apollo.dataadapter.ensj19
Class EnsJSequence

java.lang.Object
  apollo.datamodel.AbstractSequence
      apollo.datamodel.seq.AbstractLazySequence
          apollo.dataadapter.ensj19.EnsJSequence

All Implemented Interfaces:

LazySequenceI, SequenceI, java.io.Serializable

public class EnsJSequence
extends AbstractLazySequence
implements LazySequenceI

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class apollo.datamodel.seq.AbstractLazySequence

AbstractLazySequence.LazyLoadControlledObject

Field Summary

protected static org.apache.log4j.Logger

logger

Fields inherited from class apollo.datamodel.seq.AbstractLazySequence

cacher, llco

Fields inherited from class apollo.datamodel.AbstractSequence

genomic_errors, genomicRange, length

Fields inherited from interface apollo.datamodel.SequenceI

AA, CLEAR_EDIT, DELETION, DNA, INSERTION, RNA, SUBSTITUTION

Constructor Summary

EnsJSequence(java.lang.String id, Controller c, org.ensembl19.datamodel.Location loc, java.lang.String driverPath)

Method Summary

protected java.lang.String	getResiduesFromSourceImpl(int start, int end)
SequenceI	getSubSequence(int start, int end) Clean up dangling reference as listener to controller that will make old instances persist - no longer needed as doesnt listen to controller anymore
static void	main(java.lang.String[] argv)
void	setDriverPath(java.lang.String path)

Methods inherited from class apollo.datamodel.seq.AbstractLazySequence

createCacher, getCacher, getRange, getResiduesFromSource, getResiduesImpl, getResiduesImpl, isLazy, needInclusiveEnd, setCacher, setController

Methods inherited from class apollo.datamodel.AbstractSequence

addDbXref, addDbXref, addDbXref, addSequenceEdit, addSequencingErrorPosition, clearResidues, getAccessionNo, getBaseAt, getChecksum, getDbXrefs, getDescription, getFrame, getGenomicErrors, getLength, getName, getOrganism, getResidues, getResidues, getResidueType, getReverseComplement, getSequencingErrorAtPosition, hasName, hasRange, hasResidues, hasResidueType, isAA, isNewerThan, isSequenceAvailable, isSequencingErrorPosition, needShiftFromOneToZeroBasedCoords, pegLimits, removeSequenceEdit, setAccessionNo, setChecksum, setDate, setDescription, setLength, setName, setNeedShiftFromOneToZeroBasedCoords, setOrganism, setRange, setResidues, setResidueType, shiftFromOneToZeroBased, usesGenomicCoords

Methods inherited from class java.lang.Object

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

Methods inherited from interface apollo.datamodel.seq.LazySequenceI

getResiduesFromSource

Methods inherited from interface apollo.datamodel.SequenceI

addDbXref, addDbXref, addDbXref, addSequenceEdit, addSequencingErrorPosition, clearResidues, getAccessionNo, getBaseAt, getChecksum, getDbXrefs, getDescription, getFrame, getGenomicErrors, getLength, getName, getOrganism, getRange, getResidues, getResidues, getResidueType, getReverseComplement, getSequencingErrorAtPosition, hasName, hasResidues, hasResidueType, isAA, isLazy, isSequenceAvailable, isSequencingErrorPosition, removeSequenceEdit, setAccessionNo, setChecksum, setDate, setDescription, setLength, setName, setOrganism, setRange, setResidues, setResidueType, usesGenomicCoords

Field Detail

logger

protected static final org.apache.log4j.Logger logger

Constructor Detail

EnsJSequence

public EnsJSequence(java.lang.String id,
                    Controller c,
                    org.ensembl19.datamodel.Location loc,
                    java.lang.String driverPath)

Method Detail

setDriverPath

public void setDriverPath(java.lang.String path)

getSubSequence

public SequenceI getSubSequence(int start,
                                int end)

Description copied from class: AbstractLazySequence

Clean up dangling reference as listener to controller that will make old instances persist - no longer needed as doesnt listen to controller anymore

Specified by:

getSubSequence in interface SequenceI

Specified by:

getSubSequence in class AbstractLazySequence

getResiduesFromSourceImpl

protected java.lang.String getResiduesFromSourceImpl(int start,
                                                     int end)

Specified by:

getResiduesFromSourceImpl in class AbstractLazySequence

main

public static void main(java.lang.String[] argv)
                 throws java.lang.Exception

Throws:

java.lang.Exception