Interface | Description |
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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 | Description |
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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 | Description |
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AlignmentParseException |
Exception thrown by ReadAlignment
|