Uses of Interface
org.biojava.bio.alignment.Alignment

Packages that use Alignment

Package	Description
org.biojava.bio.alignment	Classes to generate and describe sequence alignments.
org.biojava.bio.chromatogram	Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
org.biojava.bio.dist	Probability distributions over Alphabets.
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.program.abi	ABI Trace Handling.
org.biojava.bio.program.phred	Parser for Phred output
org.biojava.bio.search	Interfaces and classes for representing sequence similarity search results.
org.biojava.bio.seq.homol	The classes and interfaces for defining sequence similarity and honology.
org.biojava.bio.seq.impl	Standard in-memory implementations of Sequence and Feature.
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.symbol	Representation of the Symbols that make up a sequence, and locations within them.
org.biojavax.bio.phylo.io.phylip	Classes to support the reading and writing of PHYLIP format.

Uses of Alignment in org.biojava.bio.alignment

Subinterfaces of Alignment in org.biojava.bio.alignment

Modifier and Type	Interface and Description
interface	ARAlignment ARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.
interface	UnequalLengthAlignment UnequalLengthAlignment has the following behavior.

Classes in org.biojava.bio.alignment that implement Alignment

Modifier and Type	Class and Description
class	AbstractULAlignment
class	AbstractULAlignment.SubULAlignment
class	AlignmentPair This class stores the result of an alignment procedure that creates a pairwise alignment of two sequences.
class	FlexibleAlignment 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.
class	SimpleAlignment A simple implementation of an Alignment.

Methods in org.biojava.bio.alignment that return Alignment

Modifier and Type	Method and Description
Alignment	AbstractULAlignment.subAlignment(Set<String> labels, int min, int max) Retreives a subAlignment
Alignment	AbstractULAlignment.subAlignment(Set<String> labels, Location loc) Retrieves a subalignment specified by the location.
Alignment	AbstractULAlignment.SubULAlignment.subAlignment(Set<String> labels, Location loc)
Alignment	SimpleAlignment.subAlignment(Set<String> labels, Location loc)
Alignment	Alignment.subAlignment(Set<String> labels, Location loc) Make a view onto this alignment.

Constructors in org.biojava.bio.alignment with parameters of type Alignment

Constructor and Description
Alignment.SymbolListIterator(Alignment ali) Creates a SymbolListIterator for a given alignment object.

Uses of Alignment in org.biojava.bio.chromatogram

Methods in org.biojava.bio.chromatogram that return Alignment

Modifier and Type	Method and Description
protected Alignment	AbstractChromatogram.createImmutableAlignment(Map labelsToSymLists) A factory method for creating new immutable alignments, particularly for use as base call alignments.
Alignment	Chromatogram.getBaseCalls() Returns an alignment that describes the base calls for this chromatogram.
Alignment	AbstractChromatogram.getBaseCalls() Return the total number of base calls.
protected Alignment	AbstractChromatogram.reverseComplementBaseCalls() Returns a new base call alignment that is the reverse complement of one in this chromatogram.

Methods in org.biojava.bio.chromatogram with parameters of type Alignment

Modifier and Type	Method and Description
protected void	AbstractChromatogram.setBaseCallAlignment(Alignment align) Provides the list of base calls.

Uses of Alignment in org.biojava.bio.dist

Methods in org.biojava.bio.dist with parameters of type Alignment

Modifier and Type	Method and Description
static Distribution[]	DistributionTools.distOverAlignment(Alignment a) Equivalent to distOverAlignment(a, false, 0.0).
static Distribution[]	DistributionTools.distOverAlignment(Alignment a, boolean countGaps) Creates an array of distributions, one for each column of the alignment.
static Distribution[]	DistributionTools.distOverAlignment(Alignment a, boolean countGaps, double nullWeight) Creates an array of distributions, one for each column of the alignment.
static Distribution	DistributionTools.jointDistOverAlignment(Alignment a, boolean countGaps, double nullWeight, int[] cols) Creates a joint distribution.

Uses of Alignment in org.biojava.bio.dp

Subinterfaces of Alignment in org.biojava.bio.dp

Modifier and Type	Interface and Description
interface	StatePath Extends the Alignment interface so that it is explicitly used to represent a state path through an HMM, and the associated emitted sequence and likelihoods.

Classes in org.biojava.bio.dp that implement Alignment

Modifier and Type	Class and Description
class	SimpleStatePath A no-frills implementation of StatePath.

Methods in org.biojava.bio.dp that return Alignment

Modifier and Type	Method and Description
Alignment	SimpleStatePath.subAlignment(Set labels, Location loc)

Uses of Alignment in org.biojava.bio.program.abi

Methods in org.biojava.bio.program.abi that return Alignment

Modifier and Type	Method and Description
static Alignment	ABITools.getAlignment(SymbolList abiSeq) View a symbol list over the QUALITY alphabet as an alignment.

Uses of Alignment in org.biojava.bio.program.phred

Methods in org.biojava.bio.program.phred with parameters of type Alignment

Modifier and Type	Method and Description
static Distribution[]	PhredTools.phredAlignmentToDistArray(Alignment a) converts an Alignment of PhredSequences to a Distribution[] where each position is the average distribution of the underlying column of the alignment.

Uses of Alignment in org.biojava.bio.search

Methods in org.biojava.bio.search that return Alignment

Modifier and Type	Method and Description
Alignment	SimpleSeqSimilaritySearchSubHit.getAlignment()
Alignment	SequenceDBSearchSubHit.getAlignment() Deprecated.
Alignment	SeqSimilaritySearchSubHit.getAlignment() Return an alignment of (possibly part of) the query sequence against (possibly part of) this hit sequence.

