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

G

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

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

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

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

Get the actual best alignment, in the form of a string consisting of tuples representing positions in the alignment.

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

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

Get the best alignment score, as defined by this algorithm.

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

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

Get the set of best alignments, in the form of a matrix.

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

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

Get the set of best alignments, in the form of an array of strings consisting of tuples representing positions in the alignment.

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

getByCode(char) - Static method in class org.aisb.bio.things.Monomer

Given the one-character code of a monomer, return the representation of that monomer.

getByCode(Character) - Static method in class org.aisb.bio.things.Monomer

Given the one-character code of a monomer, return the representation of that monomer.

getByName(String) - Static method in class org.aisb.bio.things.Monomer

Given the name of a monomer, perhaps such as "tyrosine" or "fructose", return the representation of that monomer.

getByNumber(int) - Static method in class org.aisb.bio.things.Monomer

Given the numberic code for a monomer, return the representation of that monomer.

getByNumber(Integer) - Static method in class org.aisb.bio.things.Monomer

Given the numberic code for a monomer, return the representation of that monomer.

getCode() - Method in class org.aisb.bio.things.Monomer

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

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

Set the comparator to use to match each pair of elements.

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

Return this sequence in FASTA format.

getFeatures() - Method in class org.aisb.bio.tools.images.WaveletFeatureExtractor

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

Get the first sequence to align.

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

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

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

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

getImage() - Method in class org.aisb.bio.tools.images.WaveletFeatureExtractor

getLevel() - Method in class org.aisb.bio.tools.images.WaveletFeatureExtractor

getMaximumScore() - Method in class org.aisb.bio.tools.PSSMFitnessFunction

Calculate and return the maximum score.

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

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

getName() - Method in class org.aisb.bio.things.Monomer

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

getNumber() - Method in class org.aisb.bio.things.Monomer

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

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

Get the number of alignments that have the best score.

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

getProperty(String) - Method in class org.aisb.bio.things.Monomer

Get a property from a monomer by name.

getQuantity() - Static method in class org.aisb.bio.things.Monomer

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

Get the second sequence to align.

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

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

getType() - Method in class org.aisb.bio.things.Monomer

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

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