4 * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
6 #ifndef FASTPAIRWISEALIGN_H
7 #define FASTPAIRWISEALIGN_H
9 #include "PairwiseAlignBase.h"
14 class FastPairwiseAlign : public PairwiseAlignBase
19 virtual ~FastPairwiseAlign(){};
21 virtual void pairwiseAlign(Alignment *alignPtr, DistMatrix *distMat, int iStart,
22 int iEnd, int jStart, int jEnd);
27 void pairAlign(const vector<int>* seq, int l1, int l2);
28 void makePPtrs(vector<int>& tptr, vector<int>& pl, const vector<int>* seq,
30 void makeNPtrs(vector<int>& tptr, vector<int>& pl, const vector<int>* seq,
32 void putFrag(int fs, int v1, int v2, int flen);
33 int fragRelPos(int a1, int b1, int a2, int b2);
34 void desQuickSort(vector<int>& array1, vector<int>& array2, int arraySize);
49 vector<int> diagIndex;