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java.lang.Objectorg.biojava.bio.structure.align.ce.CeCalculatorEnhanced
public class CeCalculatorEnhanced
This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3), as has been originally developed by I. Shindyalov and P.Bourne (1998). The original CE paper is available from here: http://peds.oxfordjournals.org/cgi/content/short/11/9/739. This class is a pretty much exact 1:1 port from C, where I cared about exact reproduce of the CE results and not about Java style.
Field Summary | |
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protected int[] |
bestTrace1
|
protected int[] |
bestTrace2
|
protected int[][] |
bestTraces1
|
protected int[][] |
bestTraces2
|
protected double |
bestTraceScore
|
protected int[] |
bestTracesN
|
protected double[] |
bestTracesScores
|
static boolean |
GLOBAL_ALIGN1
|
static boolean |
GLOBAL_ALIGN2
|
protected static boolean |
isPrint
|
protected double[][] |
mat
|
protected int |
nBestTrace
|
protected int |
nBestTraces
|
protected static int |
nIter
|
protected int |
nTrace
|
protected int |
nTraces
|
protected CeParameters |
params
|
protected int[] |
trace1
|
protected int[] |
trace2
|
protected static double |
zThr
|
Constructor Summary | |
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CeCalculatorEnhanced(CeParameters params)
|
Method Summary | |
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void |
addMatrixListener(MatrixListener li)
|
double |
calc_rmsd(Atom[] pro1,
Atom[] pro2,
int strLen,
boolean storeTransform,
boolean show)
superimpose and get rmsd |
void |
convertAfpChain(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2)
copy data from this class into AFPChain container object. |
protected int |
doIter0(int newBestTrace,
double traceTotalScore,
double bestTracesMax)
|
AFPChain |
extractFragments(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2)
|
int[] |
getAlign_se1()
|
int[] |
getAlign_se2()
|
double[][] |
getDist1()
|
double[][] |
getDist2()
|
int |
getLcmp()
|
double[][] |
getMatMatrix()
Caution: this matrix is overwriten with very different data at several points in the alignment algorithm. |
int |
getnAtom()
|
Matrix |
getRotationMatrix()
Gets the rotation matrix from the last call to calc_rmsd . |
protected double |
getScore2(int jse1,
int jse2,
double[][] traceScore,
int traceIndex_,
int[] traceIndex,
int winSizeComb1,
int winSizeComb2,
double score0,
double score1)
|
protected double |
getScoreFromDistanceMatrices(int mse1,
int mse2,
int winSize)
|
Atom |
getShift()
Gets the shift from the last call to calc_rmsd . |
double[][] |
initSumOfDistances(int nse1,
int nse2,
int winSize,
int winSizeComb1,
Atom[] ca1,
Atom[] ca2)
|
void |
nextStep(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2)
|
void |
setAlign_se1(int[] alignSe1)
|
void |
setAlign_se2(int[] alignSe2)
|
void |
setDist1(double[][] dist1)
|
void |
setDist2(double[][] dist2)
|
void |
setLcmp(int lcmp)
|
void |
setMatMatrix(double[][] matrix)
|
void |
setnAtom(int nAtom)
|
void |
traceFragmentMatrix(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2)
|
static double[][] |
updateMatrixWithSequenceConservation(double[][] max,
Atom[] ca1,
Atom[] ca2,
CeParameters params)
Modifies an alignment matrix by favoring the alignment of similar and identical amino acids and penalizing the alignment of unrelated ones. |
protected double |
zStrAlign(int winSize,
int nTrace,
double score,
int nGaps)
|
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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protected static final boolean isPrint
protected double[][] mat
protected int[] bestTrace1
protected int[] bestTrace2
protected int[][] bestTraces1
protected int[][] bestTraces2
protected int nBestTrace
protected int nBestTraces
protected int[] bestTracesN
protected double bestTraceScore
protected int nTrace
protected double[] bestTracesScores
protected int[] trace1
protected int[] trace2
protected static final double zThr
protected int nTraces
protected CeParameters params
protected static final int nIter
public static final boolean GLOBAL_ALIGN1
public static final boolean GLOBAL_ALIGN2
Constructor Detail |
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public CeCalculatorEnhanced(CeParameters params)
Method Detail |
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public AFPChain extractFragments(AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws StructureException
afpChain
- A new AFPChain, which will be filled in by this functionca1
- ca2
-
StructureException
public double[][] initSumOfDistances(int nse1, int nse2, int winSize, int winSizeComb1, Atom[] ca1, Atom[] ca2)
public void traceFragmentMatrix(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
protected double getScore2(int jse1, int jse2, double[][] traceScore, int traceIndex_, int[] traceIndex, int winSizeComb1, int winSizeComb2, double score0, double score1)
protected int doIter0(int newBestTrace, double traceTotalScore, double bestTracesMax)
protected double getScoreFromDistanceMatrices(int mse1, int mse2, int winSize)
public void nextStep(AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws StructureException
StructureException
public static double[][] updateMatrixWithSequenceConservation(double[][] max, Atom[] ca1, Atom[] ca2, CeParameters params)
max
- alignment matrixca1
- Atoms for protein 1ca2
- Atoms for Protein 2params
- alignment parameters
public void addMatrixListener(MatrixListener li)
public double calc_rmsd(Atom[] pro1, Atom[] pro2, int strLen, boolean storeTransform, boolean show) throws StructureException
pro1
- pro2
- strLen
- storeTransform
- show
-
StructureException
protected double zStrAlign(int winSize, int nTrace, double score, int nGaps)
public void convertAfpChain(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
afpChain
- ca1
- ca2
- public int getnAtom()
public void setnAtom(int nAtom)
public int getLcmp()
public void setLcmp(int lcmp)
public int[] getAlign_se1()
public void setAlign_se1(int[] alignSe1)
public int[] getAlign_se2()
public void setAlign_se2(int[] alignSe2)
public double[][] getMatMatrix()
initSumOfDistances
is run, this will hold the distance matrix between AFPs.
public void setMatMatrix(double[][] matrix)
public Matrix getRotationMatrix()
calc_rmsd
.
public Atom getShift()
calc_rmsd
.
public double[][] getDist1()
public void setDist1(double[][] dist1)
public double[][] getDist2()
public void setDist2(double[][] dist2)
|
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