apollo.datamodel
Interface SequenceI

All Superinterfaces:

java.io.Serializable

All Known Subinterfaces:

LazySequenceI

All Known Implementing Classes:

AbstractLazySequence, AbstractSequence, AlternateEnsJSequence, AlternateEnsJSequence, DASLazySequence, DebugLazySequence, EnsCGISequence, EnsJSequence, GAMESequence, GenbankSequence, PFetchSequence, Sequence, SRSSequence

public interface SequenceI
extends java.io.Serializable

Field Summary

static java.lang.String	AA
static java.lang.String	CLEAR_EDIT I question if CLEAR_EDIT shouold be a separate type - its just a deletion of the above types - refactor?
static java.lang.String	DELETION
static java.lang.String	DNA
static java.lang.String	INSERTION These are SO terms (under general family of sequence_variation) changed insertion to nucleotide_insertion as its more specific and i believe thats what we are doing here, same with deletion eventually should come from SO (should this be in tiers file?)
static java.lang.String	RNA
static java.lang.String	SUBSTITUTION

Method Summary

void	addDbXref(DbXref xref)
void	addDbXref(java.lang.String db, java.lang.String id)
void	addDbXref(java.lang.String db, java.lang.String id, int isCurrent)
boolean	addSequenceEdit(SequenceEdit seq_edit)
boolean	addSequencingErrorPosition(java.lang.String operation, int pos, java.lang.String residue)
void	clearResidues() clears out residues (set to empty string)
java.lang.String	getAccessionNo()
char	getBaseAt(int loc)
java.lang.String	getChecksum()
java.util.Vector	getDbXrefs()
java.lang.String	getDescription()
int	getFrame(long position, boolean forward)
java.util.HashMap	getGenomicErrors()
int	getLength()
java.lang.String	getName()
java.lang.String	getOrganism()
RangeI	getRange()
java.lang.String	getResidues()
java.lang.String	getResidues(int start, int end)
java.lang.String	getResidueType()
java.lang.String	getReverseComplement()
SequenceEdit	getSequencingErrorAtPosition(int base_position)
SequenceI	getSubSequence(int start, int end) I can see this being a handy method but its actually not used at all - delete?
boolean	hasName()
boolean	hasResidues() This will return false if there are no residues (null || "", cleared).
boolean	hasResidueType() Calculates residue type by comparing seq length to feat length.
boolean	isAA() Return true if getResidueType() == AA
boolean	isLazy() Cleanup dangling references when SequenceI not needed anymore.
boolean	isSequenceAvailable(long position)
boolean	isSequencingErrorPosition(int base_position)
boolean	removeSequenceEdit(SequenceEdit seqEdit)
void	setAccessionNo(java.lang.String id)
void	setChecksum(java.lang.String checksum)
void	setDate(java.util.Date update_date)
void	setDescription(java.lang.String desc)
void	setLength(int length)
void	setName(java.lang.String id)
void	setOrganism(java.lang.String organism)
void	setRange(RangeI loc)
void	setResidues(java.lang.String residues)
void	setResidueType(java.lang.String res_type)
boolean	usesGenomicCoords()

Field Detail

AA

static final java.lang.String AA

See Also:

Constant Field Values

DNA

static final java.lang.String DNA

See Also:

Constant Field Values

RNA

static final java.lang.String RNA

See Also:

Constant Field Values

INSERTION

static final java.lang.String INSERTION

These are SO terms (under general family of sequence_variation) changed insertion to nucleotide_insertion as its more specific and i believe thats what we are doing here, same with deletion eventually should come from SO (should this be in tiers file?)

See Also:

Constant Field Values

DELETION

static final java.lang.String DELETION

See Also:

Constant Field Values

SUBSTITUTION

static final java.lang.String SUBSTITUTION

See Also:

Constant Field Values

CLEAR_EDIT

static final java.lang.String CLEAR_EDIT

I question if CLEAR_EDIT shouold be a separate type - its just a deletion of the above types - refactor?

See Also:

Constant Field Values

Method Detail

getLength

int getLength()

setLength

void setLength(int length)

getResidues

java.lang.String getResidues()

getResidues

java.lang.String getResidues(int start,
                             int end)

setResidues

void setResidues(java.lang.String residues)

clearResidues

void clearResidues()

clears out residues (set to empty string)

hasResidues

boolean hasResidues()

This will return false if there are no residues (null || "", cleared).

getResidueType

java.lang.String getResidueType()

setResidueType

void setResidueType(java.lang.String res_type)

hasResidueType

boolean hasResidueType()

Calculates residue type by comparing seq length to feat length. If there is more than 2 base pairs per residue than its assigned AA.

isAA

boolean isAA()

Return true if getResidueType() == AA

getSubSequence

SequenceI getSubSequence(int start,
                         int end)

I can see this being a handy method but its actually not used at all - delete?

getName

java.lang.String getName()

setName

void setName(java.lang.String id)

hasName

boolean hasName()

getAccessionNo

java.lang.String getAccessionNo()

setAccessionNo

void setAccessionNo(java.lang.String id)

addDbXref

void addDbXref(java.lang.String db,
               java.lang.String id,
               int isCurrent)

addDbXref

void addDbXref(java.lang.String db,
               java.lang.String id)

addDbXref

void addDbXref(DbXref xref)

getDbXrefs

java.util.Vector getDbXrefs()

getChecksum

java.lang.String getChecksum()

setChecksum

void setChecksum(java.lang.String checksum)

getBaseAt

char getBaseAt(int loc)

getDescription

java.lang.String getDescription()

setDescription

void setDescription(java.lang.String desc)

getReverseComplement

java.lang.String getReverseComplement()

isSequenceAvailable

boolean isSequenceAvailable(long position)

getFrame

int getFrame(long position,
             boolean forward)

usesGenomicCoords

boolean usesGenomicCoords()

setRange

void setRange(RangeI loc)

getRange

RangeI getRange()

isLazy

boolean isLazy()

Cleanup dangling references when SequenceI not needed anymore. Is this funny to have in SequenceI? (needed for AbstractLazySequence)

getGenomicErrors

java.util.HashMap getGenomicErrors()

isSequencingErrorPosition

boolean isSequencingErrorPosition(int base_position)

getSequencingErrorAtPosition

SequenceEdit getSequencingErrorAtPosition(int base_position)

addSequencingErrorPosition

boolean addSequencingErrorPosition(java.lang.String operation,
                                   int pos,
                                   java.lang.String residue)

addSequenceEdit

boolean addSequenceEdit(SequenceEdit seq_edit)

removeSequenceEdit

boolean removeSequenceEdit(SequenceEdit seqEdit)

getOrganism

java.lang.String getOrganism()

setOrganism

void setOrganism(java.lang.String organism)

setDate

void setDate(java.util.Date update_date)