4 * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
7 * NOTE: This profile is not used in the multiple alignment part. It is used for the
8 * the clustal Qt part. It is used in the calculation of low scoring segments.
10 #ifndef LOWSCORESEGPROFILE_H
11 #define LOWSCORESEGPROFILE_H
13 #include "../alignment/Alignment.h"
18 class LowScoreSegProfile
22 LowScoreSegProfile(int prfLen, int firstS, int lastS);
23 void calcLowScoreSegProfile(const SeqArray* seqArray,
24 int matrix[NUMRES][NUMRES], vector<int>* seqWeight);
25 const SeqArray* getProfilePtr(){return &profile;};
34 int firstSeq, lastSeq;