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A B C E G I L N O P R S T U V W

A

addToBioSequence_list(BioSequence) - Method in class org.biomage.BioSequence.BioSequence_package
Method to add BioSequence to BioSequence_list
addToBioSequence_list(int, BioSequence) - Method in class org.biomage.BioSequence.BioSequence_package
Method to add BioSequence at position to BioSequence_list
addToOntologyEntries(OntologyEntry) - Method in class org.biomage.BioSequence.BioSequence
Method to add OntologyEntry to OntologyEntries_list
addToOntologyEntries(int, OntologyEntry) - Method in class org.biomage.BioSequence.BioSequence
Method to add OntologyEntry at position to OntologyEntries_list
addToRegions(SeqFeatureLocation) - Method in class org.biomage.BioSequence.SeqFeature
Method to add SeqFeatureLocation to Regions_list
addToRegions(int, SeqFeatureLocation) - Method in class org.biomage.BioSequence.SeqFeature
Method to add SeqFeatureLocation at position to Regions_list
addToSeqFeatures(SeqFeature) - Method in class org.biomage.BioSequence.BioSequence
Method to add SeqFeature to SeqFeatures_list
addToSeqFeatures(int, SeqFeature) - Method in class org.biomage.BioSequence.BioSequence
Method to add SeqFeature at position to SeqFeatures_list
addToSequenceDatabases(DatabaseEntry) - Method in class org.biomage.BioSequence.BioSequence
Method to add DatabaseEntry to SequenceDatabases_list
addToSequenceDatabases(int, DatabaseEntry) - Method in class org.biomage.BioSequence.BioSequence
Method to add DatabaseEntry at position to SequenceDatabases_list
addToSubregions(SeqFeatureLocation) - Method in class org.biomage.BioSequence.SeqFeatureLocation
Method to add SeqFeatureLocation to Subregions_list
addToSubregions(int, SeqFeatureLocation) - Method in class org.biomage.BioSequence.SeqFeatureLocation
Method to add SeqFeatureLocation at position to Subregions_list

B

BOTH - Variable in class org.biomage.BioSequence.SeqFeature.Basis
 
BioSequence - class org.biomage.BioSequence.BioSequence.
A BioSequence is a representation of a DNA, RNA, or protein sequence.
BioSequence() - Constructor for class org.biomage.BioSequence.BioSequence
Default constructor.
BioSequence(Attributes) - Constructor for class org.biomage.BioSequence.BioSequence
Attribute constructor.
BioSequence_package - class org.biomage.BioSequence.BioSequence_package.
Describes a known gene or sequence.
BioSequence_package() - Constructor for class org.biomage.BioSequence.BioSequence_package
Default constructor.
BioSequence_package(Attributes) - Constructor for class org.biomage.BioSequence.BioSequence_package
Attribute constructor.
BioSequence_package.BioSequence_list - class org.biomage.BioSequence.BioSequence_package.BioSequence_list.
Inner list class for holding multiple entries for attribute bioSequence_list.
BioSequence_package.BioSequence_list() - Constructor for class org.biomage.BioSequence.BioSequence_package.BioSequence_list
 
basis - Variable in class org.biomage.BioSequence.SeqFeature
How the evidence for a SeqFeature was determined.
bioSequence_list - Variable in class org.biomage.BioSequence.BioSequence_package
A BioSequence is a representation of a DNA, RNA, or protein sequence.

C

COMPUTATIONAL - Variable in class org.biomage.BioSequence.SeqFeature.Basis
 
coordinate - Variable in class org.biomage.BioSequence.SeqFeatureLocation
At which base pairs or amino acid this SeqFeature begins and ends.

E

EXPERIMENTAL - Variable in class org.biomage.BioSequence.SeqFeature.Basis
 
end - Variable in class org.biomage.BioSequence.SequencePosition
The location of the base, for nucleotides, that the SeqFeature ends.

G

getBasis() - Method in class org.biomage.BioSequence.SeqFeature
Get method for basis
getBioSequence_list() - Method in class org.biomage.BioSequence.BioSequence_package
Get method for bioSequence_list
getCoordinate() - Method in class org.biomage.BioSequence.SeqFeatureLocation
Get method for coordinate
getEnd() - Method in class org.biomage.BioSequence.SequencePosition
Get method for end
getFromBioSequence_list(int) - Method in class org.biomage.BioSequence.BioSequence_package
Method to get BioSequence from BioSequence_list
getFromOntologyEntries(int) - Method in class org.biomage.BioSequence.BioSequence
Method to get OntologyEntry from OntologyEntries_list
getFromRegions(int) - Method in class org.biomage.BioSequence.SeqFeature
Method to get SeqFeatureLocation from Regions_list
getFromSeqFeatures(int) - Method in class org.biomage.BioSequence.BioSequence
Method to get SeqFeature from SeqFeatures_list
getFromSequenceDatabases(int) - Method in class org.biomage.BioSequence.BioSequence
Method to get DatabaseEntry from SequenceDatabases_list
getFromSubregions(int) - Method in class org.biomage.BioSequence.SeqFeatureLocation
Method to get SeqFeatureLocation from Subregions_list
getIsApproximateLength() - Method in class org.biomage.BioSequence.BioSequence
Get method for isApproximateLength
getIsCircular() - Method in class org.biomage.BioSequence.BioSequence
Get method for isCircular
getLength() - Method in class org.biomage.BioSequence.BioSequence
Get method for length
getOntologyEntries() - Method in class org.biomage.BioSequence.BioSequence
Get method for ontologyEntries
getPolymerType() - Method in class org.biomage.BioSequence.BioSequence
Get method for polymerType
getRegions() - Method in class org.biomage.BioSequence.SeqFeature
Get method for regions
getSeqFeatures() - Method in class org.biomage.BioSequence.BioSequence
Get method for seqFeatures
getSequence() - Method in class org.biomage.BioSequence.BioSequence
Get method for sequence
getSequenceDatabases() - Method in class org.biomage.BioSequence.BioSequence
Get method for sequenceDatabases
getSpecies() - Method in class org.biomage.BioSequence.BioSequence
Get method for species
getStart() - Method in class org.biomage.BioSequence.SequencePosition
Get method for start
getStrandType() - Method in class org.biomage.BioSequence.SeqFeatureLocation
Get method for strandType
getSubregions() - Method in class org.biomage.BioSequence.SeqFeatureLocation
Get method for subregions
getType() - Method in class org.biomage.BioSequence.BioSequence
Get method for type

I

isApproximateLength - Variable in class org.biomage.BioSequence.BioSequence
If length not positively known will be true
isCircular - Variable in class org.biomage.BioSequence.BioSequence
Indicates if the BioSequence is circular in nature.

L

length - Variable in class org.biomage.BioSequence.BioSequence
The number of residues in the biosequence.

N

NA - Variable in class org.biomage.BioSequence.SeqFeature.Basis
 
nameToValue - Variable in class org.biomage.BioSequence.SeqFeature.Basis
 

O

ontologyEntries - Variable in class org.biomage.BioSequence.BioSequence
Ontology entries referring to common values associated with BioSequences, such as gene names, go ids, etc.
org.biomage.BioSequence - package org.biomage.BioSequence
 

P

polymerType - Variable in class org.biomage.BioSequence.BioSequence
A choice of protein, RNA, or DNA.

