apollo.dataadapter.ensj19
Class AnnotationEnsJAdapter

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

All Implemented Interfaces:

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

public class AnnotationEnsJAdapter
extends EnsJAdapter

Field Summary

protected static org.apache.log4j.Logger

logger

Fields inherited from class apollo.dataadapter.ensj19.EnsJAdapter

STABLE_ID_PREFIX, stateInformation, tend, 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

AnnotationEnsJAdapter()

Method Summary

java.lang.Boolean	addToCurationSet()
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) Write the (now edited) curation set back to the otter server or file, depending on what was nominated.
CurationSet	getExistingCurationSet()
java.io.InputStream	getInputStream()
DataInputType	getInputType() This is an arcane requirement to get the File->Save menu to light up.
java.lang.String	getName() Name label for use in Data Adapter Chooser.
java.io.OutputStream	getOutputStream()
SequenceI	getSequence(DbXref dbxref) We will either draw our sequence from the main database, or from another sequence database, if it was passed in.
org.bdgp.io.IOOperation[]	getSupportedOperations() Returns a list of all operations supported by this data adapter
org.bdgp.io.DataAdapterUI	getUI(org.bdgp.io.IOOperation op) need to cache guis.
protected boolean	rollbackAnnotations(CurationSet curationSet) Overridden by AnnotationEnsJAdapter and EfeatchSequenceAdapter
void	setInputStream(java.io.InputStream newValue)
void	setOutputStream(java.io.OutputStream newValue)
void	setStateInformation(java.util.Properties stateInformation) In addition to superclass processing, We will be passed otter-i/o file names.
void	setWritingStateInformation(java.util.Properties stateInformation)

Methods inherited from class apollo.dataadapter.ensj19.EnsJAdapter

getAnnotatedRegion, getCurationSet, getCurationSetWithoutClearingData, getDriver, getDriverConf, getInput, getLocation, getLoggingFile, getMode, getOrganism, getRawAnalysisResults, getReferenceSequence, getRegion, getSequence, getSequence, getSequences, getSequences, getStateInformation, getType, init, main, printTime, setDriverConf, setLoggingFile, setRegion, validateRegionSpecified

Methods inherited from class apollo.dataadapter.AbstractApolloAdapter

cacheUI, canWriteData, clearOldData, commitChanges, commitChanges, commitChanges, commitChanges, commitChanges, getAdapters, getCachedUI, getChildAdapter, getChildAdapter, getCurationState, getDatabase, getDataInput, getDefaultStyle, getFilename, getNameAdapter, getNumberOfChildAdapters, getSpecies, getStyle, hasLinkData, isComposite, loadNewSpeciesFromLink, operationIsSupported, 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

logger

protected static final org.apache.log4j.Logger logger

Constructor Detail

AnnotationEnsJAdapter

public AnnotationEnsJAdapter()

Method Detail

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

Specified by:

getSupportedOperations in interface org.bdgp.io.DataAdapter

Overrides:

getSupportedOperations in class EnsJAdapter

getInputType

public DataInputType getInputType()

This is an arcane requirement to get the File->Save menu to light up.

Specified by:

getInputType in interface ApolloDataAdapterI

Overrides:

getInputType in class EnsJAdapter

See Also:

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

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 EnsJAdapter

getInputStream

public java.io.InputStream getInputStream()

setInputStream

public void setInputStream(java.io.InputStream newValue)

getOutputStream

public java.io.OutputStream getOutputStream()

setOutputStream

public void setOutputStream(java.io.OutputStream newValue)

getSequence

public SequenceI getSequence(DbXref dbxref)
                      throws ApolloAdapterException

We will either draw our sequence from the main database, or from another sequence database, if it was passed in.

Specified by:

getSequence in interface ApolloDataAdapterI

Overrides:

getSequence in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getUI

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

need to cache guis. getUI called 6 times by the chooser (who knows why) for each load - that means if its not cached the gui gets recreated 6 times inefficient! so its now cached

commitChanges

public void commitChanges(CurationSet curationSet)
                   throws ApolloAdapterException

Write the (now edited) curation set back to the otter server or file, depending on what was nominated.

Specified by:

commitChanges in interface ApolloDataAdapterI

Overrides:

commitChanges in class EnsJAdapter

Throws:

ApolloAdapterException

setStateInformation

public void setStateInformation(java.util.Properties stateInformation)

In addition to superclass processing, We will be passed otter-i/o file names. Create file handles from these.

Specified by:

setStateInformation in interface ApolloDataAdapterI

Overrides:

setStateInformation in class EnsJAdapter

setWritingStateInformation

public void setWritingStateInformation(java.util.Properties stateInformation)

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 EnsJAdapter

rollbackAnnotations

protected boolean rollbackAnnotations(CurationSet curationSet)

Description copied from class: AbstractApolloAdapter

Overridden by AnnotationEnsJAdapter and EfeatchSequenceAdapter

Overrides:

rollbackAnnotations in class AbstractApolloAdapter

addToCurationSet

public java.lang.Boolean addToCurationSet()
                                   throws ApolloAdapterException

Specified by:

addToCurationSet in interface ApolloDataAdapterI

Overrides:

addToCurationSet in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getExistingCurationSet

public CurationSet getExistingCurationSet()