public class CrochemoreLandauZivUkelsonGlobalAlignment
extends CrochemoreLandauZivUkelson
This class implements the global pairwise sequence alignment algorithm (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal Ziv-Ukelson (2002).
This implementation derives from the paper of M.Crochemore, G.Landau and M.Ziv-Ukelson, A Sub-quadratic Sequence Alignment Algorithm for Unrestricted Scoring Matrices (available here as PDF or Postscript).
For a general description of the algorithm, please refer to the specification of the abstract class CrochemoreLandauZivUkelson superclass.
This class consist mainly of methods that:
net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonGlobalAlignment$createBlock(net.maizegenetics.analysis.gbs.neobio.Factor,net.maizegenetics.analysis.gbs.neobio.Factor,kotlin.Int,kotlin.Int)net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonGlobalAlignment$computeOutputBorder(net.maizegenetics.analysis.gbs.neobio.AlignmentBlock,kotlin.Int,kotlin.Int,kotlin.Int,kotlin.Int,kotlin.Int)net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonGlobalAlignment$locateScore()net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonGlobalAlignment$buildOptimalAlignment()class CrochemoreLandauZivUkelson,
net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonGlobalAlignment$createBlock(net.maizegenetics.analysis.gbs.neobio.Factor,net.maizegenetics.analysis.gbs.neobio.Factor,kotlin.Int,kotlin.Int),
net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonGlobalAlignment$computeOutputBorder(net.maizegenetics.analysis.gbs.neobio.AlignmentBlock,kotlin.Int,kotlin.Int,kotlin.Int,kotlin.Int,kotlin.Int),
net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonGlobalAlignment$locateScore(),
net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonGlobalAlignment$buildOptimalAlignment(),
class CrochemoreLandauZivUkelson,
class CrochemoreLandauZivUkelsonLocalAlignmentprotected AlignmentBlock createBlock(Factor factor1, Factor factor2, int row, int col)
Creates and computes all information of an alignment block. Its main job is to compute the DIST column for the block. It then request the computeOutputBorder method to compute the block's output border.
factor1 - factor of the first sequencefactor2 - factor of the second sequencerow - row index of the block in the block tablecol - column index of the block in the block tableIncompatibleScoringSchemeException - if the scoring scheme is not compatible with the sequences being alignedprotected AlignmentBlock createRootBlock(Factor factor1, Factor factor2)
Creates the root block. This is a special case of the createBlock method. No information is actually computed.
factor1 - factor of the first sequencefactor2 - factor of the second sequenceIncompatibleScoringSchemeException - If the scoring scheme is not compatible with the loaded sequences.protected AlignmentBlock createFirstRowBlock(Factor factor1, Factor factor2, int col)
Creates and computes all information of an alignment block of the first row of the block table. This is a special case of the createBlock method.
factor1 - factor of the first sequencefactor2 - factor of the second sequencecol - column index of the block in the block tableIncompatibleScoringSchemeException - if the scoring scheme is not compatible with the sequences being aligned#createBlockprotected AlignmentBlock createFirstColumnBlock(Factor factor1, Factor factor2, int row)
Creates and computes all information of an alignment block of the first column of the block table. This is a special case of the createBlock method.
factor1 - factor of the first sequencefactor2 - factor of the second sequencerow - row index of the block in the block tableIncompatibleScoringSchemeException - if the scoring scheme is not compatible with the sequences being aligned#createBlockprotected void computeOutputBorder(AlignmentBlock block, int row, int col, int dim, int lc, int lr)
Computes the output border of a block. This is performed in five steps:
class OutMatrix matrix from the input border and DIST matrix; class Smawk to compute all column maxima of the OUT matrix (SMAWK finds the index of the row that contains the maximum value of a column); block - the block for which the output border is to be computedrow - row index of the block in the block tablecol - column index of the block in the block tabledim - dimension of the output borderlc - number of columns of the blocklr - number of row of the blockclass OutMatrix,
class Smawkprotected PairwiseAlignment buildOptimalAlignment()
Builds an optimal global alignment between the loaded sequences after the block table has been computed. This method traces a path back in the block table, from the last block to the first.
IncompatibleScoringSchemeException - If the scoring scheme is not compatible with the loaded sequences.CrochemoreLandauZivUkelson#traverseBlockprotected int locateScore()
Locate the score of the highest scoring global alignment in the block table. This value is found in the output border of the last block (last row, last column).
IncompatibleScoringSchemeException - If the scoring scheme is not compatible with the loaded sequences.