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apollo.dataadapter.das.simple
Class SimpleDASAdapter  

java.lang.Object
  AbstractDataAdapter
      apollo.dataadapter.AbstractApolloAdapter
          apollo.dataadapter.das.simple.SimpleDASAdapter

All Implemented Interfaces:

apollo.dataadapter.ApolloDataAdapterI

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public class SimpleDASAdapter

extends apollo.dataadapter.AbstractApolloAdapter

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

My whole reason-for-being is to have a das-reading adapter which doesn't rely on a big external codebase (e.g. omnigene or biojava).

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Field Summary
(package private)  apollo.dataadapter.das.DASServerI	dasServer
(package private)  apollo.dataadapter.das.DASDsn	dsn
private  apollo.datamodel.SequenceI	genomeSeq
private static long	groupIdInt
(package private)  int	high
(package private)  int	low
(package private)  apollo.dataadapter.das.DASSegment	segment
(package private)  java.lang.String	server
(package private)  IOOperation[]	supportedOperations

 

Fields inherited from class apollo.dataadapter.AbstractApolloAdapter

 

Fields inherited from interface apollo.dataadapter.ApolloDataAdapterI

OP_READ_DATA, OP_READ_RAW_ANALYSIS, OP_READ_SEQUENCE, OP_WRITE_DATA

 

Constructor Summary

SimpleDASAdapter()

 

Method Summary
private  void	addFeaturePairToGroupFeatureSet(apollo.datamodel.FeatureSetI groupFeatureSet, apollo.dataadapter.das.DASFeature theFeature)
void	commitChanges(apollo.datamodel.CurationSet curationSet)           writes the changes from a featureChangeLog to a writeable datasource.
apollo.datamodel.StrandedFeatureSetI	getAnalysisRegion(apollo.datamodel.CurationSet curation)            Make a call to the chosen DSN, passing in the chosen segment/range into a das "features" command.
apollo.datamodel.FeatureSetI	getAnnotatedRegion()
apollo.datamodel.CurationSet	getCurationSet()           returns a saved CurationSet.
apollo.dataadapter.das.DASServerI	getDASServer()
apollo.dataadapter.das.DASDsn	getDSN()
int	getHigh()
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?
apollo.dataadapter.DataInputType	getInputType()           Returns the type of input data (gene,file,band...)
int	getLow()
private  java.lang.String	getMethodAndFeatureType(apollo.dataadapter.das.DASFeature theFeature)           Concatenates a DAS Feature's method label (if not null) and feature type into a string, separated by a colon.
java.lang.String	getName()
java.lang.String	getRawAnalysisResults(java.lang.String id)
apollo.dataadapter.das.DASSegment	getSegment()
apollo.datamodel.SequenceI	getSequence(apollo.datamodel.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.
apollo.datamodel.SequenceI	getSequence(apollo.datamodel.DbXref dbxref, int start, int end)
apollo.datamodel.SequenceI	getSequence(java.lang.String id)
java.util.Vector	getSequences(apollo.datamodel.DbXref[] dbxref)
java.util.Vector	getSequences(apollo.datamodel.DbXref[] dbxref, int[] start, int[] end)
java.util.Properties	getStateInformation()           The adapter is characterised by dsn (e.g.
private  int	getStrandForOrientation(java.lang.String orientation)           Direct conversion of a DAS feature orientation +,-,0 into +1, -1, 0.
IOOperation[]	getSupportedOperations()
java.lang.String	getType()
DataAdapterUI	getUI(IOOperation op)
void	init()
private  void	initializeGroupFeatureSet(apollo.datamodel.FeatureSetI groupFeatureSet, apollo.dataadapter.das.DASFeature theFeature, boolean setIsHolder)
private  void	initializeMethodNameFeatureTypeFeatureSet(apollo.datamodel.FeatureSetI targetFeatureSet, apollo.dataadapter.das.DASFeature theSourceFeature)
private  java.util.List	parseFeatureSet()
void	setDASServer(apollo.dataadapter.das.DASServerI newValue)
void	setDSN(apollo.dataadapter.das.DASDsn dsn)
void	setHigh(int high)
void	setLow(int low)
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	setSegment(apollo.dataadapter.das.DASSegment segment)
void	setStateInformation(java.util.Properties props)           With the following keys in the adapter properties, we can re-create a our internal state and start a new das-call.

