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.xml.sax.ContentHandler;
/**
- * Class DbRef.
+ * Store a list of database
+ * references for this
+ * sequence record - with
+ * optional mapping from
+ * database sequence to the
+ * given sequence record
+ *
*
* @version $Revision$ $Date$
*/
//--------------------------/
/**
- * Field _source
+ * TODO Database
+ * Naming
+ * Convention:
+ * either start
+ * using LSID (so
+ * change type to
+ * URI) or leave
+ * this as an
+ * uncontrolled/unspecified
+ * string ID
+ *
*/
private java.lang.String _source;
/**
- * Field _version
+ * Version must be
+ * specified -
+ *
*/
private java.lang.String _version;
/**
- * Field _accessionId
+ * TODO: make some
+ * specification of
+ * the database
+ * field from which
+ * this accessionId
+ * is taken from -
+ * should that be a
+ * special property
+ * of the dbRef
+ * object ?
+ *
*/
private java.lang.String _accessionId;
/**
- * Field _id
+ * Primary Key for
+ * vamsas object
+ * referencing
+ *
*/
private java.lang.String _id;
+ /**
+ * Field _mapList
+ */
+ private java.util.Vector _mapList;
+
+ /**
+ * Field _linkList
+ */
+ private java.util.Vector _linkList;
+
+ /**
+ * Field _propertyList
+ */
+ private java.util.Vector _propertyList;
+
//----------------/
//- Constructors -/
public DbRef()
{
super();
+ _mapList = new Vector();
+ _linkList = new Vector();
+ _propertyList = new Vector();
} //-- org.vamsas.objects.core.DbRef()
//-----------/
/**
+ * Method addLink
+ *
+ *
+ *
+ * @param vLink
+ */
+ public void addLink(org.vamsas.objects.core.Link vLink)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _linkList.addElement(vLink);
+ } //-- void addLink(org.vamsas.objects.core.Link)
+
+ /**
+ * Method addLink
+ *
+ *
+ *
+ * @param index
+ * @param vLink
+ */
+ public void addLink(int index, org.vamsas.objects.core.Link vLink)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _linkList.insertElementAt(vLink, index);
+ } //-- void addLink(int, org.vamsas.objects.core.Link)
+
+ /**
+ * Method addMap
+ *
+ *
+ *
+ * @param vMap
+ */
+ public void addMap(org.vamsas.objects.core.Map vMap)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _mapList.addElement(vMap);
+ } //-- void addMap(org.vamsas.objects.core.Map)
+
+ /**
+ * Method addMap
+ *
+ *
+ *
+ * @param index
+ * @param vMap
+ */
+ public void addMap(int index, org.vamsas.objects.core.Map vMap)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _mapList.insertElementAt(vMap, index);
+ } //-- void addMap(int, org.vamsas.objects.core.Map)
+
+ /**
+ * 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 enumerateLink
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateLink()
+ {
+ return _linkList.elements();
+ } //-- java.util.Enumeration enumerateLink()
+
+ /**
+ * Method enumerateMap
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateMap()
+ {
+ return _mapList.elements();
+ } //-- java.util.Enumeration enumerateMap()
+
+ /**
+ * Method enumerateProperty
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateProperty()
+ {
+ return _propertyList.elements();
+ } //-- java.util.Enumeration enumerateProperty()
+
+ /**
* Note: hashCode() has not been overriden
*
* @param obj
}
else if (temp._id != null)
return false;
+ if (this._mapList != null) {
+ if (temp._mapList == null) return false;
+ else if (!(this._mapList.equals(temp._mapList)))
+ return false;
+ }
+ else if (temp._mapList != null)
+ return false;
+ if (this._linkList != null) {
+ if (temp._linkList == null) return false;
+ else if (!(this._linkList.equals(temp._linkList)))
+ return false;
+ }
+ else if (temp._linkList != 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)
/**
- * Returns the value of field 'accessionId'.
+ * Returns the value of field 'accessionId'. The field
+ * 'accessionId' has the following description: TODO: make some
+ * specification of
+ * the database
+ * field from which
+ * this accessionId
+ * is taken from -
+ * should that be a
+ * special property
+ * of the dbRef
+ * object ?
+ *
*
* @return String
* @return the value of field 'accessionId'.
} //-- java.lang.String getAccessionId()
/**
- * Returns the value of field 'id'.
+ * 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'.
} //-- java.lang.String getId()
/**
- * Returns the value of field 'source'.
+ * Method getLink
+ *
+ *
+ *
+ * @param index
+ * @return Link
+ */
+ public org.vamsas.objects.core.Link getLink(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _linkList.size())) {
+ throw new IndexOutOfBoundsException("getLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Link) _linkList.elementAt(index);
+ } //-- org.vamsas.objects.core.Link getLink(int)
+
+ /**
+ * Method getLink
+ *
+ *
+ *
+ * @return Link
+ */
+ public org.vamsas.objects.core.Link[] getLink()
+ {
+ int size = _linkList.size();
+ org.vamsas.objects.core.Link[] mArray = new org.vamsas.objects.core.Link[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Link) _linkList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Link[] getLink()
+
+ /**
+ * Method getLinkCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getLinkCount()
+ {
+ return _linkList.size();
+ } //-- int getLinkCount()
+
+ /**
+ * Method getMap
+ *
+ *
+ *
+ * @param index
+ * @return Map
+ */
+ public org.vamsas.objects.core.Map getMap(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _mapList.size())) {
+ throw new IndexOutOfBoundsException("getMap: Index value '"+index+"' not in range [0.."+_mapList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Map) _mapList.elementAt(index);
+ } //-- org.vamsas.objects.core.Map getMap(int)
+
+ /**
+ * Method getMap
+ *
+ *
+ *
+ * @return Map
+ */
+ public org.vamsas.objects.core.Map[] getMap()
+ {
+ int size = _mapList.size();
+ org.vamsas.objects.core.Map[] mArray = new org.vamsas.objects.core.Map[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Map) _mapList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Map[] getMap()
+
+ /**
+ * Method getMapCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getMapCount()
+ {
+ return _mapList.size();
+ } //-- int getMapCount()
+
+ /**
+ * 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()
+
+ /**
+ * Returns the value of field 'source'. The field 'source' has
+ * the following description: TODO Database
+ * Naming
+ * Convention:
+ * either start
+ * using LSID (so
+ * change type to
+ * URI) or leave
+ * this as an
+ * uncontrolled/unspecified
+ * string ID
+ *
*
* @return String
* @return the value of field 'source'.
