apollo.datamodel.seq
Class PFetchSequence

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

All Implemented Interfaces:

LazySequenceI, SequenceI, java.io.Serializable

public class PFetchSequence
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

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

Method Summary

int	getLength()
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?
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)
void	setRange(RangeI loc) I (SUZ) am removing the call to setLength, because the length of the viewed range should not logically change the length of the sequence.

Methods inherited from class apollo.datamodel.seq.AbstractLazySequence

createCacher, getCacher, 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, 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, getResidues, getResidues, getResidueType, getReverseComplement, getSequencingErrorAtPosition, hasName, hasResidues, hasResidueType, isAA, isLazy, isSequenceAvailable, isSequencingErrorPosition, removeSequenceEdit, setAccessionNo, setChecksum, setDate, setDescription, setLength, setName, setOrganism, setResidues, setResidueType, usesGenomicCoords

Constructor Detail

PFetchSequence

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

Method Detail

getRange

public RangeI getRange()

Description copied from class: AbstractLazySequence

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 AbstractLazySequence

setRange

public void setRange(RangeI loc)

Description copied from class: AbstractSequence

I (SUZ) am removing the call to setLength, because the length of the viewed range should not logically change the length of the sequence. This may have a negative effect if there is any code around that was assuming the length of the sequence would be set this way. When this happens the code should be changed to independently call seq.setLength() This was having very bad effects when the sequence length was already being set. Then when setRefSequence was called the length was being silently changed to 1 (because the range was not yet set) Then the range could no longer be set because the sequence length was 0. Ugh.

Specified by:

setRange in interface SequenceI

Overrides:

setRange in class AbstractSequence

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)