Package org.biojava.nbio.structure.align.model

Class AFPChain

java.lang.Object

org.biojava.nbio.structure.align.model.AFPChain

All Implemented Interfaces:

Serializable, Cloneable

public class AFPChain
extends Object
implements Serializable, Cloneable

A bean to contain the core of a structure alignment. The FatCat aligner class is working on the AFPChain class.

Author:

Andreas Prlic, Aleix Lafita

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static final String	newline
static final String	UNKNOWN_ALGORITHM

Constructor Summary

Constructors

Constructor	Description
AFPChain(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

Method Summary

Modifier and Type	Method	Description
protected void	calcSimilarity()
Object	clone()	Creates and returns a copy of this object.
boolean	equals(Object obj)	A week equality metric.
int[][]	getAfpAftIndex()
int[][]	getAfpBefIndex()
int	getAfpChainLen()
int[]	getAfpChainList()
double[]	getAfpChainTwiBin()
double[]	getAfpChainTwiList()
int	getAfpChainTwiNum()
int[][]	getAfpIndex()
List<AFP>	getAfpSet()	Get the set of AFPs for this alignment.
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()
Double	getConn()
int	getCoverage1()	Get the coverage of protein 1 with the alignment
int	getCoverage2()	Get the coverage of protein 2 with the alignment
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.
Double	getDVar()
int[]	getFocusAfpList()
int	getFocusAfpn()
int[]	getFocusRes1()
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()
String	getName1()
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()	The number of aligned residues in the final alignment.
double[]	getOptRmsd()
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.
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()
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(List<AFP> afpSet)	Set the set of AFPs for this alignment.
void	setAlgorithmName(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)
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(Double conn)
void	setDescription2(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(Double dvar)
void	setFocusAfpList(int[] focusAfpList)
void	setFocusAfpn(int focusAfpn)
void	setFocusRes1(int[] focusRes1)
void	setFocusRes2(int[] focusRes2)
void	setFocusResn(int focusResn)
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(String name1)
void	setName2(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(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(String version)
String	toCE(Atom[] ca1, Atom[] ca2)
String	toDBSearchResult()
String	toFatcat(Atom[] ca1, Atom[] ca2)
String	toRotMat()
String	toString()

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Field Details

newline

public static final String newline

UNKNOWN_ALGORITHM

public static final String UNKNOWN_ALGORITHM

See Also:

• Constant Field Values

Constructor Details

AFPChain

public AFPChain(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).

Parameters:

algorithmName -

AFPChain

public AFPChain(AFPChain o)

Copy constructor

Parameters:

o - AFPChain to duplicate

Method Details

clone

public Object clone()

Creates and returns a copy of this object.

Overrides:

clone in class Object

getId

public long getId()

setId

public void setId(long id)

toCE

public String toCE(Atom[] ca1,
 Atom[] ca2)

toRotMat

public String toRotMat()

toFatcat

public String toFatcat(Atom[] ca1,
 Atom[] ca2)

toDBSearchResult

public String toDBSearchResult()

calcSimilarity

protected void calcSimilarity()

getNrEQR

public int getNrEQR()

Get the number of structurally equivalent residues

Returns:

nr of EQR

getCoverage1

public int getCoverage1()

Get the coverage of protein 1 with the alignment

Returns:

percentage of coverage, between 0 and 100.

getCoverage2

public int getCoverage2()

Get the coverage of protein 2 with the alignment

Returns:

percentage of coverage, between 0 and 100.

toString

public String toString()

Overrides:

toString in class Object

isSignificantResult

public boolean isSignificantResult()

getPdbAln

public String[][][] getPdbAln()

used temporarily during XML serialization to track the PDB positions of the alignmnet

Returns:

String array

setPdbAln

public void setPdbAln(String[][][] pdbAln)

getConn

public Double getConn()

setConn

public void setConn(Double conn)

getDVar

public Double getDVar()

setDVar

public void setDVar(Double dvar)

getMaxTra

public int getMaxTra()

get the maximum nr of Twists that are allowed...

