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
           
 

Methods in org.biojava.bio.alignment that return Alignment
 Alignment NeedlemanWunsch.getAlignment(Sequence query, Sequence target)
          This method is good if one wants to reuse the alignment calculated by this class in another BioJava class.
abstract  Alignment SequenceAlignment.getAlignment(Sequence query, Sequence subject)
          This method also performs a sequence alignment of the two given sequences but it returns an Alignment object instead of the score.
 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)
           
 

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 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
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 SeqSimilaritySearchSubHit.getAlignment()
          Return an alignment of (possibly part of) the query sequence against (possibly part of) this hit sequence.
 Alignment SequenceDBSearchSubHit.getAlignment()
          Deprecated.  
 

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 Homology.getAlignment()
          Retrieve the Alignment that specifies how the homologous regions are aligned.
 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 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 AlignmentFormat.read(BufferedReader reader)
          Read in an alignment from a buffered reader object
 Alignment FastaAlignmentFormat.read(BufferedReader br)
          Reads an alignment in FASTA format.
 Alignment MSFAlignmentFormat.read(BufferedReader reader)
          Reads an MSF Alignment File
 

Methods in org.biojava.bio.seq.io with parameters of type Alignment
 void 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 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 RelabeledAlignment.subAlignment(Set labels, Location loc)
           
 Alignment Alignment.subAlignment(Set labels, Location loc)
           Make a view onto this alignment.
 Alignment SimpleAlignment.subAlignment(Set labels, Location loc)
           
 

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.