Constructors in org.biojava.bio.search with parameters of type Alignment

Constructor and Description
SequenceDBSearchSubHit(double score, double eValue, double pValue, int queryStart, int queryEnd, StrandedFeature.Strand queryStrand, int subjectStart, int subjectEnd, StrandedFeature.Strand subjectStrand, Alignment alignment, Annotation annotation) Deprecated. Creates a new SequenceDBSearchSubHit object.
SimpleSeqSimilaritySearchSubHit(double score, double eValue, double pValue, int queryStart, int queryEnd, StrandedFeature.Strand queryStrand, int subjectStart, int subjectEnd, StrandedFeature.Strand subjectStrand, Alignment alignment, Annotation annotation) Creates a new SimpleSeqSimilaritySearchSubHit object.

Uses of Alignment in org.biojava.bio.seq.homol

Classes in org.biojava.bio.seq.homol that implement Alignment

Modifier and Type	Class and Description
static class	SimilarityPairFeature.EmptyPairwiseAlignment EmptyPairwiseAlignment empty pairwise alignment which has labels to empty symbol lists.

Fields in org.biojava.bio.seq.homol declared as Alignment

Modifier and Type	Field and Description
Alignment	SimilarityPairFeature.Template.alignment alignment Alignment field.
static Alignment	SimilarityPairFeature.EMPTY_PAIRWISE Constant EMPTY_PAIRWISE is an empty alignment for situations where there is no available alignment data or the implementation does not want to create one.

Methods in org.biojava.bio.seq.homol that return Alignment

Modifier and Type	Method and Description
Alignment	SimpleHomology.getAlignment() getAlignment returns the alignment, which uses the HomologyFeatures as keys.
Alignment	SimilarityPairFeature.getAlignment() getAlignment returns the Alignment of two similar features.
Alignment	Homology.getAlignment() Retrieve the Alignment that specifies how the homologous regions are aligned.
Alignment	SimilarityPairFeature.EmptyPairwiseAlignment.subAlignment(Set<String> labels, Location loc)

Methods in org.biojava.bio.seq.homol with parameters of type Alignment

Modifier and Type	Method and Description
void	SimpleHomology.setAlignment(Alignment alignment) setAlignment sets the alignment which describes the homology.

Uses of Alignment in org.biojava.bio.seq.impl

Methods in org.biojava.bio.seq.impl that return Alignment

Modifier and Type	Method and Description
Alignment	SimpleSimilarityPairFeature.getAlignment() getAlignment returns the alignment between the two features.

Uses of Alignment in org.biojava.bio.seq.io

Methods in org.biojava.bio.seq.io that return Alignment

Modifier and Type	Method and Description
Alignment	MSFAlignmentFormat.read(BufferedReader reader) Reads an MSF Alignment File
Alignment	FastaAlignmentFormat.read(BufferedReader br) Reads an alignment in FASTA format.
Alignment	AlignmentFormat.read(BufferedReader reader) Read in an alignment from a buffered reader object

Methods in org.biojava.bio.seq.io with parameters of type Alignment

Modifier and Type	Method and Description
void	MSFAlignmentFormat.write(OutputStream os, Alignment align, int fileType)
void	FastaAlignmentFormat.write(OutputStream os, Alignment align, int fileType) Writes out the alignment to an FASTA file.
void	MSFAlignmentFormat.writeDna(OutputStream os, Alignment align)
void	FastaAlignmentFormat.writeDna(OutputStream os, Alignment align)
void	MSFAlignmentFormat.writeProtein(OutputStream os, Alignment align)
void	FastaAlignmentFormat.writeProtein(OutputStream os, Alignment align)

Uses of Alignment in org.biojava.bio.symbol

Classes in org.biojava.bio.symbol that implement Alignment

Modifier and Type	Class and Description
class	RelabeledAlignment An alignment that relabels another alignment.

Methods in org.biojava.bio.symbol that return Alignment

Modifier and Type	Method and Description
static Alignment	SymbolListViews.alignment(List labels, SymbolList symList) View a SymbolList over a cross-product Alphabet as an Alignment.
static Alignment	SymbolListViews.alignment(Map labelToSymList) Construct an alignment of the SymbolLists contained in the values collection of labelToSymList.
Alignment	RelabeledAlignment.subAlignment(Set<String> labels, Location loc)

Constructors in org.biojava.bio.symbol with parameters of type Alignment

Constructor and Description
RelabeledAlignment(Alignment delegate)

Uses of Alignment in org.biojavax.bio.phylo.io.phylip

Methods in org.biojavax.bio.phylo.io.phylip that return Alignment

Modifier and Type	Method and Description
Alignment	PHYLIPFileBuilder.getAlignment()

Methods in org.biojavax.bio.phylo.io.phylip with parameters of type Alignment

Modifier and Type	Method and Description
static void	PHYLIPFileFormat.writeFile(File file, Alignment alignment) Writes the given Alignment in PHYLIP format to a file.
static void	PHYLIPFileFormat.writeStream(OutputStream os, Alignment alignment) Writes the given Alignment in PHYLIP format to a stream.
static void	PHYLIPFileFormat.writeWriter(Writer writer, Alignment alignment) Writes the given Alignment in PHYLIP format to a writer.