Returns:

maxTra, the max nr of twists

setMaxTra

public void setMaxTra(int maxTra)

Set the maximum number of Twists that are allowed...

Parameters:

maxTra -

getAlignScore

public double getAlignScore()

setAlignScore

public void setAlignScore(double alignScore)

getAlignScoreUpdate

public double getAlignScoreUpdate()

setAlignScoreUpdate

public void setAlignScoreUpdate(double alignScoreUpdate)

getAfpChainTwiNum

public int getAfpChainTwiNum()

setAfpChainTwiNum

public void setAfpChainTwiNum(int afpChainTwiNum)

getMinLen

public int getMinLen()

setMinLen

public void setMinLen(int minLen)

getAfpSet

public List<AFP> getAfpSet()

Get the set of AFPs for this alignment. An AFP is a local ungapped alignment between the two peptides. AFPs are set before the final optimization step. To get the final alignment, look at the aligned pairs from getOptAln().

Returns:

The optimal set of AFPs

See Also:

• getOptAln()

setAfpSet

public void setAfpSet(List<AFP> afpSet)

Set the set of AFPs for this alignment. An AFP is a local ungapped alignment between the two peptides. AFPs are set before the final optimization step. To get the final alignment, look at the aligned pairs from getOptAln().

getAfpIndex

public int[][] getAfpIndex()

setAfpIndex

public void setAfpIndex(int[][] afpIndex)

getAfpAftIndex

public int[][] getAfpAftIndex()

setAfpAftIndex

public void setAfpAftIndex(int[][] afpAftIndex)

getAfpBefIndex

public int[][] getAfpBefIndex()

setAfpBefIndex

public void setAfpBefIndex(int[][] afpBefIndex)

getDisTable1

public Matrix getDisTable1()

setDisTable1

public void setDisTable1(Matrix disTable1)

getDisTable2

public Matrix getDisTable2()

setDisTable2

public void setDisTable2(Matrix disTable2)

getTwi

public int[] getTwi()

setTwi

public void setTwi(int[] twi)

getAfpChainLen

public int getAfpChainLen()

setAfpChainLen

public void setAfpChainLen(int afpChainLen)

getAfpChainList

public int[] getAfpChainList()

setAfpChainList

public void setAfpChainList(int[] afpChainList)

getAfpChainTwiBin

public double[] getAfpChainTwiBin()

setAfpChainTwiBin

public void setAfpChainTwiBin(double[] afpChainTwiBin)

getAfpChainTwiList

public double[] getAfpChainTwiList()

setAfpChainTwiList

public void setAfpChainTwiList(double[] afpChainTwiList)

getChainRmsd

public double getChainRmsd()

setChainRmsd

public void setChainRmsd(double chainRmsd)

The RMSD of the chain of AFPs. Set during AFPCHainer.traceBack();

Parameters:

chainRmsd -

getChainLen

public int getChainLen()

setChainLen

public void setChainLen(int chainLen)

getMisLen

public int getMisLen()

setMisLen

public void setMisLen(int misLen)

getGapLen

public int getGapLen()

setGapLen

public void setGapLen(int gapLen)

getBlockNum

public int getBlockNum()

The number of blocks in the alignment

Returns:

the nr of blocks in alignment

setBlockNum

public void setBlockNum(int blockNum)

getBlockNumIni

public int getBlockNumIni()

setBlockNumIni

public void setBlockNumIni(int blockNumIni)

getBlockNumClu

public int getBlockNumClu()

setBlockNumClu

public void setBlockNumClu(int blockNumClu)

getBlockNumSpt

public int getBlockNumSpt()

setBlockNumSpt

public void setBlockNumSpt(int blockNumSpt)

getBlockRmsd

public double[] getBlockRmsd()

setBlockRmsd

public void setBlockRmsd(double[] blockRmsd)

getBlock2Afp

public int[] getBlock2Afp()

