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CDnaString2.h
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CDnaString2.h
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#ifndef DNASTRING_H
#define DNASTRING_H
#include "primefactors.h"
#include "faststring2.h"
#include <cctype>
#include "basic-DNA-RNA-AA-routines.h"
// Todo:
// - Check for correct nucl. in push_back, set routine
inline bool isReducibleUnit_global(const char *beg, const char* end)
{
unsigned len = end-beg;
const char *test_pos;
int factor_index;
unsigned factor;
unsigned factor_len;
unsigned i;
bool composite;
factor_index = 0;
while( (factor = primeFactors[len][factor_index]) != 0 )
{
composite = true;
factor_len = len/factor;
test_pos = beg;
for (i=1; i<factor; ++i, test_pos += factor_len)
if ( strncmp(test_pos, (test_pos + factor_len), factor_len) != 0)
composite = false;
if (composite)
return true;
++factor_index;
}
return false;
}
class CDnaString : public faststring
{
public:
/* using faststring::c_str; */
/* using faststring::reserve; */
/* using faststring::size; */
/* using faststring::capacity; */
/* using faststring::clear; */
/* using faststring::check_pos; */
/* using faststring::set_unckecked; */
/* using faststring::assign; */
/* using faststring::push_back; */
/* using faststring::set_unchecked; */
/* using faststring::begin; */
/* using faststring::end; */
/* using faststring::tolower; */
/* using faststring::toupper; */
CDnaString():faststring()
{}
CDnaString(const char *s):faststring(s)
{}
CDnaString(const faststring &s):faststring(s)
{}
void toupper_assign(const char *str)
{
faststring::assign(str);
toupper();
}
void toupper_assign(const char *str_begin, const char *str_end)
{
faststring::assign(str_begin, str_end);
toupper();
}
void toupper_push_back(char c)
{
faststring::push_back(std::toupper(c));
}
void toupper_set_unckecked(unsigned pos, char c)
{
faststring::set_unckecked(pos, std::toupper(c));
}
bool toupper_set(unsigned pos, char c)
{
return faststring::set(pos, std::toupper(c));
}
unsigned countUnknownBases()
{
char *b = begin();
char *e = end();
char c;
unsigned errors = 0;
while (b != e)
{
c = *b;
if (c != 'A' && c != 'C' && c != 'G' && c != 'T' &&
c != 'R' && c != 'Y' &&
c != 'M' && c != 'K' &&
c != 'B' && c != 'V' &&
c != 'D' && c != 'H' &&
c != 'N' )
++errors;
++b;
}
return errors;
}
unsigned setToComplementOf(const CDnaString &a)
{
unsigned len = a.size();
const char *pos = a.begin();
const char *pos_end = a.end();
unsigned error = 0;
reserve(len);
clear();
while( pos != pos_end )
{
switch (*pos)
{
case 'A': faststring::push_back('T'); break;
case 'T': faststring::push_back('A'); break;
case 'G': faststring::push_back('C'); break;
case 'C': faststring::push_back('G'); break;
case 'R': faststring::push_back('Y'); break;
case 'Y': faststring::push_back('R'); break;
case 'M': faststring::push_back('K'); break;
case 'K': faststring::push_back('M'); break;
case 'B': faststring::push_back('V'); break;
case 'V': faststring::push_back('B'); break;
case 'D': faststring::push_back('H'); break;
case 'H': faststring::push_back('D'); break;
case 'N': faststring::push_back('N'); break;
default:
++error;
push_back('?');
break;
};
++pos;
}
return error;
}
unsigned setToReverseComplementOf(const CDnaString &a)
{
unsigned len = a.size();
const char *pos = a.rbegin();
const char *pos_end = a.rend();
unsigned error = 0;
reserve(len);
clear();
while( pos != pos_end )
{
switch (*pos)
{
case 'A': faststring::push_back('T'); break;
case 'T': faststring::push_back('A'); break;
case 'G': faststring::push_back('C'); break;
case 'C': faststring::push_back('G'); break;
case 'R': faststring::push_back('Y'); break;
case 'Y': faststring::push_back('R'); break;
case 'M': faststring::push_back('K'); break;
case 'K': faststring::push_back('M'); break;
case 'B': faststring::push_back('V'); break;
case 'V': faststring::push_back('B'); break;
case 'D': faststring::push_back('H'); break;
case 'H': faststring::push_back('D'); break;
case 'N': faststring::push_back('N'); break;
default:
++error;
push_back('?');
break;
};
--pos;
}
return error;
}
void setToReverseOf(const CDnaString &a)
{
unsigned len = a.size();
const char *pos = a.rbegin();
const char *pos_end = a.rend();
reserve(len);
clear();
while( pos != pos_end )
{
faststring::push_back(*pos);
--pos;
}
}
// Returns true if a subpattern has been found,
// false if no subpattern has been found.
