CoreDump

Full name SMRUCC.genomics.Analysis.SequenceAlignment.BestLocalAlignment.CoreDump Assembly SMRUCC.genomics.Analysis.SequenceAlignment Members 3

01 Syntax

SMRUCC.genomics.Analysis.SequenceAlignment.BestLocalAlignment.CoreDump

02 Methods

Name	Overloads	Summary
printDPMatrix	1	print the dynmaic programming matrix
printAlignments	2	Output the local alignments ending in the (i, j) cell.

03 Members

method printDPMatrix #

printDPMatrix``1(GSW(Of ``0), StreamWriter)

print the dynmaic programming matrix

method printAlignments overload 2 #

printAlignments``1(GSW(Of ``0), TextWriter)

Output the local alignments with the maximum score.

Remarks

Note: empty alignments are not printed.

method printAlignments #

printAlignments``1(GSW(Of ``0), Int32, Int32, String, String, TextWriter)

Output the local alignments ending in the (i, j) cell. aligned1 and aligned2 are suffixes of final aligned strings found in backtracking before calling this function. Note: the strings are replicated at each recursive call. Use buffers or stacks to improve efficiency.