* \r
* @version $Revision$ $Date$\r
*/\r
-public class SequenceMapping extends uk.ac.vamsas.client.Vobject \r
+public class SequenceMapping extends uk.ac.vamsas.objects.core.MapType \r
implements java.io.Serializable\r
{\r
\r
//--------------------------/\r
\r
/**\r
- * Field _sequenceA.\r
+ * Object on which the local\r
+ * range is defined. \r
*/\r
- private java.lang.Object _sequenceA;\r
+ private java.lang.Object _loc;\r
\r
/**\r
- * Field _sequenceB.\r
+ * Object on which the mapped\r
+ * range is defined. \r
*/\r
- private java.lang.Object _sequenceB;\r
+ private java.lang.Object _map;\r
\r
/**\r
* Field _id.\r
private java.lang.String _id;\r
\r
/**\r
- * Field _rangeList.\r
- */\r
- private java.util.Vector _rangeList;\r
-\r
- /**\r
* Field _provenance.\r
*/\r
private uk.ac.vamsas.objects.core.Provenance _provenance;\r
\r
public SequenceMapping() {\r
super();\r
- this._rangeList = new java.util.Vector();\r
}\r
\r
\r
//-----------/\r
\r
/**\r
- * \r
- * \r
- * @param vRange\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addRange(\r
- final uk.ac.vamsas.objects.core.Range vRange)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._rangeList.addElement(vRange);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vRange\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addRange(\r
- final int index,\r
- final uk.ac.vamsas.objects.core.Range vRange)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._rangeList.add(index, vRange);\r
- }\r
-\r
- /**\r
- * Method enumerateRange.\r
- * \r
- * @return an Enumeration over all\r
- * uk.ac.vamsas.objects.core.Range elements\r
- */\r
- public java.util.Enumeration enumerateRange(\r
- ) {\r
- return this._rangeList.elements();\r
- }\r
-\r
- /**\r
* Overrides the java.lang.Object.equals method.\r
* \r
* @param obj\r
if (obj instanceof SequenceMapping) {\r
\r
SequenceMapping temp = (SequenceMapping)obj;\r
- if (this._sequenceA != null) {\r
- if (temp._sequenceA == null) return false;\r
- else if (!(this._sequenceA.equals(temp._sequenceA))) \r
- return false;\r
- }\r
- else if (temp._sequenceA != null)\r
+ boolean thcycle;\r
+ boolean tmcycle;\r
+ if (this._loc != null) {\r
+ if (temp._loc == null) return false;\r
+ if (this._loc != temp._loc) {\r
+ thcycle=org.castor.util.CycleBreaker.startingToCycle(this._loc);\r
+ tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._loc);\r
+ if (thcycle!=tmcycle) {\r
+ if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._loc); };\r
+ if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._loc); };\r
+ return false;\r
+ }\r
+ if (!thcycle) {\r
+ if (!this._loc.equals(temp._loc)) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._loc);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._loc);\r
+ return false;\r
+ }\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._loc);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._loc);\r
+ }\r
+ }\r
+ } else if (temp._loc != null)\r
return false;\r
- if (this._sequenceB != null) {\r
- if (temp._sequenceB == null) return false;\r
- else if (!(this._sequenceB.equals(temp._sequenceB))) \r
- return false;\r
- }\r
- else if (temp._sequenceB != null)\r
+ if (this._map != null) {\r
+ if (temp._map == null) return false;\r
+ if (this._map != temp._map) {\r
+ thcycle=org.castor.util.CycleBreaker.startingToCycle(this._map);\r
+ tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._map);\r
+ if (thcycle!=tmcycle) {\r
+ if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._map); };\r
+ if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._map); };\r
+ return false;\r
+ }\r
+ if (!thcycle) {\r
+ if (!this._map.equals(temp._map)) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._map);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._map);\r
+ return false;\r
+ }\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._map);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._map);\r
+ }\r
+ }\r
+ } else if (temp._map != null)\r
return false;\r
if (this._id != null) {\r
if (temp._id == null) return false;\r
- else if (!(this._id.equals(temp._id))) \r
- return false;\r
- }\r
- else if (temp._id != null)\r
- return false;\r
- if (this._rangeList != null) {\r
- if (temp._rangeList == null) return false;\r
- else if (!(this._rangeList.equals(temp._rangeList))) \r
- return false;\r
- }\r
- else if (temp._rangeList != null)\r
+ if (this._id != temp._id) {\r
+ thcycle=org.castor.util.CycleBreaker.startingToCycle(this._id);\r
+ tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._id);\r
+ if (thcycle!=tmcycle) {\r
+ if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._id); };\r
+ if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); };\r
+ return false;\r
+ }\r
+ if (!thcycle) {\r
+ if (!this._id.equals(temp._id)) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);\r
