apollo.dataadapter.synteny
Class SyntenyComparaAdapter

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

All Implemented Interfaces:

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

public class SyntenyComparaAdapter
extends AbstractApolloAdapter

Field Summary

static int	BUFFER_SIZE
protected java.util.Properties	driverConf
protected static org.apache.log4j.Logger	logger
protected java.util.Properties	stateInformation

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

SyntenyComparaAdapter()

Method Summary

java.lang.String	convertLogicalNameToSpeciesName(java.lang.String logicalName) Use the synteny style to convert from logical to actual species names.
java.util.List	fetchAllAlignFeatures(java.lang.String speciesName, java.lang.String chromosome, int start, int end, java.util.HashMap sequenceHash, java.lang.String type)
java.lang.String	getChromosome()
java.lang.String	getCoordSystemString()
CurationSet	getCurationSet() returns a saved CurationSet.
int	getEnd()
java.lang.String	getHitChromosome()
java.lang.String	getHitCoordSystemString()
int	getHitEnd()
java.lang.String	getHitSpecies()
java.lang.String	getHitStableId()
int	getHitStart()
java.lang.String	getQuerySpecies()
java.lang.String	getQueryStableId()
java.lang.String	getStableId()
int	getStart()
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
org.bdgp.io.DataAdapterUI	getUI(org.bdgp.io.IOOperation op) BEWARE: this method creates a brand-new instance of this adapter's UI and hands it back!
org.ensembl.datamodel.AssemblyLocation	getUserChoice(java.util.HashMap locationHash)
void	setChromosome(java.lang.String newValue)
void	setCoordSystemString(java.lang.String newValue)
void	setDriverConf(java.util.Properties v)
void	setEnd(int newValue)
void	setHitChromosome(java.lang.String newValue)
void	setHitCoordSystemString(java.lang.String newValue)
void	setHitEnd(int newValue)
void	setHitSpecies(java.lang.String newValue)
void	setHitStart(int newValue)
void	setLoggingFile(java.lang.String v)
void	setQuerySpecies(java.lang.String newValue)
void	setStart(int newValue)
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, clearStateInformation, commitChanges, commitChanges, commitChanges, commitChanges, commitChanges, commitChanges, getAdapters, getCachedUI, getChildAdapter, getChildAdapter, getCurationState, getDatabase, getDataInput, getDefaultStyle, getFilename, getInput, getInputType, getName, getNameAdapter, getNumberOfChildAdapters, getRawAnalysisResults, getSequence, getSequence, getSequence, getSequences, getSequences, getSpecies, getStyle, getType, hasLinkData, init, isComposite, loadNewSpeciesFromLink, operationIsSupported, rollbackAnnotations, rollbackAnnotations, setCuration, setCurationNumber, setCurationState, setDatabase, setDataInput, setDataLoadListener, setInput, setInputType, setLocation, setName, setPadLeft, setPadRight, setRegion, 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

BUFFER_SIZE

public static int BUFFER_SIZE

stateInformation

protected java.util.Properties stateInformation

driverConf

protected java.util.Properties driverConf

Constructor Detail

SyntenyComparaAdapter

public SyntenyComparaAdapter()

Method Detail

getUI

public org.bdgp.io.DataAdapterUI getUI(org.bdgp.io.IOOperation op)

BEWARE: this method creates a brand-new instance of this adapter's UI and hands it back!

setLoggingFile

public void setLoggingFile(java.lang.String v)

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

setDriverConf

public void setDriverConf(java.util.Properties v)

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

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

getUserChoice

public org.ensembl.datamodel.AssemblyLocation getUserChoice(java.util.HashMap locationHash)

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

getQuerySpecies

public java.lang.String getQuerySpecies()

getHitSpecies

public java.lang.String getHitSpecies()

getHitStart

public int getHitStart()

getHitEnd

public int getHitEnd()

getHitChromosome

public java.lang.String getHitChromosome()

getHitCoordSystemString

public java.lang.String getHitCoordSystemString()

setQuerySpecies

public void setQuerySpecies(java.lang.String newValue)

setHitSpecies

public void setHitSpecies(java.lang.String newValue)

setHitStart

public void setHitStart(int newValue)

setHitEnd

public void setHitEnd(int newValue)

setHitChromosome

public void setHitChromosome(java.lang.String newValue)

setHitCoordSystemString

public void setHitCoordSystemString(java.lang.String newValue)

setStart

public void setStart(int newValue)

setEnd

public void setEnd(int newValue)

setChromosome

public void setChromosome(java.lang.String newValue)

setCoordSystemString

public void setCoordSystemString(java.lang.String newValue)

getStart

public int getStart()

getEnd

public int getEnd()

getChromosome

public java.lang.String getChromosome()

getCoordSystemString

public java.lang.String getCoordSystemString()

convertLogicalNameToSpeciesName

public java.lang.String convertLogicalNameToSpeciesName(java.lang.String logicalName)

Use the synteny style to convert from logical to actual species names.

fetchAllAlignFeatures

public java.util.List fetchAllAlignFeatures(java.lang.String speciesName,
                                            java.lang.String chromosome,
                                            int start,
                                            int end,
                                            java.util.HashMap sequenceHash,
                                            java.lang.String type)
                                     throws ApolloAdapterException

Throws:

ApolloAdapterException

getQueryStableId

public java.lang.String getQueryStableId()

getHitStableId

public java.lang.String getHitStableId()

getStableId

public java.lang.String getStableId()