Class SequenceAlignmentCluster
- java.lang.Object
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- org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
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- All Implemented Interfaces:
java.lang.Cloneable
public class SequenceAlignmentCluster extends java.lang.Object implements java.lang.Cloneable
Represents a cluster of equivalent sequences
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Constructor Summary
Constructors Constructor Description SequenceAlignmentCluster(QuatSymmetryParameters parameters)
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Method Summary
All Methods Instance Methods Concrete Methods 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()
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Constructor Detail
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SequenceAlignmentCluster
public SequenceAlignmentCluster(QuatSymmetryParameters parameters)
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Method Detail
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isPseudoStoichiometric
public boolean isPseudoStoichiometric()
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getMinSequenceIdentity
public double getMinSequenceIdentity()
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setMinSequenceIdentity
public void setMinSequenceIdentity(double minSequenceIdentity)
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getMaxSequenceIdentity
public double getMaxSequenceIdentity()
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setMaxSequenceIdentity
public void setMaxSequenceIdentity(double maxSequenceIdentity)
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addUniqueSequenceList
public void addUniqueSequenceList(UniqueSequenceList sequenceList)
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getSequenceCount
public int getSequenceCount()
- Returns:
- the number of sequences which have been added to this cluster
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getSequenceAlignmentLength
public int getSequenceAlignmentLength()
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getUniqueSequenceList
public java.util.List<UniqueSequenceList> getUniqueSequenceList()
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getChainIds
public java.util.List<java.lang.String> getChainIds()
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getModelNumbers
public java.util.List<java.lang.Integer> getModelNumbers()
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getStructureIds
public java.util.List<java.lang.Integer> getStructureIds()
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getAlignedCalphaAtoms
public java.util.List<Atom[]> getAlignedCalphaAtoms()
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identityMatch
public 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. If the given sequence matches the cluster seed (100%), then performs an alignment to the seed and adds it to theunique sequence list
.- Parameters:
cAlphaAtoms
-chainId
-modelNumber
-structureId
-sequence
-- Returns:
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getPairwiseAlignment
public PairwiseAlignment getPairwiseAlignment(SequenceAlignmentCluster other)
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clone
public java.lang.Object clone()
- Overrides:
clone
in classjava.lang.Object
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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