Index (alignment 1.9.7 API)

A C D E F G I L M N O P Q R S T U
All Classes and Interfaces|All Packages|Serialized Form

A

AbstractULAlignment - Class in org.biojava.bio.alignment
AbstractULAlignment() - Constructor for class org.biojava.bio.alignment.AbstractULAlignment
AbstractULAlignment.LeftRightLocationComparator<T> - Class in org.biojava.bio.alignment: Orders by location left to right.
AbstractULAlignment.SubULAlignment - Class in org.biojava.bio.alignment
ADD_LABEL - Static variable in interface org.biojava.bio.alignment.ARAlignment
addSequence(AlignmentElement) - Method in interface org.biojava.bio.alignment.ARAlignment
addSequence(AlignmentElement) - Method in class org.biojava.bio.alignment.FlexibleAlignment: add a new a alignment usings a location to the reference sequence.
align(Sequence, Sequence, AlignmentAlgorithm) - Static method in class org.biojava.bio.alignment.AlignmentPair
alignAll(SequenceIterator, SequenceDB) - Method in class org.biojava.bio.alignment.AlignmentAlgorithm
AlignmentAlgorithm - Class in org.biojava.bio.alignment: This Interface provides methods for the alignment of bio-sequences.
AlignmentAlgorithm() - Constructor for class org.biojava.bio.alignment.AlignmentAlgorithm
AlignmentElement - Interface in org.biojava.bio.alignment: AlignmentElement is a class which represents a SymbolList and its location within an Alignment This is for use in UnequalLengthAlignments and ARAlignments.
AlignmentPair - Class in org.biojava.bio.alignment: This class stores the result of an alignment procedure that creates a pairwise alignment of two sequences.
AlignmentPair(Sequence, Sequence, int, int, int, int, SubstitutionMatrix) - Constructor for class org.biojava.bio.alignment.AlignmentPair
AlignmentPair(Sequence, Sequence, SubstitutionMatrix) - Constructor for class org.biojava.bio.alignment.AlignmentPair
alignmentRange - Variable in class org.biojava.bio.alignment.FlexibleAlignment
allGaps(SymbolList, int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment: make sure that all Symbols in this range are gaps
alphabet - Variable in class org.biojava.bio.alignment.AbstractULAlignment
ARAlignment - Interface in org.biojava.bio.alignment: ARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.

C

compare(Object, Object) - Method in class org.biojava.bio.alignment.AbstractULAlignment.LeftRightLocationComparator
CostMatrix - Variable in class org.biojava.bio.alignment.NeedlemanWunsch: A matrix with the size length(sequence1) times length(sequence2)

D

data - Variable in class org.biojava.bio.alignment.FlexibleAlignment
debug(String) - Method in class org.biojava.bio.alignment.AbstractULAlignment

E

edit(Object, Edit) - Method in interface org.biojava.bio.alignment.EditableAlignment: edit() allows edits on an individual sequence, they should be reflected back to the underlying SymbolList.
edit(Object, Edit) - Method in class org.biojava.bio.alignment.FlexibleAlignment
EditableAlignment - Interface in org.biojava.bio.alignment: EditableAlignment is an interface that defines methods for shifting bases within an Alignment.

F

FlexibleAlignment - Class in org.biojava.bio.alignment: FlexibleAlignment is a class which implements UnequalLengthAlignment, ARAlignment and EditableAlignment It places no restriction on where any sequence can be in the alignment so there could be gaps in the alignment.
FlexibleAlignment(List<AlignmentElement>) - Constructor for class org.biojava.bio.alignment.FlexibleAlignment: construct this object with the reference sequence which can either be a gappedSymbolList or not label in all cases refers to an object that holds the display name (generally just a String). since more than one sequence in an alignment could have the same name this works as long as the labels are different objects even though they may hold the same name.
formatOutput() - Method in class org.biojava.bio.alignment.AlignmentPair
formatOutput(int) - Method in class org.biojava.bio.alignment.AlignmentPair: This method provides a BLAST-like formated alignment from the given Strings, in which the sequence coordinates and the information "Query" or "Sbjct", respectively is added to each line.