+ return false;\r
+ }\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);\r
+ }\r
+ }\r
+ } else if (temp._id != null)\r
return false;\r
if (this._provenance != null) {\r
if (temp._provenance == null) return false;\r
- else if (!(this._provenance.equals(temp._provenance))) \r
- return false;\r
- }\r
- else if (temp._provenance != null)\r
+ if (this._provenance != temp._provenance) {\r
+ thcycle=org.castor.util.CycleBreaker.startingToCycle(this._provenance);\r
+ tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._provenance);\r
+ if (thcycle!=tmcycle) {\r
+ if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); };\r
+ if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); };\r
+ return false;\r
+ }\r
+ if (!thcycle) {\r
+ if (!this._provenance.equals(temp._provenance)) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);\r
+ return false;\r
+ }\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);\r
+ }\r
+ }\r
+ } else if (temp._provenance != null)\r
return false;\r
return true;\r
}\r
}\r
\r
/**\r
- * Returns the value of field 'provenance'.\r
- * \r
- * @return the value of field 'Provenance'.\r
- */\r
- public uk.ac.vamsas.objects.core.Provenance getProvenance(\r
- ) {\r
- return this._provenance;\r
- }\r
-\r
- /**\r
- * Method getRange.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- * @return the value of the uk.ac.vamsas.objects.core.Range at\r
- * the given index\r
- */\r
- public uk.ac.vamsas.objects.core.Range getRange(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._rangeList.size()) {\r
- throw new IndexOutOfBoundsException("getRange: Index value '" + index + "' not in range [0.." + (this._rangeList.size() - 1) + "]");\r
- }\r
- \r
- return (uk.ac.vamsas.objects.core.Range) _rangeList.get(index);\r
- }\r
-\r
- /**\r
- * Method getRange.Returns the contents of the collection in an\r
- * Array. <p>Note: Just in case the collection contents are\r
- * changing in another thread, we pass a 0-length Array of the\r
- * correct type into the API call. This way we <i>know</i>\r
- * that the Array returned is of exactly the correct length.\r
+ * Returns the value of field 'loc'. The field 'loc' has the\r
+ * following description: Object on which the local\r
+ * range is defined. \r
* \r
- * @return this collection as an Array\r
+ * @return the value of field 'Loc'.\r
*/\r
- public uk.ac.vamsas.objects.core.Range[] getRange(\r
+ public java.lang.Object getLoc(\r
) {\r
- uk.ac.vamsas.objects.core.Range[] array = new uk.ac.vamsas.objects.core.Range[0];\r
- return (uk.ac.vamsas.objects.core.Range[]) this._rangeList.toArray(array);\r
+ return this._loc;\r
}\r
\r
/**\r
- * Method getRangeAsReference.Returns a reference to\r
- * '_rangeList'. No type checking is performed on any\r
- * modifications to the Vector.\r
+ * Returns the value of field 'map'. The field 'map' has the\r
+ * following description: Object on which the mapped\r
+ * range is defined. \r
* \r
- * @return a reference to the Vector backing this class\r
+ * @return the value of field 'Map'.\r
*/\r
- public java.util.Vector getRangeAsReference(\r
+ public java.lang.Object getMap(\r
) {\r
- return this._rangeList;\r
+ return this._map;\r
}\r
\r
/**\r
- * Method getRangeCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getRangeCount(\r
- ) {\r
- return this._rangeList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'sequenceA'.\r
- * \r
- * @return the value of field 'SequenceA'.\r
- */\r
- public java.lang.Object getSequenceA(\r
- ) {\r
- return this._sequenceA;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'sequenceB'.\r
+ * Returns the value of field 'provenance'.\r
* \r
- * @return the value of field 'SequenceB'.\r
+ * @return the value of field 'Provenance'.\r
*/\r
- public java.lang.Object getSequenceB(\r
+ public uk.ac.vamsas.objects.core.Provenance getProvenance(\r
) {\r
- return this._sequenceB;\r
+ return this._provenance;\r
}\r
\r
/**\r
int result = super.hashCode();\r
\r
long tmp;\r
- if (_sequenceA != null) {\r
- result = 37 * result + _sequenceA.hashCode();\r
+ if (_loc != null\r
+ && !org.castor.util.CycleBreaker.startingToCycle(_loc)) {\r
+ result = 37 * result + _loc.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_loc);\r
}\r
- if (_sequenceB != null) {\r
- result = 37 * result + _sequenceB.hashCode();\r
+ if (_map != null\r
+ && !org.castor.util.CycleBreaker.startingToCycle(_map)) {\r
+ result = 37 * result + _map.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_map);\r
}\r
- if (_id != null) {\r
+ if (_id != null\r
+ && !org.castor.util.CycleBreaker.startingToCycle(_id)) {\r
result = 37 * result + _id.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_id);\r
}\r
- if (_rangeList != null) {\r
