apollo.dataadapter.analysis
Class AnalysisAdapter

java.lang.Object
  org.bdgp.io.AbstractDataAdapter
      apollo.dataadapter.AbstractApolloAdapter
          apollo.dataadapter.analysis.AnalysisAdapter

All Implemented Interfaces:

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

public class AnalysisAdapter
extends AbstractApolloAdapter

Field Summary

protected static org.apache.log4j.Logger

logger

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

AnalysisAdapter()

Method Summary

java.lang.Boolean	addToCurationSet() from ApolloDataAdapterI interface.
CurationSet	getCurationSet() from ApolloDataAdapterI interface.
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() org.bdgp.io.DataAdapter method
org.bdgp.io.DataAdapterUI	getUI(org.bdgp.io.IOOperation op) Returns a user interface for the requested IOOperation.
void	init() From org.bdgp.io.DataAdapter interface.
void	setAnalysisInput(AnalysisInput input)
void	setFilter(AnalysisFilterI filter)
void	setParser(AnalysisParserI parser)
void	setRegion(SequenceI seq)
void	setRegion(java.lang.String seq_file) This region doesnt seem to be used anywhere?
void	setStateInformation(java.util.Properties props) DataLoader calls this

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, getInputType, getName, getNameAdapter, getNumberOfChildAdapters, getRawAnalysisResults, getSequence, 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

logger

protected static final org.apache.log4j.Logger logger

Constructor Detail

AnalysisAdapter

public AnalysisAdapter()

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

getType

public java.lang.String getType()

org.bdgp.io.DataAdapter method

Specified by:

getType in interface org.bdgp.io.DataAdapter

Overrides:

getType 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

getUI

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

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

Returns a user interface for the requested IOOperation. Most VisualDataAdapters will return a different user interface for each supported IOOperation.

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)

DataLoader calls this

Specified by:

setStateInformation in interface ApolloDataAdapterI

Overrides:

setStateInformation in class AbstractApolloAdapter

setAnalysisInput

public void setAnalysisInput(AnalysisInput input)

setParser

public void setParser(AnalysisParserI parser)

setFilter

public void setFilter(AnalysisFilterI filter)

setRegion

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

Description copied from class: AbstractApolloAdapter

This region doesnt seem to be used anywhere?

Specified by:

setRegion in interface ApolloDataAdapterI

Overrides:

setRegion in class AbstractApolloAdapter

Throws:

ApolloAdapterException

setRegion

public void setRegion(SequenceI seq)
               throws ApolloAdapterException

Throws:

ApolloAdapterException

getCurationSet

public CurationSet getCurationSet()
                           throws ApolloAdapterException

from ApolloDataAdapterI interface. input type and input should be set previous to this. This is called when loading analysis results as a fresh curation set.

Specified by:

getCurationSet in interface ApolloDataAdapterI

Overrides:

getCurationSet in class AbstractApolloAdapter

Throws:

ApolloAdapterException

addToCurationSet

public java.lang.Boolean addToCurationSet()
                                   throws ApolloAdapterException

from ApolloDataAdapterI interface. input type and input should be set previous to this. This is used when adding analysis results to already-loaded curation set.

Specified by:

addToCurationSet in interface ApolloDataAdapterI

Overrides:

addToCurationSet in class AbstractApolloAdapter

Throws:

ApolloAdapterException