G

GAPS - Static variable in interface org.biojava.bio.alignment.EditableAlignment

getAE(Object) - Method in class org.biojava.bio.alignment.FlexibleAlignment

getAlphabet() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment

getAlphabet() - Method in class org.biojava.bio.alignment.FlexibleAlignment

getAlphabet() - Method in class org.biojava.bio.alignment.SubstitutionMatrix

Gives the alphabet used by this matrix.

getBlosum100() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM100 amino acid substitution matrix.

getBlosum100_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM100.50 amino acid substitution matrix.

getBlosum30() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM30 amino acid substitution matrix.

getBlosum30_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM30.50 amino acid substitution matrix.

getBlosum35() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM35 amino acid substitution matrix.

getBlosum35_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM35.50 amino acid substitution matrix.

getBlosum40() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM40 amino acid substitution matrix.

getBlosum40_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM40.50 amino acid substitution matrix.

getBlosum45() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM45 amino acid substitution matrix.

getBlosum45_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM45.50 amino acid substitution matrix.

getBlosum50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM50 amino acid substitution matrix.

getBlosum50_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM50.50 amino acid substitution matrix.

getBlosum55() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM55 amino acid substitution matrix.

getBlosum55_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM55.50 amino acid substitution matrix.

getBlosum60() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM60 amino acid substitution matrix.

getBlosum60_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM60.50 amino acid substitution matrix.

getBlosum62() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM62 amino acid substitution matrix.

getBlosum62_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM62.50 amino acid substitution matrix.

getBlosum65() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM65 amino acid substitution matrix.

getBlosum65_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM65.50 amino acid substitution matrix.

getBlosum70() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM70 amino acid substitution matrix.

getBlosum70_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM70.50 amino acid substitution matrix.

getBlosum75() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM75 amino acid substitution matrix.

getBlosum75_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM75.50 amino acid substitution matrix.

getBlosum80() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM80 amino acid substitution matrix.

getBlosum80_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM80.50 amino acid substitution matrix.

getBlosum85() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM85 amino acid substitution matrix.

getBlosum85_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM85.50 amino acid substitution matrix.

getBlosum90() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM90 amino acid substitution matrix.

getBlosum90_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUM90.50 amino acid substitution matrix.

getBlosumn() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUMN amino acid substitution matrix.

getBlosumn_50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the BLOSUMN.50 amino acid substitution matrix.

getComputationTime() - Method in class org.biojava.bio.alignment.AlignmentPair

getDayhoff() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the DAYHOFF amino acid substitution matrix.

getDelete() - Method in class org.biojava.bio.alignment.NeedlemanWunsch

Returns the current expenses of a single delete operation.

getDelete() - Method in class org.biojava.bio.alignment.SmithWaterman

getDescription() - Method in class org.biojava.bio.alignment.SubstitutionMatrix

This gives you the description of this matrix if there is one.

getEditDistance() - Method in class org.biojava.bio.alignment.NeedlemanWunsch

This gives the edit distance according to the given parameters of this certain object.

getGapExt() - Method in class org.biojava.bio.alignment.NeedlemanWunsch

Returns the current expenses of any extension of a gap operation.

getGapExt() - Method in class org.biojava.bio.alignment.SmithWaterman

getGonnet() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the GONNET amino acid substitution matrix.

getIdentity() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the IDENTITY amino acid substitution matrix.

getInsert() - Method in class org.biojava.bio.alignment.NeedlemanWunsch

Returns the current expenses of a single insert operation.

getInsert() - Method in class org.biojava.bio.alignment.SmithWaterman

getLabel() - Method in interface org.biojava.bio.alignment.AlignmentElement

getLabel() - Method in class org.biojava.bio.alignment.SimpleAlignmentElement

getLabels() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment

getLabels() - Method in class org.biojava.bio.alignment.FlexibleAlignment

getLabels will return a list of labels in left to right order

getLabelsAt(int) - Method in class org.biojava.bio.alignment.FlexibleAlignment

getLoc() - Method in interface org.biojava.bio.alignment.AlignmentElement

getLoc() - Method in class org.biojava.bio.alignment.SimpleAlignmentElement

getMatch() - Method in class org.biojava.bio.alignment.NeedlemanWunsch

Returns the current expenses of a single match operation.

getMatch() - Method in class org.biojava.bio.alignment.SmithWaterman

getMatch() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the MATCH amino acid substitution matrix.

getMax() - Method in class org.biojava.bio.alignment.SubstitutionMatrix

The maximum score in this matrix.

getMin() - Method in class org.biojava.bio.alignment.SubstitutionMatrix

The minimum score of this matrix.

getName() - Method in class org.biojava.bio.alignment.SubstitutionMatrix

Every substitution matrix has a name like "BLOSUM30" or "PAM160".

