[Biojava-dev] [Bug 2301] New: Initialization error of org.biojava.bio.alignment.NeedlemanWunsch when considering affine gap penalty

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2301

           Summary: Initialization error of
                    org.biojava.bio.alignment.NeedlemanWunsch when
                    considering affine gap penalty
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: alignment
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: cwu2 at eecs.wsu.edu
                CC: cwu2 at eecs.wsu.edu


In the class org.biojava.bio.alignment.NeedlemanWunsch, the initilization of
the first row and first column should be the following code when considering
affine gap. Otherwise, the first CostMatrix[1][0] will not get the right value!
Thanks!
        for (i=1; i<=query.length();i++) {
//          CostMatrix[i][0]  = CostMatrix[i-1][0] + delete;
          E[i][0] = Double.POSITIVE_INFINITY;
          CostMatrix[i][0] = F[i][0] = delete + i*gapExt;
        }
        for (j=1; j<=subject.length(); j++) {
//          CostMatrix[0][j]  = CostMatrix[0][j-1] + insert;
          F[0][j] = Double.POSITIVE_INFINITY;
          CostMatrix[0][j] = E[0][j] = insert + j*gapExt;
        }


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