Package org.snpeff.pdb

Class DistanceResult

java.lang.Object

org.snpeff.pdb.DistanceResult

public class DistanceResult
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field	Description
char	aa1
char	aa2
int	aaPos1
int	aaPos2
java.lang.String	chr1
java.lang.String	chr2
static boolean	debug
double	distance
java.lang.String	pdbChainId1
java.lang.String	pdbChainId2
java.lang.String	pdbId
int	pos1
int	pos2
java.lang.String	trId1
java.lang.String	trId2

Constructor Summary

Constructors

Constructor	Description
DistanceResult()
DistanceResult(java.lang.String line)
DistanceResult(org.biojava.nbio.structure.AminoAcid aa1, org.biojava.nbio.structure.AminoAcid aa2, Transcript tr1, Transcript tr2, double distance)

Method Summary

Modifier and Type	Method	Description
int	compareByPos(DistanceResult d)	Compare by genomic position
boolean	equalPos(DistanceResult d)	Same genomic positions
java.lang.String	getId()
boolean	hasValidCoords()
void	setAa1(org.biojava.nbio.structure.AminoAcid aa)
void	setAa2(org.biojava.nbio.structure.AminoAcid aa)
void	setTr1(Transcript tr)
void	setTr2(Transcript tr)
java.lang.String	toString()
java.lang.String	toStringPos()	Show genomic positions only

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

debug

public static boolean debug

pdbId

public java.lang.String pdbId

pdbChainId1

public java.lang.String pdbChainId1

pdbChainId2

public java.lang.String pdbChainId2

aaPos1

public int aaPos1

aaPos2

public int aaPos2

aa1

public char aa1

aa2

public char aa2

distance

public double distance

trId1

public java.lang.String trId1

trId2

public java.lang.String trId2

chr1

public java.lang.String chr1

chr2

public java.lang.String chr2

pos1

public int pos1

pos2

public int pos2

Constructor Detail

DistanceResult

public DistanceResult()

DistanceResult

public DistanceResult(org.biojava.nbio.structure.AminoAcid aa1,
                      org.biojava.nbio.structure.AminoAcid aa2,
                      Transcript tr1,
                      Transcript tr2,
                      double distance)

DistanceResult

public DistanceResult(java.lang.String line)

Method Detail

compareByPos

public int compareByPos(DistanceResult d)

Compare by genomic position

equalPos

public boolean equalPos(DistanceResult d)

Same genomic positions

getId

public java.lang.String getId()

hasValidCoords

public boolean hasValidCoords()

setAa1

public void setAa1(org.biojava.nbio.structure.AminoAcid aa)

setAa2

public void setAa2(org.biojava.nbio.structure.AminoAcid aa)

setTr1

public void setTr1(Transcript tr)

setTr2

public void setTr2(Transcript tr)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

toStringPos

public java.lang.String toStringPos()

Show genomic positions only