Msa.MSA_FORMAT
Modifier and Type | Method | Description |
---|---|---|
double[] |
calcGappiness() |
|
static int |
calcGapSumPerColumn(Msa msa,
int col) |
|
static DeleteableMsa |
createInstance(java.util.List<MolecularSequence> seqs) |
|
static DeleteableMsa |
createInstance(Msa msa) |
|
void |
deleteGapColumns(double max_allowed_gap_ratio) |
|
void |
deleteGapOnlyColumns() |
|
MolecularSequence |
deleteRow(java.lang.String id,
boolean return_removed_seq) |
|
short |
determineMaxIdLength() |
|
java.lang.String |
getIdentifier(int row) |
|
int |
getLength() |
|
int |
getNumberOfSequences() |
|
char |
getResidueAt(int row,
int col) |
|
MolecularSequence |
getSequence(int row) |
|
boolean |
isAllGap(int col) |
|
void |
setIdentifier(int row,
java.lang.String id) |
|
void |
setResidueAt(int row,
int col,
char residue) |
asSequenceList, getColumnAt, getSequence, getSequenceAsString, getType, isGapAt, toString, write
public final double[] calcGappiness()
public static int calcGapSumPerColumn(Msa msa, int col)
public short determineMaxIdLength()
public final void deleteGapColumns(double max_allowed_gap_ratio)
public final void deleteGapOnlyColumns()
public final MolecularSequence deleteRow(java.lang.String id, boolean return_removed_seq)
public final java.lang.String getIdentifier(int row)
getIdentifier
in interface Msa
getIdentifier
in class BasicMsa
public final int getLength()
public final int getNumberOfSequences()
getNumberOfSequences
in interface Msa
getNumberOfSequences
in class BasicMsa
public final char getResidueAt(int row, int col)
getResidueAt
in interface Msa
getResidueAt
in class BasicMsa
public MolecularSequence getSequence(int row)
getSequence
in interface Msa
getSequence
in class BasicMsa
public final boolean isAllGap(int col)
public final void setIdentifier(int row, java.lang.String id)
setIdentifier
in interface Msa
setIdentifier
in class BasicMsa
public final void setResidueAt(int row, int col, char residue)
setResidueAt
in interface Msa
setResidueAt
in class BasicMsa
public static final DeleteableMsa createInstance(java.util.List<MolecularSequence> seqs)
public static final DeleteableMsa createInstance(Msa msa)