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:

  • Field Details

  • 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:

    • 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:

    • 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: