apollo.dataadapter.ensj19
Class EnsJAdapter

java.lang.Object
  org.bdgp.io.AbstractDataAdapter
      apollo.dataadapter.AbstractApolloAdapter
          apollo.dataadapter.ensj19.EnsJAdapter

All Implemented Interfaces:

ApolloDataAdapterI, org.bdgp.io.DataAdapter, org.bdgp.io.VisualDataAdapter

Direct Known Subclasses:

AnnotationEnsJAdapter

public abstract class EnsJAdapter
extends AbstractApolloAdapter

Adaptor providing access to the ensembl database via the ensj-core library.

Originally based on EnsCGIAdaptor.

Field Summary

static java.lang.String	STABLE_ID_PREFIX
protected java.util.Properties	stateInformation
long	tend
long	tstart

Fields inherited from class apollo.dataadapter.AbstractApolloAdapter

curation_set, style

Fields inherited from class org.bdgp.io.AbstractDataAdapter

listeners

Fields inherited from interface apollo.dataadapter.ApolloDataAdapterI

OP_APPEND_DATA, OP_READ_DATA, OP_READ_RAW_ANALYSIS, OP_READ_SEQUENCE, OP_WRITE_DATA

Constructor Summary

EnsJAdapter()

Method Summary

void	clearStateInformation() This SHOULD reset all the contents of the stateInformation being held by an adapter: with setStateInformation, this is not guaranteed.
void	commitChanges(CurationSet curationSet) writes the changes from a featureChangeLog to a writeable datasource.
protected StrandedFeatureSetI	getAnnotatedRegion(CurationSet curationSet)
CurationSet	getCurationSet() returns a saved CurationSet.
protected CurationSet	getCurationSetWithoutClearingData()
protected org.ensembl19.driver.Driver	getDriver()
java.util.Properties	getDriverConf() Get the value of driverConf.
java.lang.String	getInput() Returns the input String passed to the DataAdapter, the input is of course associated with the input type Should this go into org.bdgp.io.DataAdapter?
DataInputType	getInputType() Returns the type of input data (gene,file,band...)
protected org.ensembl19.datamodel.LinearLocation	getLocation()
java.lang.String	getLoggingFile() Get the value of loggingFile.
protected int	getMode()
java.lang.String	getName() Name label for use in Data Adapter Chooser.
protected java.lang.String	getOrganism() An ugly hack to tease the organism name from the database name Ignore it if this doesn't parse out
java.lang.String	getRawAnalysisResults(java.lang.String id)
protected SequenceI	getReferenceSequence()
protected java.lang.String	getRegion()
SequenceI	getSequence(DbXref dbxref, int start, int end)
SequenceI	getSequence(java.lang.String id) Strings for input types
java.util.Vector	getSequences(DbXref[] dbxref)
java.util.Vector	getSequences(DbXref[] dbxref, int[] start, int[] end)
java.util.Properties	getStateInformation() State info Properties carries all the info needed for the adapter to do its query This is an alternative to setDataInput.
org.bdgp.io.IOOperation[]	getSupportedOperations() Returns a list of all operations supported by this data adapter
java.lang.String	getType() From org.bdgp.io.DataAdapter.
void	init() From org.bdgp.io.DataAdapter interface.
static void	main(java.lang.String[] args)
void	printTime(java.lang.String message)
void	setDriverConf(java.util.Properties v) Set the value of driverConf.
void	setLoggingFile(java.lang.String v) Set the value of loggingFile.
void	setRegion(java.lang.String region) Set the region to be retrieved by subsequent calls to getCurrationSet().
void	setStateInformation(java.util.Properties props) This should set StateInformation object! see StateInformation for Strings to use for keys.
protected void	validateRegionSpecified(java.util.Properties properties)

Methods inherited from class apollo.dataadapter.AbstractApolloAdapter

addToCurationSet, cacheUI, canWriteData, clearOldData, commitChanges, commitChanges, commitChanges, commitChanges, commitChanges, getAdapters, getCachedUI, getChildAdapter, getChildAdapter, getCurationState, getDatabase, getDataInput, getDefaultStyle, getFilename, getNameAdapter, getNumberOfChildAdapters, getSequence, getSpecies, getStyle, hasLinkData, isComposite, loadNewSpeciesFromLink, operationIsSupported, rollbackAnnotations, rollbackAnnotations, setCuration, setCurationNumber, setCurationState, setDatabase, setDataInput, setDataLoadListener, setInput, setInputType, setLocation, setName, setPadLeft, setPadRight, setSpecies, setStyle