R

regions - Variable in class org.biomage.BioSequence.SeqFeature
Association to classes that describe the location with the sequence of the SeqFeature.
removeElementAtFromBioSequence_list(int) - Method in class org.biomage.BioSequence.BioSequence_package
Method to remove by position from BioSequence_list
removeElementAtFromOntologyEntries(int) - Method in class org.biomage.BioSequence.BioSequence
Method to remove by position from OntologyEntries_list
removeElementAtFromRegions(int) - Method in class org.biomage.BioSequence.SeqFeature
Method to remove by position from Regions_list
removeElementAtFromSeqFeatures(int) - Method in class org.biomage.BioSequence.BioSequence
Method to remove by position from SeqFeatures_list
removeElementAtFromSequenceDatabases(int) - Method in class org.biomage.BioSequence.BioSequence
Method to remove by position from SequenceDatabases_list
removeElementAtFromSubregions(int) - Method in class org.biomage.BioSequence.SeqFeatureLocation
Method to remove by position from Subregions_list
removeFromBioSequence_list(BioSequence) - Method in class org.biomage.BioSequence.BioSequence_package
Method to remove first BioSequence from BioSequence_list
removeFromOntologyEntries(OntologyEntry) - Method in class org.biomage.BioSequence.BioSequence
Method to remove first OntologyEntry from OntologyEntries_list
removeFromRegions(SeqFeatureLocation) - Method in class org.biomage.BioSequence.SeqFeature
Method to remove first SeqFeatureLocation from Regions_list
removeFromSeqFeatures(SeqFeature) - Method in class org.biomage.BioSequence.BioSequence
Method to remove first SeqFeature from SeqFeatures_list
removeFromSequenceDatabases(DatabaseEntry) - Method in class org.biomage.BioSequence.BioSequence
Method to remove first DatabaseEntry from SequenceDatabases_list
removeFromSubregions(SeqFeatureLocation) - Method in class org.biomage.BioSequence.SeqFeatureLocation
Method to remove first SeqFeatureLocation from Subregions_list

S

SeqFeature - class org.biomage.BioSequence.SeqFeature.
Represents, in general, what would be a GenBank Feature Table annotation for a sequence.
SeqFeature() - Constructor for class org.biomage.BioSequence.SeqFeature
Default constructor.
SeqFeature(Attributes) - Constructor for class org.biomage.BioSequence.SeqFeature
Attribute constructor.
SeqFeature.Basis - class org.biomage.BioSequence.SeqFeature.Basis.
Inner class for the enumeration values that the attribute basis can assume.
SeqFeature.Basis() - Constructor for class org.biomage.BioSequence.SeqFeature.Basis
 
SeqFeatureLocation - class org.biomage.BioSequence.SeqFeatureLocation.
The location of the SeqFeature annotation.
SeqFeatureLocation() - Constructor for class org.biomage.BioSequence.SeqFeatureLocation
Default constructor.
SeqFeatureLocation(Attributes) - Constructor for class org.biomage.BioSequence.SeqFeatureLocation
Attribute constructor.
SequencePosition - class org.biomage.BioSequence.SequencePosition.
Designates the position of the Feature in its BioSequence.
SequencePosition() - Constructor for class org.biomage.BioSequence.SequencePosition
Default constructor.
SequencePosition(Attributes) - Constructor for class org.biomage.BioSequence.SequencePosition
Attribute constructor.
seqFeatures - Variable in class org.biomage.BioSequence.BioSequence
Association to annotations for subsequences.
sequence - Variable in class org.biomage.BioSequence.BioSequence
The actual components of the sequence, for instance, for DNA a string consisting of A,T,C and G.
sequenceDatabases - Variable in class org.biomage.BioSequence.BioSequence
References an entry in a species database, like GenBank, UniGene, etc.
setBasis(SeqFeature.Basis) - Method in class org.biomage.BioSequence.SeqFeature
Set method for basis
setBioSequence_list(BioSequence_package.BioSequence_list) - Method in class org.biomage.BioSequence.BioSequence_package
Set method for bioSequence_list
setCoordinate(SequencePosition) - Method in class org.biomage.BioSequence.SeqFeatureLocation
Set method for coordinate
setEnd(int) - Method in class org.biomage.BioSequence.SequencePosition
Set method for end
setIsApproximateLength(boolean) - Method in class org.biomage.BioSequence.BioSequence
Set method for isApproximateLength
setIsCircular(boolean) - Method in class org.biomage.BioSequence.BioSequence
Set method for isCircular
setLength(int) - Method in class org.biomage.BioSequence.BioSequence
Set method for length
setOntologyEntries(HasOntologyEntries.OntologyEntries_list) - Method in class org.biomage.BioSequence.BioSequence
Set method for ontologyEntries
setPolymerType(OntologyEntry) - Method in class org.biomage.BioSequence.BioSequence
Set method for polymerType
setRegions(HasRegions.Regions_list) - Method in class org.biomage.BioSequence.SeqFeature
Set method for regions
setSeqFeatures(HasSeqFeatures.SeqFeatures_list) - Method in class org.biomage.BioSequence.BioSequence
Set method for seqFeatures
setSequence(String) - Method in class org.biomage.BioSequence.BioSequence
Set method for sequence
setSequenceDatabases(HasSequenceDatabases.SequenceDatabases_list) - Method in class org.biomage.BioSequence.BioSequence
Set method for sequenceDatabases
setSpecies(OntologyEntry) - Method in class org.biomage.BioSequence.BioSequence
Set method for species
setStart(int) - Method in class org.biomage.BioSequence.SequencePosition
Set method for start
setStrandType(String) - Method in class org.biomage.BioSequence.SeqFeatureLocation
Set method for strandType
setSubregions(HasSubregions.Subregions_list) - Method in class org.biomage.BioSequence.SeqFeatureLocation
Set method for subregions
setType(OntologyEntry) - Method in class org.biomage.BioSequence.BioSequence
Set method for type
setValueByName(String) - Method in class org.biomage.BioSequence.SeqFeature.Basis
 
