public class MultipleAlignmentWriter
extends java.lang.Object
MultipleAlignment
to various String outputs.
Supported formats: FASTA, FatCat, Aligned Residues
Constructor and Description |
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MultipleAlignmentWriter() |
Modifier and Type | Method and Description |
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static java.lang.String |
toAlignedResidues(MultipleAlignment multAln)
Converts the alignment to its simplest form: a list of groups of aligned residues.
|
static java.lang.String |
toFASTA(MultipleAlignment alignment)
Converts the
MultipleAlignment into a multiple sequence alignment String in FASTA format. |
static java.lang.String |
toFatCat(MultipleAlignment alignment)
Converts the
MultipleAlignment into a FatCat String format. |
static java.lang.String |
toTransformMatrices(MultipleAlignment alignment)
Converts the transformation Matrices of the alignment into a String output.
|
public static java.lang.String toFASTA(MultipleAlignment alignment)
MultipleAlignment
into a multiple sequence alignment String in FASTA format.alignment
- MultipleAlignmentpublic static java.lang.String toFatCat(MultipleAlignment alignment)
MultipleAlignment
into a FatCat String format. Includes summary information
about the alignment in the top and a multiple sequence alignment at the bottom.alignment
- MultipleAlignmentpublic static java.lang.String toAlignedResidues(MultipleAlignment multAln)
52 A ALA 102 A VAL 154 A THR
Note that this format loses information about blocks.
multAln
- MultipleAlignment objectpublic static java.lang.String toTransformMatrices(MultipleAlignment alignment)
afpChain
-