java.io.Serializable
, java.lang.Cloneable
public class AFPChain
extends java.lang.Object
implements java.io.Serializable, java.lang.Cloneable
Modifier and Type | Field | Description |
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static java.lang.String |
newline |
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static java.lang.String |
UNKNOWN_ALGORITHM |
Constructor | Description |
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AFPChain() |
Deprecated.
|
AFPChain(java.lang.String algorithmName) |
Construction of an AFPChain needs the algorithm name, since downstream
analysis methods (scores, display, etc) behave differently if the
alignment is flexible (created with FatCat).
|
AFPChain(AFPChain o) |
Copy constructor
|
Modifier and Type | Method | Description |
---|---|---|
protected void |
calcSimilarity() |
|
java.lang.Object |
clone() |
Creates and returns a copy of this object.
|
boolean |
equals(java.lang.Object obj) |
A week equality metric.
|
int[][] |
getAfpAftIndex() |
|
int[][] |
getAfpBefIndex() |
|
int |
getAfpChainLen() |
|
int[] |
getAfpChainList() |
|
double[] |
getAfpChainTwiBin() |
|
double[] |
getAfpChainTwiList() |
|
int |
getAfpChainTwiNum() |
|
int[][] |
getAfpIndex() |
|
java.util.List<AFP> |
getAfpSet() |
Get the set of AFPs for this alignment.
|
java.lang.String |
getAlgorithmName() |
|
double |
getAlignScore() |
|
double |
getAlignScoreUpdate() |
|
int |
getAlnbeg1() |
|
int |
getAlnbeg2() |
|
int |
getAlnLength() |
|
char[] |
getAlnseq1() |
|
char[] |
getAlnseq2() |
|
char[] |
getAlnsymb() |
|
int[] |
getBlock2Afp() |
|
int[] |
getBlockGap() |
|
int |
getBlockNum() |
The number of blocks in the alignment
|
int |
getBlockNumClu() |
|
int |
getBlockNumIni() |
|
int |
getBlockNumSpt() |
|
int[][][] |
getBlockResList() |
tracks the residues of the initial blocks (before optimization)
|
int[] |
getBlockResSize() |
|
double[] |
getBlockRmsd() |
|
Matrix[] |
getBlockRotationMatrix() |
|
double[] |
getBlockScore() |
|
Atom[] |
getBlockShiftVector() |
|
int[] |
getBlockSize() |
|
int |
getCa1Length() |
|
int |
getCa2Length() |
|
long |
getCalculationTime() |
|
int |
getChainLen() |
|
double |
getChainRmsd() |
|
java.lang.Double |
getConn() |
|
int |
getCoverage1() |
Get the coverage of protein 1 with the alignment
|
int |
getCoverage2() |
Get the coverage of protein 2 with the alignment
|
java.lang.String |
getDescription2() |
Get a textual description for the protein 2 of the alignment.
|
Matrix |
getDisTable1() |
|
Matrix |
getDisTable2() |
|
Matrix |
getDistanceMatrix() |
A matrix with ca1length rows and ca2length columns.
|
java.lang.Double |
getDVar() |
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int[] |
getFocusAfpList() |
|
int |
getFocusAfpn() |
|
int[] |
getFocusRes1() |
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int[] |
getFocusRes2() |
|
int |
getFocusResn() |
|
int |
getGapLen() |
|
long |
getId() |
|
double |
getIdentity() |
The percent of residues that are sequence-identical in the alignment.
|
long |
getIoTime() |
|
int |
getMaxTra() |
get the maximum nr of Twists that are allowed...
|
int |
getMinLen() |
|
int |
getMisLen() |
|
java.lang.String |
getName1() |
|
java.lang.String |
getName2() |
|
double |
getNormAlignScore() |
|
int |
getNrEQR() |
Get the number of structurally equivalent residues
|
int[][][] |
getOptAln() |
Tracks the Atom positions in the optimal alignment.
|
int[] |
getOptLen() |
The length of each block
|
int |
getOptLength() |
|
double[] |
getOptRmsd() |
|
java.lang.String[][][] |
getPdbAln() |
used temporarily during XML serialization to track the PDB positions of the alignmnet
|
double |
getProbability() |
The probability (FATCAT) or Z-score (CE) of the alignment.
|
double |
getSimilarity() |
Returns the similarity score for the alignment.
|
int |
getSimilarity1() |
Deprecated.
