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Packages that use Alignment | |
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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 |
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Subinterfaces of Alignment in org.biojava.bio.alignment | |
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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 | |
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class |
AbstractULAlignment
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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 | |
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protected Alignment |
NeedlemanWunsch.pairalign
The result of a successful alignment |
Methods in org.biojava.bio.alignment that return Alignment | |
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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(java.util.Set labels,
int min,
int max)
Retreives a subAlignment |
Alignment |
AbstractULAlignment.subAlignment(java.util.Set labels,
Location loc)
Retrieves a subalignment specified by the location. |
Alignment |
AbstractULAlignment.SubULAlignment.subAlignment(java.util.Set labels,
Location loc)
|
Methods in org.biojava.bio.alignment that return types with arguments of type Alignment | |
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java.util.List<Alignment> |
NeedlemanWunsch.alignAll(SequenceIterator source,
SequenceDB subjectDB)
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Uses of Alignment in org.biojava.bio.chromatogram |
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Methods in org.biojava.bio.chromatogram that return Alignment | |
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protected Alignment |
AbstractChromatogram.createImmutableAlignment(java.util.Map labelsToSymLists)
A factory method for creating new immutable alignments, particularly for use as base call alignments. |
Alignment |
AbstractChromatogram.getBaseCalls()
Return the total number of base calls. |
Alignment |
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 Alignment | |
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protected void |
AbstractChromatogram.setBaseCallAlignment(Alignment align)
Provides the list of base calls. |
Uses of Alignment in org.biojava.bio.dist |
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Methods in org.biojava.bio.dist with parameters of type Alignment | |
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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 |
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Subinterfaces of Alignment in org.biojava.bio.dp | |
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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 | |
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class |
SimpleStatePath
A no-frills implementation of StatePath. |
Methods in org.biojava.bio.dp that return Alignment | |
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Alignment |
SimpleStatePath.subAlignment(java.util.Set labels,
Location loc)
|
Uses of Alignment in org.biojava.bio.program.abi |
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Methods in org.biojava.bio.program.abi that return Alignment | |
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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 |
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Methods in org.biojava.bio.program.phred with parameters of type Alignment | |
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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 |
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Methods in org.biojava.bio.search that return Alignment | |
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Alignment |
SequenceDBSearchSubHit.getAlignment()
Deprecated. |
Alignment |
SimpleSeqSimilaritySearchSubHit.getAlignment()
|
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 | |
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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 |
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Classes in org.biojava.bio.seq.homol that implement Alignment | |
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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 | |
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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 | |
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Alignment |
SimilarityPairFeature.getAlignment()
getAlignment returns the Alignment of
two similar features. |
Alignment |
SimpleHomology.getAlignment()
getAlignment returns the alignment, which uses the
HomologyFeature s as keys. |
Alignment |
Homology.getAlignment()
Retrieve the Alignment that specifies how the homologous regions are aligned. |
Alignment |
SimilarityPairFeature.EmptyPairwiseAlignment.subAlignment(java.util.Set labels,
Location loc)
|
Methods in org.biojava.bio.seq.homol with parameters of type Alignment | |
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void |
SimpleHomology.setAlignment(Alignment alignment)
setAlignment sets the alignment which describes
the homology. |
Uses of Alignment in org.biojava.bio.seq.impl |
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Methods in org.biojava.bio.seq.impl that return Alignment | |
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Alignment |
SimpleSimilarityPairFeature.getAlignment()
getAlignment returns the alignment between the two
features. |
Uses of Alignment in org.biojava.bio.seq.io |
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Methods in org.biojava.bio.seq.io that return Alignment | |
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Alignment |
MSFAlignmentFormat.read(java.io.BufferedReader reader)
Reads an MSF Alignment File |
Alignment |
FastaAlignmentFormat.read(java.io.BufferedReader br)
Reads an alignment in FASTA format. |
Alignment |
AlignmentFormat.read(java.io.BufferedReader reader)
Read in an alignment from a buffered reader object |
Methods in org.biojava.bio.seq.io with parameters of type Alignment | |
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void |
MSFAlignmentFormat.write(java.io.OutputStream os,
Alignment align,
int fileType)
|
void |
FastaAlignmentFormat.write(java.io.OutputStream os,
Alignment align,
int fileType)
Writes out the alignment to an FASTA file. |
void |
MSFAlignmentFormat.writeDna(java.io.OutputStream os,
Alignment align)
|
void |
FastaAlignmentFormat.writeDna(java.io.OutputStream os,
Alignment align)
|
void |
MSFAlignmentFormat.writeProtein(java.io.OutputStream os,
Alignment align)
|
void |
FastaAlignmentFormat.writeProtein(java.io.OutputStream os,
Alignment align)
|
Uses of Alignment in org.biojava.bio.symbol |
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Classes in org.biojava.bio.symbol that implement Alignment | |
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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 | |
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static Alignment |
SymbolListViews.alignment(java.util.List labels,
SymbolList symList)
View a SymbolList over a cross-product Alphabet as an Alignment. |
static Alignment |
SymbolListViews.alignment(java.util.Map labelToSymList)
Construct an alignment of the SymbolLists contained in the values collection of labelToSymList . |
Alignment |
SimpleAlignment.subAlignment(java.util.Set labels,
Location loc)
|
Alignment |
RelabeledAlignment.subAlignment(java.util.Set labels,
Location loc)
|
Alignment |
Alignment.subAlignment(java.util.Set labels,
Location loc)
Make a view onto this alignment. |
Constructors in org.biojava.bio.symbol with parameters of type Alignment | |
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Alignment.SymbolListIterator(Alignment ali)
|
|
RelabeledAlignment(Alignment delegate)
|
Uses of Alignment in org.biojavax.bio.phylo.io.phylip |
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Methods in org.biojavax.bio.phylo.io.phylip that return Alignment | |
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Alignment |
PHYLIPFileBuilder.getAlignment()
|
Methods in org.biojavax.bio.phylo.io.phylip with parameters of type Alignment | |
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static void |
PHYLIPFileFormat.writeFile(java.io.File file,
Alignment alignment)
Writes the given Alignment in PHYLIP format to a file. |
static void |
PHYLIPFileFormat.writeStream(java.io.OutputStream os,
Alignment alignment)
Writes the given Alignment in PHYLIP format to a stream. |
static void |
PHYLIPFileFormat.writeWriter(java.io.Writer writer,
Alignment alignment)
Writes the given Alignment in PHYLIP format to a writer. |
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