apollo.dataadapter.ensj
Class DataFetcher

java.lang.Object
  apollo.dataadapter.ensj.DataFetcher

public class DataFetcher
extends java.lang.Object

I am just a separate helper class to stop the EnsJAdapter from becoming too huge. I keep all the code that drives ensj to fetch stuff.

Field Summary

protected static org.apache.log4j.Logger

logger

Constructor Summary

DataFetcher(EnsJAdapter adapter)

Method Summary

int	addContigFeatures(CurationSet curationSet, java.util.List flatFeatures, org.ensembl.datamodel.Location location)
int	addDitagFeatures(CurationSet curationSet, java.util.List flatFeatures, org.ensembl.datamodel.Location location, java.util.List includedTypes)
int	addDnaAlignFeatures(CurationSet curationSet, java.util.List flatFeatures, org.ensembl.datamodel.Location location, java.util.List includedTypes)
java.util.List	addGenes(StrandedFeatureSet results, org.ensembl.datamodel.Location location, java.util.List includedTypes, boolean aggressiveNaming, java.lang.String typePrefix) Retrieves ensJ genes/transcripts/exons, converts them into seq features and adds them to the curation set.
int	addPredictionTranscripts(StrandedFeatureSet results, org.ensembl.datamodel.Location location, java.util.List includedTypes)
int	addProteinAlignFeatures(CurationSet curationSet, java.util.List flatFeatures, org.ensembl.datamodel.Location location, java.util.List includedTypes)
int	addProteinAnnotations(CurationSet curationSet, java.util.List flatFeatures, java.util.List retrievedGenes)
int	addRepeatFeatures(CurationSet curationSet, java.util.List flatFeatures, org.ensembl.datamodel.Location location) Add all repeat features into the input set.
int	addSimpleFeatures(CurationSet curationSet, java.util.List flatFeatures, org.ensembl.datamodel.Location location, java.util.List includedTypes)
protected StrandedFeatureSetI	getAnnotations(CurationSet curationSet, java.util.List genes, boolean addTranscriptSupport)

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static final org.apache.log4j.Logger logger

Constructor Detail

DataFetcher

public DataFetcher(EnsJAdapter adapter)

Method Detail

addGenes

public java.util.List addGenes(StrandedFeatureSet results,
                               org.ensembl.datamodel.Location location,
                               java.util.List includedTypes,
                               boolean aggressiveNaming,
                               java.lang.String typePrefix)
                        throws org.ensembl.driver.AdaptorException

Retrieves ensJ genes/transcripts/exons, converts them into seq features and adds them to the curation set. Passes out the list of ensj-genes retreived: this so that the simple-feature adapter can, if it wants, use the translations to retrieve protein annotations.

Throws:

org.ensembl.driver.AdaptorException

addRepeatFeatures

public int addRepeatFeatures(CurationSet curationSet,
                             java.util.List flatFeatures,
                             org.ensembl.datamodel.Location location)
                      throws org.ensembl.driver.AdaptorException

Add all repeat features into the input set.

Throws:

org.ensembl.driver.AdaptorException

addProteinAlignFeatures

public int addProteinAlignFeatures(CurationSet curationSet,
                                   java.util.List flatFeatures,
                                   org.ensembl.datamodel.Location location,
                                   java.util.List includedTypes)
                            throws org.ensembl.driver.AdaptorException

Throws:

org.ensembl.driver.AdaptorException

addDnaAlignFeatures

public int addDnaAlignFeatures(CurationSet curationSet,
                               java.util.List flatFeatures,
                               org.ensembl.datamodel.Location location,
                               java.util.List includedTypes)
                        throws org.ensembl.driver.AdaptorException

Throws:

org.ensembl.driver.AdaptorException

addDitagFeatures

public int addDitagFeatures(CurationSet curationSet,
                            java.util.List flatFeatures,
                            org.ensembl.datamodel.Location location,
                            java.util.List includedTypes)
                     throws org.ensembl.driver.AdaptorException

Throws:

org.ensembl.driver.AdaptorException

addPredictionTranscripts

public int addPredictionTranscripts(StrandedFeatureSet results,
                                    org.ensembl.datamodel.Location location,
                                    java.util.List includedTypes)
                             throws org.ensembl.driver.AdaptorException

Throws:

org.ensembl.driver.AdaptorException

addSimpleFeatures

public int addSimpleFeatures(CurationSet curationSet,
                             java.util.List flatFeatures,
                             org.ensembl.datamodel.Location location,
                             java.util.List includedTypes)
                      throws org.ensembl.driver.AdaptorException

Throws:

org.ensembl.driver.AdaptorException

addContigFeatures

public int addContigFeatures(CurationSet curationSet,
                             java.util.List flatFeatures,
                             org.ensembl.datamodel.Location location)
                      throws org.ensembl.driver.AdaptorException

Throws:

org.ensembl.driver.AdaptorException

addProteinAnnotations

public int addProteinAnnotations(CurationSet curationSet,
                                 java.util.List flatFeatures,
                                 java.util.List retrievedGenes)
                          throws org.ensembl.driver.AdaptorException

Throws:

org.ensembl.driver.AdaptorException

getAnnotations

protected StrandedFeatureSetI getAnnotations(CurationSet curationSet,
                                             java.util.List genes,
                                             boolean addTranscriptSupport)
                                      throws ApolloAdapterException,
                                             org.ensembl.driver.AdaptorException

Throws:

ApolloAdapterException

org.ensembl.driver.AdaptorException