apollo.dataadapter
Class AbstractApolloAdapter

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

All Implemented Interfaces:

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

Direct Known Subclasses:

AnalysisAdapter, BaseGFFAdapter, BuilderAdapter, ChadoAdapter, ChadoXmlAdapter, DAS2Adapter, DummySequenceAdapter, EfetchSequenceAdapter, EnsCGIAdapter, EnsJAdapter, EnsJAdapter, GAMEAdapter, GbrowseAdapter, GenbankAdapter, GFF3Adapter, GraphAdapter, OtterAdapter, OtterXMLAdapter, SampleAdapter, SerialDiskAdapter, SimpleDASAdapter, SyntenyAdapter, SyntenyComparaAdapter

public abstract class AbstractApolloAdapter
extends org.bdgp.io.AbstractDataAdapter
implements ApolloDataAdapterI

All the dataadapters now subclass AbstractApolloAdapter, which new data adapters should do as well. In AbstractApolloAdapter.getCurationSet() apollo.config.Config.newDataAdapter(this) is called. This sets up the new style before the data loads. So all the subclasses have to call super.getCurationSet() at the start of their getCurationSet() method. A data adapter has to subclass AbstactApolloAdapter and call super.getCurationSet(). (AAA.getCS() also clears out all the old data that is still lingering). I know this is a bit of an awkward requirement and is easy to miss on coding a new data adapter. I am certainly open to other suggestions on how to get the notification out before the data loads. The problem is that org.bdgp.swing.widget.DataAdapterChooser is a bit of a black box and the first point of control one gets in apollo is in data adapters with DataAdapterGUI.doOperation which then calls DataAdapter.getCurationSet. One idea I had was to have DataAdapterChooser send out some sort of notification of whether its going to do a load or cancel. I've ran this by John Richter who is more or less in charge of org.bdgp utilities but I havent heard back yet. - MG

Field Summary

protected CurationSet	curation_set
protected static org.apache.log4j.Logger	logger
protected java.lang.String	region
protected Style	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

AbstractApolloAdapter()

Method Summary

java.lang.Boolean	addToCurationSet()
protected void	cacheUI(org.bdgp.io.IOOperation op, org.bdgp.io.DataAdapterUI ui)
boolean	canWriteData() Whether write operation is supported by data adapter
protected void	clearOldData() This has to be called in the subclass.getCurationSet (super.clearOldData()) to do the new data notification(clears old features) - also it notifies Config of style change.
void	clearStateInformation() This SHOULD reset all the contents of the stateInformation being held by an adapter: with setStateInformation, this is not guaranteed.
void	commitChanges(CompositeDataHolder cdh) SyntenyAdapter and SerialDiskAdapter override this
void	commitChanges(CompositeDataHolder cdh, boolean saveAnnots, boolean saveResults)
void	commitChanges(CurationSet curation) writes the changes from a featureChangeLog to a writeable datasource.
void	commitChanges(CurationSet curation, boolean saveAnnots, boolean saveResults)
void	commitChanges(java.lang.Object values) Straight from DataAdapterGUI.doOp.
void	commitChanges(java.lang.Object values, boolean saveAnnots, boolean saveResults) GAMEAdapter and ChadoXMLAdapter can specify whether to save annots and whether to save results
java.util.Map	getAdapters()
protected org.bdgp.io.DataAdapterUI	getCachedUI(org.bdgp.io.IOOperation op)
ApolloDataAdapterI	getChildAdapter(int i) Throws not implemented exception as by default data adapter dont have species adapter (isComposite()=false).
ApolloDataAdapterI	getChildAdapter(java.lang.String species) Throws not implemented exception as by default data adapter dont have species adapter (isComposite()=false).
CurationSet	getCurationSet() returns a saved CurationSet.
CurationState	getCurationState() Get CurationState associated with data adapter.
java.lang.String	getDatabase()
DataInput	getDataInput()
protected Style	getDefaultStyle() Return style to use if no db (file) or db is not listed.
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.lang.String	getName() Name label for use in Data Adapter Chooser.
ApolloNameAdapterI	getNameAdapter(AnnotatedFeatureI annot)
int	getNumberOfChildAdapters() Returns 0 by default.
java.lang.String	getRawAnalysisResults(java.lang.String id)
SequenceI	getSequence(DbXref dbxref)
SequenceI	getSequence(DbXref dbxref, int start, int end)
SequenceI	getSequence(java.lang.String id) Strings for input types
java.util.Vector	getSequences(DbXref[] dbxref)
java.util.Vector	getSequences(DbXref[] dbxref, int[] start, int[] end)
java.lang.String	getSpecies() Synteny gives a species to each adapter to help keep track of them
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.
Style	getStyle() By default return style associated with the adapter in apollo.cfg.
java.lang.String	getType() From org.bdgp.io.DataAdapter.
boolean	hasLinkData() Whether data adapter contains link data used for synteny, returns false by default override if otherwise
void	init() From org.bdgp.io.DataAdapter interface.
boolean	isComposite() By default return false - data adapter is not composite.
void	loadNewSpeciesFromLink(SeqFeatureI link, CompositeDataHolder c) Bring up the link as a species in synteny.
protected boolean	operationIsSupported(org.bdgp.io.IOOperation op) I think this should be taken out to force a data adapter to implement it.
boolean	rollbackAnnotations(CompositeDataHolder cdh) Send any necessary signals to the server to release annotation locks or undo edits --after the user has been prompted that these will be lost.
protected boolean	rollbackAnnotations(CurationSet curationSet) Overridden by AnnotationEnsJAdapter and EfeatchSequenceAdapter
void	setCuration(CurationSet curation) This region is used for overlay onto this existing curation
void	setCurationNumber(int curationNumber)
void	setCurationState(CurationState curationState)
void	setDatabase(java.lang.String database) Presently only game adapter uses this
void	setDataInput(DataInput dataInput) This should replace setInput.
void	setDataLoadListener(DataLoadListener l) We currently only need one DataLoadListener(curSet controller) if we need more than one change this to addDataLoadListener
void	setInput(java.lang.String input) Input string that corresponds with the input type (eg gene name for gene input type)
void	setInputType(DataInputType type) DataInputType describes the type of input (gene,cytology,scaffold...) does this belong in the abstract class?
void	setLocation(GenomicRange chromosomeLocation) GenomicRange is a convenient object to carry chromosome, start and end.
void	setName(java.lang.String n)
void	setPadLeft(int padLeft) Request to "pad" the input padLeft basepairs to the left(5' forward strand) - default noop - presently only used by game adapter in synteny context
void	setPadRight(int padRight) Request to "pad" the input padRight basepairs to the right(3' forward strand)
void	setRegion(java.lang.String region) This region doesnt seem to be used anywhere?
void	setSpecies(java.lang.String species)
void	setStateInformation(java.util.Properties p) This should set StateInformation object! see StateInformation for Strings to use for keys.
void	setStyle(Style style) By default a data adapter uses the style listed with it in the config file.

