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See:
Description
Interface Summary | |
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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 | |
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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 | |
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AlignmentParseException | Exception thrown by ReadAlignment |
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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