Msa
DeleteableMsa
, ResampleableMsa
public class BasicMsa extends java.lang.Object implements Msa
Msa.MSA_FORMAT
Constructor | Description |
---|---|
BasicMsa(int rows,
int columns,
MolecularSequence.TYPE type) |
Modifier and Type | Method | Description |
---|---|---|
java.util.List<MolecularSequence> |
asSequenceList() |
|
static Msa |
createInstance(java.util.List<MolecularSequence> seqs) |
|
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 id) |
|
void |
setResidueAt(int row,
int col,
char residue) |
|
java.lang.String |
toString() |
|
void |
write(java.io.Writer w,
Msa.MSA_FORMAT format) |
public BasicMsa(int rows, int columns, MolecularSequence.TYPE type)
public java.util.List<MolecularSequence> asSequenceList()
asSequenceList
in interface Msa
public java.util.List<java.lang.Character> getColumnAt(int col)
getColumnAt
in interface Msa
public java.lang.String getIdentifier(int row)
getIdentifier
in interface Msa
public int getNumberOfSequences()
getNumberOfSequences
in interface Msa
public char getResidueAt(int row, int col)
getResidueAt
in interface Msa
public MolecularSequence getSequence(int row)
getSequence
in interface Msa
public MolecularSequence getSequence(java.lang.String id)
getSequence
in interface Msa
public java.lang.StringBuffer getSequenceAsString(int row)
getSequenceAsString
in interface Msa
public MolecularSequence.TYPE getType()
public void setIdentifier(int row, java.lang.String id)
setIdentifier
in interface Msa
public void setResidueAt(int row, int col, char residue)
setResidueAt
in interface Msa
public java.lang.String toString()
toString
in class java.lang.Object
public void write(java.io.Writer w, Msa.MSA_FORMAT format) throws java.io.IOException
public static Msa createInstance(java.util.List<MolecularSequence> seqs)