Package pal.alignment
Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.
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Interface Summary Interface Description 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 Class Description 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 receivedAlignmentReceiver.SingleReceiver The SingleReceiver only keeps track of one alignment, the last one it receivedAlignmentTool Simple access for alignment functions.AlignmentUtils Helper utilities for alignments.BootstrappedAlignment generates bootstrapped alignments from a raw alignmentConcatenatedAlignment concatenates a list of alignments to one single alignment, increasing the number of sitesConcatenatedAnnotatedAlignment 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 patternsStrippedAlignment takes an alignment and repeatedly removes sitesStrippedAnnotatedAlignment This is the stripped implementation of the Annotation interface, which is designed to provide stripped and annotated alignments. -
Exception Summary Exception Description AlignmentParseException Exception thrown by ReadAlignment