList != null) {
+ if (temp._annotationElementList == null) return false;
+ else if (!(this._annotationElementList.equals(temp._annotationElementList)))
+ return false;
+ }
+ else if (temp._annotationElementList != null)
+ return false;
+ if (this._scoreList != null) {
+ if (temp._scoreList == null) return false;
+ else if (!(this._scoreList.equals(temp._scoreList)))
+ return false;
+ }
+ else if (temp._scoreList != null)
+ return false;
+ if (this._urlList != null) {
+ if (temp._urlList == null) return false;
+ else if (!(this._urlList.equals(temp._urlList)))
+ return false;
+ }
+ else if (temp._urlList != null)
+ return false;
+ if (this._propertyList != null) {
+ if (temp._propertyList == null) return false;
+ else if (!(this._propertyList.equals(temp._propertyList)))
+ return false;
+ }
+ else if (temp._propertyList != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Method getAnnotationElement
+ *
+ *
+ *
+ * @param index
+ * @return AnnotationElement
+ */
+ public org.vamsas.objects.core.AnnotationElement getAnnotationElement(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _annotationElementList.size())) {
+ throw new IndexOutOfBoundsException("getAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);
+ } //-- org.vamsas.objects.core.AnnotationElement getAnnotationElement(int)
+
+ /**
+ * Method getAnnotationElement
+ *
+ *
+ *
+ * @return AnnotationElement
+ */
+ public org.vamsas.objects.core.AnnotationElement[] getAnnotationElement()
+ {
+ int size = _annotationElementList.size();
+ org.vamsas.objects.core.AnnotationElement[] mArray = new org.vamsas.objects.core.AnnotationElement[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.AnnotationElement[] getAnnotationElement()
+
+ /**
+ * Method getAnnotationElementCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getAnnotationElementCount()
+ {
+ return _annotationElementList.size();
+ } //-- int getAnnotationElementCount()
+
+ /**
+ * Returns the value of field 'description'. The field
+ * 'description' has the following description: Human readable
+ * description of the annotation
+ *
+ *
+ * @return String
+ * @return the value of field 'description'.
+ */
+ public java.lang.String getDescription()
+ {
+ return this._description;
+ } //-- java.lang.String getDescription()
+
+ /**
+ * Returns the value of field 'group'. The field 'group' has
+ * the following description: Annotation with the same
+ * non-empty group
+ * name are grouped together
+ *
+ *
+ * @return String
+ * @return the value of field 'group'.
+ */
+ public java.lang.String getGroup()
+ {
+ return this._group;
+ } //-- java.lang.String getGroup()
+
+ /**
+ * 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'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ } //-- java.lang.String getId()
+
+ /**
+ * Returns the value of field 'label'. The field 'label' has
+ * the following description: Short, meaningful name for the
+ * annotation - if this is absent, then the type string should
+ * be used in its place.
+ *
+ *
+ * @return String
+ * @return the value of field 'label'.
+ */
+ public java.lang.String getLabel()
+ {
+ return this._label;
+ } //-- java.lang.String getLabel()
+
+ /**
+ * Returns the value of field 'modifiable'. The field
+ * 'modifiable' has the following description: objects with
+ * modifiable=false will not be
+ * modified by a vamsas client update
+ *
+ *
+ * @return boolean
+ * @return the value of field 'modifiable'.