} //-- java.lang.String getSource()
/**
- * Returns the value of field 'version'.
+ * Returns the value of field 'version'. The field 'version'
+ * has the following description: Version must be
+ * specified -
+ *
*
* @return String
* @return the value of field 'version'.
} //-- void marshal(org.xml.sax.ContentHandler)
/**
- * Sets the value of field 'accessionId'.
+ * Method removeAllLink
+ *
+ */
+ public void removeAllLink()
+ {
+ _linkList.removeAllElements();
+ } //-- void removeAllLink()
+
+ /**
+ * Method removeAllMap
+ *
+ */
+ public void removeAllMap()
+ {
+ _mapList.removeAllElements();
+ } //-- void removeAllMap()
+
+ /**
+ * Method removeAllProperty
+ *
+ */
+ public void removeAllProperty()
+ {
+ _propertyList.removeAllElements();
+ } //-- void removeAllProperty()
+
+ /**
+ * Method removeLink
+ *
+ *
+ *
+ * @param index
+ * @return Link
+ */
+ public org.vamsas.objects.core.Link removeLink(int index)
+ {
+ java.lang.Object obj = _linkList.elementAt(index);
+ _linkList.removeElementAt(index);
+ return (org.vamsas.objects.core.Link) obj;
+ } //-- org.vamsas.objects.core.Link removeLink(int)
+
+ /**
+ * Method removeMap
+ *
+ *
+ *
+ * @param index
+ * @return Map
+ */
+ public org.vamsas.objects.core.Map removeMap(int index)
+ {
+ java.lang.Object obj = _mapList.elementAt(index);
+ _mapList.removeElementAt(index);
+ return (org.vamsas.objects.core.Map) obj;
+ } //-- org.vamsas.objects.core.Map removeMap(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)
+
+ /**
+ * Sets the value of field 'accessionId'. The field
+ * 'accessionId' has the following description: TODO: make some
+ * specification of
+ * the database
+ * field from which
+ * this accessionId
+ * is taken from -
+ * should that be a
+ * special property
+ * of the dbRef
+ * object ?
+ *
*
* @param accessionId the value of field 'accessionId'.
*/
} //-- void setAccessionId(java.lang.String)
/**
- * Sets the value of field 'id'.
+ * 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'.
*/
} //-- void setId(java.lang.String)
/**
- * Sets the value of field 'source'.
+ * Method setLink
+ *
+ *
+ *
+ * @param index
+ * @param vLink
+ */
+ public void setLink(int index, org.vamsas.objects.core.Link vLink)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _linkList.size())) {
+ throw new IndexOutOfBoundsException("setLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]");
+ }
+ _linkList.setElementAt(vLink, index);
+ } //-- void setLink(int, org.vamsas.objects.core.Link)
+
+ /**
+ * Method setLink
+ *
+ *
+ *
+ * @param linkArray
+ */
+ public void setLink(org.vamsas.objects.core.Link[] linkArray)
+ {
+ //-- copy array
+ _linkList.removeAllElements();
+ for (int i = 0; i < linkArray.length; i++) {
+ _linkList.addElement(linkArray[i]);
+ }
+ } //-- void setLink(org.vamsas.objects.core.Link)
+
+ /**
+ * Method setMap
+ *
+ *
+ *
+ * @param index
+ * @param vMap
+ */
+ public void setMap(int index, org.vamsas.objects.core.Map vMap)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _mapList.size())) {
+ throw new IndexOutOfBoundsException("setMap: Index value '"+index+"' not in range [0.."+_mapList.size()+ "]");
+ }
+ _mapList.setElementAt(vMap, index);
+ } //-- void setMap(int, org.vamsas.objects.core.Map)
+
+ /**
+ * Method setMap
+ *
+ *
+ *
+ * @param mapArray
+ */
+ public void setMap(org.vamsas.objects.core.Map[] mapArray)
+ {
+ //-- copy array
+ _mapList.removeAllElements();
+ for (int i = 0; i < mapArray.length; i++) {
+ _mapList.addElement(mapArray[i]);
+ }
+ } //-- void setMap(org.vamsas.objects.core.Map)
+
+ /**
+ * 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)
+
+ /**
+ * Sets the value of field 'source'. The field 'source' has the
+ * following description: TODO Database
+ * Naming
+ * Convention:
+ * either start
+ * using LSID (so
+ * change type to
+ * URI) or leave
+ * this as an
+ * uncontrolled/unspecified
+ * string ID
+ *
*
* @param source the value of field 'source'.
*/
} //-- void setSource(java.lang.String)
/**
- * Sets the value of field 'version'.
+ * Sets the value of field 'version'. The field 'version' has
+ * the following description: Version must be
+ * specified -
+ *
*
* @param version the value of field 'version'.
*/
git://source.jalview.org / vamsas.git / blobdiff