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, getUI, removeProgressListener

Methods inherited from interface org.bdgp.io.DataAdapter

getSupportedOperations

Field Detail

logger

protected static final org.apache.log4j.Logger logger

region

protected java.lang.String region

curation_set

protected CurationSet curation_set

style

protected Style style

Constructor Detail

AbstractApolloAdapter

public AbstractApolloAdapter()

Method Detail

init

public void init()

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

getName

public java.lang.String getName()

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

setName

public void setName(java.lang.String n)

getType

public java.lang.String getType()

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

setCurationNumber

public void setCurationNumber(int curationNumber)

setCurationState

public void setCurationState(CurationState curationState)

getCurationState

public CurationState getCurationState()

Description copied from interface: ApolloDataAdapterI

Get CurationState associated with data adapter.

Specified by:

getCurationState in interface ApolloDataAdapterI

getNameAdapter

public ApolloNameAdapterI getNameAdapter(AnnotatedFeatureI annot)

setDataInput

public void setDataInput(DataInput dataInput)

Description copied from interface: ApolloDataAdapterI

This should replace setInput. setInput is limited to just a String which is awkward for locations where you have to jam several fields into one String. DataInput deals with locations much better. DataInput can complement stateInfo (hopefully?)

Specified by:

setDataInput in interface ApolloDataAdapterI

getDataInput

public DataInput getDataInput()

getFilename

protected java.lang.String getFilename()

Returns null if not file

setInputType

public void setInputType(DataInputType type)

DataInputType describes the type of input (gene,cytology,scaffold...) does this belong in the abstract class?

Specified by:

setInputType in interface ApolloDataAdapterI

getInputType

public DataInputType getInputType()

Returns the type of input data (gene,file,band...)

Specified by:

getInputType in interface ApolloDataAdapterI

See Also:

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

getInput

public 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?

Specified by:

getInput in interface ApolloDataAdapterI

setInput

public void setInput(java.lang.String input)

Input string that corresponds with the input type (eg gene name for gene input type)

Specified by:

setInput in interface ApolloDataAdapterI

clearOldData

protected void clearOldData()
                     throws ApolloAdapterException

This has to be called in the subclass.getCurationSet (super.clearOldData()) to do the new data notification(clears old features) - also it notifies Config of style change. This needs to be called after it has been verified that the user input is ok. e.g. that the filename is a valid filename. Otherwise old data will be cleared out but the new has failed. Split into 2 methods? fireDataLoadEvent and setStyle? or rename newDataLoading?

