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