getNuc4_2() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the NUC.4.2 nucleotide substitution matrix.

getNuc4_4() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the NUC.4.4 nucleotide substitution matrix.

getNumGapsInQuery() - Method in class org.biojava.bio.alignment.AlignmentPair

getNumGapsInSubject() - Method in class org.biojava.bio.alignment.AlignmentPair

getNumIdenticals() - Method in class org.biojava.bio.alignment.AlignmentPair

getNumSimilars() - Method in class org.biojava.bio.alignment.AlignmentPair

getPam10() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM10 amino acid substitution matrix.

getPam100() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM100 amino acid substitution matrix.

getPam110() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM110 amino acid substitution matrix.

getPam120() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM120 amino acid substitution matrix.

getPam130() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM130 amino acid substitution matrix.

getPam140() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM140 amino acid substitution matrix.

getPam150() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM150 amino acid substitution matrix.

getPam160() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM160 amino acid substitution matrix.

getPam170() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM170 amino acid substitution matrix.

getPam180() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM180 amino acid substitution matrix.

getPam190() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM190 amino acid substitution matrix.

getPam20() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM20 amino acid substitution matrix.

getPam200() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM200 amino acid substitution matrix.

getPam210() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM210 amino acid substitution matrix.

getPam220() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM220 amino acid substitution matrix.

getPam230() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM230 amino acid substitution matrix.

getPam240() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM240 amino acid substitution matrix.

getPam250() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM250 amino acid substitution matrix.

getPam260() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM260 amino acid substitution matrix.

getPam270() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM270 amino acid substitution matrix.

getPam280() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM280 amino acid substitution matrix.

getPam290() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM290 amino acid substitution matrix.

getPam30() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM30 amino acid substitution matrix.

getPam300() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM300 amino acid substitution matrix.

getPam310() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM310 amino acid substitution matrix.

getPam320() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM320 amino acid substitution matrix.

getPam330() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM330 amino acid substitution matrix.

getPam340() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM340 amino acid substitution matrix.

getPam350() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM350 amino acid substitution matrix.

getPam360() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM360 amino acid substitution matrix.

getPam370() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM370 amino acid substitution matrix.

getPam380() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM380 amino acid substitution matrix.

getPam390() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM390 amino acid substitution matrix.

getPam40() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM40 amino acid substitution matrix.

getPam400() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM400 amino acid substitution matrix.

getPam410() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM410 amino acid substitution matrix.

getPam420() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM420 amino acid substitution matrix.

getPam430() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM430 amino acid substitution matrix.

getPam440() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM440 amino acid substitution matrix.

getPam450() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM450 amino acid substitution matrix.

getPam460() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM460 amino acid substitution matrix.

getPam470() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM470 amino acid substitution matrix.

getPam480() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM480 amino acid substitution matrix.

getPam490() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM490 amino acid substitution matrix.

getPam50() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM50 amino acid substitution matrix.

getPam500() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM500 amino acid substitution matrix.

getPam60() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM60 amino acid substitution matrix.

getPam70() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM70 amino acid substitution matrix.

getPam80() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM80 amino acid substitution matrix.

getPam90() - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return the PAM90 amino acid substitution matrix.

getPercentGapsQuery() - Method in class org.biojava.bio.alignment.AlignmentPair

getPercentGapsTarget() - Method in class org.biojava.bio.alignment.AlignmentPair

getPercentIdentityQuery() - Method in class org.biojava.bio.alignment.AlignmentPair

getPercentIdentitySubject() - Method in class org.biojava.bio.alignment.AlignmentPair

getPercentSimilarityQuery() - Method in class org.biojava.bio.alignment.AlignmentPair

getPercentSimilaritySubject() - Method in class org.biojava.bio.alignment.AlignmentPair

getQuery() - Method in class org.biojava.bio.alignment.AlignmentPair

Return the query sequence as a gapped sequence.

getQueryEnd() - Method in class org.biojava.bio.alignment.AlignmentPair

getQueryLength() - Method in class org.biojava.bio.alignment.AlignmentPair

getQueryStart() - Method in class org.biojava.bio.alignment.AlignmentPair

getReplace() - Method in class org.biojava.bio.alignment.NeedlemanWunsch

Returns the current expenses of a single replace operation.

getReplace() - Method in class org.biojava.bio.alignment.SmithWaterman

getSubject() - Method in class org.biojava.bio.alignment.AlignmentPair

Return the subject sequence as a gapped sequence.

