java.lang.Cloneable
public class SequenceAlignmentCluster
extends java.lang.Object
implements java.lang.Cloneable
Constructor | Description |
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SequenceAlignmentCluster(QuatSymmetryParameters parameters) |
Modifier and Type | Method | 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) |
Match a sequence to this cluster at 100% identity.
|
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)
unique sequence list
.cAlphaAtoms
- chainId
- modelNumber
- structureId
- 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