org.intermine.bio.postprocess
Class TransferSequences

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

public class TransferSequences
extends java.lang.Object

Transfer sequences from the Assembly objects to the other objects that are located on the Assemblys and to the objects that the Assemblys are located on (eg. Chromosomes).

Field Summary

protected ObjectStoreWriter

osw

Constructor Summary

TransferSequences(ObjectStoreWriter osw)
Create a new TransferSequences object from the given ObjectStoreWriter

Method Summary

void	transferToLocatedSequenceFeatures() Use the Location relations to copy the sequence from the Chromosomes to every SequenceFeature that is located on a Chromosome and which doesn't already have a sequence (ie. don't copy to Assembly).
void	transferToTranscripts() For each Transcript, join and transfer the sequences from the child Exons to a new Sequence object for the Transcript.

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

TransferSequences

public TransferSequences(ObjectStoreWriter osw)

Create a new TransferSequences object from the given ObjectStoreWriter

Parameters:

osw - writer on genomic ObjectStore

Method Detail

transferToLocatedSequenceFeatures

public void transferToLocatedSequenceFeatures()
                                       throws java.lang.Exception

Use the Location relations to copy the sequence from the Chromosomes to every SequenceFeature that is located on a Chromosome and which doesn't already have a sequence (ie. don't copy to Assembly). Uses the ObjectStoreWriter that was passed to the constructor.

Throws:

java.lang.Exception - if there are problems with the transfer

transferToTranscripts

public void transferToTranscripts()
                           throws java.lang.Exception

For each Transcript, join and transfer the sequences from the child Exons to a new Sequence object for the Transcript. Uses the ObjectStoreWriter that was passed to the constructor

Throws:

java.lang.Exception - if there are problems with the transfer