htswanalysis/src/ValidationDesign/peak.cpp

   1 /*
   2  *  peak.cpp
   3  *  PeakLocator
   4  *
   5  *  Created by Alan You on 8/11/08.
   6  *  Copyright 2008 Hudson Alpha. All rights reserved.
   7  *
   8  */
   9
  10 #include <vector>
  11 #include <string>
  12
  13 #include "peak.h"
  14 #include "util.h"
  15
  16 using namespace std;
  17
  18 Peak::Peak()
  19 {
  20         this->startBP = 0;
  21         this->endBP = 0;
  22         this->length = 0;
  23         this->chrom = "";
  24         this->score = 0;
  25         this->sequence = "";
  26 }
  27
  28 Peak::Peak(string line)
  29 {
  30         istringstream outStream;
  31
  32         vector<string> fields;
  33         string delim("\t");
  34         split(line,delim,fields);
  35
  36         this->chrom = fields[0];
  37         this->startBP = atoi(fields[1].c_str());
  38         this->endBP = atoi(fields[2].c_str());
  39         this->score = strtod(fields[3].c_str(), NULL);
  40         this->length = this->endBP - this->startBP;
  41         this->sequence = "";
  42 }
  43
  44 Peak::Peak(const Peak& p)
  45 {
  46         this->startBP = p.startBP;
  47         this->endBP = p.endBP;
  48         this->length = p.length;
  49         this->chrom = p.chrom;
  50         this->score = p.score;
  51         this->sequence = p.sequence;
  52 }
  53
  54 Peak::~Peak()
  55 {
  56 ;
  57 }
  58
  59 void Peak::print()
  60 {
  61         cout << "Chromosome:\t\t" << this->chrom.c_str() << endl;
  62         cout << "Starting Base Pair:\t" << this->startBP << endl;
  63         cout << "Ending Base Pair:\t" << this->endBP << endl;
  64         cout << "Sequence Length:\t" << this->length << endl;
  65         cout << "Sequence Score:\t\t" << this->score << endl;
  66         cout << "Sequence:\t\t" << this->sequence << endl;
  67 }
  68
  69 void Peak::printToFile(ofstream &outputFile)
  70 {
  71         outputFile << "Chromosome:\t\t" << this->chrom.c_str() << endl;
  72         outputFile << "Starting Base Pair:\t" << this->startBP << endl;
  73         outputFile << "Ending Base Pair:\t" << this->endBP << endl;
  74         outputFile << "Sequence Length:\t" << this->length << endl;
  75         outputFile << "Sequence Score:\t\t" << this->score << endl;
  76         outputFile << "Sequence:\t\t" << this->sequence << endl;
  77         outputFile << endl;
  78 }
  79
  80 bool Peak::operator<(const Peak& that) const
  81 {
  82         if (this->chrom == that.chrom) { return(this->startBP < that.startBP);
  83         } else { return(this->chrom < that.chrom); }
  84 }
  85
  86 bool Peak::operator>(const Peak& that) const
  87 {
  88         if (this->chrom == that.chrom) { return(this->startBP > that.startBP);
  89         } else { return(this->chrom > that.chrom); }
  90
  91 }
  92
  93 Peak& Peak:: operator=(const Peak& that)
  94 {
  95         if (this != &that)
  96         {
  97                 this->chrom = that.chrom;
  98                 this->startBP = that.startBP;
  99                 this->endBP = that.endBP;
 100                 this->length = that.length;
 101                 this->score = that.score;
 102                 this->sequence = that.sequence;
 103         }
 104
 105         return *this;
 106 }