X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=RefSeq.h;h=88b149e0068e8aa342e14aedf126dac79deac136;hp=1b2e58e26b90efa40717a0567df06f263e1e88ea;hb=2d71eb92104693ca9baa5a2e1c23eeca776d8fd3;hpb=a95154919f950f86de9104b2b9dcf1f0c7e83387

diff --git a/RefSeq.h b/RefSeq.h
index 1b2e58e..88b149e 100644
--- a/RefSeq.h
+++ b/RefSeq.h
@@ -10,132 +10,131 @@
 
 //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