Methods inherited from class org.bdgp.io.AbstractDataAdapter

addProgressListener, fireProgressEvent, removeProgressListener, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.bdgp.io.VisualDataAdapter

addProgressListener, fireProgressEvent, getUI, removeProgressListener

Field Detail

tstart

public long tstart

tend

public long tend

STABLE_ID_PREFIX

public static final java.lang.String STABLE_ID_PREFIX

See Also:

Constant Field Values

stateInformation

protected java.util.Properties stateInformation

Constructor Detail

EnsJAdapter

public EnsJAdapter()

Method Detail

init

public void init()

Description copied from class: AbstractApolloAdapter

From org.bdgp.io.DataAdapter interface. no-op default implementation. A data adapter should override this if it needs to do some initialization.

Specified by:

init in interface org.bdgp.io.DataAdapter

Overrides:

init in class AbstractApolloAdapter

printTime

public void printTime(java.lang.String message)

getName

public java.lang.String getName()

Description copied from class: AbstractApolloAdapter

Name label for use in Data Adapter Chooser. Don't override this method--call setName from your constructor.

Specified by:

getName in interface org.bdgp.io.DataAdapter

Overrides:

getName in class AbstractApolloAdapter

getType

public java.lang.String getType()

Description copied from class: AbstractApolloAdapter

From org.bdgp.io.DataAdapter. Default implementation returns "". Override this to return a string describing the data adapter. The reason for the default implementation is that as far as I can tell getType is not used by apollo nor org.bdgp, so seems silly to require it. Am i missing something?

Specified by:

getType in interface org.bdgp.io.DataAdapter

Overrides:

getType in class AbstractApolloAdapter

getInputType

public DataInputType getInputType()

Description copied from class: AbstractApolloAdapter

Returns the type of input data (gene,file,band...)

Specified by:

getInputType in interface ApolloDataAdapterI

Overrides:

getInputType in class AbstractApolloAdapter

See Also:

Should this go into org.bdgp.io.DataAdapter?

getInput

public java.lang.String getInput()

Description copied from class: AbstractApolloAdapter

Returns the input String passed to the DataAdapter, the input is of course associated with the input type Should this go into org.bdgp.io.DataAdapter?

Specified by:

getInput in interface ApolloDataAdapterI

Overrides:

getInput in class AbstractApolloAdapter

getSupportedOperations

public org.bdgp.io.IOOperation[] getSupportedOperations()

Description copied from interface: org.bdgp.io.DataAdapter

Returns a list of all operations supported by this data adapter

setRegion

public void setRegion(java.lang.String region)
               throws ApolloAdapterException

Set the region to be retrieved by subsequent calls to getCurrationSet().

Specified by:

setRegion in interface ApolloDataAdapterI

Overrides:

setRegion in class AbstractApolloAdapter

Parameters:

region - region to be retrieved. Region is encoded as parameters separated by spaces "CHR START END".

Throws:

ApolloAdapterException

getStateInformation

public java.util.Properties getStateInformation()

Description copied from interface: ApolloDataAdapterI

State info Properties carries all the info needed for the adapter to do its query This is an alternative to setDataInput. For most cases setDataInput should be sufficient. This should return StateInformation

Specified by:

getStateInformation in interface ApolloDataAdapterI

Overrides:

getStateInformation in class AbstractApolloAdapter

setStateInformation

public void setStateInformation(java.util.Properties props)

Description copied from interface: ApolloDataAdapterI

This should set StateInformation object! see StateInformation for Strings to use for keys.

Specified by:

setStateInformation in interface ApolloDataAdapterI

Overrides:

setStateInformation in class AbstractApolloAdapter

getCurationSetWithoutClearingData

protected CurationSet getCurationSetWithoutClearingData()
                                                 throws ApolloAdapterException

Throws:

ApolloAdapterException

getCurationSet

public CurationSet getCurationSet()
                           throws ApolloAdapterException

Description copied from interface: ApolloDataAdapterI

returns a saved CurationSet.

