apollo.dataadapter.ensj
Class EnsJAdapter

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

All Implemented Interfaces:

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

public class EnsJAdapter
extends AbstractApolloAdapter

EnsJ - Direct Access for Ensembl Databases (Schema 20 and above)

Field Summary

static java.lang.String	COORD_SYSTEM
static java.lang.String	END
static java.lang.String	ID
static java.lang.String	ID_PATTERN
protected static org.apache.log4j.Logger	logger
static java.lang.String	NUMBER_OF_FEATURES
static java.lang.String	REGION_PATTERN
static java.lang.String	REGION_PATTERN_2
static java.lang.String	REGION_PATTERN_3
static java.lang.String	SEQ_REGION
static java.lang.String	STABLE_ID_PREFIX
static java.lang.String	START
static java.lang.String	VERSION

Fields inherited from class apollo.dataadapter.AbstractApolloAdapter

curation_set, region, 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

java.lang.Boolean	addToCurationSet()
StrandedFeatureSet	getAnnotations()
CurationSet	getCurationSet() This is the main data-retrieval method.
org.ensembl.driver.Driver	getDriver()
DataInputType	getInputType() This is queried by Apollo's FileMenu
SequenceI	getSequence(DbXref dbxref) There is no longer a notion of a 'sequence' database - it is now assumed to come from the standard db (use the BuilderAdapter to stack up results from different db's).
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() From bdgp DataAdapter.
java.lang.String	getType() From bdgp DataAdapter.
org.bdgp.io.DataAdapterUI	getUI(org.bdgp.io.IOOperation op) This method traditionally creates a new UI for the adapter, based on the operation - read or write (each creates a different UI instance).
void	init() From org.bdgp.DataAdapter interface.
void	setRegion(java.lang.String region) This region doesnt seem to be used anywhere?
void	setSequence(FeaturePair pair, CurationSet curationSet)
void	setStateInformation(java.util.Properties properties) This is a convenient way of passing in the adapter's state: each part of the state is a key-value pair in the input Properties.

Methods inherited from class apollo.dataadapter.AbstractApolloAdapter

cacheUI, canWriteData, clearOldData, clearStateInformation, commitChanges, commitChanges, commitChanges, commitChanges, commitChanges, commitChanges, getAdapters, getCachedUI, getChildAdapter, getChildAdapter, getCurationState, getDatabase, getDataInput, getDefaultStyle, getFilename, getInput, getName, getNameAdapter, getNumberOfChildAdapters, getRawAnalysisResults, getSequence, getSequence, getSequences, getSequences, 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, removeProgressListener

Field Detail

NUMBER_OF_FEATURES

public static final java.lang.String NUMBER_OF_FEATURES

See Also:

Constant Field Values

REGION_PATTERN

public static final java.lang.String REGION_PATTERN

See Also:

Constant Field Values

REGION_PATTERN_2

public static final java.lang.String REGION_PATTERN_2

See Also:

Constant Field Values

REGION_PATTERN_3

public static final java.lang.String REGION_PATTERN_3

See Also:

Constant Field Values

ID_PATTERN

public static final java.lang.String ID_PATTERN

See Also:

Constant Field Values

logger

protected static final org.apache.log4j.Logger logger

ID

public static final java.lang.String ID

See Also:

Constant Field Values

VERSION

public static final java.lang.String VERSION

See Also:

Constant Field Values

COORD_SYSTEM

public static final java.lang.String COORD_SYSTEM

See Also:

Constant Field Values

SEQ_REGION

public static final java.lang.String SEQ_REGION

See Also:

Constant Field Values

START

public static final java.lang.String START

See Also:

Constant Field Values

END

public static final java.lang.String END

See Also:

Constant Field Values

STABLE_ID_PREFIX

public static final java.lang.String STABLE_ID_PREFIX

See Also:

Constant Field Values

Constructor Detail

EnsJAdapter

public EnsJAdapter()

Method Detail

getType

public java.lang.String getType()

From bdgp DataAdapter. No idea where this is used.

Specified by:

getType in interface org.bdgp.io.DataAdapter

Overrides:

getType in class AbstractApolloAdapter

getSupportedOperations

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

From bdgp DataAdapter. If you want the adapter to WRITE stuff, it needs to add OP_WRITE_DATA to the list.

getUI

public org.bdgp.io.DataAdapterUI getUI(org.bdgp.io.IOOperation op)

This method traditionally creates a new UI for the adapter, based on the operation - read or write (each creates a different UI instance).

setStateInformation

public void setStateInformation(java.util.Properties properties)

This is a convenient way of passing in the adapter's state: each part of the state is a key-value pair in the input Properties. Use the static constant(s) on this dataadapter for the keys - it's just safer!

Specified by:

setStateInformation in interface ApolloDataAdapterI

Overrides:

setStateInformation in class AbstractApolloAdapter

setRegion

public void setRegion(java.lang.String region)

Description copied from class: AbstractApolloAdapter

This region doesnt seem to be used anywhere?

Specified by:

setRegion in interface ApolloDataAdapterI

Overrides:

setRegion in class AbstractApolloAdapter

init

public void init()

From org.bdgp.DataAdapter interface. This is called when the adapter is created and added to the registry (see org.bdgp.io.DataAdapterChooser).

Specified by:

init in interface org.bdgp.io.DataAdapter

Overrides:

init in class AbstractApolloAdapter

getCurationSet

public CurationSet getCurationSet()
                           throws ApolloAdapterException

This is the main data-retrieval method.

Specified by:

getCurationSet in interface ApolloDataAdapterI

Overrides:

getCurationSet in class AbstractApolloAdapter

Throws:

ApolloAdapterException

addToCurationSet

public java.lang.Boolean addToCurationSet()
                                   throws ApolloAdapterException

Specified by:

addToCurationSet in interface ApolloDataAdapterI

Overrides:

addToCurationSet in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getAnnotations

public StrandedFeatureSet getAnnotations()

getInputType

public DataInputType getInputType()

This is queried by Apollo's FileMenu

Specified by:

getInputType in interface ApolloDataAdapterI

Overrides:

getInputType in class AbstractApolloAdapter

See Also:

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

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

getDriver

public org.ensembl.driver.Driver getDriver()

getSequence

public SequenceI getSequence(DbXref dbxref)
                      throws ApolloAdapterException

There is no longer a notion of a 'sequence' database - it is now assumed to come from the standard db (use the BuilderAdapter to stack up results from different db's).

Specified by:

getSequence in interface ApolloDataAdapterI

Overrides:

getSequence in class AbstractApolloAdapter

Throws:

ApolloAdapterException

setSequence

public void setSequence(FeaturePair pair,
                        CurationSet curationSet)