Class UniqueSequenceList
- java.lang.Object
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- org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
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- All Implemented Interfaces:
java.lang.Cloneable
public class UniqueSequenceList extends java.lang.Object implements java.lang.Cloneable
Bean for a single sequence. These are intended to be unique sequences (100% id) as an imput to clustering.
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Constructor Summary
Constructors Constructor Description UniqueSequenceList(Atom[] cAlphaAtoms, java.lang.String chainId, int modelNumber, int structureId, java.lang.String seqResSequence)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.Object
clone()
java.util.List<java.lang.Integer>
getAlignment1()
java.util.List<java.lang.Integer>
getAlignment2()
Atom[]
getCalphaAtoms()
java.lang.String
getChainId()
int
getModelNumber()
java.lang.String
getSeqResSequence()
static java.lang.String
getSequenceString(Atom[] caAlphaAtoms)
int
getStructureId()
boolean
isMatch(Atom[] caAlphaAtoms)
Return true is the sequence and residues numbers of the passed in array of atoms matches those of this unique sequence listvoid
setAlignment1(java.util.List<java.lang.Integer> alignment1)
void
setAlignment2(java.util.List<java.lang.Integer> alignment2)
void
setSequenceString(java.lang.String sequenceString)
java.lang.String
toString()
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Constructor Detail
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UniqueSequenceList
public UniqueSequenceList(Atom[] cAlphaAtoms, java.lang.String chainId, int modelNumber, int structureId, java.lang.String seqResSequence)
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Method Detail
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isMatch
public boolean isMatch(Atom[] caAlphaAtoms)
Return true is the sequence and residues numbers of the passed in array of atoms matches those of this unique sequence list- Parameters:
caAlphaAtoms
-- Returns:
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getChainId
public java.lang.String getChainId()
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getModelNumber
public int getModelNumber()
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getStructureId
public int getStructureId()
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getCalphaAtoms
public Atom[] getCalphaAtoms()
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getSeqResSequence
public java.lang.String getSeqResSequence()
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setSequenceString
public void setSequenceString(java.lang.String sequenceString)
- Parameters:
sequenceString
- the sequenceString to set
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getAlignment1
public java.util.List<java.lang.Integer> getAlignment1()
- Returns:
- the alignment1
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setAlignment1
public void setAlignment1(java.util.List<java.lang.Integer> alignment1)
- Parameters:
alignment1
- the alignment1 to set
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getAlignment2
public java.util.List<java.lang.Integer> getAlignment2()
- Returns:
- the alignment2
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setAlignment2
public void setAlignment2(java.util.List<java.lang.Integer> alignment2)
- Parameters:
alignment2
- the alignment2 to set
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clone
public java.lang.Object clone()
- Overrides:
clone
in classjava.lang.Object
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getSequenceString
public static java.lang.String getSequenceString(Atom[] caAlphaAtoms)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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