Throws:

ApolloAdapterException

rollbackAnnotations

public boolean rollbackAnnotations(CompositeDataHolder cdh)

Send any necessary signals to the server to release annotation locks or undo edits --after the user has been prompted that these will be lost. By default this method has an empty implementation: it is overridden, for instance, in the ensj-adapter

Specified by:

rollbackAnnotations in interface ApolloDataAdapterI

rollbackAnnotations

protected boolean rollbackAnnotations(CurationSet curationSet)

Overridden by AnnotationEnsJAdapter and EfeatchSequenceAdapter

getSequence

public SequenceI getSequence(java.lang.String id)
                      throws ApolloAdapterException

Description copied from interface: ApolloDataAdapterI

Strings for input types

Specified by:

getSequence in interface ApolloDataAdapterI

Throws:

ApolloAdapterException

getSequence

public SequenceI getSequence(DbXref dbxref)
                      throws ApolloAdapterException

Specified by:

getSequence in interface ApolloDataAdapterI

Throws:

ApolloAdapterException

getSequence

public SequenceI getSequence(DbXref dbxref,
                             int start,
                             int end)
                      throws ApolloAdapterException

Specified by:

getSequence in interface ApolloDataAdapterI

Throws:

ApolloAdapterException

getSequences

public java.util.Vector getSequences(DbXref[] dbxref)
                              throws ApolloAdapterException

Specified by:

getSequences in interface ApolloDataAdapterI

Throws:

ApolloAdapterException

getSequences

public java.util.Vector getSequences(DbXref[] dbxref,
                                     int[] start,
                                     int[] end)
                              throws ApolloAdapterException

Specified by:

getSequences in interface ApolloDataAdapterI

Throws:

ApolloAdapterException

getRawAnalysisResults

public java.lang.String getRawAnalysisResults(java.lang.String id)
                                       throws ApolloAdapterException

Specified by:

getRawAnalysisResults in interface ApolloDataAdapterI

Throws:

ApolloAdapterException

setRegion

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

This region doesnt seem to be used anywhere?

Specified by:

setRegion in interface ApolloDataAdapterI

Throws:

ApolloAdapterException

setCuration

public void setCuration(CurationSet curation)
                 throws ApolloAdapterException

This region is used for overlay onto this existing curation

Specified by:

setCuration in interface ApolloDataAdapterI

Throws:

ApolloAdapterException

commitChanges

public void commitChanges(CurationSet curation)
                   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

Throws:

ApolloAdapterException

commitChanges

public void commitChanges(CompositeDataHolder cdh)
                   throws ApolloAdapterException

SyntenyAdapter and SerialDiskAdapter override this

Specified by:

commitChanges in interface ApolloDataAdapterI

Throws:

ApolloAdapterException

commitChanges

public void commitChanges(java.lang.Object values)
                   throws ApolloAdapterException

Description copied from interface: ApolloDataAdapterI

Straight from DataAdapterGUI.doOp. Could be cur set or comp data holder

Specified by:

commitChanges in interface ApolloDataAdapterI

Throws:

ApolloAdapterException

commitChanges

public void commitChanges(java.lang.Object values,
                          boolean saveAnnots,
                          boolean saveResults)
                   throws ApolloAdapterException

GAMEAdapter and ChadoXMLAdapter can specify whether to save annots and whether to save results

Specified by:

commitChanges in interface ApolloDataAdapterI

Throws:

ApolloAdapterException

commitChanges

public void commitChanges(CurationSet curation,
                          boolean saveAnnots,
                          boolean saveResults)
                   throws ApolloAdapterException

Throws:

ApolloAdapterException

commitChanges

public void commitChanges(CompositeDataHolder cdh,
                          boolean saveAnnots,
                          boolean saveResults)
                   throws ApolloAdapterException

Throws:

ApolloAdapterException

getCurationSet

public CurationSet getCurationSet()
                           throws ApolloAdapterException

Description copied from interface: ApolloDataAdapterI

returns a saved CurationSet.

Specified by:

getCurationSet in interface ApolloDataAdapterI

Throws:

ApolloAdapterException

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

setStateInformation

public void setStateInformation(java.util.Properties p)

Description copied from interface: ApolloDataAdapterI

This should set StateInformation object! see StateInformation for Strings to use for keys.