+ */
+ public boolean getModifiable()
+ {
+ return this._modifiable;
+ } //-- boolean getModifiable()
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property getProperty(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _propertyList.size())) {
+ throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ } //-- org.vamsas.objects.core.Property getProperty(int)
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property[] getProperty()
+ {
+ int size = _propertyList.size();
+ org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Property[] getProperty()
+
+ /**
+ * Method getPropertyCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getPropertyCount()
+ {
+ return _propertyList.size();
+ } //-- int getPropertyCount()
+
+ /**
+ * Method getScore
+ *
+ *
+ *
+ * @param index
+ * @return Score
+ */
+ public org.vamsas.objects.core.Score getScore(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _scoreList.size())) {
+ throw new IndexOutOfBoundsException("getScore: Index value '"+index+"' not in range [0.."+_scoreList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Score) _scoreList.elementAt(index);
+ } //-- org.vamsas.objects.core.Score getScore(int)
+
+ /**
+ * Method getScore
+ *
+ *
+ *
+ * @return Score
+ */
+ public org.vamsas.objects.core.Score[] getScore()
+ {
+ int size = _scoreList.size();
+ org.vamsas.objects.core.Score[] mArray = new org.vamsas.objects.core.Score[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Score) _scoreList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Score[] getScore()
+
+ /**
+ * Method getScoreCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getScoreCount()
+ {
+ return _scoreList.size();
+ } //-- int getScoreCount()
+
+ /**
+ * Returns the value of field 'status'. The field 'status' has
+ * the following description: TODO: specify this - we have
+ * considered taking the GO evidence codes as a model for
+ * assessing a measure of quality to an annotation.
+ *
+ *
+ * @return String
+ * @return the value of field 'status'.
+ */
+ public java.lang.String getStatus()
+ {
+ return this._status;
+ } //-- java.lang.String getStatus()
+
+ /**
+ * Returns the value of field 'type'. The field 'type' has the
+ * following description: A Das Feature has both a type and a
+ * Type ID.
+ * We go the route of requiring the type string
+ * to be taken from a controlled vocabulary if
+ * an application expects others to make sense
+ * of it.
+ * The type may qualified - so uniprot:CHAIN is a valid type
+ * name,
+ * and considered distinct from someotherDB:CHAIN
+ *
+ *
+ * @return String
+ * @return the value of field 'type'.
+ */
+ public java.lang.String getType()
+ {
+ return this._type;
+ } //-- java.lang.String getType()
+
+ /**
+ * Method getUrl
+ *
+ *
+ *
+ * @param index
+ * @return Url
+ */
+ public org.vamsas.objects.core.Url getUrl(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _urlList.size())) {
+ throw new IndexOutOfBoundsException("getUrl: Index value '"+index+"' not in range [0.."+_urlList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Url) _urlList.elementAt(index);
+ } //-- org.vamsas.objects.core.Url getUrl(int)
+
+ /**
+ * Method getUrl
+ *
+ *
+ *
+ * @return Url
+ */
+ public org.vamsas.objects.core.Url[] getUrl()
+ {
+ int size = _urlList.size();
+ org.vamsas.objects.core.Url[] mArray = new org.vamsas.objects.core.Url[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Url) _urlList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Url[] getUrl()
+
+ /**
+ * Method getUrlCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getUrlCount()
+ {
+ return _urlList.size();
+ } //-- int getUrlCount()
+
+ /**
+ * Method hasModifiable
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasModifiable()
+ {
+ return this._has_modifiable;
+ } //-- boolean hasModifiable()
+
+ /**
+ * 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 removeAllAnnotationElement
+ *
+ */
+ public void removeAllAnnotationElement()
+ {
+ _annotationElementList.removeAllElements();
+ } //-- void removeAllAnnotationElement()
+
+ /**
+ * Method removeAllProperty
+ *
+ */
+ public void removeAllProperty()
+ {
+ _propertyList.removeAllElements();
+ } //-- void removeAllProperty()
+
+ /**
+ * Method removeAllScore