species - Variable in class org.biomage.BioSequence.BioSequence
The organism from which this sequence was obtained.
start - Variable in class org.biomage.BioSequence.SequencePosition
The location of the base, for nucleotides, that the SeqFeature starts.
strandType - Variable in class org.biomage.BioSequence.SeqFeatureLocation
Indicates the direction and/or type of the SeqFeature, i.e.
subregions - Variable in class org.biomage.BioSequence.SeqFeatureLocation
Regions within the SeqFeature.

T

type - Variable in class org.biomage.BioSequence.BioSequence
The type of biosequence, i.e.

U

UNKNOWN - Variable in class org.biomage.BioSequence.SeqFeature.Basis
 

V

value - Variable in class org.biomage.BioSequence.SeqFeature.Basis
 

W

writeAssociations(Writer) - Method in class org.biomage.BioSequence.BioSequence
writeAssociations
writeAssociations(Writer) - Method in class org.biomage.BioSequence.BioSequence_package
writeAssociations
writeAssociations(Writer) - Method in class org.biomage.BioSequence.SeqFeature
writeAssociations
writeAssociations(Writer) - Method in class org.biomage.BioSequence.SeqFeatureLocation
writeAssociations
writeAssociations(Writer) - Method in class org.biomage.BioSequence.SequencePosition
writeAssociations
writeAttributes(Writer) - Method in class org.biomage.BioSequence.BioSequence
writeAttributes
writeAttributes(Writer) - Method in class org.biomage.BioSequence.BioSequence_package
writeAttributes
writeAttributes(Writer) - Method in class org.biomage.BioSequence.SeqFeature
writeAttributes
writeAttributes(Writer) - Method in class org.biomage.BioSequence.SeqFeatureLocation
writeAttributes
writeAttributes(Writer) - Method in class org.biomage.BioSequence.SequencePosition
writeAttributes
writeMAGEML(Writer) - Method in class org.biomage.BioSequence.BioSequence
writeMAGEML
writeMAGEML(Writer) - Method in class org.biomage.BioSequence.BioSequence_package
writeMAGEML
writeMAGEML(Writer) - Method in class org.biomage.BioSequence.SeqFeature
writeMAGEML
writeMAGEML(Writer) - Method in class org.biomage.BioSequence.SeqFeatureLocation
writeMAGEML
writeMAGEML(Writer) - Method in class org.biomage.BioSequence.SequencePosition
writeMAGEML

A B C E G I L N O P R S T U V W