5 #include "textfile.h"
\r
8 SCORE AlignTwoMSAs(const MSA &msa1, const MSA &msa2, MSA &msaOut, PWPath &Path,
\r
9 bool bLockLeft, bool bLockRight)
\r
11 const unsigned uLengthA = msa1.GetColCount();
\r
12 const unsigned uLengthB = msa2.GetColCount();
\r
14 ProfPos *PA = ProfileFromMSA(msa1);
\r
15 ProfPos *PB = ProfileFromMSA(msa2);
\r
19 PA[0].m_scoreGapOpen = MINUS_INFINITY;
\r
20 PB[0].m_scoreGapOpen = MINUS_INFINITY;
\r
25 PA[uLengthA-1].m_scoreGapClose = MINUS_INFINITY;
\r
26 PB[uLengthB-1].m_scoreGapClose = MINUS_INFINITY;
\r
29 float r = (float) uLengthA/ (float) (uLengthB + 1); // +1 to prevent div 0
\r
33 SCORE Score = GlobalAlign(PA, uLengthA, PB, uLengthB, Path);
\r
35 AlignTwoMSAsGivenPath(Path, msa1, msa2, msaOut);
\r