Package | Description |
---|---|
pal.alignment |
Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.
|
Modifier and Type | Method | Description |
---|---|---|
static Alignment[] |
AlignmentReaders.readAllPhylipClustalAlignments(java.io.Reader r,
DataType dt) |
Read an alignment in phylip/clustal/simple format.
|
static Alignment |
AlignmentReaders.readPhylipClustalAlignment(java.io.Reader r,
DataType dt) |
Read an alignment in phylip/clustal/simple format.
|
static void |
AlignmentReaders.readPhylipClustalAlignment(java.io.Reader r,
DataType dt,
AlignmentReceiver receiver) |
Read an alignment in phylip/clustal/simple format.
|
Constructor | Description |
---|---|
ReadAlignment(java.io.PushbackReader input) |
read from stream
|
ReadAlignment(java.lang.String file) |
read from file
|
ReadAlignmentOld(java.io.PushbackReader input) |
read from stream
|
ReadAlignmentOld(java.lang.String file) |
read from file
|