Specified by:

setStateInformation in interface ApolloDataAdapterI

setLocation

public void setLocation(GenomicRange chromosomeLocation)

GenomicRange is a convenient object to carry chromosome, start and end. May at some point replace this with a more generic Location object, for non chromosome locations, this will do for now. This sets state info properties INPUT_TYPE = "Location", INPUT_ID = chromName, START & END

clearStateInformation

public void clearStateInformation()

This SHOULD reset all the contents of the stateInformation being held by an adapter: with setStateInformation, this is not guaranteed.

addToCurationSet

public java.lang.Boolean addToCurationSet()
                                   throws ApolloAdapterException

Specified by:

addToCurationSet in interface ApolloDataAdapterI

Throws:

ApolloAdapterException

operationIsSupported

protected boolean operationIsSupported(org.bdgp.io.IOOperation op)

I think this should be taken out to force a data adapter to implement it. If a data adapter doesnt have a ui it can return null for this.

canWriteData

public boolean canWriteData()

Whether write operation is supported by data adapter

Specified by:

canWriteData in interface ApolloDataAdapterI

cacheUI

protected void cacheUI(org.bdgp.io.IOOperation op,
                       org.bdgp.io.DataAdapterUI ui)

getCachedUI

protected org.bdgp.io.DataAdapterUI getCachedUI(org.bdgp.io.IOOperation op)

hasLinkData

public boolean hasLinkData()

Whether data adapter contains link data used for synteny, returns false by default override if otherwise

Specified by:

hasLinkData in interface ApolloDataAdapterI

isComposite

public boolean isComposite()

By default return false - data adapter is not composite. SyntenyAdpapter overrides this to return true.

Specified by:

isComposite in interface ApolloDataAdapterI

getChildAdapter

public ApolloDataAdapterI getChildAdapter(java.lang.String species)

Throws not implemented exception as by default data adapter dont have species adapter (isComposite()=false). SyntenyAdapter overrides this, and returns its species adapters

Specified by:

getChildAdapter in interface ApolloDataAdapterI

getChildAdapter

public ApolloDataAdapterI getChildAdapter(int i)

Throws not implemented exception as by default data adapter dont have species adapter (isComposite()=false). SyntenyAdapter overrides this, and returns its species adapters

Specified by:

getChildAdapter in interface ApolloDataAdapterI

getNumberOfChildAdapters

public int getNumberOfChildAdapters()

Returns 0 by default. SyntenyAdapter overrides.

Specified by:

getNumberOfChildAdapters in interface ApolloDataAdapterI

getAdapters

public java.util.Map getAdapters()

Specified by:

getAdapters in interface ApolloDataAdapterI

setSpecies

public void setSpecies(java.lang.String species)

getSpecies

public java.lang.String getSpecies()

Description copied from interface: ApolloDataAdapterI

Synteny gives a species to each adapter to help keep track of them

Specified by:

getSpecies in interface ApolloDataAdapterI

getStyle

public Style getStyle()

By default return style associated with the adapter in apollo.cfg. This can be overridden by setStyle, which is used by SyntenyAdapter to overrides its childrens style with its own. Once we have the ability to switch between single and multi species, the style will need to be synched with it (not there yet). Also a style can have other styles it loads depending on the db that is being loaded (yes this is a little quirky and perhaps needs a revisit).

Specified by:

getStyle in interface ApolloDataAdapterI

getDefaultStyle

protected Style getDefaultStyle()

Return style to use if no db (file) or db is not listed. This is the style listed in apollo.cfg with the data adapter

setDatabase

public void setDatabase(java.lang.String database)

Presently only game adapter uses this

Specified by:

setDatabase in interface ApolloDataAdapterI

getDatabase

public java.lang.String getDatabase()

loadNewSpeciesFromLink

public void loadNewSpeciesFromLink(SeqFeatureI link,
                                   CompositeDataHolder c)
                            throws org.bdgp.io.DataAdapterException

Bring up the link as a species in synteny. Presently this can only be done in synteny mode - eventually would be nice to do from regular apollo From ApolloDataAdapterI - default throws exception - SyntenyAdapter overrides

Specified by:

loadNewSpeciesFromLink in interface ApolloDataAdapterI

Throws:

org.bdgp.io.DataAdapterException

setPadLeft

public void setPadLeft(int padLeft)

Request to "pad" the input padLeft basepairs to the left(5' forward strand) - default noop - presently only used by game adapter in synteny context

Specified by:

setPadLeft in interface ApolloDataAdapterI

setPadRight

public void setPadRight(int padRight)

Request to "pad" the input padRight basepairs to the right(3' forward strand)

Specified by:

setPadRight in interface ApolloDataAdapterI

setStyle

public void setStyle(Style style)

By default a data adapter uses the style listed with it in the config file. In synteny mode the childrens default style needs to be overridden by the synteny adapters style. This method is for the synteny override of its child adapters style. also using for SpeciesToStyle override(game).

Specified by:

setStyle in interface ApolloDataAdapterI

setDataLoadListener

public void setDataLoadListener(DataLoadListener l)

We currently only need one DataLoadListener(curSet controller) if we need more than one change this to addDataLoadListener

Specified by:

setDataLoadListener in interface ApolloDataAdapterI