//Each Object can only be used once
class RefSeq {
- public:
-
- RefSeq() {
- fullLen = totLen = 0;
- name = ""; seq = "";
- fmasks.clear();
+public:
+ RefSeq() {
+ fullLen = totLen = 0;
+ name = ""; seq = "";
+ fmasks.clear();
+ }
+
+ //Constructor , seq : the forward strand of the reference
+ //tag does not contain ">"
+ //polyALen : length of polyA tail we add
+ RefSeq(const std::string& name, const std::string& seq, int polyALen) {
+ fullLen = seq.length();
+ totLen = fullLen + polyALen;
+ this->name = name;
+ this->seq = seq;
+ this->seq.append(polyALen, 'A');
+
+ assert(fullLen > 0 && totLen >= fullLen);
+
+ int len = (fullLen - 1) / NBITS + 1;
+ fmasks.assign(len, 0);
+ // set mask if poly(A) tail is added
+ if (polyALen > 0) {
+ for (int i = std::max(fullLen - OLEN + 1, 0); i < fullLen; i++) setMask(i);
+ }
}
- //Constructor , seq : the forward strand of the reference
- //tag does not contain ">"
- //polyALen : length of polyA tail we add
- RefSeq(const std::string& name, const std::string& seq, int polyALen) {
- fullLen = seq.length();
- totLen = fullLen + polyALen;
- this->name = name;
- this->seq = seq;
- this->seq.append(polyALen, 'A');
-
- assert(fullLen > 0 && totLen >= fullLen);
-
- int len = (fullLen - 1) / NBITS + 1;
- fmasks.clear(); fmasks.resize(len, 0);
- // ask read to be at least OLEN long!
- for (int i = std::max(fullLen - OLEN + 1, 0); i < fullLen; i++) setMask(i);
- }
+ RefSeq(const RefSeq& o) {
+ fullLen = o.fullLen;
+ totLen = o.totLen;
+ name = o.name;
+ seq = o.seq;
+ fmasks = o.fmasks;
+ }
- RefSeq(const RefSeq& o) {
- fullLen = o.fullLen;
- totLen = o.totLen;
- name = o.name;
- seq = o.seq;
- fmasks = o.fmasks;
- }
+ RefSeq& operator= (const RefSeq &rhs) {
+ if (this != &rhs) {
+ fullLen = rhs.fullLen;
+ totLen = rhs.totLen;
+ name = rhs.name;
+ seq = rhs.seq;
+ fmasks = rhs.fmasks;
+ }
- RefSeq& operator= (const RefSeq &rhs) {
- if (this != &rhs) {
- fullLen = rhs.fullLen;
- totLen = rhs.totLen;
- name = rhs.name;
- seq = rhs.seq;
- fmasks = rhs.fmasks;
- }
+ return *this;
+ }
- return *this;
- }
+ ~RefSeq() {}
- ~RefSeq() {
- }
+ bool read(std::ifstream&, int = 0);
+ void write(std::ofstream&);
- bool read(std::ifstream&, int = 0);
- void write(std::ofstream&);
+ int getFullLen() const { return fullLen; }
- int getFullLen() const { return fullLen; }
+ int getTotLen() const { return totLen; }
- int getTotLen() const { return totLen; }
+ const std::string& getName() const { return name; }
- const std::string& getName() const { return name; }
+ std::string getSeq() const { return seq; }
- std::string getSeq() const { return seq; }
-
- std::string getRSeq() const {
- std::string rseq = "";
- for (int i = totLen - 1; i >= 0; i--) rseq.push_back(getCharacter(get_rbase_id(seq[i])));
- return rseq;
- }
-
- //get the sequence dir 0 : + 1 : -
- std::string getSeq(int dir) const {
- return (dir == 0 ? getSeq() : getRSeq());
- }
+ std::string getRSeq() const {
+ std::string rseq = "";
+ for (int i = totLen - 1; i >= 0; i--) rseq.push_back(getCharacter(get_rbase_id(seq[i])));
+ return rseq;
+ }
+ //get the sequence dir 0 : + 1 : -
+ std::string getSeq(int dir) const {
+ return (dir == 0 ? getSeq() : getRSeq());
+ }
- int get_id(int pos, int dir) const {
