apollo.datamodel
Class Sequence

java.lang.Object
  apollo.datamodel.AbstractSequence
      apollo.datamodel.Sequence

All Implemented Interfaces:

SequenceI, java.io.Serializable

Direct Known Subclasses:

GenbankSequence

public class Sequence
extends AbstractSequence
implements SequenceI

Update this to take to use Range - used to ignore Range and use residueOffset, which was redundat with using Range. I believe this makes GAMESequence pase as the main function of GAMESequence was to be Range sensitive. If no Range then 0 offset

See Also:

Serialized Form

Field Summary

protected java.lang.String

residues

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

Sequence(java.lang.String id, java.lang.String residues)

Method Summary

void	clearResidues() sets residues to empty string
char	getBaseAt(int loc)
int	getLength()
java.lang.String	getResidues()
protected java.lang.String	getResiduesImpl(int start)
protected java.lang.String	getResiduesImpl(int rangeStart, int rangeEnd) this does a plus one to the end which i assume is to be inclucsive, the only problem i think is AbstractSequence.getResudes calls pegLimits which sutracts one from start to convert from one based to zero based, but one is not subtracted from the end which i think is also an act of inclusivity.
SequenceI	getSubSequence(int start, int end) this method actually isnt used at all - take out of SequenceI? calls AbstractSequence.getResidues which calls getResiduesImpl
void	setResidues(java.lang.String seqString)

Methods inherited from class apollo.datamodel.AbstractSequence

addDbXref, addDbXref, addDbXref, addSequenceEdit, addSequencingErrorPosition, getAccessionNo, getChecksum, getDbXrefs, getDescription, getFrame, getGenomicErrors, getName, getOrganism, getRange, getResidues, getResidueType, getReverseComplement, getSequencingErrorAtPosition, hasName, hasRange, hasResidues, hasResidueType, isAA, isLazy, isNewerThan, isSequenceAvailable, isSequencingErrorPosition, needInclusiveEnd, 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, getAccessionNo, getChecksum, getDbXrefs, getDescription, getFrame, getGenomicErrors, getName, getOrganism, getRange, getResidues, getResidueType, getReverseComplement, getSequencingErrorAtPosition, hasName, hasResidues, hasResidueType, isAA, isLazy, isSequenceAvailable, isSequencingErrorPosition, removeSequenceEdit, setAccessionNo, setChecksum, setDate, setDescription, setLength, setName, setOrganism, setRange, setResidueType, usesGenomicCoords

Field Detail

residues

protected java.lang.String residues

Constructor Detail

Sequence

public Sequence(java.lang.String id,
                java.lang.String residues)

Method Detail

getLength

public int getLength()

Specified by:

getLength in interface SequenceI

Overrides:

getLength in class AbstractSequence

getBaseAt

public char getBaseAt(int loc)

Specified by:

getBaseAt in interface SequenceI

Overrides:

getBaseAt in class AbstractSequence

getSubSequence

public SequenceI getSubSequence(int start,
                                int end)

this method actually isnt used at all - take out of SequenceI? calls AbstractSequence.getResidues which calls getResiduesImpl

Specified by:

getSubSequence in interface SequenceI

Specified by:

getSubSequence in class AbstractSequence

setResidues

public void setResidues(java.lang.String seqString)

Specified by:

setResidues in interface SequenceI

Overrides:

setResidues in class AbstractSequence

clearResidues

public void clearResidues()

Description copied from class: AbstractSequence

sets residues to empty string

Specified by:

clearResidues in interface SequenceI

Overrides:

clearResidues in class AbstractSequence

getResidues

public java.lang.String getResidues()

Specified by:

getResidues in interface SequenceI

Overrides:

getResidues in class AbstractSequence

getResiduesImpl

protected java.lang.String getResiduesImpl(int rangeStart,
                                           int rangeEnd)

this does a plus one to the end which i assume is to be inclucsive, the only problem i think is AbstractSequence.getResudes calls pegLimits which sutracts one from start to convert from one based to zero based, but one is not subtracted from the end which i think is also an act of inclusivity. By inclusivity i mean that java substring includes the start but not end, the apollo standard is to include both. This seems to accomodated for twice and is thus adding an extra base. Am I right about this?

Specified by:

getResiduesImpl in class AbstractSequence

getResiduesImpl

protected java.lang.String getResiduesImpl(int start)

Specified by:

getResiduesImpl in class AbstractSequence