## Uses of Interface
org.biojava.bio.symbol.Alignment

Packages that use Alignment
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
`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
`class` `AbstractULAlignment`
`class` `AbstractULAlignment.SubULAlignment`
`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.

Fields in org.biojava.bio.alignment declared as Alignment
`protected Alignment` `NeedlemanWunsch.pairalign` The result of a successful alignment

Methods in org.biojava.bio.alignment that return Alignment
`abstract Alignment` `SequenceAlignment.getAlignment(SymbolList query, SymbolList subject)` This method also performs a sequence alignment of the two given sequences but it returns an Alignment object instead of the score.
`Alignment` `NeedlemanWunsch.getAlignment(SymbolList query, SymbolList target)` This method is good if one wants to reuse the alignment calculated by this class in another BioJava class.
`Alignment` `AbstractULAlignment.subAlignment(Set labels, int min, int max)` Retreives a subAlignment
`Alignment` `AbstractULAlignment.subAlignment(Set labels, Location loc)` Retrieves a subalignment specified by the location.
`Alignment` `AbstractULAlignment.SubULAlignment.subAlignment(Set labels, Location loc)`

Methods in org.biojava.bio.alignment that return types with arguments of type Alignment
`List<Alignment>` `NeedlemanWunsch.alignAll(SequenceIterator source, SequenceDB subjectDB)`

Uses of Alignment in org.biojava.bio.chromatogram

Methods in org.biojava.bio.chromatogram that return Alignment
`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
`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
`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
`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
`class` `SimpleStatePath` A no-frills implementation of StatePath.

Methods in org.biojava.bio.dp that return Alignment
`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
`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
`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
`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
`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
`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
`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
`Alignment` `SimpleHomology.getAlignment()` `getAlignment` returns the alignment, which uses the `HomologyFeature`s 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 labels, Location loc)`

Methods in org.biojava.bio.seq.homol with parameters of type Alignment
`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
`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
`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
`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
`class` `RelabeledAlignment` An alignment that relabels another alignment.
`class` `SimpleAlignment` A simple implementation of an Alignment.

Methods in org.biojava.bio.symbol that return Alignment
`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` `SimpleAlignment.subAlignment(Set labels, Location loc)`
`Alignment` `RelabeledAlignment.subAlignment(Set labels, Location loc)`
`Alignment` `Alignment.subAlignment(Set labels, Location loc)` Make a view onto this alignment.

Constructors in org.biojava.bio.symbol with parameters of type Alignment
`Alignment.SymbolListIterator(Alignment ali)`
`RelabeledAlignment(Alignment delegate)`

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

Methods in org.biojavax.bio.phylo.io.phylip that return Alignment
`Alignment` `PHYLIPFileBuilder.getAlignment()`

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