 

Methods inherited from class apollo.dataadapter.AbstractApolloAdapter

addDataListener, clearOldData, notifyLoadingDone, rollbackAnnotations, setInput, setInputType

 

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

 

Field Detail

server

java.lang.String server

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dsn

apollo.dataadapter.das.DASDsn dsn

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segment

apollo.dataadapter.das.DASSegment segment

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genomeSeq

private apollo.datamodel.SequenceI genomeSeq

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low

int low

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high

int high

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groupIdInt

private static long groupIdInt

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dasServer

apollo.dataadapter.das.DASServerI dasServer

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supportedOperations

IOOperation[] supportedOperations

Constructor Detail

SimpleDASAdapter

public SimpleDASAdapter()

Method Detail

getDASServer

public apollo.dataadapter.das.DASServerI getDASServer()

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setDASServer

public void setDASServer(apollo.dataadapter.das.DASServerI newValue)

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init

public void init()

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getDSN

public apollo.dataadapter.das.DASDsn getDSN()

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getName

public java.lang.String getName()

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getType

public java.lang.String getType()

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getInputType

public apollo.dataadapter.DataInputType getInputType()

Description copied from class: apollo.dataadapter.AbstractApolloAdapter

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

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getInput

public java.lang.String getInput()

Description copied from class: apollo.dataadapter.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?

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getSupportedOperations

public IOOperation[] getSupportedOperations()

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getUI

public DataAdapterUI getUI(IOOperation op)

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setDSN

public void setDSN(apollo.dataadapter.das.DASDsn dsn)

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setSegment

public void setSegment(apollo.dataadapter.das.DASSegment segment)

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getSegment

public apollo.dataadapter.das.DASSegment getSegment()

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setLow

public void setLow(int low)

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setHigh

public void setHigh(int high)

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getLow

public int getLow()

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getHigh

public int getHigh()

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setRegion

public void setRegion(java.lang.String region)
               throws apollo.dataadapter.DataAdapterException

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).

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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.

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setStateInformation

public void setStateInformation(java.util.Properties props)

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

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

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getCurationSet

public apollo.datamodel.CurationSet getCurationSet()
                                            throws apollo.dataadapter.DataAdapterException

Description copied from interface: apollo.dataadapter.ApolloDataAdapterI

returns a saved CurationSet.

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parseFeatureSet

private java.util.List parseFeatureSet()

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initializeMethodNameFeatureTypeFeatureSet

private void initializeMethodNameFeatureTypeFeatureSet(apollo.datamodel.FeatureSetI targetFeatureSet,
                                                       apollo.dataadapter.das.DASFeature theSourceFeature)

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initializeGroupFeatureSet

private void initializeGroupFeatureSet(apollo.datamodel.FeatureSetI groupFeatureSet,
                                       apollo.dataadapter.das.DASFeature theFeature,
                                       boolean setIsHolder)

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addFeaturePairToGroupFeatureSet

private void addFeaturePairToGroupFeatureSet(apollo.datamodel.FeatureSetI groupFeatureSet,
                                             apollo.dataadapter.das.DASFeature theFeature)

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getAnalysisRegion

public apollo.datamodel.StrandedFeatureSetI getAnalysisRegion(apollo.datamodel.CurationSet curation)
                                                       throws apollo.dataadapter.DataAdapterException

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.

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getAnnotatedRegion

public apollo.datamodel.FeatureSetI getAnnotatedRegion()
                                                throws apollo.dataadapter.DataAdapterException

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getSequence

public apollo.datamodel.SequenceI getSequence(java.lang.String id)
                                       throws apollo.dataadapter.DataAdapterException

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getSequence

public apollo.datamodel.SequenceI getSequence(apollo.datamodel.DbXref dbxref)
                                       throws apollo.dataadapter.DataAdapterException

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.

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getSequence

public apollo.datamodel.SequenceI getSequence(apollo.datamodel.DbXref dbxref,
                                              int start,
                                              int end)
                                       throws apollo.dataadapter.DataAdapterException

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getSequences

public java.util.Vector getSequences(apollo.datamodel.DbXref[] dbxref)
                              throws apollo.dataadapter.DataAdapterException

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getSequences

public java.util.Vector getSequences(apollo.datamodel.DbXref[] dbxref,
                                     int[] start,
                                     int[] end)
                              throws apollo.dataadapter.DataAdapterException

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commitChanges

public void commitChanges(apollo.datamodel.CurationSet curationSet)
                   throws apollo.dataadapter.DataAdapterException

Description copied from interface: apollo.dataadapter.ApolloDataAdapterI

writes the changes from a featureChangeLog to a writeable datasource.

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getRawAnalysisResults

public java.lang.String getRawAnalysisResults(java.lang.String id)
                                       throws apollo.dataadapter.DataAdapterException

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getStrandForOrientation

private int getStrandForOrientation(java.lang.String orientation)

Direct conversion of a DAS feature orientation +,-,0 into +1, -1, 0.

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getMethodAndFeatureType

private java.lang.String getMethodAndFeatureType(apollo.dataadapter.das.DASFeature theFeature)

Concatenates a DAS Feature's method label (if not null) and feature type into a string, separated by a colon.

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> apollo >> dataadapter >> das >> [ simple overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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