- assert(pos >= 0 && pos < totLen);
- return (dir == 0 ? get_base_id(seq[pos]) : get_rbase_id(seq[totLen - pos - 1]));
- }
-
- bool getMask(int seedPos) const {
- assert(seedPos >= 0 && seedPos < totLen);
- return fmasks[seedPos / NBITS] & mask_codes[seedPos % NBITS];
- }
-
- void setMask(int seedPos) {
- assert(seedPos >= 0 && seedPos < totLen);
- fmasks[seedPos / NBITS] |= mask_codes[seedPos % NBITS];
- }
+ int get_id(int pos, int dir) const {
+ assert(pos >= 0 && pos < totLen);
+ return (dir == 0 ? get_base_id(seq[pos]) : get_rbase_id(seq[totLen - pos - 1]));
+ }
+
+ bool getMask(int seedPos) const {
+ assert(seedPos >= 0 && seedPos < totLen);
+ return fmasks[seedPos / NBITS] & mask_codes[seedPos % NBITS];
+ }
+
+ void setMask(int seedPos) {
+ assert(seedPos >= 0 && seedPos < totLen);
+ fmasks[seedPos / NBITS] |= mask_codes[seedPos % NBITS];
+ }
- private:
- int fullLen; // fullLen : the original length of an isoform
- int totLen; // totLen : the total length, included polyA tails, if any
- std::string name; // the tag
- std::string seq; // the raw sequence, in forward strand
- std::vector<unsigned int> fmasks; // record masks for forward strand, each position occupies 1 bit
+private:
+ int fullLen; // fullLen : the original length of an isoform
+ int totLen; // totLen : the total length, included polyA tails, if any
+ std::string name; // the tag
+ std::string seq; // the raw sequence, in forward strand
+ std::vector<unsigned int> fmasks; // record masks for forward strand, each position occupies 1 bit
};
-//internal read; option 0 : read all 1 : do not read seqence and name
+//internal read; option 0 : read all 1 : do not read seqences
bool RefSeq::read(std::ifstream& fin, int option) {
- std::string line;
+ std::string line;
- if (!(fin>>fullLen>>totLen)) return false;
- assert(fullLen > 0 && totLen >= fullLen);
- getline(fin, line);
- if (!getline(fin, name)) return false;
- if (!getline(fin, seq)) return false;
-
- int len = (fullLen - 1) / NBITS + 1; // assume each cell contains NBITS bits
- fmasks.resize(len, 0);
- for (int i = 0; i < len; i++)
- if (!(fin>>fmasks[i])) return false;
- getline(fin, line);
+ if (!(fin>>fullLen>>totLen)) return false;
+ assert(fullLen > 0 && totLen >= fullLen);
+ getline(fin, line);
+ if (!getline(fin, name)) return false;
+ if (!getline(fin, seq)) return false;
+
+ int len = (fullLen - 1) / NBITS + 1; // assume each cell contains NBITS bits
+ fmasks.assign(len, 0);
+ for (int i = 0; i < len; i++)
+ if (!(fin>>fmasks[i])) return false;
+ getline(fin, line);
- assert(option == 0 || option == 1);
- if (option == 1) { name = seq = ""; }
+ assert(option == 0 || option == 1);
+ if (option == 1) { seq = ""; }
- return true;
+ return true;
}
//write to file in "internal" format
void RefSeq::write(std::ofstream& fout) {
- fout<<fullLen<<" "<<totLen<<std::endl;
- fout<<name<<std::endl;
- fout<<seq<<std::endl;
-
- int len = fmasks.size();
- for (int i = 0; i < len - 1; i++) fout<<fmasks[i]<<" ";
- fout<<fmasks[len - 1]<<std::endl;
+ fout<<fullLen<<" "<<totLen<<std::endl;
+ fout<<name<<std::endl;
+ fout<<seq<<std::endl;
+
+ int len = fmasks.size();
+ for (int i = 0; i < len - 1; i++) fout<<fmasks[i]<<" ";
+ fout<<fmasks[len - 1]<<std::endl;
}
#endif
projects / rsem.git / blobdiff