apollo.datamodel.seq
Class GAMESequence

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

All Implemented Interfaces:

LazySequenceI, SequenceI, java.io.Serializable

public class GAMESequence
extends AbstractLazySequence

Currently GAMESequence is not lazy. I think it extends AbstractLazySequence because it intends to be lazy at some point. GAMESequence is the main genomic sequence for game data(but not the result sequences) I think the main thing it does is deal with mapping genomic range coords (genomic start and end) to sequence coords (1 to length). This is done in getResidueFromSourceImpl. I know Sequence does not do this, and as far as I can tell, this is the only sequence object that does this. Should Sequence do this? or should this be given a more general name? so Sequence now does do this (actually has for quite some time) - so there is no longer a reason for GAMESequence to exist and should probably be vanquished - the only possible reason would be if game adapter holds off on sucking in sequences and then reparses game file on demand - which actually seems silly - a better scenario would be to have a game file with no sequence and seq is retrieved on demand from chado db using ChadoLazySeq - or through url? but game comes in pretty fast so the only reason would be to save on memory flybase chado needs to use this so it should its more general than GAME. The main thing is GAMESequence has a non null Range. The non-null Range is not enforced, but if Range is not set null pointers will fly. Should it be more flexible and be able to deal with null ranges (null range being one to one mapping) Usual place Range gets set is in CurationSet.setRefSequence, where CurationSet sets the sequences range to itself. Currently this object is only used for the game adapter, and chado flybase adapters curation sets. Regular Sequence objects are used for FeaturePairs hit seqs. Maybe this should be renamed CurationSetSequence?

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

GAMESequence(java.lang.String id, Controller c, java.lang.String dna)

Method Summary

protected CacheSequenceLoader	createCacher() Overriden by GAMESequence
java.lang.String	getResiduesFromSource(int low, int high)
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
boolean	hasSequence()
boolean	isLazy() Change this to return true when GAMESequence actually becomes lazy
protected boolean	needInclusiveEnd() Whether the end needs adding to, to make it inclusive.
void	setResidues(java.lang.String seqString)

Methods inherited from class apollo.datamodel.seq.AbstractLazySequence

getCacher, getRange, getResiduesImpl, getResiduesImpl, 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, 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, setResidueType, usesGenomicCoords

Constructor Detail

GAMESequence

public GAMESequence(java.lang.String id,
                    Controller c,
                    java.lang.String dna)

Method Detail

createCacher

protected CacheSequenceLoader createCacher()

Description copied from class: AbstractLazySequence

Overriden by GAMESequence

Overrides:

createCacher in class AbstractLazySequence

getResiduesFromSource

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

Specified by:

getResiduesFromSource in interface LazySequenceI

Overrides:

getResiduesFromSource in class AbstractLazySequence

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

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 AbstractLazySequence

getResiduesFromSourceImpl

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

Specified by:

getResiduesFromSourceImpl in class AbstractLazySequence

hasSequence

public boolean hasSequence()

setResidues

public void setResidues(java.lang.String seqString)

Specified by:

setResidues in interface SequenceI

Overrides:

setResidues in class AbstractSequence

isLazy

public boolean isLazy()

Change this to return true when GAMESequence actually becomes lazy

Specified by:

isLazy in interface SequenceI

Overrides:

isLazy in class AbstractLazySequence