setBlock2Afp

public void setBlock2Afp(int[] block2Afp)

getBlockSize

public int[] getBlockSize()

setBlockSize

public void setBlockSize(int[] blockSize)

getBlockScore

public double[] getBlockScore()

setBlockScore

public void setBlockScore(double[] blockScore)

getBlockGap

public int[] getBlockGap()

setBlockGap

public void setBlockGap(int[] blockGap)

getBlockResSize

public int[] getBlockResSize()

setBlockResSize

public void setBlockResSize(int[] blockResSize)

getBlockResList

public int[][][] getBlockResList()

tracks the residues of the initial blocks (before optimization)

Returns:

list of block residues

setBlockResList

public void setBlockResList(int[][][] blockResList)

getFocusResn

public int getFocusResn()

setFocusResn

public void setFocusResn(int focusResn)

getFocusRes1

public int[] getFocusRes1()

setFocusRes1

public void setFocusRes1(int[] focusRes1)

getFocusRes2

public int[] getFocusRes2()

setFocusRes2

public void setFocusRes2(int[] focusRes2)

getFocusAfpn

public int getFocusAfpn()

setFocusAfpn

public void setFocusAfpn(int focusAfpn)

getFocusAfpList

public int[] getFocusAfpList()

setFocusAfpList

public void setFocusAfpList(int[] focusAfpList)

isShortAlign

public boolean isShortAlign()

setShortAlign

public void setShortAlign(boolean shortAlign)

getOptAln

public int[][][] getOptAln()

Tracks the Atom positions in the optimal alignment. Note: only considers the equivalent positions, gaps are ignored... first dimension is the block nr second dimension is 0 or 1 (the alignment chain index) third is the position

Returns:

int array

setOptAln

public void setOptAln(int[][][] optAln)

getOptLen

public int[] getOptLen()

The length of each block

Returns:

lengths

setOptLen

public void setOptLen(int[] optLen)

getOptRmsd

public double[] getOptRmsd()

setOptRmsd

public void setOptRmsd(double[] optRmsd)

getOptLength

public int getOptLength()

The number of aligned residues in the final alignment.

Returns:

setOptLength

public void setOptLength(int optLength)

The length of the optimal alignment. Set by AFPOptimizer.optimizeAln(). This should be the sum of the elements in optLen

Parameters:

optLength -

getAlnsymb

public char[] getAlnsymb()

setAlnsymb

public void setAlnsymb(char[] alnsymb)

getAlnseq1

public char[] getAlnseq1()

setAlnseq1

public void setAlnseq1(char[] alnseq1)

getAlnseq2

public char[] getAlnseq2()

setAlnseq2

public void setAlnseq2(char[] alnseq2)

getAlnLength

public int getAlnLength()

Returns:

The total length of the alignment, including gaps

See Also:

• getOptLength()

setAlnLength

public void setAlnLength(int alnLength)

getAlnbeg1

public int getAlnbeg1()

Returns:

The index of the first aligned residue in protein 1

setAlnbeg1

public void setAlnbeg1(int alnbeg1)

getAlnbeg2

public int getAlnbeg2()

Returns:

The index of the first aligned residue in protein 2

setAlnbeg2

public void setAlnbeg2(int alnbeg2)

getTotalLenIni

public int getTotalLenIni()

setTotalLenIni

public void setTotalLenIni(int totalLenIni)

getTotalLenOpt

public int getTotalLenOpt()

setTotalLenOpt

public void setTotalLenOpt(int totalLenOpt)

getTotalRmsdIni

public double getTotalRmsdIni()

this is the init-RMSD, not the final RMSD after refinement.

Returns:

totalRmsdIni

setTotalRmsdIni

public void setTotalRmsdIni(double totalRmsdIni)

this is the init-RMSD, not the final RMSD after refinement.

Parameters:

totalRmsdIni -

getTotalRmsdOpt

public double getTotalRmsdOpt()

The RMSD of the final alignment. Use this to print overal alignment RMSD.

