aln.h

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#ifndef MLOCALS_STR_H
#define MLOCALS_STR_H
/* alignment base class to be used for global, local derived classes 
 * */

#include "../../../cadbc/cadbc.h"
#include "dynamicaln.h"
#include <iostream.h>
#include <utility>

class aln {
        private:
                struct SEQALN_SEQUENCE *seq1,*seq2; /* 1st & 2nd sequences */
                struct SEQALN_CONSTANTS *scoring; /*Parameters of scoring operation*/
                struct SEQALN_RESULTS *results;  /* Computation results. */
                struct SEQALN_IO *io;

                /* helper function */
                void allocateMem();
                void initParameter();  // initialize default behavior

                /* parameters the caller should set these values */
                char distrib_file1[51]; //="distr1.aa";  for profile comparison
                char distrib_file2[51]; // = "distr2.aa";  // we don't need them
                /* sorted residue frequence from big to small */
                pair<float, char> sortedFreq1[20], sortedFreq2[20];

        public:
                dyaln();
                ~dyaln(); // { free(seq1str); free(seq2str); }
                /* return 0 for success */
                int align(const char s1n[], const char s1str[], const char s2n[], const char s2str[]);
                void setup();

                /* return true if matches region is just simple repeats */
                void outputTab(ostream &os);
                void freeTrace() { freeTraceList(results); }
                /* performs trace back inside */
                void outputAln(FILE* ou=stdout);

                // set alignment parameters
                void setMatrix(char m[]) { load_mat(m, scoring, io); }
                /* alpha -> gap open, beta -> gap extension */
                void setGapCost(int alpha, int beta);
                void setcsub(int cs) { scoring->csub=cs; }
                bool isSimple() const;
                void setNaligns(int n) { scoring->naligns = n; }
};

#endif