source: tags/initial/ARBDB_COMPRESS/AC_sequence.cxx

#include <stdio.h>
#include <stdlib.h>
#include <memory.h>
#include <malloc.h>
#include <string.h>
#include <ctype.h>

#include <arbdb.h>
#include <arbdbt.h>

#include "ac.hxx"




//********************************************************************
//
//              class AC_SEQUENCE : Konstruktor/Destruktor
//
//********************************************************************
AC_SEQUENCE::AC_SEQUENCE(GBDATA *gb_data_i) {   // gb_data is nur Link
//r     sequence                = seq;
        gb_data                 = gb_data_i;
        quality                 = 0;
        seq_len                 = GB_read_string_count(gb_data);
}

AC_SEQUENCE::~AC_SEQUENCE(){

}
//*********************************************************************


//*********************************************************************
//      class AC_SEQUENCE::get_quality(GBDATA *gb_data)
//
//              bestimmt die Anzahl der Buchstaben einer Sequenz.
//*********************************************************************
long  AC_SEQUENCE::get_quality() {

        char *runner;
        long counter = 0;
        char *temp_sequence  = GB_read_char_pntr(gb_data);
        for(runner = temp_sequence; *runner; runner++) {
                if(isalpha(*runner)) counter++;
        }

        return counter;
} // end AC_SEQUENCE::get_quality(GBDATA *gb_data)
//*********************************************************************


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//*********************************************************************
//
//              class AC_SEQUENCE_ALIGNED : Konstruktor/Destruktor
//
//*********************************************************************
AC_SEQUENCE_ALIGNED::AC_SEQUENCE_ALIGNED(GBDATA *gb_data_i) : AC_SEQUENCE (gb_data_i) {
        ac_dbdata_state = ALIGNED_SEQUENCES;
}



AC_SEQUENCE_ALIGNED::~AC_SEQUENCE_ALIGNED()  {

}
//*********************************************************************



//*********************************************************************
//      class AC_SEQUENCE_ALIGNED::get_distance()
//
//              liefert die Distanz zwischen der aktuellen Sequenz und 
//              der Referenzsequenz.
//              Es muessen zwei vergleichbare Zeichen (= Buchstaben)
//              aufeinandertreffen. Sind die Zeichen unterschiedlich,
//              erhoeht sich die Distanz um + 1 .
//
//*********************************************************************
double AC_SEQUENCE_ALIGNED::get_distance(AC_SEQUENCE *that)  {
        
        register long   distance, equals;
        register char   *revptr, *seqptr;

        revptr = that->sequence;                // Reverenzsequenz

        seqptr  = GB_read_char_pntr(gb_data);

//      seqptr = this->sequence;                // aktuelle Sequenz
        distance = 0;
        equals = 0;
        register char   reg1, reg2;
        for( ; (reg1 = *revptr) && (reg2 = *seqptr); revptr++, seqptr++ ) {
                if( (!isalpha(reg1)) || !isalpha(reg2))  continue;
                if (reg1==reg2) {
                        equals++;
                }else{
                        distance++;
                } // endif
        } // endfor
        
        return distance/(distance + equals + 1.0);

} // end AC_SEQUENCE_ALIGNED::get_distance()
//*********************************************************************


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//*********************************************************************
//
//              class AC_SEQUENCE_UNALIGNED : Konstruktor/Destruktor
//
//*********************************************************************
AC_SEQUENCE_UNALIGNED::AC_SEQUENCE_UNALIGNED(GBDATA *gb_data_i) : AC_SEQUENCE (gb_data_i) {
        ac_dbdata_state = UNALIGNED_SEQUENCES;
}



AC_SEQUENCE_UNALIGNED::~AC_SEQUENCE_UNALIGNED()  {

}
//*********************************************************************



//*********************************************************************
//      class AC_SEQUENCE_ALIGNED::get_distance()
//
//              Dummyfunktion zum Compilerberuhigen
//
//
//*********************************************************************
double AC_SEQUENCE_UNALIGNED::get_distance(AC_SEQUENCE *that)  {

        return 0;
} // end AC_SEQUENCE_UNALIGNED::get_distance()
//*********************************************************************