Add GLprobs and MSAprobs to binaries

[jabaws.git] / binaries / src / GLProbs-1.0 / MSA.h

diff --git a/binaries/src/GLProbs-1.0/MSA.h b/binaries/src/GLProbs-1.0/MSA.h
new file mode 100644 (file)
index 0000000..2e37e85
--- /dev/null
+++ b/binaries/src/GLProbs-1.0/MSA.h
@@ -0,0 +1,95 @@
+#ifndef _MSA_H
+#define _MSA_H
+#include "MSADef.h"
+#include "MSAGuideTree.h"
+
+#include "SafeVector.h"
+#include "MultiSequence.h"
+#include "ScoreType.h"
+#include "ProbabilisticModel.h"
+#include "SparseMatrix.h"
+#include <string>
+using namespace std;
+
+class MSAGuideTree;
+struct TreeNode;
+class MSA {
+public:
+       MSA(int argc, char* argv[]);
+       ~MSA();
+
+       static void getSysTime(double * dtime);
+       MSAGuideTree* getGuideTree() {
+               return tree;
+       }
+       int * getSeqsWeights() {
+               return seqsWeights;
+       }
+private:
+       //print usage
+       void printUsage();
+       //do multiple sequence alignment
+       void doAlign();
+
+       //for sequence weights
+       void createSeqsWeights(int seqsNum);
+       void releaseSeqsWeights();
+
+       //weights of sequences
+       int * seqsWeights;
+       //guide tree
+       MSAGuideTree* tree;
+       //output file
+       string alignOutFileName;
+       std::ostream* alignOutFile;
+private:
+       SafeVector<string> ParseParams(int argc, char *argv[]);
+       void PrintParameters(const char *message, const VF &initDistrib,
+                       const VF &gapOpen, const VF &gapExtend, const VVF &emitPairs,
+                       const VF &emitSingle, const char *filename);
+
+       SafeVector<string> PostProbsParseParams(int argc, char **argv);
+       MultiSequence *doAlign(MultiSequence *sequence,
+                       const ProbabilisticModel &model, int levelid);
+       void ReadParameters();
+       MultiSequence* ProcessTree(TreeNode *tree, MultiSequence *sequences,
+                       const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+                       const ProbabilisticModel &model);
+       MultiSequence *ComputeFinalAlignment(MSAGuideTree *tree,
+                       MultiSequence *sequences,
+                       const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+                       const ProbabilisticModel &model,int levelid);
+       MultiSequence *AlignAlignments(MultiSequence *align1, MultiSequence *align2,
+                       const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+                       const ProbabilisticModel &model);
+       SafeVector<SafeVector<SparseMatrix *> > DoRelaxation(float* seqsWeights,
+                       MultiSequence *sequences,
+                       SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices);
+       void Relax(float weight, SparseMatrix *matXZ, SparseMatrix *matZY,
+                       VF &posterior);
+       void Relax1(float weight, SparseMatrix *matXZ, SparseMatrix *matZY,
+                       VF &posterior);
+       int DoIterativeRefinement(
+                       const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+                       const ProbabilisticModel &model, MultiSequence* &alignment);
+       void DoIterativeRefinementTreeNode(
+                       const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+                       const ProbabilisticModel &model, MultiSequence* &alignment,
+                       int nodeIndex);
+       void WriteAnnotation(MultiSequence *alignment,
+                       const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices);
+       int ComputeScore(const SafeVector<pair<int, int> > &active,
+                       const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices);
+        int AdjustmentTest(MultiSequence *sequences,const ProbabilisticModel &model);
+#ifdef _OPENMP
+       //private struct
+       struct SeqsPair {
+               int seq1;
+               int seq2;
+       };
+       int numPairs;
+       SeqsPair* seqsPairs;
+#endif
+};
+
+#endif