getSubjectEnd() - Method in class org.biojava.bio.alignment.AlignmentPair

getSubjectLength() - Method in class org.biojava.bio.alignment.AlignmentPair

getSubjectStart() - Method in class org.biojava.bio.alignment.AlignmentPair

getSubMatrix() - Method in class org.biojava.bio.alignment.SmithWaterman

getSubstitutionMatrix() - Method in class org.biojava.bio.alignment.AlignmentPair

getSubstitutionMatrix(BufferedReader) - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

This constructor can be used to guess the alphabet of this substitution matrix.

getSubstitutionMatrix(FiniteAlphabet, BufferedReader) - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return a new substitution matrix with the specified alphabet.

getSubstitutionMatrix(FiniteAlphabet, BufferedReader, String) - Static method in class org.biojava.bio.alignment.SubstitutionMatrix

Return a new substitution matrix with the specified alphabet and name.

getSymbolList() - Method in interface org.biojava.bio.alignment.AlignmentElement

getSymbolList() - Method in class org.biojava.bio.alignment.SimpleAlignmentElement

getValueAt(Symbol, Symbol) - Method in class org.biojava.bio.alignment.SubstitutionMatrix

There are some substitution matrices containing more columns than lines.

greater(int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment

I

IllegalAlignmentEditException - Exception Class in org.biojava.bio.alignment

The usual reason for throwing an IllegalAlignmentEditException is that you are trying to shift a group of bases in such a way that it would require deleting bases.

IllegalAlignmentEditException() - Constructor for exception class org.biojava.bio.alignment.IllegalAlignmentEditException

Just make the exception.

IllegalAlignmentEditException(String) - Constructor for exception class org.biojava.bio.alignment.IllegalAlignmentEditException

Make the exception with a message.

IllegalAlignmentEditException(Throwable) - Constructor for exception class org.biojava.bio.alignment.IllegalAlignmentEditException

IllegalAlignmentEditException(Throwable, String) - Constructor for exception class org.biojava.bio.alignment.IllegalAlignmentEditException

L

label - Variable in class org.biojava.bio.alignment.SimpleAlignmentElement

labelOrder - Variable in class org.biojava.bio.alignment.FlexibleAlignment

labelsAt(int) - Method in class org.biojava.bio.alignment.AbstractULAlignment

labelsAt(int) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment

labelsAt(int) - Method in interface org.biojava.bio.alignment.UnequalLengthAlignment

Returns a list labels, of all seqs that cover that column

labelsInRange(Location) - Method in class org.biojava.bio.alignment.AbstractULAlignment

labelsInRange(Location) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment

labelsInRange(Location) - Method in interface org.biojava.bio.alignment.UnequalLengthAlignment

Returns list of all the labels that intersect that range

leftMost() - Method in class org.biojava.bio.alignment.AbstractULAlignment

leftMost and rightMost return labels.

LeftRightLocationComparator() - Constructor for class org.biojava.bio.alignment.AbstractULAlignment.LeftRightLocationComparator

length() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment

length() - Method in class org.biojava.bio.alignment.FlexibleAlignment

lesser(int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment

listIntersection(List<String>, List<String>) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment

loc - Variable in class org.biojava.bio.alignment.SimpleAlignmentElement

LOCATION - Static variable in interface org.biojava.bio.alignment.EditableAlignment

locInAlignment(Object) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment

The location of an individual SymbolList relative to overall Alignment

locInAlignment(Object) - Method in class org.biojava.bio.alignment.FlexibleAlignment

The location of an individual SymbolList relative to overall Alignment

locInAlignment(Object) - Method in interface org.biojava.bio.alignment.UnequalLengthAlignment

The location of an individual SymbolList relative to overall Alignment

locInSeq(Object, Location) - Method in class org.biojava.bio.alignment.FlexibleAlignment

M

min(int, int, int) - Static method in class org.biojava.bio.alignment.NeedlemanWunsch

This just computes the minimum of three integer values.

N

NeedlemanWunsch - Class in org.biojava.bio.alignment

Needleman and Wunsch defined the problem of global sequence alignments, from the first till the last symbol of a sequence.

