Class AFPChain

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.

• 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

• 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 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)