Returns:

total RMSD of the optimal alignment.

setTotalRmsdOpt

public void setTotalRmsdOpt(double totalRmsdOpt)

The RMSD of the final alignment. Use this to print overal alignment RMSD.

Parameters:

totalRmsdOpt - : total RMSD of the optimal alignment

getName1

public String getName1()

setName1

public void setName1(String name1)

getName2

public String getName2()

setName2

public void setName2(String name2)

getCalculationTime

public long getCalculationTime()

setCalculationTime

public void setCalculationTime(long calculationTime)

getCa1Length

public int getCa1Length()

setCa1Length

public void setCa1Length(int ca1Length)

getCa2Length

public int getCa2Length()

setCa2Length

public void setCa2Length(int ca2Length)

getIoTime

public long getIoTime()

setIoTime

public void setIoTime(long ioTime)

getProbability

public double getProbability()

The probability (FATCAT) or Z-score (CE) of the alignment.

Returns:

either the probability (FATCAT) or the Z-score (CE) of the alignment.

setProbability

public void setProbability(double probability)

getIdentity

public double getIdentity()

The percent of residues that are sequence-identical in the alignment.

Returns:

a value between 0 and 1

setIdentity

public void setIdentity(double identity)

getSimilarity

public double getSimilarity()

Returns the similarity score for the alignment. This gives the percent of sequence similar residues in the alignment.

Returns:

a double between 0 and 1

setSimilarity

public void setSimilarity(double similarity)

getNormAlignScore

public double getNormAlignScore()

setNormAlignScore

public void setNormAlignScore(double normAlignScore)

getBlockRotationMatrix

public Matrix[] getBlockRotationMatrix()

setBlockRotationMatrix

public void setBlockRotationMatrix(Matrix[] blockRotationMatrix)

getBlockShiftVector

public Atom[] getBlockShiftVector()

setBlockShiftVector

public void setBlockShiftVector(Atom[] blockShiftVector)

getAlgorithmName

public String getAlgorithmName()

setAlgorithmName

public void setAlgorithmName(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).

Parameters:

algorithmName -

getVersion

public String getVersion()

setVersion

public void setVersion(String version)

isSequentialAlignment

public boolean isSequentialAlignment()

Get whether this alignment has the normal topology, ie the residues aligned in each block increase sequentially over the original protein. This will be false if a circular permutation was detected.

Returns:

true if the alignment is sequential

setSequentialAlignment

public 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. This will be false if a circular permutation was detected.

getDistanceMatrix

public Matrix getDistanceMatrix()

A matrix with ca1length rows and ca2length columns. For CE this is the distance matrix, but the exact interpretation is left up to the alignment algorithm.

Note: The org.biojava.nbio.structure.gui.JMatrixPanel, 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.

Returns:

A matrix with dimensions ca1length x ca2length, or null

setDistanceMatrix

public void setDistanceMatrix(Matrix distanceMatrix)

A matrix with ca1length rows and ca2length columns. For CE this is the distance matrix, but the exact interpretation is left up to the alignment algorithm.

Parameters:

distanceMatrix - A matrix with dimensions ca1length x ca2length

setTMScore

public void setTMScore(double tmScore)

getTMScore

public double getTMScore()

Returns the tmScore of the alignment. If the score has not been calcualted yet, returns -1. To calculate it call AFPChainScorer.getTMScore(afpChain, ca1, ca2);

Returns:

-1, if not calculated, or the TM-score, a score between 0 and 1

getDescription2

public String getDescription2()

Get a textual description for the protein 2 of the alignment.

Returns:

setDescription2

public void setDescription2(String desc)

Set the textual description for protein 2.

Parameters:

desc -

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

A week equality metric. Checks if the optAlign is the same, and if the objects being compared seem to be the same (same names, lengths). Does not check properties of the alignment such as scores or superposition matrices.

Overrides:

equals in class Object

See Also:

• Object.equals(java.lang.Object)