apollo.datamodel.seq
Class GenbankSequence

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

All Implemented Interfaces:

SequenceI, java.io.Serializable

public class GenbankSequence
extends Sequence

Currently GenbankSequence is not lazy. It won't ever be because it simply loads a complete EMBL/Genbank entry in its entirety.

See Also:

Serialized Form

Field Summary

protected java.lang.String	header
protected java.util.Hashtable	properties

Fields inherited from class apollo.datamodel.Sequence

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

GenbankSequence(java.lang.String id, java.lang.String dna)

Method Summary

void	addProperty(java.lang.String name, java.lang.String value)
java.lang.String	getHeader()
java.util.Hashtable	getProperties()
java.lang.String	getProperty(java.lang.String name)
protected java.lang.String	getResiduesImpl(int low, int high) 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.
void	removeProperty(java.lang.String key)
void	setHeader(java.lang.String header)

Methods inherited from class apollo.datamodel.Sequence

clearResidues, getBaseAt, getLength, getResidues, getResiduesImpl, getSubSequence, setResidues

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

header

protected java.lang.String header

properties

protected java.util.Hashtable properties

Constructor Detail

GenbankSequence

public GenbankSequence(java.lang.String id,
                       java.lang.String dna)

Method Detail

setHeader

public void setHeader(java.lang.String header)

getHeader

public java.lang.String getHeader()

addProperty

public void addProperty(java.lang.String name,
                        java.lang.String value)

removeProperty

public void removeProperty(java.lang.String key)

getProperty

public java.lang.String getProperty(java.lang.String name)

getProperties

public java.util.Hashtable getProperties()

getResiduesImpl

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

Description copied from class: Sequence

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?

Overrides:

getResiduesImpl in class Sequence