org.intermine.bio.postprocess
Class CreateReferences

java.lang.Object
  org.intermine.bio.postprocess.CreateReferences

public class CreateReferences
extends java.lang.Object

Fill in additional references/collections in genomic model

Field Summary

protected ObjectStoreWriter

osw

Constructor Summary

CreateReferences(ObjectStoreWriter osw)
Construct with an ObjectStoreWriter, read and write from same ObjectStore

Method Summary

void	createUtrRefs() Read the UTRs collection of MRNA then set the fivePrimeUTR and threePrimeUTR fields with the corresponding UTRs.
protected void	insertCollectionField(java.lang.Class<? extends InterMineObject> firstClass, java.lang.String firstClassFieldName, java.lang.Class<? extends InterMineObject> connectingClass, java.lang.String connectingClassFieldName, java.lang.Class<? extends InterMineObject> secondClass, java.lang.String createFieldName, boolean createInFirstClass) Add a collection of objects of type X to objects of type Y by using a connecting class.
protected void	insertReferenceField(java.lang.Class<? extends InterMineObject> sourceClass, java.lang.String sourceClassFieldName, java.lang.Class<? extends InterMineObject> connectingClass, java.lang.String connectingClassFieldName, java.lang.Class<? extends InterMineObject> destinationClass, java.lang.String createFieldName) Add a reference to and object of type X in objects of type Y by using a connecting class.
void	insertReferences() Fill in missing references/collections in model by querying relations

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

osw

protected ObjectStoreWriter osw

Constructor Detail

CreateReferences

public CreateReferences(ObjectStoreWriter osw)

Construct with an ObjectStoreWriter, read and write from same ObjectStore

Parameters:

osw - an ObjectStore to write to

Method Detail

insertReferences

public void insertReferences()
                      throws java.lang.Exception

Fill in missing references/collections in model by querying relations

Throws:

java.lang.Exception - if anything goes wrong

insertReferenceField

protected void insertReferenceField(java.lang.Class<? extends InterMineObject> sourceClass,
                                    java.lang.String sourceClassFieldName,
                                    java.lang.Class<? extends InterMineObject> connectingClass,
                                    java.lang.String connectingClassFieldName,
                                    java.lang.Class<? extends InterMineObject> destinationClass,
                                    java.lang.String createFieldName)
                             throws java.lang.Exception

Add a reference to and object of type X in objects of type Y by using a connecting class. Eg. Add a reference to Gene objects in Exon by examining the Transcript objects in the transcripts collection of the Gene, which would use a query like: SELECT DISTINCT gene FROM Gene AS gene, Transcript AS transcript, Exon AS exon WHERE (gene.transcripts CONTAINS transcript AND transcript.exons CONTAINS exon) ORDER BY gene and then set exon.gene in overview we are doing: BioEntity1 -> BioEntity2 -> BioEntity3 ==> BioEntitiy1 -> BioEntity3

Parameters:

sourceClass - the first class in the query

sourceClassFieldName - the field in the sourceClass which should contain the connectingClass

connectingClass - the class referred to by sourceClass.sourceFieldName

connectingClassFieldName - the field in connectingClass which should contain destinationClass

destinationClass - the class referred to by connectingClass.connectingClassFieldName

createFieldName - the reference field in the destinationClass - the collection to create/set

Throws:

java.lang.Exception - if anything goes wrong

insertCollectionField

protected void insertCollectionField(java.lang.Class<? extends InterMineObject> firstClass,
                                     java.lang.String firstClassFieldName,
                                     java.lang.Class<? extends InterMineObject> connectingClass,
                                     java.lang.String connectingClassFieldName,
                                     java.lang.Class<? extends InterMineObject> secondClass,
                                     java.lang.String createFieldName,
                                     boolean createInFirstClass)
                              throws java.lang.Exception

Add a collection of objects of type X to objects of type Y by using a connecting class. Eg. Add a collection of Protein objects to Gene by examining the Transcript objects in the transcripts collection of the Gene, which would use a query like: SELECT DISTINCT gene FROM Gene AS gene, Transcript AS transcript, Protein AS protein WHERE (gene.transcripts CONTAINS transcript AND transcript.protein CONTAINS protein) ORDER BY gene and then set protected gene.protein (if created BioEntity1 -> BioEntity2 -> BioEntity3 ==> BioEntity1 -> BioEntity3

Parameters:

firstClass - the first class in the query

firstClassFieldName - the field in the firstClass which should contain the connectingClass

connectingClass - the class referred to by firstClass.sourceFieldName

connectingClassFieldName - the field in connectingClass which should contain secondClass

secondClass - the class referred to by connectingClass.connectingClassFieldName

createFieldName - the collection field in the secondClass - the collection to create/set

createInFirstClass - if true create the new collection field in firstClass, otherwise create in secondClass

Throws:

java.lang.Exception - if anything goes wrong

createUtrRefs

public void createUtrRefs()
                   throws java.lang.Exception

Read the UTRs collection of MRNA then set the fivePrimeUTR and threePrimeUTR fields with the corresponding UTRs.

Throws:

java.lang.Exception - if anything goes wrong