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java.lang.Object
  |
  +--neobio.alignment.PairwiseAlignmentAlgorithm
        |
        +--neobio.alignment.CrochemoreLandauZivUkelson
              |
              +--neobio.alignment.CrochemoreLandauZivUkelsonGlobalAlignment
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 CrochemoreLandauZivUkelson superclass.
This class consist mainly of methods that:
createBlock
 and its variants);
 computeOutputBorder;
 locateScore;
 buildOptimalAlignment.
 
CrochemoreLandauZivUkelson, 
CrochemoreLandauZivUkelsonLocalAlignment| Field Summary | 
| Fields inherited from class neobio.alignment.CrochemoreLandauZivUkelson | 
| block_table, DIAGONAL_DIRECTION, LEFT_DIRECTION, num_cols, num_rows, out_matrix, seq1, seq2, smawk, STOP_DIRECTION, TOP_DIRECTION | 
| Fields inherited from class neobio.alignment.PairwiseAlignmentAlgorithm | 
| alignment, APPROXIMATE_MATCH_TAG, GAP_CHARACTER, GAP_TAG, MATCH_TAG, MISMATCH_TAG, score, score_computed, scoring, sequences_loaded, use_match_tag | 
| Constructor Summary | |
| CrochemoreLandauZivUkelsonGlobalAlignment() | |
| Method Summary | |
| protected  PairwiseAlignment | buildOptimalAlignment()Builds an optimal global alignment between the loaded sequences after the block table has been computed. | 
| protected  void | computeOutputBorder(AlignmentBlock block,
                                       int row,
                                       int col,
                                       int dim,
                                       int lc,
                                       int lr)Computes the output border of a block. | 
| protected  AlignmentBlock | createBlock(Factor factor1,
                       Factor factor2,
                       int row,
                       int col)Creates and computes all information of an alignment block. | 
| protected  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. | 
| 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. | 
| protected  AlignmentBlock | createRootBlock(Factor factor1,
                               Factor factor2)Creates the root block. | 
| protected  int | locateScore()Locate the score of the highest scoring global alignment in the block table. | 
| Methods inherited from class neobio.alignment.CrochemoreLandauZivUkelson | 
| assembleDistMatrix, assembleInputBorder, computeBlockTable, computePairwiseAlignment, computeScore, getDiagonalPrefix, getLeftPrefix, getTopPrefix, loadSequencesInternal, traverseBlock, unloadSequencesInternal | 
| Methods inherited from class neobio.alignment.PairwiseAlignmentAlgorithm | 
| getPairwiseAlignment, getScore, loadSequences, max, max, max, scoreDeletion, scoreInsertion, scoreSubstitution, setScoringScheme, unloadSequences, useMatchTag | 
| Methods inherited from class java.lang.Object | 
| clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait | 
| Constructor Detail | 
public CrochemoreLandauZivUkelsonGlobalAlignment()
| Method Detail | 
protected AlignmentBlock createBlock(Factor factor1,
                                     Factor factor2,
                                     int row,
                                     int col)
                              throws IncompatibleScoringSchemeException
computeOutputBorder method to compute the block's output border.
createBlock in class CrochemoreLandauZivUkelsonfactor1 - 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 table
IncompatibleScoringSchemeException - if the scoring scheme is not compatible
 with the sequences being aligned
protected AlignmentBlock createRootBlock(Factor factor1,
                                         Factor factor2)
createBlock
 method. No information is actually computed.
createRootBlock in class CrochemoreLandauZivUkelsonfactor1 - factor of the first sequencefactor2 - factor of the second sequence
protected AlignmentBlock createFirstRowBlock(Factor factor1,
                                             Factor factor2,
                                             int col)
                                      throws IncompatibleScoringSchemeException
createBlock method.
createFirstRowBlock in class CrochemoreLandauZivUkelsonfactor1 - factor of the first sequencefactor2 - factor of the second sequencecol - column index of the block in the block table
IncompatibleScoringSchemeException - if the scoring scheme is not compatible
 with the sequences being alignedcreateBlock
protected AlignmentBlock createFirstColumnBlock(Factor factor1,
                                                Factor factor2,
                                                int row)
                                         throws IncompatibleScoringSchemeException
createBlock method.
createFirstColumnBlock in class CrochemoreLandauZivUkelsonfactor1 - factor of the first sequencefactor2 - factor of the second sequencerow - row index of the block in the block table
IncompatibleScoringSchemeException - if the scoring scheme is not compatible
 with the sequences being alignedcreateBlock
protected void computeOutputBorder(AlignmentBlock block,
                                   int row,
                                   int col,
                                   int dim,
                                   int lc,
                                   int lr)
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 block
protected PairwiseAlignment buildOptimalAlignment()
                                           throws IncompatibleScoringSchemeException
buildOptimalAlignment in class CrochemoreLandauZivUkelsonIncompatibleScoringSchemeException - If the scoring scheme is not compatible
 with the loaded sequences.CrochemoreLandauZivUkelson.traverseBlock(neobio.alignment.AlignmentBlock, int, java.lang.StringBuffer, java.lang.StringBuffer, java.lang.StringBuffer)protected int locateScore()
locateScore in class CrochemoreLandauZivUkelson| 
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