+ *
+ */
+ public void removeAllScore()
+ {
+ _scoreList.removeAllElements();
+ } //-- void removeAllScore()
+
+ /**
+ * Method removeAllUrl
+ *
+ */
+ public void removeAllUrl()
+ {
+ _urlList.removeAllElements();
+ } //-- void removeAllUrl()
+
+ /**
+ * Method removeAnnotationElement
+ *
+ *
+ *
+ * @param index
+ * @return AnnotationElement
+ */
+ public org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int index)
+ {
+ java.lang.Object obj = _annotationElementList.elementAt(index);
+ _annotationElementList.removeElementAt(index);
+ return (org.vamsas.objects.core.AnnotationElement) obj;
+ } //-- org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int)
+
+ /**
+ * Method removeProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property removeProperty(int index)
+ {
+ java.lang.Object obj = _propertyList.elementAt(index);
+ _propertyList.removeElementAt(index);
+ return (org.vamsas.objects.core.Property) obj;
+ } //-- org.vamsas.objects.core.Property removeProperty(int)
+
+ /**
+ * Method removeScore
+ *
+ *
+ *
+ * @param index
+ * @return Score
+ */
+ public org.vamsas.objects.core.Score removeScore(int index)
+ {
+ java.lang.Object obj = _scoreList.elementAt(index);
+ _scoreList.removeElementAt(index);
+ return (org.vamsas.objects.core.Score) obj;
+ } //-- org.vamsas.objects.core.Score removeScore(int)
+
+ /**
+ * Method removeUrl
+ *
+ *
+ *
+ * @param index
+ * @return Url
+ */
+ public org.vamsas.objects.core.Url removeUrl(int index)
+ {
+ java.lang.Object obj = _urlList.elementAt(index);
+ _urlList.removeElementAt(index);
+ return (org.vamsas.objects.core.Url) obj;
+ } //-- org.vamsas.objects.core.Url removeUrl(int)
+
+ /**
+ * Method setAnnotationElement
+ *
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ */
+ public void setAnnotationElement(int index, org.vamsas.objects.core.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _annotationElementList.size())) {
+ throw new IndexOutOfBoundsException("setAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");
+ }
+ _annotationElementList.setElementAt(vAnnotationElement, index);
+ } //-- void setAnnotationElement(int, org.vamsas.objects.core.AnnotationElement)
+
+ /**
+ * Method setAnnotationElement
+ *
+ *
+ *
+ * @param annotationElementArray
+ */
+ public void setAnnotationElement(org.vamsas.objects.core.AnnotationElement[] annotationElementArray)
+ {
+ //-- copy array
+ _annotationElementList.removeAllElements();
+ for (int i = 0; i < annotationElementArray.length; i++) {
+ _annotationElementList.addElement(annotationElementArray[i]);
+ }
+ } //-- void setAnnotationElement(org.vamsas.objects.core.AnnotationElement)
+
+ /**
+ * Sets the value of field 'description'. The field
+ * 'description' has the following description: Human readable
+ * description of the annotation
+ *
+ *
+ * @param description the value of field 'description'.
+ */
+ public void setDescription(java.lang.String description)
+ {
+ this._description = description;
+ } //-- void setDescription(java.lang.String)
+
+ /**
+ * Sets the value of field 'group'. The field 'group' has the
+ * following description: Annotation with the same non-empty
+ * group
+ * name are grouped together
+ *
+ *
+ * @param group the value of field 'group'.
+ */
+ public void setGroup(java.lang.String group)
+ {
+ this._group = group;
+ } //-- void setGroup(java.lang.String)
+
+ /**
+ * Sets the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas object
+ * referencing
+ *
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(java.lang.String id)
+ {
+ this._id = id;
+ } //-- void setId(java.lang.String)
+
+ /**
+ * Sets the value of field 'label'. The field 'label' has the
+ * following description: Short, meaningful name for the
+ * annotation - if this is absent, then the type string should
+ * be used in its place.
+ *
+ *
+ * @param label the value of field 'label'.
+ */
+ public void setLabel(java.lang.String label)
+ {
+ this._label = label;
+ } //-- void setLabel(java.lang.String)
+
+ /**
+ * Sets the value of field 'modifiable'. The field 'modifiable'
+ * has the following description: objects with modifiable=false
+ * will not be
+ * modified by a vamsas client update
+ *
+ *
+ * @param modifiable the value of field 'modifiable'.
