Class AFPChain

    • 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

        public AFPChain​(AFPChain o)
        Copy constructor
        Parameters:
        o - AFPChain to duplicate
    • Method Detail

      • getId

        public long getId()
      • setId

        public void setId​(long id)
      • 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.
      • getPdbAln

        public String[][][] getPdbAln()
        used temporarily during XML serialization to track the PDB positions of the alignmnet
        Returns:
        String array
      • 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 -
      • setAlignScore

        public void setAlignScore​(double alignScore)
      • setMinLen

        public void setMinLen​(int minLen)
      • getAfpSet

        public List<AFPgetAfpSet()
        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().
      • setAfpIndex

        public void setAfpIndex​(int[][] afpIndex)
      • setAfpAftIndex

        public void setAfpAftIndex​(int[][] afpAftIndex)
      • setAfpBefIndex

        public void setAfpBefIndex​(int[][] afpBefIndex)
      • getTwi

        public int[] getTwi()
      • setTwi

        public void setTwi​(int[] twi)
      • setChainRmsd

        public void setChainRmsd​(double chainRmsd)
        The RMSD of the chain of AFPs. Set during AFPCHainer.traceBack();
        Parameters:
        chainRmsd -
      • setChainLen

        public void setChainLen​(int chainLen)
      • setMisLen

        public void setMisLen​(int misLen)
      • 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)
      • setBlockRmsd

        public void setBlockRmsd​(double[] blockRmsd)
      • setBlock2Afp

        public void setBlock2Afp​(int[] block2Afp)
      • setBlockSize

        public void setBlockSize​(int[] blockSize)
      • setBlockScore

        public void setBlockScore​(double[] blockScore)
      • setBlockGap

        public void setBlockGap​(int[] blockGap)
      • getBlockResList

        public int[][][] getBlockResList()
        tracks the residues of the initial blocks (before optimization)
        Returns:
        list of block residues
      • setBlockResList

        public void setBlockResList​(int[][][] blockResList)
      • setFocusResn

        public void setFocusResn​(int focusResn)
      • setFocusRes1

        public void setFocusRes1​(int[] focusRes1)
      • setFocusRes2

        public void setFocusRes2​(int[] focusRes2)
      • setFocusAfpn

        public void setFocusAfpn​(int focusAfpn)
      • 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)
      • setOptRmsd

        public void setOptRmsd​(double[] optRmsd)
      • 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 -
      • setAlnsymb

        public void setAlnsymb​(char[] alnsymb)
      • setAlnseq1

        public void setAlnseq1​(char[] alnseq1)
      • 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)
      • 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
      • setCa1Length

        public void setCa1Length​(int ca1Length)
      • setCa2Length

        public void setCa2Length​(int ca2Length)
      • 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.
      • 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)
      • 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 -
      • 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 -
      • 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)