use getCoverage1() instead
|
int |
getSimilarity2() |
Deprecated.
use getCoverage2() instead
|
double |
getTMScore() |
Returns the tmScore of the alignment.
|
int |
getTotalLenIni() |
|
int |
getTotalLenOpt() |
|
double |
getTotalRmsdIni() |
this is the init-RMSD, not the final RMSD after refinement.
|
double |
getTotalRmsdOpt() |
The RMSD of the final alignment.
|
int[] |
getTwi() |
|
java.lang.String |
getVersion() |
|
int |
hashCode() |
|
boolean |
isSequentialAlignment() |
Get whether this alignment has the normal topology, ie the residues
aligned in each block increase sequentially over the original protein.
|
boolean |
isShortAlign() |
|
boolean |
isSignificantResult() |
|
void |
setAfpAftIndex(int[][] afpAftIndex) |
|
void |
setAfpBefIndex(int[][] afpBefIndex) |
|
void |
setAfpChainLen(int afpChainLen) |
|
void |
setAfpChainList(int[] afpChainList) |
|
void |
setAfpChainTwiBin(double[] afpChainTwiBin) |
|
void |
setAfpChainTwiList(double[] afpChainTwiList) |
|
void |
setAfpChainTwiNum(int afpChainTwiNum) |
|
void |
setAfpIndex(int[][] afpIndex) |
|
void |
setAfpSet(java.util.List<AFP> afpSet) |
Set the set of AFPs for this alignment.
|
void |
setAlgorithmName(java.lang.String algorithmName) |
Caution has to be made when changing the algorithmName of an AFPChain,
since downstream analysis methods (scores, display, etc) behave
differently if the alignment is flexible (created with FatCat).
|
void |
setAlignScore(double alignScore) |
|
void |
setAlignScoreUpdate(double alignScoreUpdate) |
|
void |
setAlnbeg1(int alnbeg1) |
|
void |
setAlnbeg2(int alnbeg2) |
|
void |
setAlnLength(int alnLength) |
|
void |
setAlnseq1(char[] alnseq1) |
|
void |
setAlnseq2(char[] alnseq2) |
|
void |
setAlnsymb(char[] alnsymb) |
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void |
setBlock2Afp(int[] block2Afp) |
|
void |
setBlockGap(int[] blockGap) |
|
void |
setBlockNum(int blockNum) |
|
void |
setBlockNumClu(int blockNumClu) |
|
void |
setBlockNumIni(int blockNumIni) |
|
void |
setBlockNumSpt(int blockNumSpt) |
|
void |
setBlockResList(int[][][] blockResList) |
|
void |
setBlockResSize(int[] blockResSize) |
|
void |
setBlockRmsd(double[] blockRmsd) |
|
void |
setBlockRotationMatrix(Matrix[] blockRotationMatrix) |
|
void |
setBlockScore(double[] blockScore) |
|
void |
setBlockShiftVector(Atom[] blockShiftVector) |
|
void |
setBlockSize(int[] blockSize) |
|
void |
setCa1Length(int ca1Length) |
|
void |
setCa2Length(int ca2Length) |
|
void |
setCalculationTime(long calculationTime) |
|
void |
setChainLen(int chainLen) |
|
void |
setChainRmsd(double chainRmsd) |
The RMSD of the chain of AFPs.
|
void |
setConn(java.lang.Double conn) |
|
void |
setDescription2(java.lang.String desc) |
Set the textual description for protein 2.
|
void |
setDisTable1(Matrix disTable1) |
|
void |
setDisTable2(Matrix disTable2) |
|
void |
setDistanceMatrix(Matrix distanceMatrix) |
A matrix with ca1length rows and ca2length columns.
|
void |
setDVar(java.lang.Double dvar) |
|
void |
setFocusAfpList(int[] focusAfpList) |
|
void |
setFocusAfpn(int focusAfpn) |
|
void |
setFocusRes1(int[] focusRes1) |
|
void |
setFocusRes2(int[] focusRes2) |
|
void |
setFocusResn(int focusResn) |
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void |
setGapLen(int gapLen) |
|
void |
setId(long id) |
|
void |
setIdentity(double identity) |
|
void |
setIoTime(long ioTime) |
|
void |
setMaxTra(int maxTra) |
Set the maximum number of Twists that are allowed...
