apollo.dataadapter.synteny
Class SyntenyAdapter

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

All Implemented Interfaces:

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

public class SyntenyAdapter
extends AbstractApolloAdapter

When the user selects "Synteny" from the datachooser menu, I am the adapter that's loaded. Note that all of my hard work is really done by my GUI - SyntenyAdapterGUI. In particular, the data-fetching is run by the doOperation method on the GUI.

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

SyntenyAdapter()

Method Summary

void	clearStateInformation() Does nothing yet, because the state info isn't being used on this adapter yet.
void	commitChanges(CompositeDataHolder cdh) Write out composite data holder to multiple data adapters - called by DataLoader/FileMenu not SynAdapGUI
void	commitChanges(CurationSet curationSet) I think this is now pase and should be deleted - always gets a CompositeDataHolder now - this is actually not called by SyntenyAdapterGUI.doOp(WRITE) - calls child adapter guis doOp this is called by DataLoader though
java.util.Map	getAdapters() maps adapter "logical name"/label to the adapter itself
ApolloDataAdapterI	getChildAdapter(int i) Throws not implemented exception as by default data adapter dont have species adapter (isComposite()=false).
CurationSet	getCurationSet() Visit each child adapter and ask each one for its CurationSet.
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() 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.
int	getNumberOfChildAdapters() From ApolloDataAdapterI
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)
ApolloDataAdapterI	getSpeciesAdapter(java.lang.String species)
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) gets ui for op from cache.
void	init() From org.bdgp.io.DataAdapter interface.
boolean	isComposite() By default return false - data adapter is not composite.
void	loadNewSpeciesFromLink(SeqFeatureI link, CompositeDataHolder compData) From ApolloDataAdapterI.
CompositeDataHolder	loadSpeciesThatContainLinks(int numberOfSpecies) Load data from dataadapters where the link information is embedded in the species data (rather than coming from a separate source).
void	setRegion(java.lang.String region) 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, commitChanges, commitChanges, commitChanges, commitChanges, getCachedUI, getChildAdapter, getCurationState, getDatabase, getDataInput, getDefaultStyle, getFilename, getNameAdapter, getSpecies, getStyle, hasLinkData, 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

SyntenyAdapter

public SyntenyAdapter()

Method Detail

getAdapters

public java.util.Map getAdapters()

maps adapter "logical name"/label to the adapter itself

Specified by:

getAdapters in interface ApolloDataAdapterI

Overrides:

getAdapters in class AbstractApolloAdapter

getSpeciesAdapter

public ApolloDataAdapterI getSpeciesAdapter(java.lang.String species)

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

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 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)

gets ui for op from cache. if not there creates new one, adds to cache

setRegion

public void setRegion(java.lang.String region)
               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

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

getCurationSet

public CurationSet getCurationSet()
                           throws ApolloAdapterException

Visit each child adapter and ask each one for its CurationSet. combine the results into a composite curation set.

Specified by:

getCurationSet in interface ApolloDataAdapterI

Overrides:

getCurationSet in class AbstractApolloAdapter

Throws:

ApolloAdapterException

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

Overrides:

getSequence in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getSequence

public SequenceI getSequence(DbXref dbxref)
                      throws ApolloAdapterException

Specified by:

getSequence in interface ApolloDataAdapterI

Overrides:

getSequence in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getSequence

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

Specified by:

getSequence in interface ApolloDataAdapterI

Overrides:

getSequence in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getSequences

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

Specified by:

getSequences in interface ApolloDataAdapterI

Overrides:

getSequences in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getSequences

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

Specified by:

getSequences in interface ApolloDataAdapterI

Overrides:

getSequences in class AbstractApolloAdapter

Throws:

ApolloAdapterException

commitChanges

public void commitChanges(CompositeDataHolder cdh)
                   throws ApolloAdapterException

Write out composite data holder to multiple data adapters - called by DataLoader/FileMenu not SynAdapGUI

Specified by:

commitChanges in interface ApolloDataAdapterI

Overrides:

commitChanges in class AbstractApolloAdapter

Throws:

ApolloAdapterException

commitChanges

public void commitChanges(CurationSet curationSet)
                   throws ApolloAdapterException

I think this is now pase and should be deleted - always gets a CompositeDataHolder now - this is actually not called by SyntenyAdapterGUI.doOp(WRITE) - calls child adapter guis doOp this is called by DataLoader though

Specified by:

commitChanges in interface ApolloDataAdapterI

Overrides:

commitChanges in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getRawAnalysisResults

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

Specified by:

getRawAnalysisResults in interface ApolloDataAdapterI

Overrides:

getRawAnalysisResults in class AbstractApolloAdapter

Throws:

ApolloAdapterException

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

getNumberOfChildAdapters

public int getNumberOfChildAdapters()

From ApolloDataAdapterI

Specified by:

getNumberOfChildAdapters in interface ApolloDataAdapterI

Overrides:

getNumberOfChildAdapters in class AbstractApolloAdapter

getChildAdapter

public ApolloDataAdapterI getChildAdapter(int i)

Description copied from class: AbstractApolloAdapter

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

Overrides:

getChildAdapter in class AbstractApolloAdapter

loadSpeciesThatContainLinks

public CompositeDataHolder loadSpeciesThatContainLinks(int numberOfSpecies)
                                                throws org.bdgp.io.DataAdapterException

Load data from dataadapters where the link information is embedded in the species data (rather than coming from a separate source). Presently only the game adapter does this. This is public because TestApollo uses it.

Throws:

org.bdgp.io.DataAdapterException

loadNewSpeciesFromLink

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

From ApolloDataAdapterI. Bring up the link as a species in synteny.

Specified by:

loadNewSpeciesFromLink in interface ApolloDataAdapterI

Overrides:

loadNewSpeciesFromLink in class AbstractApolloAdapter

Throws:

org.bdgp.io.DataAdapterException

clearStateInformation

public void clearStateInformation()

Does nothing yet, because the state info isn't being used on this adapter yet.

Overrides:

clearStateInformation in class AbstractApolloAdapter

isComposite

public boolean isComposite()

Description copied from class: AbstractApolloAdapter

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

Specified by:

isComposite in interface ApolloDataAdapterI

Overrides:

isComposite in class AbstractApolloAdapter