NeedlemanWunsch(short, short, short, short, short, SubstitutionMatrix) - Constructor for class org.biojava.bio.alignment.NeedlemanWunsch

Constructs a new Object with the given parameters based on the Needleman-Wunsch algorithm The alphabet of sequences to be aligned will be taken from the given substitution matrix.

normalizeMatrix() - Method in class org.biojava.bio.alignment.SubstitutionMatrix

With this method you can get a “normalized” SubstitutionMatrix object; however, since this implementation uses an short matrix, the normalized matrix will be scaled by ten.

O

orderedLables(Comparator<String>) - Method in class org.biojava.bio.alignment.AbstractULAlignment

org.biojava.bio.alignment - package org.biojava.bio.alignment

Classes to generate and describe sequence alignments.

P

pairwiseAlignment(SymbolList, SymbolList) - Method in class org.biojava.bio.alignment.AlignmentAlgorithm

Performs a pairwise sequence alignment of the two given sequences.

pairwiseAlignment(SymbolList, SymbolList) - Method in class org.biojava.bio.alignment.NeedlemanWunsch

Global pairwise sequence alignment of two BioJava-Sequence objects according to the Needleman-Wunsch-algorithm.

pairwiseAlignment(SymbolList, SymbolList) - Method in class org.biojava.bio.alignment.SmithWaterman

Overrides the method inherited from the NeedlemanWunsch and performs only a local alignment.

posInSeq(Object, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment

get the position in the sequence corresponding to the postion within the alignment

printCostMatrix(int[][], char[], char[]) - Static method in class org.biojava.bio.alignment.NeedlemanWunsch

Prints a String representation of the CostMatrix for the given Alignment on the screen.

printMatrix() - Method in class org.biojava.bio.alignment.SubstitutionMatrix

Just to perform some test.

Q

QualitativeAlignment - Interface in org.biojava.bio.alignment

qualityAt(Object, int) - Method in interface org.biojava.bio.alignment.QualitativeAlignment

Returns a quality score for label/position

R

REMOVE_LABEL - Static variable in interface org.biojava.bio.alignment.ARAlignment

removeGaps(GappedSymbolList, int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment

because there is a bug in GappedSymbolList

removeSequence(Object) - Method in interface org.biojava.bio.alignment.ARAlignment

removeSequence(Object) - Method in class org.biojava.bio.alignment.FlexibleAlignment

resetRange() - Method in class org.biojava.bio.alignment.FlexibleAlignment

check that begining is at 1 otherwise shift everything over

rightMost() - Method in class org.biojava.bio.alignment.AbstractULAlignment

S

seq - Variable in class org.biojava.bio.alignment.SimpleAlignmentElement

setDelete(short) - Method in class org.biojava.bio.alignment.NeedlemanWunsch

Sets the penalty for a delete operation to the specified value.

setDelete(short) - Method in class org.biojava.bio.alignment.SmithWaterman

Overrides the method inherited from the NeedlemanWunsch and sets the penalty for a delete operation to the specified value.

setDescription(String) - Method in class org.biojava.bio.alignment.SubstitutionMatrix

Sets the description to the given value.

setGapExt(short) - Method in class org.biojava.bio.alignment.NeedlemanWunsch

Sets the penalty for an extension of any gap (insert or delete) to the specified value.

setGapExt(short) - Method in class org.biojava.bio.alignment.SmithWaterman

Overrides the method inherited from the NeedlemanWunsch and sets the penalty for an extension of any gap (insert or delete) to the specified value.

setInsert(short) - Method in class org.biojava.bio.alignment.NeedlemanWunsch

Sets the penalty for an insert operation to the specified value.

setInsert(short) - Method in class org.biojava.bio.alignment.SmithWaterman

Overrides the method inherited from the NeedlemanWunsch and sets the penalty for an insert operation to the specified value.

setLoc(Location) - Method in interface org.biojava.bio.alignment.AlignmentElement

setLoc(Location) - Method in class org.biojava.bio.alignment.SimpleAlignmentElement

setMatch(short) - Method in class org.biojava.bio.alignment.NeedlemanWunsch

Sets the penalty for a match operation to the specified value.

setMatch(short) - Method in class org.biojava.bio.alignment.SmithWaterman

Overrides the method inherited from the NeedlemanWunsch and sets the penalty for a match operation to the specified value.

setReplace(short) - Method in class org.biojava.bio.alignment.NeedlemanWunsch

Sets the penalty for a replace operation to the specified value.

setReplace(short) - Method in class org.biojava.bio.alignment.SmithWaterman

Overrides the method inherited from the NeedlemanWunsch and sets the penalty for a replace operation to the specified value.