void correct_unit_with_subpattern(unsigned &ulen)
{
unsigned len = size();
char *tmp = new char [2*len+1];
const char *orig = c_str();
char *pos = tmp;
char *pos_end = pos + len;
int strncmp_result;
strcpy(tmp, orig);
strcpy(tmp+len, orig);
// std::cerr << "Correcting unit: " << *this << std::endl;
++pos;
for (; pos != pos_end; ++pos)
{
strncmp_result = strncmp(tmp, pos, len);
if ( strncmp_result == 0 ) // Subpattern has been found
{
ulen = pos-tmp;
shorten(ulen);
// std::cerr << "New unit: " << ulen << " " << *this << std::endl;
break;
}
}
delete [] tmp;
}
// Returns true if a subpattern has been found,
// false if no subpattern has been found.
bool setToMinAlphaRepModCyclicPermOf(const CDnaString &s)
{
unsigned len = s.size();
char *tmp = new char [2*len+1];
const char *orig = const_cast<CDnaString&>(s).c_str();
char *pos = tmp;
char *pos_end = pos + len;
//unsigned i;
char *min_str;
int strncmp_result;
bool found_subpattern = false;
strcpy(tmp, orig);
strcpy(tmp+len, orig);
min_str = tmp;
++pos;
for (; pos != pos_end; ++pos)
{
strncmp_result = strncmp(pos, min_str, len);
if ( strncmp_result < 0 )
min_str = pos;
else if ( strncmp_result == 0 )
{
// New pattern is from
found_subpattern = true;
}
}
*(min_str+len) = '\0'; /* At this position within tmp we have the end of the unit */
faststring::assign(min_str);
delete [] tmp;
return found_subpattern;
}
// Returns true if a subpattern has been found,
// false if no subpattern has been found.
bool setToMinAlphaRepModRevCompAndCyclicPermOf(const CDnaString &s)
{
CDnaString tmp;
bool found_subpattern;
tmp.setToReverseComplementOf(s);
found_subpattern = setToMinAlphaRepModCyclicPermOf(tmp); // *this contains minimum representation of rev comp of s
tmp.setToMinAlphaRepModCyclicPermOf(s); // tmp contains minimum representation of s itself
if ( strcmp(c_str(), tmp.c_str() ) > 0 )
{
assign( tmp.c_str() );
}
return found_subpattern;
}
// Returns true if a subpattern has been found,
// false if no subpattern has been found.
bool setToMinAlphaRepModRevCompAndCyclicPermOf(const CDnaString &s, signed char &direction)
{
CDnaString tmp;
bool found_subpattern;
tmp.setToReverseComplementOf(s);
found_subpattern = setToMinAlphaRepModCyclicPermOf(tmp); // *this contains minimum representation of rev comp of s
tmp.setToMinAlphaRepModCyclicPermOf(s); // tmp contains minimum representation of s itself
direction = 1;
if ( strcmp(c_str(), tmp.c_str() ) > 0 )
{
assign( tmp.c_str() );
direction = -1;
}
return found_subpattern;
}
bool isCompositeUnitLength(int x)
{
return primeFactors[x][0];
}
// Old and inefficient:
/* bool isReducibleUnit_old() */
/* { */
/* unsigned len = size(); */
/* char *tmp = new char [2*len+1]; */
/* const char *orig = c_str(); */
/* int factor_index; */
/* unsigned shift; */
/* strcpy(tmp, orig); */
/* strcpy(tmp+len, orig); */
/* factor_index = 0; */
/* while( (shift = primeFactors[len][factor_index]) != 0 ) */
/* { */
/* if ( strncmp(tmp, tmp+shift, len) == 0) */
/* return true; */
/* ++factor_index; */
/* } */
/* return false; */
/* } */
// New and works but is redundent - equivalent to current version
/* bool isReducibleUnit_ok() */
/* { */
/* unsigned len = size(); */
/* const char *orig = c_str(); */
/* int factor_index; */
/* unsigned factor; */
/* unsigned factor_len; */
/* unsigned i; */
/* bool composite; */
/* factor_index = 0; */
/* while( (factor = primeFactors[len][factor_index]) != 0 ) */
/* { */
/* composite = true; */
/* factor_len = len/factor; */
/* orig = c_str(); */
/* for (i=1; i<factor; ++i, orig += factor_len) */
/* if ( strncmp(orig, orig+factor_len, factor_len) != 0) */
/* composite = false; */
/* if (composite) */
/* return true; */
/* ++factor_index; */
/* } */
/* return false; */
/* } */
bool isReducibleUnit()
{
return isReducibleUnit_global(c_str(), c_str()+size());
}
friend bool operator<(const CDnaString &a, const CDnaString &b)
{
// Possibly more efficient would be a strncmp. If equally long, take the shorter one.
// Not tested yet - thats why its not used!
// unsigned minlen = (a.length() < b.length() ? a.length() : b.length());
// short test = strncmp(a.begin(), b.begin(), minlen);
// if (test == 0)
// return a.length() < b.length();
// else
// return (test < 0);
// Hi compiler - how do you like this: Haahaahaahaaaaaaaa
return (strcmp(const_cast<CDnaString&>(a).c_str(), const_cast<CDnaString&>(b).c_str() ) < 0);
}
};
#endif