apollo.dataadapter
Class SerialDiskAdapter

java.lang.Object
  org.bdgp.io.AbstractDataAdapter
      apollo.dataadapter.AbstractApolloAdapter
          apollo.dataadapter.SerialDiskAdapter

All Implemented Interfaces:

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

public class SerialDiskAdapter
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

SerialDiskAdapter()

SerialDiskAdapter(java.lang.String filename)

Method Summary

void	commitChanges(CompositeDataHolder cdh) If multi cur set, appends curset name to filename - or should it appends the cur set # so its retrievable?
void	commitChanges(CurationSet curationSet) writes the changes from a featureChangeLog to a writeable datasource.
CurationSet	getCurationSet() What about getCompositeDataHolder?
protected java.lang.String	getFilename() Returns null if not file
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...)
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.
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	setFilename(java.lang.String filename)
void	setRegion(java.lang.String extId) This region doesnt seem to be used anywhere?
void	setStateInformation(java.util.Properties props) This should set StateInformation object! see StateInformation for Strings to use for keys.

Methods inherited from class apollo.dataadapter.AbstractApolloAdapter

addToCurationSet, cacheUI, canWriteData, clearOldData, clearStateInformation, commitChanges, commitChanges, commitChanges, commitChanges, getAdapters, getCachedUI, getChildAdapter, getChildAdapter, getCurationState, getDatabase, getDataInput, getDefaultStyle, 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

SerialDiskAdapter

public SerialDiskAdapter()

SerialDiskAdapter

public SerialDiskAdapter(java.lang.String filename)

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()

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

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.

setFilename

public void setFilename(java.lang.String filename)

getFilename

protected java.lang.String getFilename()

Description copied from class: AbstractApolloAdapter

Returns null if not file

Overrides:

getFilename in class AbstractApolloAdapter

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

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

commitChanges

public void commitChanges(CompositeDataHolder cdh)
                   throws ApolloAdapterException

If multi cur set, appends curset name to filename - or should it appends the cur set # so its retrievable?

Specified by:

commitChanges in interface ApolloDataAdapterI

Overrides:

commitChanges in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getCurationSet

public CurationSet getCurationSet()
                           throws ApolloAdapterException

What about getCompositeDataHolder?

Specified by:

getCurationSet in interface ApolloDataAdapterI

Overrides:

getCurationSet in class AbstractApolloAdapter

Throws:

ApolloAdapterException

setRegion

public void setRegion(java.lang.String extId)
               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