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#ifndef KMERTABLE_H
#define KMERTABLE_H
//class KmerSequence;
//KmerSequence * GetGlobalSeq();
const string defaultKmerDBName = "kmers.db";
inline void TempFile(string & out, const string & in)
{
char tmp[1024];
strcpy(tmp, in.c_str());
for (int i=0; i>=0; i--) {
if (tmp[i] == '/') {
tmp[i+1] = 0;
break;
}
}
out = tmp;
out += defaultKmerDBName;
}
class KmerEntry
{
public:
KmerEntry() {
m_index = -1;
m_pos = -1;
}
KmerEntry(int i, int pos) {
m_index = i;
m_pos = pos;
}
void SetIndex(int index, int pos) {
m_index = index;
m_pos = pos;
}
int Index() const {return m_index;}
int Pos() const {return m_pos;}
bool operator < (const KmerEntry & k) const;
private:
int m_index;
int m_pos;
};
class IDS
{
public:
IDS() {
m_id = -1;
m_start = -1;
m_edge = -1;
m_ori = 1;
}
IDS(int id, int start, int edge) {
m_id = id;
m_start = start;
m_edge = edge;
m_ori = 1;
}
int ID() const {return m_id;}
int Start() const {return m_start;}
int Edge() const {return m_edge;}
int Ori() const {return m_ori;}
void SetStart(int s) {m_start = s;}
const string & Name() const {return m_name;}
void SetEdge(int i) {m_edge = i;}
void SetName(const string & n) {
m_name = n;
}
bool operator < (const IDS & d) const {
#ifndef NO_REVERSE_OUT
if (m_ori < d.m_ori)
return true;
if (m_ori > d.m_ori)
return false;
#endif
if (m_id < d.m_id)
return true;
if (m_id == d.m_id) {
if (m_start < d.m_start)
return true;
}
return false;
}
// bool operator < (const IDS & d) const {
// /*if (m_id < d.m_id)
// return true;
// if (m_id == d.m_id) {
// if (m_start < d.m_start)/
// return true;
// }
// return false;*/
// return m_name < d.m_name;
// }
void SetOri(int n) {
m_ori = n;
}
private:
int m_id;
int m_start;
int m_edge;
int m_ori;
string m_name;
};
inline double FracAlign(const DNAVector & d, int startSeq, const DNAVector & read, int startRead)
{
int i;
int fit = 0;
int k = startRead;
for (i=startSeq; i<d.isize(); i++) {
if (k >= read.isize())
break;
if (d[i] == read[k])
fit++;
}
return (double)fit/(double)read.isize();
}
class KmerSequence
{
public:
KmerSequence(int k, const vecDNAVector * p);
//void SetK(long long k) {m_k = k;}
//long long K() const {return m_k;}
void Read(const string & fileName);
void Write(const string & fileName);
long long GetBoundValue() const {return m_count;}
void Add(const vecDNAVector & all);
void AddRestrict(const vecDNAVector & all, const vecDNAVector & restrict);
void Count(svec<int> & counts) {
long long i, j;
for (i=0; i<m_kmers.lsize(); i++) {
int c = 0;
for (j=i; j<m_kmers.lsize(); j++) {
if (m_kmers[j] < m_kmers[i])
break;
if (m_kmers[i] < m_kmers[j])
break;
c++;
}
counts[i] = c;
i = j-1;
}
}
long long BasesToNumber(const DNAVector & d, int off);
long long BasesToNumberCount(int & count, const DNAVector & d, int off);
long long BasesToNumberCountPlus(svec<IDS> & ids, long long & count, const DNAVector & d, int edge);
int GetK() const;
private:
svec<KmerEntry> m_kmers;
long long m_count;
};
//===================================================================
//========================================================================
//========================================================================
#endif
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