Specified by:

getCurationSet in interface ApolloDataAdapterI

Overrides:

getCurationSet in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getOrganism

protected java.lang.String getOrganism()

An ugly hack to tease the organism name from the database name Ignore it if this doesn't parse out

getLocation

protected org.ensembl19.datamodel.LinearLocation getLocation()
                                                      throws org.ensembl19.driver.AdaptorException,
                                                             org.ensembl19.driver.ConfigurationException

Returns:

ensj location corresponding to region, or null if no match exists.

Throws:

org.ensembl19.driver.AdaptorException

org.ensembl19.driver.ConfigurationException

getAnnotatedRegion

protected StrandedFeatureSetI getAnnotatedRegion(CurationSet curationSet)
                                          throws ApolloAdapterException

Returns:

object graph containing genes, transcripts and exons from the currently specified region as apollo annotation objects. Reads otter source (server or file) for annotations. Converts those annotations into Apollo objects. ONLY if the adapter has been specified an input server/file name. THAT will only happen if EditingEnabled has been marked as "true" on the style file for the adapter.

Throws:

ApolloAdapterException

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

Throws:

java.lang.Exception

getSequence

public SequenceI getSequence(java.lang.String id)
                      throws ApolloAdapterException

Description copied from interface: ApolloDataAdapterI

Strings for input types

Specified by:

getSequence in interface ApolloDataAdapterI

Overrides:

getSequence in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getSequence

public SequenceI getSequence(DbXref dbxref,
                             int start,
                             int end)
                      throws ApolloAdapterException

Specified by:

getSequence in interface ApolloDataAdapterI

Overrides:

getSequence in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getSequences

public java.util.Vector getSequences(DbXref[] dbxref)
                              throws ApolloAdapterException

Specified by:

getSequences in interface ApolloDataAdapterI

Overrides:

getSequences in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getSequences

public java.util.Vector getSequences(DbXref[] dbxref,
                                     int[] start,
                                     int[] end)
                              throws ApolloAdapterException

Specified by:

getSequences in interface ApolloDataAdapterI

Overrides:

getSequences in class AbstractApolloAdapter

Throws:

ApolloAdapterException

commitChanges

public void commitChanges(CurationSet curationSet)
                   throws ApolloAdapterException

Description copied from interface: ApolloDataAdapterI

writes the changes from a featureChangeLog to a writeable datasource. Not just a featureChangeLog - this writes out the whole curationSet

Specified by:

commitChanges in interface ApolloDataAdapterI

Overrides:

commitChanges in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getRawAnalysisResults

public java.lang.String getRawAnalysisResults(java.lang.String id)
                                       throws ApolloAdapterException

Specified by:

getRawAnalysisResults in interface ApolloDataAdapterI

Overrides:

getRawAnalysisResults in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getLoggingFile

public java.lang.String getLoggingFile()

Get the value of loggingFile.

Returns:

value of loggingFile.

setLoggingFile

public void setLoggingFile(java.lang.String v)

Set the value of loggingFile.

Parameters:

v - Value to assign to loggingFile.

getDriverConf

public java.util.Properties getDriverConf()

Get the value of driverConf.

Returns:

value of driverConf.

getDriver

protected org.ensembl19.driver.Driver getDriver()

getMode

protected int getMode()

setDriverConf

public void setDriverConf(java.util.Properties v)

Set the value of driverConf.

Parameters:

v - Value to assign to driverConf.

getRegion

protected java.lang.String getRegion()

getReferenceSequence

protected SequenceI getReferenceSequence()

clearStateInformation

public void clearStateInformation()

Description copied from class: AbstractApolloAdapter

This SHOULD reset all the contents of the stateInformation being held by an adapter: with setStateInformation, this is not guaranteed.

Overrides:

clearStateInformation in class AbstractApolloAdapter

validateRegionSpecified

protected void validateRegionSpecified(java.util.Properties properties)
                                throws ApolloAdapterException

Throws:

ApolloAdapterException