AFPChain (biojava-structure 5.0.0-alpha2 API)

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 and Description

static String newline

static String UNKNOWN_ALGORITHM

Fields
Modifier and Type	Field and Description
`static String`	`newline`
`static String`	`UNKNOWN_ALGORITHM`

Constructor Summary

Constructors
Constructor and Description
`AFPChain()` Deprecated.
`AFPChain(AFPChain o)` Copy constructor
`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).

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and 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()`
`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.
`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()`
`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 Detail
  - newline
```
public static final String newline
```
  - UNKNOWN_ALGORITHM
```
public static final String UNKNOWN_ALGORITHM
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - 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
```
@Deprecated
public AFPChain()
```
    Deprecated.
    
    Use the constructor with the algorithmName (design condition).
    
    See Also:
    
    AFPChain(String)
  - AFPChain
```
public AFPChain(AFPChain o)
```
    Copy constructor
    
    Parameters:
    
    o - AFPChain to duplicate
- Method Detail
  - 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.
  - getSimilarity1
```
@Deprecated
public int getSimilarity1()
```
    Deprecated. use getCoverage1() instead
    
    get the coverage of protein 1 with the alignment
    
    Returns:
    
    percentage of coverage, between 0 and 100.
  - getSimilarity2
```
@Deprecated
public int getSimilarity2()
```
    Deprecated. use getCoverage2() instead
    
    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()
```
  - 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(), the number of aligned residues in the final alignment.
  - 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: A org.biojava.nbio.structure.gui.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.
    
    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)

Class AFPChain

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

newline

UNKNOWN_ALGORITHM

Constructor Detail

AFPChain

AFPChain

AFPChain

Method Detail

clone

getId

setId

toCE

toRotMat

toFatcat

toDBSearchResult

calcSimilarity

getNrEQR

getCoverage1

getCoverage2

getSimilarity1

getSimilarity2

toString

isSignificantResult

getPdbAln

setPdbAln

getConn

setConn

getDVar

setDVar

getMaxTra

setMaxTra

getAlignScore

setAlignScore

getAlignScoreUpdate

setAlignScoreUpdate

getAfpChainTwiNum

setAfpChainTwiNum

getMinLen

setMinLen

getAfpSet

setAfpSet

getAfpIndex

setAfpIndex

getAfpAftIndex

setAfpAftIndex

getAfpBefIndex

setAfpBefIndex

getDisTable1

setDisTable1

getDisTable2

setDisTable2

getTwi

setTwi

getAfpChainLen

setAfpChainLen

getAfpChainList

setAfpChainList

getAfpChainTwiBin

setAfpChainTwiBin

getAfpChainTwiList

setAfpChainTwiList

getChainRmsd

setChainRmsd

getChainLen

setChainLen

getMisLen

setMisLen

getGapLen

setGapLen

getBlockNum

setBlockNum

getBlockNumIni

setBlockNumIni

getBlockNumClu

setBlockNumClu