ppALIGN API documentation

DynCellMoments< TYPE, N > Struct Template Reference

#include <firstmoment.hpp>

List of all members.

Public Attributes

TYPE M [N]
TYPE I [N]
TYPE D [N]

Detailed Description

template<typename TYPE, int N = 1>
struct DynCellMoments< TYPE, N >

A cell of the dynamic programming workspace for higher moments computation. 

  int gap_open = 11;
  int gap_extension = 1;
  AlignmentType atype = LocalBounded;
  bool allow_ID = true;
  bool allow_DI = false;
  PartitionWorkspace ws(100000);
  HmmWeight weights(proteinAlphabet,
		    proteinAlphabet,
		    "blosum62",
		    gap_open,
		    gap_extension,
		    atype,
		    allow_DI,
		    allow_ID);
  ProteinScoring score_matrix("blosum62");
  ProteinSequence seq1,seq2;
  DriverFirstMoment first_moment(score_matrix,
				 gap_open,
				 gap_extension);
  ws.AddDriver(first_moment);

  seq1 = "TSILIVKLKVILPEVLCVKMRRNDDSRIIMKGLVGGVRLA";
  seq2 = "LRQVSRSDTTVSYKQISQDWCSIIPTTIGRNNQESASACR";
  ws.PartitionFunction(seq1,seq2,weights);
  cout << "ExpectedScore: " << first_moment.FirstMoment() << endl;
Template Parameters:
TYPE numerical type
N the highest moment to be computed

Definition at line 65 of file firstmoment.hpp.

Member Data Documentation

template<typename TYPE , int N = 1>
TYPE DynCellMoments< TYPE, N >::D[N]

vaues for delete state

Definition at line 74 of file firstmoment.hpp.

template<typename TYPE , int N = 1>
TYPE DynCellMoments< TYPE, N >::I[N]

values for insert state

Definition at line 71 of file firstmoment.hpp.

template<typename TYPE , int N = 1>
TYPE DynCellMoments< TYPE, N >::M[N]

values for match state

Definition at line 68 of file firstmoment.hpp.

The documentation for this struct was generated from the following file: