private java.lang.String _id;
/**
- * From: Offset to first
- * position in dataset sequence record that
- * this database entry maps to To: Offset
- * to last position in dataset sequence
- * record that this database entry maps to
- * Start: Offset to first last position in
- * database entry that first (or offset)
- * position in sequence maps to End: Offset
- * to last position in database entry that
- * last (offset) position in sequence maps
- * to
+ * the local mapType maps from the parent
+ * sequence coordinate frame to the reference
+ * frame defined by the dbRef element.
+ * The mapped mapType is the mapped range defined
+ * on the dbRef element's reference frame.
+ * Conventionally, the unit attribute defaults to 1, or
+ * will be inferred from the local sequence's
+ * dictionary type and any dictionary type associated
+ * with the database being mapped to.
+ * However, it may be used to avoid ambiguity.
+ *
*/
- private java.util.Vector _mapList;
+ private uk.ac.vamsas.objects.core.Map _map;
/**
* Field _linkList.
public DbRef() {
super();
- this._mapList = new java.util.Vector();
this._linkList = new java.util.Vector();
this._propertyList = new java.util.Vector();
}
/**
*
*
- * @param vMap
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addMap(
- final uk.ac.vamsas.objects.core.Map vMap)
- throws java.lang.IndexOutOfBoundsException {
- this._mapList.addElement(vMap);
- }
-
- /**
- *
- *
- * @param index
- * @param vMap
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addMap(
- final int index,
- final uk.ac.vamsas.objects.core.Map vMap)
- throws java.lang.IndexOutOfBoundsException {
- this._mapList.add(index, vMap);
- }
-
- /**
- *
- *
* @param vProperty
* @throws java.lang.IndexOutOfBoundsException if the index
* given is outside the bounds of the collection
}
/**
- * Method enumerateMap.
- *
- * @return an Enumeration over all
- * uk.ac.vamsas.objects.core.Map elements
- */
- public java.util.Enumeration enumerateMap(
- ) {
- return this._mapList.elements();
- }
-
- /**
* Method enumerateProperty.
*
* @return an Enumeration over all
if (obj instanceof DbRef) {
DbRef temp = (DbRef)obj;
+ boolean thcycle;
+ boolean tmcycle;
if (this._source != null) {
if (temp._source == null) return false;
- else if (!(this._source.equals(temp._source)))
- return false;
- }
- else if (temp._source != null)
+ if (this._source != temp._source) {
+ thcycle=org.castor.util.CycleBreaker.startingToCycle(this._source);
+ tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._source);
+ if (thcycle!=tmcycle) {
+ if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._source); };
+ if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._source); };
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._source.equals(temp._source)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._source);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._source);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._source);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._source);
+ }
+ }
+ } else if (temp._source != null)
return false;
if (this._version != null) {
if (temp._version == null) return false;
- else if (!(this._version.equals(temp._version)))
- return false;
- }
- else if (temp._version != null)
+ if (this._version != temp._version) {
+ thcycle=org.castor.util.CycleBreaker.startingToCycle(this._version);
+ tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._version);
+ if (thcycle!=tmcycle) {
+ if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._version); };
+ if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._version); };
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._version.equals(temp._version)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
+ }
+ }
+ } else if (temp._version != null)
return false;
if (this._accessionId != null) {
if (temp._accessionId == null) return false;
- else if (!(this._accessionId.equals(temp._accessionId)))
- return false;
- }
- else if (temp._accessionId != null)
+ if (this._accessionId != temp._accessionId) {
+ thcycle=org.castor.util.CycleBreaker.startingToCycle(this._accessionId);
+ tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._accessionId);
+ if (thcycle!=tmcycle) {
+ if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._accessionId); };
+ if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._accessionId); };
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._accessionId.equals(temp._accessionId)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._accessionId);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._accessionId);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._accessionId);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._accessionId);
+ }
+ }
+ } else if (temp._accessionId != null)
return false;
if (this._id != null) {
if (temp._id == null) return false;
- else if (!(this._id.equals(temp._id)))
- return false;
- }
- else if (temp._id != null)
+ if (this._id != temp._id) {
+ thcycle=org.castor.util.CycleBreaker.startingToCycle(this._id);
+ tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._id);
+ if (thcycle!=tmcycle) {
+ if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._id); };
+ if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); };
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._id.equals(temp._id)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ }
+ } 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)
+ if (this._map != null) {
+ if (temp._map == null) return false;
+ if (this._map != temp._map) {
+ thcycle=org.castor.util.CycleBreaker.startingToCycle(this._map);
+ tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._map);
+ if (thcycle!=tmcycle) {
+ if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._map); };
+ if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._map); };
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._map.equals(temp._map)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._map);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._map);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._map);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._map);
+ }
+ }
+ } else if (temp._map != 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)
+ if (this._linkList != temp._linkList) {
+ thcycle=org.castor.util.CycleBreaker.startingToCycle(this._linkList);
+ tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._linkList);
+ if (thcycle!=tmcycle) {
+ if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList); };
+ if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList); };
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._linkList.equals(temp._linkList)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList);
+ }
+ }
+ } 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)
+ if (this._propertyList != temp._propertyList) {
+ thcycle=org.castor.util.CycleBreaker.startingToCycle(this._propertyList);
+ tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._propertyList);
+ if (thcycle!=tmcycle) {
+ if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList); };
+ if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList); };
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._propertyList.equals(temp._propertyList)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
+ }
+ }
+ } else if (temp._propertyList != null)
return false;
return true;
}
}
/**
- * Method getMap.