|
void |
setMinLen(int minLen) |
|
void |
setMisLen(int misLen) |
|
void |
setName1(java.lang.String name1) |
|
void |
setName2(java.lang.String name2) |
|
void |
setNormAlignScore(double normAlignScore) |
|
void |
setOptAln(int[][][] optAln) |
|
void |
setOptLen(int[] optLen) |
|
void |
setOptLength(int optLength) |
The length of the optimal alignment.
|
void |
setOptRmsd(double[] optRmsd) |
|
void |
setPdbAln(java.lang.String[][][] pdbAln) |
|
void |
setProbability(double probability) |
|
void |
setSequentialAlignment(boolean sequentialAlignment) |
Set whether this alignment has the normal topology, ie the residues
aligned in each block increase sequentially over the original protein.
|
void |
setShortAlign(boolean shortAlign) |
|
void |
setSimilarity(double similarity) |
|
void |
setTMScore(double tmScore) |
|
void |
setTotalLenIni(int totalLenIni) |
|
void |
setTotalLenOpt(int totalLenOpt) |
|
void |
setTotalRmsdIni(double totalRmsdIni) |
this is the init-RMSD, not the final RMSD after refinement.
|
void |
setTotalRmsdOpt(double totalRmsdOpt) |
The RMSD of the final alignment.
|
void |
setTwi(int[] twi) |
|
void |
setVersion(java.lang.String version) |
|
java.lang.String |
toCE(Atom[] ca1,
Atom[] ca2) |
|
java.lang.String |
toDBSearchResult() |
|
java.lang.String |
toFatcat(Atom[] ca1,
Atom[] ca2) |
|
java.lang.String |
toRotMat() |
|
java.lang.String |
toString() |
public static final java.lang.String newline
public static final java.lang.String UNKNOWN_ALGORITHM
public AFPChain(java.lang.String algorithmName)
algorithmName
- @Deprecated public AFPChain()
AFPChain(String)
public AFPChain(AFPChain o)
o
- AFPChain to duplicatepublic java.lang.Object clone()
clone
in class java.lang.Object
public long getId()
public void setId(long id)
public java.lang.String toRotMat()
public java.lang.String toDBSearchResult()
protected void calcSimilarity()
public int getNrEQR()
public int getCoverage1()
public int getCoverage2()
@Deprecated public int getSimilarity1()
@Deprecated public int getSimilarity2()
public java.lang.String toString()
toString
in class java.lang.Object
public boolean isSignificantResult()
public java.lang.String[][][] getPdbAln()
public void setPdbAln(java.lang.String[][][] pdbAln)
public java.lang.Double getConn()
public void setConn(java.lang.Double conn)
public java.lang.Double getDVar()
public void setDVar(java.lang.Double dvar)
public int getMaxTra()
public void setMaxTra(int maxTra)
maxTra
- public double getAlignScore()
public void setAlignScore(double alignScore)
public double getAlignScoreUpdate()
public void setAlignScoreUpdate(double alignScoreUpdate)
public int getAfpChainTwiNum()
public void setAfpChainTwiNum(int afpChainTwiNum)
public int getMinLen()
public void setMinLen(int minLen)
public java.util.List<AFP> getAfpSet()
getOptAln()
.getOptAln()
public void setAfpSet(java.util.List<AFP> afpSet)
getOptAln()
.public int[][] getAfpIndex()
public void setAfpIndex(int[][] afpIndex)
public int[][] getAfpAftIndex()
public void setAfpAftIndex(int[][] afpAftIndex)
public int[][] getAfpBefIndex()
public void setAfpBefIndex(int[][] afpBefIndex)
public Matrix getDisTable1()
public void setDisTable1(Matrix disTable1)
public Matrix getDisTable2()
public void setDisTable2(Matrix disTable2)
public int[] getTwi()
public void setTwi(int[] twi)
public int getAfpChainLen()
public void setAfpChainLen(int afpChainLen)
public int[] getAfpChainList()
public void setAfpChainList(int[] afpChainList)
public double[] getAfpChainTwiBin()
public void setAfpChainTwiBin(double[] afpChainTwiBin)
public double[] getAfpChainTwiList()
public void setAfpChainTwiList(double[] afpChainTwiList)
public double getChainRmsd()
public void setChainRmsd(double chainRmsd)
chainRmsd
- public int getChainLen()
public void setChainLen(int chainLen)
public int getMisLen()
public void setMisLen(int misLen)
public int getGapLen()
public void setGapLen(int gapLen)
public int getBlockNum()
public void setBlockNum(int blockNum)
public int getBlockNumIni()
public void setBlockNumIni(int blockNumIni)