- result = 37 * result + _rangeList.hashCode();\r
- }\r
- if (_provenance != null) {\r
+ if (_provenance != null\r
+ && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {\r
result = 37 * result + _provenance.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);\r
}\r
\r
return result;\r
}\r
\r
/**\r
- */\r
- public void removeAllRange(\r
- ) {\r
- this._rangeList.clear();\r
- }\r
-\r
- /**\r
- * Method removeRange.\r
- * \r
- * @param vRange\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeRange(\r
- final uk.ac.vamsas.objects.core.Range vRange) {\r
- boolean removed = _rangeList.remove(vRange);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeRangeAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public uk.ac.vamsas.objects.core.Range removeRangeAt(\r
- final int index) {\r
- java.lang.Object obj = this._rangeList.remove(index);\r
- return (uk.ac.vamsas.objects.core.Range) obj;\r
- }\r
-\r
- /**\r
* Sets the value of field 'id'.\r
* \r
* @param id the value of field 'id'.\r
}\r
\r
/**\r
- * Sets the value of field 'provenance'.\r
- * \r
- * @param provenance the value of field 'provenance'.\r
- */\r
- public void setProvenance(\r
- final uk.ac.vamsas.objects.core.Provenance provenance) {\r
- this._provenance = provenance;\r
- }\r
-\r
- /**\r
+ * Sets the value of field 'loc'. The field 'loc' has the\r
+ * following description: Object on which the local\r
+ * range is defined. \r
* \r
- * \r
- * @param index\r
- * @param vRange\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setRange(\r
- final int index,\r
- final uk.ac.vamsas.objects.core.Range vRange)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._rangeList.size()) {\r
- throw new IndexOutOfBoundsException("setRange: Index value '" + index + "' not in range [0.." + (this._rangeList.size() - 1) + "]");\r
- }\r
- \r
- this._rangeList.set(index, vRange);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vRangeArray\r
+ * @param loc the value of field 'loc'.\r
*/\r
- public void setRange(\r
- final uk.ac.vamsas.objects.core.Range[] vRangeArray) {\r
- //-- copy array\r
- _rangeList.clear();\r
- \r
- for (int i = 0; i < vRangeArray.length; i++) {\r
- this._rangeList.add(vRangeArray[i]);\r
- }\r
+ public void setLoc(\r
+ final java.lang.Object loc) {\r
+ this._loc = loc;\r
}\r
\r
/**\r
- * Sets the value of '_rangeList' by copying the given Vector.\r
- * All elements will be checked for type safety.\r
+ * Sets the value of field 'map'. The field 'map' has the\r
+ * following description: Object on which the mapped\r
+ * range is defined. \r
* \r
- * @param vRangeList the Vector to copy.\r
+ * @param map the value of field 'map'.\r
*/\r
- public void setRange(\r
- final java.util.Vector vRangeList) {\r
- // copy vector\r
- this._rangeList.clear();\r
- \r
- this._rangeList.addAll(vRangeList);\r
+ public void setMap(\r
+ final java.lang.Object map) {\r
+ this._map = map;\r
}\r
\r
/**\r
- * Sets the value of '_rangeList' by setting it to the given\r
- * Vector. No type checking is performed.\r
- * @deprecated\r
- * \r
- * @param rangeVector the Vector to set.\r
- */\r
- public void setRangeAsReference(\r
- final java.util.Vector rangeVector) {\r
- this._rangeList = rangeVector;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'sequenceA'.\r
- * \r
- * @param sequenceA the value of field 'sequenceA'.\r
- */\r
- public void setSequenceA(\r
- final java.lang.Object sequenceA) {\r
- this._sequenceA = sequenceA;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'sequenceB'.\r
+ * Sets the value of field 'provenance'.\r
* \r
- * @param sequenceB the value of field 'sequenceB'.\r
+ * @param provenance the value of field 'provenance'.\r
*/\r
- public void setSequenceB(\r
- final java.lang.Object sequenceB) {\r
- this._sequenceB = sequenceB;\r
+ public void setProvenance(\r
+ final uk.ac.vamsas.objects.core.Provenance provenance) {\r
+ this._provenance = provenance;\r
}\r
\r
/**\r
* null or if any SAXException is thrown during marshaling\r
* @throws org.exolab.castor.xml.ValidationException if this\r
* object is an invalid instance according to the schema\r
- * @return the unmarshaled\r
- * uk.ac.vamsas.objects.core.SequenceMapping\r
+ * @return the unmarshaled uk.ac.vamsas.objects.core.MapType\r
*/\r
- public static uk.ac.vamsas.objects.core.SequenceMapping unmarshal(\r
+ public static uk.ac.vamsas.objects.core.MapType unmarshal(\r
final java.io.Reader reader)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- return (uk.ac.vamsas.objects.core.SequenceMapping) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.SequenceMapping.class, reader);\r
+ return (uk.ac.vamsas.objects.core.MapType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.SequenceMapping.class, reader);\r
}\r
\r
/**\r
git://source.jalview.org / vamsas.git / blobdiff