Package pal.alignment

Classes dealing with sequence alignments, including methods for reading and printing in several possible formats, as well as rearranging and concatenating.

See:
Description

Interface Summary

Alignment	interface for any alignment data.
AlignmentGenerator	A AlignmentGenerator is an object that can generate alignments! (most probably replicates for statistical tests)
AlignmentReceiver
AnnotationAlignment	The AnnotationAlignment interface is designed to provide annotation for an alignment.
CharacterAlignment	This interface is designed to hold quantitative character states.

Class Summary

AbstractAlignment	abstract base class for any alignment data.
AlignmentBuilder	A class for the gradual construction of an alignment.
AlignmentGenerator.Utils
AlignmentReaders	Temporary class for reading alignments...
AlignmentReaders.PhylipClustalAlignment
AlignmentReaders.UnalignedAlignment
AlignmentReceiver.BucketReceiver	The SingleReceiver only keeps track of one alignment, the last one it received
AlignmentReceiver.SingleReceiver	The SingleReceiver only keeps track of one alignment, the last one it received
AlignmentTool	Simple access for alignment functions.
AlignmentUtils	Helper utilities for alignments.
BootstrappedAlignment	generates bootstrapped alignments from a raw alignment
ConcatenatedAlignment	concatenates a list of alignments to one single alignment, increasing the number of sites
ConcatenatedAnnotatedAlignment	This is an annotation version of the ConcatenatedAlignment Unlike normal ConcatenatedAlignment, it permits for merges with different numbers of sequences.
DataTranslator
GapBalancedAlignment	Creates a "Gap-Balanced" alignment.
Genotype	This class provides from genotype to be constructed from separate but paired alignments.
IndelAlignment	This class extracts indels (insertion/deletion) out of an alignment, and creates an alignment of indel polymorphisms.
IndelAnnotatedAlignment	an extension of the IndelAlignment that includes annotation.
JumbledAlignment	generates jumbled alignments (randomizing input order of sequences)
MultiLocusAnnotatedAlignment	MultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci.
ReadAlignment	reads aligned sequence data from plain text files.
ReadAlignmentOld	reads aligned sequence data from plain text files.
SimpleAlignment	An alignment class that can be efficiently constructed from an array of strings.
SimpleAnnotatedAlignment	This is the basic implementation of the Annotation interface, which is designed to provide annotation for an alignment.
SimpleCharacterAlignment	This provides a basic implementation of CharacterAlignment.
SitePattern	takes an Alignment and determines its site patterns
StrippedAlignment	takes an alignment and repeatedly removes sites
StrippedAnnotatedAlignment	This is the stripped implementation of the Annotation interface, which is designed to provide stripped and annotated alignments.

Exception Summary

AlignmentParseException

Exception thrown by ReadAlignment

Package pal.alignment Description

Classes dealing with sequence alignments, including methods for reading and printing in several possible formats, as well as rearranging and concatenating.