apollo.datamodel.seq
Class EnsCGISequence

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

All Implemented Interfaces:

LazySequenceI, SequenceI, java.io.Serializable

public class EnsCGISequence
extends AbstractLazySequence
implements LazySequenceI

EnsCGISequence:

Sequence class for implementing lazy load from Ensembl Server

Copyright: Copyright (c) 2002

Ensembl

Version:

1.0 It is important to bear in mind that the retrievals and sequences at this level are 0-based. Although in the display the sequences are shown as 1 based (counting bases, not spaces) this does not apply here.

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

EnsCGISequence(java.lang.String id, Controller c, RangeI loc, java.lang.String server)

Method Summary

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)
protected boolean	needInclusiveEnd() AbstractSequence by default will add one to the end on getRes to counteract java Strings non inclusiveness.
void	setServer(java.lang.String server)

Methods inherited from class apollo.datamodel.seq.AbstractLazySequence

createCacher, getCacher, getRange, getResiduesFromSource, getResiduesImpl, getResiduesImpl, isLazy, 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, 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, getLength, getName, getOrganism, getRange, getResidues, getResidues, getResidueType, getReverseComplement, getSequencingErrorAtPosition, hasName, hasResidues, hasResidueType, isAA, isLazy, isSequenceAvailable, isSequencingErrorPosition, removeSequenceEdit, setAccessionNo, setChecksum, setDate, setDescription, setLength, setName, setOrganism, setRange, setResidues, setResidueType, usesGenomicCoords

Constructor Detail

EnsCGISequence

public EnsCGISequence(java.lang.String id,
                      Controller c,
                      RangeI loc,
                      java.lang.String server)

Method Detail

needInclusiveEnd

protected boolean needInclusiveEnd()

AbstractSequence by default will add one to the end on getRes to counteract java Strings non inclusiveness. EnsCGI already retrieves sequence with the end included. Returning false disables AbstractSequence's inclusive end.

Overrides:

needInclusiveEnd in class AbstractLazySequence

setServer

public void setServer(java.lang.String server)

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

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)