setSubMatrix(SubstitutionMatrix) - Method in class org.biojava.bio.alignment.SmithWaterman

setSubstitutionMatrix(SubstitutionMatrix) - Method in class org.biojava.bio.alignment.NeedlemanWunsch

Sets the substitution matrix to be used to the specified one.

shift(Object, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment

moves the whole sequence

shiftAll(int) - Method in class org.biojava.bio.alignment.FlexibleAlignment

shiftAtAlignmentLoc(Object, Location, int) - Method in interface org.biojava.bio.alignment.EditableAlignment

loc in this case is the Alignment Location

shiftAtAlignmentLoc(Object, Location, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment

loc in this case is the Alignment Location

shiftAtSequenceLoc(Object, Location, int) - Method in interface org.biojava.bio.alignment.EditableAlignment

loc in this case is the SymbolList Location

shiftAtSequenceLoc(Object, Location, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment

loc in this case is the SymbolList Location

SimpleAlignmentElement - Class in org.biojava.bio.alignment

SimpleSimpleAlignment is a simple implementation of AlignmentElement.

SimpleAlignmentElement(String, SymbolList, Location) - Constructor for class org.biojava.bio.alignment.SimpleAlignmentElement

SmithWaterman - Class in org.biojava.bio.alignment

Smith and Waterman developed an efficient dynamic programming algorithm to perform local sequence alignments, which returns the most conserved region of two sequences (longest common substring with modifications).

SmithWaterman() - Constructor for class org.biojava.bio.alignment.SmithWaterman

Default constructor.

SmithWaterman(short, short, short, short, short, SubstitutionMatrix) - Constructor for class org.biojava.bio.alignment.SmithWaterman

Constructs the new SmithWaterman alignment object.

stringnifyDescription() - Method in class org.biojava.bio.alignment.SubstitutionMatrix

Converts the description of the matrix to a String.

stringnifyMatrix() - Method in class org.biojava.bio.alignment.SubstitutionMatrix

Creates a String representation of this matrix.

subAlignment(Set<String>, int, int) - Method in class org.biojava.bio.alignment.AbstractULAlignment

Retreives a subAlignment

subAlignment(Set<String>, Location) - Method in class org.biojava.bio.alignment.AbstractULAlignment

Retrieves a subalignment specified by the location.

subAlignment(Set<String>, Location) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment

subMatrix - Variable in class org.biojava.bio.alignment.NeedlemanWunsch

A matrix with the size length(alphabet) times length(alphabet)

SubstitutionMatrix - Class in org.biojava.bio.alignment

This object is able to read a substitution matrix file and constructs a short matrix in memory.

SubstitutionMatrix(File) - Constructor for class org.biojava.bio.alignment.SubstitutionMatrix

This constructor can be used to guess the alphabet of this substitution matrix.

SubstitutionMatrix(FiniteAlphabet, short, short) - Constructor for class org.biojava.bio.alignment.SubstitutionMatrix

Constructs a SubstitutionMatrix with every Match and every Replace having the same expenses given by the parameters.

SubstitutionMatrix(FiniteAlphabet, File) - Constructor for class org.biojava.bio.alignment.SubstitutionMatrix

This constructs a SubstitutionMatrix object that contains two Map data structures having BioJava symbols as keys and the value being the index of the matrix containing the substitution score.

SubstitutionMatrix(FiniteAlphabet, String, String) - Constructor for class org.biojava.bio.alignment.SubstitutionMatrix

With this constructor it is possible to construct a SubstitutionMatrix object from a substitution matrix file.

SubULAlignment(Set<String>, Location) - Constructor for class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment

symbolAt(int) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment

symbolAt(int) - Method in class org.biojava.bio.alignment.AbstractULAlignment

this will return the ambiguity symbol associated with all symbols in that column

symbolAt(String, int) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment

symbolAt(String, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment

This gets the symbol for an individual sequence at position in the overall alignment If the sequence is not aligned at that location it returns null

symbolListForLabel(String) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment

symbolListForLabel(String) - Method in class org.biojava.bio.alignment.FlexibleAlignment

symbolListIterator() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment

symbolListIterator() - Method in class org.biojava.bio.alignment.AbstractULAlignment

T

toString() - Method in class org.biojava.bio.alignment.SubstitutionMatrix

Overrides the inherited method.

U

UnequalLengthAlignment - Interface in org.biojava.bio.alignment

UnequalLengthAlignment has the following behavior.

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