Package org.snpeff.pdb
Class DistanceResult
- java.lang.Object
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- org.snpeff.pdb.DistanceResult
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public class DistanceResult extends java.lang.Object
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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
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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)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
compareByPos(DistanceResult d)
Compare by genomic positionboolean
equalPos(DistanceResult d)
Same genomic positionsjava.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
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Field Detail
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debug
public static boolean debug
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pdbId
public java.lang.String pdbId
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pdbChainId1
public java.lang.String pdbChainId1
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pdbChainId2
public java.lang.String pdbChainId2
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aaPos1
public int aaPos1
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aaPos2
public int aaPos2
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aa1
public char aa1
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aa2
public char aa2
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distance
public double distance
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trId1
public java.lang.String trId1
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trId2
public java.lang.String trId2
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chr1
public java.lang.String chr1
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chr2
public java.lang.String chr2
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pos1
public int pos1
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pos2
public int pos2
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Constructor Detail
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DistanceResult
public DistanceResult()
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DistanceResult
public DistanceResult(org.biojava.nbio.structure.AminoAcid aa1, org.biojava.nbio.structure.AminoAcid aa2, Transcript tr1, Transcript tr2, double distance)
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DistanceResult
public DistanceResult(java.lang.String line)
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Method Detail
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compareByPos
public int compareByPos(DistanceResult d)
Compare by genomic position
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equalPos
public boolean equalPos(DistanceResult d)
Same genomic positions
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getId
public java.lang.String getId()
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hasValidCoords
public boolean hasValidCoords()
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setAa1
public void setAa1(org.biojava.nbio.structure.AminoAcid aa)
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setAa2
public void setAa2(org.biojava.nbio.structure.AminoAcid aa)
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setTr1
public void setTr1(Transcript tr)
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setTr2
public void setTr2(Transcript tr)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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toStringPos
public java.lang.String toStringPos()
Show genomic positions only
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