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 |
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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 Msa
public int getNumberOfSequences()
getNumberOfSequences
in interface Msa
public char getResidueAt(int row, int col)
getResidueAt
in interface Msa
public java.lang.StringBuffer getSequenceAsString(int row)
getSequenceAsString
in interface Msa
public Sequence.TYPE getType()
public void setIdentifier(int row, java.lang.Object 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) throws java.io.IOException
public java.util.List<java.lang.Character> getColumnAt(int col)
getColumnAt
in interface Msa