public interface Msa
Modifier and Type | Interface and Description |
---|---|
static class |
Msa.MSA_FORMAT |
Modifier and Type | Method and Description |
---|---|
java.util.List<MolecularSequence> |
asSequenceList() |
java.util.List<java.lang.Character> |
getColumnAt(int col) |
java.lang.String |
getIdentifier(int row) |
int |
getLength() |
int |
getNumberOfSequences() |
char |
getResidueAt(int row,
int col) |
MolecularSequence |
getSequence(int row) |
MolecularSequence |
getSequence(java.lang.String id) |
java.lang.StringBuffer |
getSequenceAsString(int row) |
MolecularSequence.TYPE |
getType() |
boolean |
isGapAt(int row,
int col) |
void |
setIdentifier(int row,
java.lang.String identifier) |
void |
setResidueAt(int row,
int col,
char residue) |
void |
write(java.io.Writer w,
Msa.MSA_FORMAT format) |
java.lang.String getIdentifier(int row)
void setIdentifier(int row, java.lang.String identifier)
int getLength()
int getNumberOfSequences()
char getResidueAt(int row, int col)
boolean isGapAt(int row, int col)
java.util.List<java.lang.Character> getColumnAt(int col)
MolecularSequence getSequence(java.lang.String id)
MolecularSequence getSequence(int row)
java.util.List<MolecularSequence> asSequenceList()
java.lang.StringBuffer getSequenceAsString(int row)
MolecularSequence.TYPE getType()
void setResidueAt(int row, int col, char residue)
void write(java.io.Writer w, Msa.MSA_FORMAT format) throws java.io.IOException
java.io.IOException