apollo.dataadapter.synteny.builder
Class BuilderAdapter

java.lang.Object
  org.bdgp.io.AbstractDataAdapter
      apollo.dataadapter.AbstractApolloAdapter
          apollo.dataadapter.synteny.builder.BuilderAdapter

All Implemented Interfaces:

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

public class BuilderAdapter
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

BuilderAdapter()

Method Summary

void	clearStateInformation() This SHOULD reset all the contents of the stateInformation being held by an adapter: with setStateInformation, this is not guaranteed.
CurationSet	getCurationSet() returns a saved CurationSet.
DataInputType	getInputType() Returns the type of input data (gene,file,band...)
Model	getModel()
java.lang.String	getName() Name label for use in Data Adapter Chooser.
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	setRegion(java.lang.String region) This method has to pass the setRegion call onto each child adapter.
void	setStateInformation(java.util.Properties properties) This stores the input properties on the adapter.

Methods inherited from class apollo.dataadapter.AbstractApolloAdapter

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

BuilderAdapter

public BuilderAdapter()

Method Detail

getModel

public Model getModel()

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

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.

setStateInformation

public void setStateInformation(java.util.Properties properties)

This stores the input properties on the adapter. It also transmits any input properties - via a direct setStateInformation call - to all child adapters.

Specified by:

setStateInformation in interface ApolloDataAdapterI

Overrides:

setStateInformation in class AbstractApolloAdapter

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

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

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?

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

setRegion

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

This method has to pass the setRegion call onto each child adapter.

Specified by:

setRegion in interface ApolloDataAdapterI

Overrides:

setRegion in class AbstractApolloAdapter

Throws:

ApolloAdapterException

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