public int getBlockNumClu()
public void setBlockNumClu(int blockNumClu)
public int getBlockNumSpt()
public void setBlockNumSpt(int blockNumSpt)
public double[] getBlockRmsd()
public void setBlockRmsd(double[] blockRmsd)
public int[] getBlock2Afp()
public void setBlock2Afp(int[] block2Afp)
public int[] getBlockSize()
public void setBlockSize(int[] blockSize)
public double[] getBlockScore()
public void setBlockScore(double[] blockScore)
public int[] getBlockGap()
public void setBlockGap(int[] blockGap)
public int[] getBlockResSize()
public void setBlockResSize(int[] blockResSize)
public int[][][] getBlockResList()
public void setBlockResList(int[][][] blockResList)
public int getFocusResn()
public void setFocusResn(int focusResn)
public int[] getFocusRes1()
public void setFocusRes1(int[] focusRes1)
public int[] getFocusRes2()
public void setFocusRes2(int[] focusRes2)
public int getFocusAfpn()
public void setFocusAfpn(int focusAfpn)
public int[] getFocusAfpList()
public void setFocusAfpList(int[] focusAfpList)
public boolean isShortAlign()
public void setShortAlign(boolean shortAlign)
public int[][][] getOptAln()
public void setOptAln(int[][][] optAln)
public int[] getOptLen()
public void setOptLen(int[] optLen)
public double[] getOptRmsd()
public void setOptRmsd(double[] optRmsd)
public int getOptLength()
public void setOptLength(int optLength)
optLength
- public char[] getAlnsymb()
public void setAlnsymb(char[] alnsymb)
public char[] getAlnseq1()
public void setAlnseq1(char[] alnseq1)
public char[] getAlnseq2()
public void setAlnseq2(char[] alnseq2)
public int getAlnLength()
public void setAlnLength(int alnLength)
public int getAlnbeg1()
public void setAlnbeg1(int alnbeg1)
public int getAlnbeg2()
public void setAlnbeg2(int alnbeg2)
public int getTotalLenIni()
public void setTotalLenIni(int totalLenIni)
public int getTotalLenOpt()
public void setTotalLenOpt(int totalLenOpt)
public double getTotalRmsdIni()
public void setTotalRmsdIni(double totalRmsdIni)
totalRmsdIni
- public double getTotalRmsdOpt()
public void setTotalRmsdOpt(double totalRmsdOpt)
totalRmsdOpt
- : total RMSD of the optimal alignmentpublic java.lang.String getName1()
public void setName1(java.lang.String name1)
public java.lang.String getName2()
public void setName2(java.lang.String name2)
public long getCalculationTime()
public void setCalculationTime(long calculationTime)
public int getCa1Length()
public void setCa1Length(int ca1Length)
public int getCa2Length()
public void setCa2Length(int ca2Length)
public long getIoTime()
public void setIoTime(long ioTime)
public double getProbability()
public void setProbability(double probability)
public double getIdentity()
public void setIdentity(double identity)
public double getSimilarity()
public void setSimilarity(double similarity)
public double getNormAlignScore()
public void setNormAlignScore(double normAlignScore)
public Matrix[] getBlockRotationMatrix()
public void setBlockRotationMatrix(Matrix[] blockRotationMatrix)
public Atom[] getBlockShiftVector()
public void setBlockShiftVector(Atom[] blockShiftVector)
public java.lang.String getAlgorithmName()
public void setAlgorithmName(java.lang.String algorithmName)
algorithmName
- public java.lang.String getVersion()
public void setVersion(java.lang.String version)
public boolean isSequentialAlignment()
public void setSequentialAlignment(boolean sequentialAlignment)
public Matrix getDistanceMatrix()
Note:
A JMatrixPanel
, which is used in
the structure-gui package to display distance matrices, will display the
transpose of this matrix. Be sure to take that into account when debugging
visually.
public void setDistanceMatrix(Matrix distanceMatrix)
distanceMatrix
- A matrix with dimensions ca1length x ca2lengthpublic void setTMScore(double tmScore)
public double getTMScore()
public java.lang.String getDescription2()
public void setDescription2(java.lang.String desc)
desc
- public int hashCode()
hashCode
in class java.lang.Object
public boolean equals(java.lang.Object obj)
equals
in class java.lang.Object
Object.equals(java.lang.Object)