binaries/src/clustalw/src/multipleAlign/MSA.h

   1 /**
   2  * Author: Mark Larkin
   3  *
   4  * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
   5  */
   6 #ifndef MSA_H
   7 #define MSA_H
   8
   9 #include <iomanip>
  10 #include "ProfileBase.h"
  11 #include "../alignment/Alignment.h"
  12 //#include "../calcAlignSteps/Tree.h"
  13 #include "../tree/AlignmentSteps.h"
  14 #include "ProfileAlignAlgorithm.h"
  15
  16 namespace clustalw
  17 {
  18 //using tree::AlignmentSteps;
  19
  20 class MSA
  21 {
  22     public:
  23         /* Functions */
  24         int multiSeqAlign(Alignment* alnPtr, DistMatrix* distMat,
  25             vector<int>* seqWeight, AlignmentSteps* progSteps, int iStart);
  26         int seqsAlignToProfile(Alignment* alnPtr, DistMatrix* distMat, vector<int>* seqWeight, int iStart,
  27                               string phylipName);
  28         int calcPairwiseForProfileAlign(Alignment* alnPtr, DistMatrix* distMat);
  29         int doProfileAlign(Alignment* alnPtr, DistMatrix* distMat, vector<int>* prof1Weight,
  30                            vector<int>* prof2Weight);
  31
  32         /* Attributes */
  33
  34     private:
  35         /* Functions */
  36
  37         /* Attributes */
  38 };
  39
  40 }
  41 #endif