public class SequenceAlignmentCluster
extends java.lang.Object
implements java.lang.Cloneable
Constructor and Description |
---|
SequenceAlignmentCluster(QuatSymmetryParameters parameters) |
Modifier and Type | Method and Description |
---|---|
void |
addUniqueSequenceList(UniqueSequenceList sequenceList) |
java.lang.Object |
clone() |
java.util.List<Atom[]> |
getAlignedCalphaAtoms() |
java.util.List<java.lang.String> |
getChainIds() |
double |
getMaxSequenceIdentity() |
double |
getMinSequenceIdentity() |
java.util.List<java.lang.Integer> |
getModelNumbers() |
PairwiseAlignment |
getPairwiseAlignment(SequenceAlignmentCluster other) |
int |
getSequenceAlignmentLength() |
int |
getSequenceCount() |
java.util.List<java.lang.Integer> |
getStructureIds() |
java.util.List<UniqueSequenceList> |
getUniqueSequenceList() |
boolean |
identityMatch(Atom[] cAlphaAtoms,
java.lang.String chainId,
int modelNumber,
int structureId,
java.lang.String sequence) |
boolean |
isPseudoStoichiometric() |
void |
setMaxSequenceIdentity(double maxSequenceIdentity) |
void |
setMinSequenceIdentity(double minSequenceIdentity) |
java.lang.String |
toString() |
public SequenceAlignmentCluster(QuatSymmetryParameters parameters)
public boolean isPseudoStoichiometric()
public double getMinSequenceIdentity()
public void setMinSequenceIdentity(double minSequenceIdentity)
public double getMaxSequenceIdentity()
public void setMaxSequenceIdentity(double maxSequenceIdentity)
public void addUniqueSequenceList(UniqueSequenceList sequenceList)
public int getSequenceCount()
public int getSequenceAlignmentLength()
public java.util.List<UniqueSequenceList> getUniqueSequenceList()
public java.util.List<java.lang.String> getChainIds()
public java.util.List<java.lang.Integer> getModelNumbers()
public java.util.List<java.lang.Integer> getStructureIds()
public java.util.List<Atom[]> getAlignedCalphaAtoms()
public boolean identityMatch(Atom[] cAlphaAtoms, java.lang.String chainId, int modelNumber, int structureId, java.lang.String sequence)
public PairwiseAlignment getPairwiseAlignment(SequenceAlignmentCluster other)
public java.lang.Object clone()
clone
in class java.lang.Object
public java.lang.String toString()
toString
in class java.lang.Object