apollo.datamodel.seq
Class SRSSequence

java.lang.Object
  apollo.datamodel.AbstractSequence
      apollo.datamodel.seq.AbstractLazySequence
          apollo.datamodel.seq.SRSSequence

All Implemented Interfaces:

LazySequenceI, SequenceI, java.io.Serializable

public class SRSSequence
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

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

SRSSequence(java.lang.String id, Controller c)

Method Summary

int	getLength()
protected java.lang.String	getResiduesFromSourceImpl(int low, int high)
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)

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, 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, 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

SRSSequence

public SRSSequence(java.lang.String id,
                   Controller c)

Method Detail

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

getLength

public int getLength()

Specified by:

getLength in interface SequenceI

Overrides:

getLength in class AbstractSequence

getResiduesFromSourceImpl

protected java.lang.String getResiduesFromSourceImpl(int low,
                                                     int high)

Specified by:

getResiduesFromSourceImpl in class AbstractLazySequence

main

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