Msa.MSA_FORMAT| Modifier and Type | Method and 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, writepublic 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 MsagetIdentifier in class BasicMsapublic final int getLength()
public final int getNumberOfSequences()
getNumberOfSequences in interface MsagetNumberOfSequences in class BasicMsapublic final char getResidueAt(int row,
int col)
getResidueAt in interface MsagetResidueAt in class BasicMsapublic MolecularSequence getSequence(int row)
getSequence in interface MsagetSequence in class BasicMsapublic final boolean isAllGap(int col)
public final void setIdentifier(int row,
java.lang.String id)
setIdentifier in interface MsasetIdentifier in class BasicMsapublic final void setResidueAt(int row,
int col,
char residue)
setResidueAt in interface MsasetResidueAt in class BasicMsapublic static final DeleteableMsa createInstance(java.util.List<MolecularSequence> seqs)
public static final DeleteableMsa createInstance(Msa msa)