apollo.dataadapter.das
Class DASLazySequence

java.lang.Object
  apollo.datamodel.AbstractSequence
      apollo.datamodel.seq.AbstractLazySequence
          apollo.dataadapter.das.DASLazySequence

All Implemented Interfaces:

LazySequenceI, SequenceI, java.io.Serializable

public class DASLazySequence
extends AbstractLazySequence
implements LazySequenceI

I am a Sequence class for implementing lazy load using a DASServer

See Also:

Serialized Form

Nested Class Summary

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

AbstractLazySequence.LazyLoadControlledObject

Field Summary

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

DASLazySequence(java.lang.String id, Controller c, RangeI loc, DASServerI theServer, DASDsn theDsn, DASSegment theSegment)

Method Summary

DASDsn	getDsn()
protected java.lang.String	getResiduesFromSourceImpl(int low, int high) Returns the sequence string
DASSegment	getSegment()
DASServerI	getServer()
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

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

Constructor Detail

DASLazySequence

public DASLazySequence(java.lang.String id,
                       Controller c,
                       RangeI loc,
                       DASServerI theServer,
                       DASDsn theDsn,
                       DASSegment theSegment)

Method Detail

getServer

public DASServerI getServer()

getDsn

public DASDsn getDsn()

getSegment

public DASSegment getSegment()

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 low,
                                                     int high)

Returns the sequence string

Specified by:

getResiduesFromSourceImpl in class AbstractLazySequence