Uses of Interface
org.biojava.bio.alignment.Alignment
Packages that use Alignment
Package
Description
Classes to generate and describe sequence alignments.
Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
Probability distributions over Alphabets.
HMM and Dynamic Programming Algorithms.
ABI Trace Handling.
Parser for Phred output
Interfaces and classes for representing sequence similarity search results.
The classes and interfaces for defining sequence similarity and
honology.
Standard in-memory implementations of
Sequence
and
Feature
.Classes and interfaces for processing and producing flat-file representations
of sequences.
Representation of the Symbols that make up a sequence, and locations within
them.
Classes to support the reading and writing of PHYLIP format.
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Uses of Alignment in org.biojava.bio.alignment
Subinterfaces of Alignment in org.biojava.bio.alignmentModifier and TypeInterfaceDescriptioninterface
ARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.interface
UnequalLengthAlignment has the following behavior.Classes in org.biojava.bio.alignment that implement AlignmentModifier and TypeClassDescriptionclass
class
class
This class stores the result of an alignment procedure that creates a pairwise alignment of two sequences.class
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
A simple implementation of an Alignment.Methods in org.biojava.bio.alignment that return AlignmentModifier and TypeMethodDescriptionAbstractULAlignment.subAlignment
(Set<String> labels, int min, int max) Retreives a subAlignmentAbstractULAlignment.subAlignment
(Set<String> labels, Location loc) Retrieves a subalignment specified by the location.AbstractULAlignment.SubULAlignment.subAlignment
(Set<String> labels, Location loc) Alignment.subAlignment
(Set<String> labels, Location loc) Make a view onto this alignment.SimpleAlignment.subAlignment
(Set<String> labels, Location loc) Constructors in org.biojava.bio.alignment with parameters of type AlignmentModifierConstructorDescriptionCreates a SymbolListIterator for a given alignment object. -
Uses of Alignment in org.biojava.bio.chromatogram
Methods in org.biojava.bio.chromatogram that return AlignmentModifier and TypeMethodDescriptionprotected Alignment
AbstractChromatogram.createImmutableAlignment
(Map labelsToSymLists) A factory method for creating new immutable alignments, particularly for use as base call alignments.AbstractChromatogram.getBaseCalls()
Return the total number of base calls.Chromatogram.getBaseCalls()
Returns an alignment that describes the base calls for this chromatogram.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 AlignmentModifier and TypeMethodDescriptionprotected final 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 AlignmentModifier and TypeMethodDescriptionstatic Distribution[]
DistributionTools.distOverAlignment
(Alignment a) Equivalent to distOverAlignment(a, false, 0.0).static final Distribution[]
DistributionTools.distOverAlignment
(Alignment a, boolean countGaps) Creates an array of distributions, one for each column of the alignment.static final Distribution[]
DistributionTools.distOverAlignment
(Alignment a, boolean countGaps, double nullWeight) Creates an array of distributions, one for each column of the alignment.static final 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.dpModifier and TypeInterfaceDescriptioninterface
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 AlignmentMethods in org.biojava.bio.dp that return Alignment -
Uses of Alignment in org.biojava.bio.program.abi
Methods in org.biojava.bio.program.abi that return AlignmentModifier and TypeMethodDescriptionstatic 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 AlignmentModifier and TypeMethodDescriptionstatic 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 AlignmentModifier and TypeMethodDescriptionSeqSimilaritySearchSubHit.getAlignment()
Return an alignment of (possibly part of) the query sequence against (possibly part of) this hit sequence.SequenceDBSearchSubHit.getAlignment()
Deprecated.SimpleSeqSimilaritySearchSubHit.getAlignment()
Constructors in org.biojava.bio.search with parameters of type AlignmentModifierConstructorDescriptionSequenceDBSearchSubHit
(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 newSequenceDBSearchSubHit
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 newSimpleSeqSimilaritySearchSubHit
object. -
Uses of Alignment in org.biojava.bio.seq.homol
Classes in org.biojava.bio.seq.homol that implement AlignmentModifier and TypeClassDescriptionstatic final class
EmptyPairwiseAlignment
empty pairwise alignment which has labels to empty symbol lists.Fields in org.biojava.bio.seq.homol declared as AlignmentModifier and TypeFieldDescriptionSimilarityPairFeature.Template.alignment
alignment
Alignment
field.static final Alignment
SimilarityPairFeature.EMPTY_PAIRWISE
ConstantEMPTY_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 AlignmentModifier and TypeMethodDescriptionHomology.getAlignment()
Retrieve the Alignment that specifies how the homologous regions are aligned.SimilarityPairFeature.getAlignment()
getAlignment
returns theAlignment
of two similar features.SimpleHomology.getAlignment()
getAlignment
returns the alignment, which uses theHomologyFeature
s as keys.SimilarityPairFeature.EmptyPairwiseAlignment.subAlignment
(Set<String> labels, Location loc) Methods in org.biojava.bio.seq.homol with parameters of type AlignmentModifier and TypeMethodDescriptionvoid
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 AlignmentModifier and TypeMethodDescriptionSimpleSimilarityPairFeature.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 AlignmentModifier and TypeMethodDescriptionAlignmentFormat.read
(BufferedReader reader) Read in an alignment from a buffered reader objectFastaAlignmentFormat.read
(BufferedReader br) Reads an alignment in FASTA format.MSFAlignmentFormat.read
(BufferedReader reader) Reads an MSF Alignment FileMethods in org.biojava.bio.seq.io with parameters of type AlignmentModifier and TypeMethodDescriptionvoid
FastaAlignmentFormat.write
(OutputStream os, Alignment align, int fileType) Writes out the alignment to an FASTA file.void
MSFAlignmentFormat.write
(OutputStream os, Alignment align, int fileType) void
FastaAlignmentFormat.writeDna
(OutputStream os, Alignment align) void
MSFAlignmentFormat.writeDna
(OutputStream os, Alignment align) void
FastaAlignmentFormat.writeProtein
(OutputStream os, Alignment align) void
MSFAlignmentFormat.writeProtein
(OutputStream os, Alignment align) -
Uses of Alignment in org.biojava.bio.symbol
Classes in org.biojava.bio.symbol that implement AlignmentModifier and TypeClassDescriptionclass
An alignment that relabels another alignment.Methods in org.biojava.bio.symbol that return AlignmentModifier and TypeMethodDescriptionstatic Alignment
SymbolListViews.alignment
(List labels, SymbolList symList) View a SymbolList over a cross-product Alphabet as an Alignment.static Alignment
Construct an alignment of the SymbolLists contained in the values collection oflabelToSymList
.RelabeledAlignment.subAlignment
(Set<String> labels, Location loc) Constructors in org.biojava.bio.symbol with parameters of type Alignment -
Uses of Alignment in org.biojavax.bio.phylo.io.phylip
Methods in org.biojavax.bio.phylo.io.phylip that return AlignmentMethods in org.biojavax.bio.phylo.io.phylip with parameters of type AlignmentModifier and TypeMethodDescriptionstatic void
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.