binaries/src/GLProbs-1.0/MSA.h

   1 #ifndef _MSA_H
   2 #define _MSA_H
   3 #include "MSADef.h"
   4 #include "MSAGuideTree.h"
   5
   6 #include "SafeVector.h"
   7 #include "MultiSequence.h"
   8 #include "ScoreType.h"
   9 #include "ProbabilisticModel.h"
  10 #include "SparseMatrix.h"
  11 #include <string>
  12 using namespace std;
  13
  14 class MSAGuideTree;
  15 struct TreeNode;
  16 class MSA {
  17 public:
  18         MSA(int argc, char* argv[]);
  19         ~MSA();
  20
  21         static void getSysTime(double * dtime);
  22         MSAGuideTree* getGuideTree() {
  23                 return tree;
  24         }
  25         int * getSeqsWeights() {
  26                 return seqsWeights;
  27         }
  28 private:
  29         //print usage
  30         void printUsage();
  31         //do multiple sequence alignment
  32         void doAlign();
  33
  34         //for sequence weights
  35         void createSeqsWeights(int seqsNum);
  36         void releaseSeqsWeights();
  37
  38         //weights of sequences
  39         int * seqsWeights;
  40         //guide tree
  41         MSAGuideTree* tree;
  42         //output file
  43         string alignOutFileName;
  44         std::ostream* alignOutFile;
  45 private:
  46         SafeVector<string> ParseParams(int argc, char *argv[]);
  47         void PrintParameters(const char *message, const VF &initDistrib,
  48                         const VF &gapOpen, const VF &gapExtend, const VVF &emitPairs,
  49                         const VF &emitSingle, const char *filename);
  50
  51         SafeVector<string> PostProbsParseParams(int argc, char **argv);
  52         MultiSequence *doAlign(MultiSequence *sequence,
  53                         const ProbabilisticModel &model, int levelid);
  54         void ReadParameters();
  55         MultiSequence* ProcessTree(TreeNode *tree, MultiSequence *sequences,
  56                         const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
  57                         const ProbabilisticModel &model);
  58         MultiSequence *ComputeFinalAlignment(MSAGuideTree *tree,
  59                         MultiSequence *sequences,
  60                         const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
  61                         const ProbabilisticModel &model,int levelid);
  62         MultiSequence *AlignAlignments(MultiSequence *align1, MultiSequence *align2,
  63                         const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
  64                         const ProbabilisticModel &model);
  65         SafeVector<SafeVector<SparseMatrix *> > DoRelaxation(float* seqsWeights,
  66                         MultiSequence *sequences,
  67                         SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices);
  68         void Relax(float weight, SparseMatrix *matXZ, SparseMatrix *matZY,
  69                         VF &posterior);
  70         void Relax1(float weight, SparseMatrix *matXZ, SparseMatrix *matZY,
  71                         VF &posterior);
  72         int DoIterativeRefinement(
  73                         const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
  74                         const ProbabilisticModel &model, MultiSequence* &alignment);
  75         void DoIterativeRefinementTreeNode(
  76                         const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
  77                         const ProbabilisticModel &model, MultiSequence* &alignment,
  78                         int nodeIndex);
  79         void WriteAnnotation(MultiSequence *alignment,
  80                         const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices);
  81         int ComputeScore(const SafeVector<pair<int, int> > &active,
  82                         const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices);
  83         int AdjustmentTest(MultiSequence *sequences,const ProbabilisticModel &model);
  84 #ifdef _OPENMP
  85         //private struct
  86         struct SeqsPair {
  87                 int seq1;
  88                 int seq2;
  89         };
  90         int numPairs;
  91         SeqsPair* seqsPairs;
  92 #endif
  93 };
  94
  95 #endif