A C D E F G H I L M N O P R S T V

S

Sequence - class org.aisb.bio.things.Sequence.

This is the basis for any implementation of any sequence.

Sequence(Class) - Constructor for class org.aisb.bio.things.Sequence

Sequence(Class, String) - Constructor for class org.aisb.bio.things.Sequence

Sequence(int) - Constructor for class org.aisb.bio.things.Sequence

Sequence() - Constructor for class org.aisb.bio.things.Sequence

SequenceAligner - class org.aisb.bio.tools.SequenceAligner.

This interface describes any algorithm for doing pair-wise alignment of sequences.

SequenceAligner() - Constructor for class org.aisb.bio.tools.SequenceAligner

SequenceFetcher - class org.aisb.bio.tools.SequenceFetcher.

Give this class the name of a sequence, and it will fetch it via the web.

SequenceFetcher() - Constructor for class org.aisb.bio.tools.SequenceFetcher

SimilarityMatrixComparator - class org.aisb.bio.tools.SimilarityMatrixComparator.

This is a simple implementation of a similarity matrix for comparing monomers.

SimilarityMatrixComparator() - Constructor for class org.aisb.bio.tools.SimilarityMatrixComparator

SomeSimpleTests - class org.aisb.bio.tests.SomeSimpleTests.

This class performs some simple unit tests of the underlying frameworks.

SomeSimpleTests() - Constructor for class org.aisb.bio.tests.SomeSimpleTests

set(int, Object) - Method in class org.aisb.bio.things.Sequence

setBirthday(double) - Method in class org.aisb.bio.things.evolution.AsexualOrganism

setComment(String) - Method in class org.aisb.bio.things.Sequence

setComparator(MonomerComparator) - Method in class org.aisb.bio.tools.Needleman

Returns the comparator currently in use.

setFirstSequence(Sequence) - Method in class org.aisb.bio.tools.SequenceAligner

Set the first sequence to align.

setFitness(int) - Method in class org.aisb.bio.things.evolution.AsexualOrganism

setGapCreationPenalty(int) - Method in class org.aisb.bio.tools.Needleman

setGapExtensionPenalty(int) - Method in class org.aisb.bio.tools.Needleman

setGenbankIdentifier(String) - Method in class org.aisb.bio.tools.SequenceFetcher

This is a "magic" setter, that builds the name correctly from a given genbank id.

setGenotype(Sequence) - Method in class org.aisb.bio.things.evolution.AsexualOrganism

setMu(double) - Method in class org.aisb.bio.things.evolution.Mutator

setMutator(Mutator) - Method in class org.aisb.bio.things.evolution.AsexualOrganism

setName(String) - Method in class org.aisb.bio.tools.SequenceFetcher

setParent(AsexualOrganism) - Method in class org.aisb.bio.things.evolution.AsexualOrganism

setProperty(String, Object) - Method in class org.aisb.bio.things.Monomer

Assign a named property to this monomer.

setSecondSequence(Sequence) - Method in class org.aisb.bio.tools.SequenceAligner

Set the second sequence to align.

setTimeToReproduce(double) - Method in class org.aisb.bio.things.evolution.AsexualOrganism

setType(String) - Method in class org.aisb.bio.things.Sequence

setType(Class) - Method in class org.aisb.bio.things.Sequence

Set the type.

setType(Class) - Method in class org.aisb.bio.tools.SequenceFetcher

size() - Method in class org.aisb.bio.things.Sequence

subList(int, int) - Method in class org.aisb.bio.things.Sequence