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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
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