+ */
+ public void setModifiable(boolean modifiable)
+ {
+ this._modifiable = modifiable;
+ this._has_modifiable = true;
+ } //-- void setModifiable(boolean)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void setProperty(int index, org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _propertyList.size())) {
+ throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
+ }
+ _propertyList.setElementAt(vProperty, index);
+ } //-- void setProperty(int, org.vamsas.objects.core.Property)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param propertyArray
+ */
+ public void setProperty(org.vamsas.objects.core.Property[] propertyArray)
+ {
+ //-- copy array
+ _propertyList.removeAllElements();
+ for (int i = 0; i < propertyArray.length; i++) {
+ _propertyList.addElement(propertyArray[i]);
+ }
+ } //-- void setProperty(org.vamsas.objects.core.Property)
+
+ /**
+ * Method setScore
+ *
+ *
+ *
+ * @param index
+ * @param vScore
+ */
+ public void setScore(int index, org.vamsas.objects.core.Score vScore)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _scoreList.size())) {
+ throw new IndexOutOfBoundsException("setScore: Index value '"+index+"' not in range [0.."+_scoreList.size()+ "]");
+ }
+ _scoreList.setElementAt(vScore, index);
+ } //-- void setScore(int, org.vamsas.objects.core.Score)
+
+ /**
+ * Method setScore
+ *
+ *
+ *
+ * @param scoreArray
+ */
+ public void setScore(org.vamsas.objects.core.Score[] scoreArray)
+ {
+ //-- copy array
+ _scoreList.removeAllElements();
+ for (int i = 0; i < scoreArray.length; i++) {
+ _scoreList.addElement(scoreArray[i]);
+ }
+ } //-- void setScore(org.vamsas.objects.core.Score)
+
+ /**
+ * Sets the value of field 'status'. The field 'status' has the
+ * following description: TODO: specify this - we have
+ * considered taking the GO evidence codes as a model for
+ * assessing a measure of quality to an annotation.
+ *
+ *
+ * @param status the value of field 'status'.
+ */
+ public void setStatus(java.lang.String status)
+ {
+ this._status = status;
+ } //-- void setStatus(java.lang.String)
+
+ /**
+ * Sets the value of field 'type'. The field 'type' has the
+ * following description: A Das Feature has both a type and a
+ * Type ID.
+ * We go the route of requiring the type string
+ * to be taken from a controlled vocabulary if
+ * an application expects others to make sense
+ * of it.
+ * The type may qualified - so uniprot:CHAIN is a valid type
+ * name,
+ * and considered distinct from someotherDB:CHAIN
+ *
+ *
+ * @param type the value of field 'type'.
+ */
+ public void setType(java.lang.String type)
+ {
+ this._type = type;
+ } //-- void setType(java.lang.String)
+
+ /**
+ * Method setUrl
+ *
+ *
+ *
+ * @param index
+ * @param vUrl
+ */
+ public void setUrl(int index, org.vamsas.objects.core.Url vUrl)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _urlList.size())) {
+ throw new IndexOutOfBoundsException("setUrl: Index value '"+index+"' not in range [0.."+_urlList.size()+ "]");
+ }
+ _urlList.setElementAt(vUrl, index);
+ } //-- void setUrl(int, org.vamsas.objects.core.Url)
+
+ /**
+ * Method setUrl
+ *
+ *
+ *
+ * @param urlArray
+ */
+ public void setUrl(org.vamsas.objects.core.Url[] urlArray)
+ {
+ //-- copy array
+ _urlList.removeAllElements();
+ for (int i = 0; i < urlArray.length; i++) {
+ _urlList.addElement(urlArray[i]);
+ }
+ } //-- void setUrl(org.vamsas.objects.core.Url)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return RangeType
+ */
+ public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.RangeAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.RangeAnnotation.class, reader);
+ } //-- org.vamsas.objects.core.RangeType 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()
+
+}
git://source.jalview.org / vamsas.git / blobdiff