apollo.datamodel.seq
Class AbstractLazySequence

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

All Implemented Interfaces:

LazySequenceI, SequenceI, java.io.Serializable

Direct Known Subclasses:

AlternateEnsJSequence, AlternateEnsJSequence, DASLazySequence, DebugLazySequence, EnsCGISequence, EnsJSequence, GAMESequence, PFetchSequence, SRSSequence

public abstract class AbstractLazySequence
extends AbstractSequence
implements LazySequenceI

i wonder if this should move to dataadapter package as its a sequence loader basically - so it loads stuff just like a data adapter

See Also:

Serialized Form

Nested Class Summary

protected class

AbstractLazySequence.LazyLoadControlledObject

Field Summary

protected CacheSequenceLoader	cacher
protected AbstractLazySequence.LazyLoadControlledObject	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

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

Method Summary

protected CacheSequenceLoader	createCacher() Overriden by GAMESequence
CacheSequenceLoader	getCacher()
RangeI	getRange() CacheSequenceLoader requires a Range - getRange will set one up from 1 to length if there has not been a range set yet - should this go in AbstractSeq?
java.lang.String	getResiduesFromSource(int low, int high)
protected abstract java.lang.String	getResiduesFromSourceImpl(int low, int high)
protected java.lang.String	getResiduesImpl(int start)
protected java.lang.String	getResiduesImpl(int start, int end)
abstract 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
boolean	isLazy() Cleanup dangling references when SequenceI not needed anymore.
protected boolean	needInclusiveEnd() Whether the end needs adding to, to make it inclusive.
void	setCacher(CacheSequenceLoader csl)
void	setController(Controller c)

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.SequenceI

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

Field Detail

llco

protected AbstractLazySequence.LazyLoadControlledObject llco

cacher

protected CacheSequenceLoader cacher

Constructor Detail

AbstractLazySequence

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

Method Detail

getRange

public RangeI getRange()

CacheSequenceLoader requires a Range - getRange will set one up from 1 to length if there has not been a range set yet - should this go in AbstractSeq?

Specified by:

getRange in interface SequenceI

Overrides:

getRange in class AbstractSequence

getSubSequence

public abstract 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

Specified by:

getSubSequence in interface SequenceI

Specified by:

getSubSequence in class AbstractSequence

createCacher

protected CacheSequenceLoader createCacher()

Overriden by GAMESequence

setController

public void setController(Controller c)

setCacher

public void setCacher(CacheSequenceLoader csl)

getCacher

public CacheSequenceLoader getCacher()

getResiduesImpl

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

Specified by:

getResiduesImpl in class AbstractSequence

getResiduesImpl

protected java.lang.String getResiduesImpl(int start)

Specified by:

getResiduesImpl in class AbstractSequence

getResiduesFromSource

public java.lang.String getResiduesFromSource(int low,
                                              int high)

Specified by:

getResiduesFromSource in interface LazySequenceI

needInclusiveEnd

protected boolean needInclusiveEnd()

Whether the end needs adding to, to make it inclusive. EnsCGISequence does not need an inclusive end and overrides this to return false.

Overrides:

needInclusiveEnd in class AbstractSequence

getResiduesFromSourceImpl

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

isLazy

public boolean isLazy()

Description copied from interface: SequenceI

Cleanup dangling references when SequenceI not needed anymore. Is this funny to have in SequenceI? (needed for AbstractLazySequence)

Specified by:

isLazy in interface SequenceI

Overrides:

isLazy in class AbstractSequence