+ * Returns the value of field 'map'. The field 'map' has the
+ * following description: the local mapType maps from the
+ * parent
+ * sequence coordinate frame to the reference
+ * frame defined by the dbRef element.
+ * The mapped mapType is the mapped range defined
+ * on the dbRef element's reference frame.
+ * Conventionally, the unit attribute defaults to 1, or
+ * will be inferred from the local sequence's
+ * dictionary type and any dictionary type associated
+ * with the database being mapped to.
+ * However, it may be used to avoid ambiguity.
+ *
*
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the uk.ac.vamsas.objects.core.Map at
- * the given index
+ * @return the value of field 'Map'.
*/
public uk.ac.vamsas.objects.core.Map getMap(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._mapList.size()) {
- throw new IndexOutOfBoundsException("getMap: Index value '" + index + "' not in range [0.." + (this._mapList.size() - 1) + "]");
- }
-
- return (uk.ac.vamsas.objects.core.Map) _mapList.get(index);
- }
-
- /**
- * Method getMap.Returns the contents of the collection in an
- * Array. <p>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 <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public uk.ac.vamsas.objects.core.Map[] getMap(
- ) {
- uk.ac.vamsas.objects.core.Map[] array = new uk.ac.vamsas.objects.core.Map[0];
- return (uk.ac.vamsas.objects.core.Map[]) this._mapList.toArray(array);
- }
-
- /**
- * Method getMapAsReference.Returns a reference to '_mapList'.
- * No type checking is performed on any modifications to the
- * Vector.
- *
- * @return a reference to the Vector backing this class
- */
- public java.util.Vector getMapAsReference(
- ) {
- return this._mapList;
- }
-
- /**
- * Method getMapCount.
- *
- * @return the size of this collection
- */
- public int getMapCount(
) {
- return this._mapList.size();
+ return this._map;
}
/**
int result = super.hashCode();
long tmp;
- if (_source != null) {
+ if (_source != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_source)) {
result = 37 * result + _source.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_source);
}
- if (_version != null) {
+ if (_version != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_version)) {
result = 37 * result + _version.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_version);
}
- if (_accessionId != null) {
+ if (_accessionId != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_accessionId)) {
result = 37 * result + _accessionId.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_accessionId);
}
- if (_id != null) {
+ if (_id != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
result = 37 * result + _id.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_id);
}
- if (_mapList != null) {
- result = 37 * result + _mapList.hashCode();
+ if (_map != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_map)) {
+ result = 37 * result + _map.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_map);
}
- if (_linkList != null) {
+ if (_linkList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_linkList)) {
result = 37 * result + _linkList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_linkList);
}
- if (_propertyList != null) {
+ if (_propertyList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
result = 37 * result + _propertyList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
}
return result;
/**
*/
- public void removeAllMap(
- ) {
- this._mapList.clear();
- }
-
- /**
- */
public void removeAllProperty(
) {
this._propertyList.clear();
}
/**
- * Method removeMap.
- *
- * @param vMap
- * @return true if the object was removed from the collection.
- */
- public boolean removeMap(
- final uk.ac.vamsas.objects.core.Map vMap) {
- boolean removed = _mapList.remove(vMap);
- return removed;
- }
-
- /**
- * Method removeMapAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public uk.ac.vamsas.objects.core.Map removeMapAt(
- final int index) {
- java.lang.Object obj = this._mapList.remove(index);
- return (uk.ac.vamsas.objects.core.Map) obj;
- }
-
- /**
* Method removeProperty.
*
* @param vProperty
}
/**
+ * Sets the value of field 'map'. The field 'map' has the
+ * following description: the local mapType maps from the
+ * parent
+ * sequence coordinate frame to the reference
+ * frame defined by the dbRef element.
+ * The mapped mapType is the mapped range defined
+ * on the dbRef element's reference frame.
+ * Conventionally, the unit attribute defaults to 1, or
+ * will be inferred from the local sequence's
+ * dictionary type and any dictionary type associated
+ * with the database being mapped to.
+ * However, it may be used to avoid ambiguity.
+ *
*
- *
- * @param index
- * @param vMap
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setMap(
- final int index,
- final uk.ac.vamsas.objects.core.Map vMap)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._mapList.size()) {
- throw new IndexOutOfBoundsException("setMap: Index value '" + index + "' not in range [0.." + (this._mapList.size() - 1) + "]");
- }
-
- this._mapList.set(index, vMap);
- }
-
- /**
- *
- *
- * @param vMapArray
- */
- public void setMap(
- final uk.ac.vamsas.objects.core.Map[] vMapArray) {
- //-- copy array
- _mapList.clear();
-
- for (int i = 0; i < vMapArray.length; i++) {
- this._mapList.add(vMapArray[i]);
- }
- }
-
- /**
- * Sets the value of '_mapList' by copying the given Vector.
- * All elements will be checked for type safety.
- *
- * @param vMapList the Vector to copy.
+ * @param map the value of field 'map'.
*/
public void setMap(
- final java.util.Vector vMapList) {
- // copy vector
- this._mapList.clear();
-
- this._mapList.addAll(vMapList);
- }
-
- /**
- * Sets the value of '_mapList' by setting it to the given
- * Vector. No type checking is performed.
- * @deprecated
- *
- * @param mapVector the Vector to set.
- */
- public void setMapAsReference(
- final java.util.Vector mapVector) {
- this._mapList = mapVector;
+ final uk.ac.vamsas.objects.core.Map map) {
+ this._map = map;
}
/**
git://source.jalview.org / vamsas.git / blobdiff