apollo.dataadapter.das2
Class DAS2Adapter

java.lang.Object
  org.bdgp.io.AbstractDataAdapter
      apollo.dataadapter.AbstractApolloAdapter
          apollo.dataadapter.das2.DAS2Adapter

All Implemented Interfaces:

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

public class DAS2Adapter
extends AbstractApolloAdapter

I implement a AbstractDataAdapter, allowing Apollo to get information from DAS datasources, using 'simple' implementions of DASServerI, DASDsn etc.

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

DAS2Adapter()

Method Summary

void	clearStateInformation() This SHOULD reset all the contents of the stateInformation being held by an adapter: with setStateInformation, this is not guaranteed.
void	commitChanges(CurationSet curation) Main method for writing DAS2XML file
StrandedFeatureSetI	getAnalysisRegion(CurationSet curation) Make a call to the chosen DSN, passing in the chosen segment/range into a das "features" command.
FeatureSetI	getAnnotatedRegion()
CurationSet	getCurationSet() returns a saved CurationSet.
DAS2Request	getDASServer()
DASDsn	getDSN()
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.
java.lang.String	getRawAnalysisResults(java.lang.String id)
SequenceI	getSequence(DbXref dbxref) The dbxref passed into this argument is only checked to make sure that the the IdValue it contains is the same as the Id for the DASSegment that this adapter is poised on.
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.util.Properties	getStateInformation() The adapter is characterised by dsn (e.g.
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.
static void	main(java.lang.String[] args) For testing directly from the command line--give a DAS2XML file as the argument.
void	setDASServer(DAS2Request newValue)
void	setDataInput(DataInput dataInput) Used when Apollo was called from the command line rather than the GUI
void	setInput(java.lang.String filename) Input string that corresponds with the input type (eg gene name for gene input type)
void	setRegion(java.lang.String region) This string is used when the user navigates around the genome - it should contain both the new segment and high/low information.
void	setStateInformation(java.util.Properties newProperties) With the following keys in the adapter properties, we can re-create a our internal state and start a new das-call.
void	validateStateInformation()

Methods inherited from class apollo.dataadapter.AbstractApolloAdapter

addToCurationSet, cacheUI, canWriteData, clearOldData, commitChanges, commitChanges, commitChanges, commitChanges, commitChanges, getAdapters, getCachedUI, getChildAdapter, getChildAdapter, getCurationState, getDatabase, getDataInput, getDefaultStyle, getFilename, getNameAdapter, getNumberOfChildAdapters, getSpecies, getStyle, hasLinkData, isComposite, loadNewSpeciesFromLink, operationIsSupported, rollbackAnnotations, rollbackAnnotations, setCuration, setCurationNumber, setCurationState, setDatabase, setDataLoadListener, 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

DAS2Adapter

public DAS2Adapter()

Method Detail

getDASServer

public DAS2Request getDASServer()

setDASServer

public void setDASServer(DAS2Request newValue)

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

getDSN

public DASDsn getDSN()

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()

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?

setInput

public void setInput(java.lang.String filename)

Description copied from class: AbstractApolloAdapter

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

Specified by:

setInput in interface ApolloDataAdapterI

Overrides:

setInput in class AbstractApolloAdapter

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

setDataInput

public void setDataInput(DataInput dataInput)

Used when Apollo was called from the command line rather than the GUI

Specified by:

setDataInput in interface ApolloDataAdapterI

Overrides:

setDataInput 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.

setRegion

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

This string is used when the user navigates around the genome - it should contain both the new segment and high/low information. Armed with this, we can set the DASSegment in this data adapter. The new data is set into the adapter with two calls: setStateInformation (copying in the "old" state of the adapter and then setRegion (copying in the new choices of region into the adapter).

Specified by:

setRegion in interface ApolloDataAdapterI

Overrides:

setRegion in class AbstractApolloAdapter

Throws:

ApolloAdapterException

getStateInformation

public java.util.Properties getStateInformation()

The adapter is characterised by dsn (e.g. http://url/.../entry_point) and segment (e.g. chr=1, start=... stop=....) With this information we can make a das-call. So we write this information out in entirety.

Specified by:

getStateInformation in interface ApolloDataAdapterI

Overrides:

getStateInformation in class AbstractApolloAdapter

setStateInformation

public void setStateInformation(java.util.Properties newProperties)

With the following keys in the adapter properties, we can re-create a our internal state and start a new das-call.

• DAS_server_url
• DSN_sourceId
• DSN_source
• DSN_sourceVersion
• DSN_mapMaster
• Segment_segment
• Segment_id
• Segment_start
• Segment_stop
• Segment_orientation
• Segment_subparts
• Segment_length

Specified by:

setStateInformation in interface ApolloDataAdapterI

Overrides:

setStateInformation 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

getAnalysisRegion

public StrandedFeatureSetI getAnalysisRegion(CurationSet curation)
                                      throws ApolloAdapterException

Make a call to the chosen DSN, passing in the chosen segment/range into a das "features" command. Parse the result into a nested heirarchy of FeatureSets.

Level 1 - StrandedFeatureSet. Common parent to all lower level sets

Level 2 - FeatureSets keyed by Method Name and Feature Type

Level 3 - FeatureSets for the parent Method and Type, keyed by GroupId, containing max score within group, and having handles to aligned sequences

Level 4 - FeaturePairs for the parent Group, containing start, end, target start, target end.

Throws:

ApolloAdapterException

getAnnotatedRegion

public FeatureSetI getAnnotatedRegion()
                               throws ApolloAdapterException

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

The dbxref passed into this argument is only checked to make sure that the the IdValue it contains is the same as the Id for the DASSegment that this adapter is poised on. The range etc passed into the lazy sequence are determined by the Segment that this adapter already has stored on it.

Note carefully: the sequence should NOT be fetched from the DASServer and DASDSN set on this adapter: that Server/DSN may not be a reference server. Instead, we must to go to the server and DSN referenced by the 'MapMaster' - this points to the URL of the reference server, which will have the raw sequence.

3/2006: Not currently used

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

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

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

validateStateInformation

public void validateStateInformation()

commitChanges

public void commitChanges(CurationSet curation)

Main method for writing DAS2XML file

Specified by:

commitChanges in interface ApolloDataAdapterI

Overrides:

commitChanges in class AbstractApolloAdapter

main

public static void main(java.lang.String[] args)

For testing directly from the command line--give a DAS2XML file as the argument.