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FastaFile.cpp
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FastaFile.cpp
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/*
* FastaFile.cpp
*
* This is the cpp file for the FastaFile object. The FastaFile object
* is a utility object designed to read in a Fasta File and keep the
* information for the file in memory.
*
* ************* WARNING ***********************************
* * There is no error handling in place for this object! *
* * This means that if the file does not exist or is *
* * formatted incorrectly, you will get an error and *
* * will not be able to use this object. *
* * *
* * If this code gets moved to a production setting *
* * appropriate error handling should be implemented! *
* *********************************************************
*
* Typical use for the file would be to use the FastaFile(pathName, fileName)
* constructor to create the object. This will automatically open the
* Fasta File specified by the pathName and fileName, and read its contents
* storing them in the firstLine, and dnaSequence attributes.
*
* populateSuffixes(vector<Suffix*>) is a convenience method that will
* populate the passed in vector with the forward and reverse complement
* suffixes for the dnaSequence read in from the Fasta file.
*
* Created on: 1-10-13
* Author: tomkolar
*/
#include "FastaFile.h"
#include "Suffix.h"
#include <sstream>
#include <iostream>
#include <fstream>
#include <vector>
using namespace std;
// Constuctors
// ==============================================
FastaFile::FastaFile() {
}
FastaFile::FastaFile(string path, string name) {
filePath = path;
fileName = name;
populate();
}
// Destructor
// ==============================================
FastaFile::~FastaFile() {
}
// Public Methods
// =============================================
// populateSuffixes(vector<Suffix*>& suffixes)
// Purpose:
// Populate the suffixes vector with the suffixes from the dnaSequence and
// its reverse complment.
// Preconditions:
// Fasta File has been read and dnaSequence has been populated
// Postconditions:
// suffixes vector contains Suffix objects for each suffix of the dnaSequence
// and its reverse complement
void FastaFile::populateSuffixes(vector<Suffix*>& suffixes) {
// Create forward suffixes
int sequenceLength = dnaSequence.length();
for (int i = 0; i < sequenceLength; i++) {
suffixes.push_back(new Suffix(&dnaSequence[i], fileName, i+1, true));
}
// Create reverse suffixes
for (int i = 0; i < sequenceLength; i++) {
suffixes.push_back(new Suffix(&reverseComplement[i], fileName, sequenceLength -i + 1, false));
}
}
// string firstLineResultString()
// Purpose:
// Returns the string value of an XML element representing the first line of
// the Fasta file.
//
// format:
// <result type='first line' file='<<fileName>>' >
// <<firstLine>>
// </result>
// Preconditions:
// Fasta File has been read and firstLine has been populated
string FastaFile::firstLineResultString() {
stringstream ss;
ss << " <result type='first line' file='" << fileName << "'>\n";
ss << " " << firstLine << "\n";
ss << " </result>\n";
return ss.str();
}
// string baseCountsResultString()
// Purpose:
// Returns the string value of an XML element representing the base counts
// of the dnaSequence.
//
// format:
// <result type='nucleotide histogram' file='<<fileName>>' >
// A=<<baseCountForA>>,C=<<baseCountForC>>,G=<<baseCountForG>>,
// A=<<baseCountForT>>,N=<<countForOtherChars>>
// </result>
// Preconditions:
// Fasta File has been read and dnaSequence has been populated
string FastaFile::baseCountsResultString() {
stringstream ss;
// Header
ss << " <result type='nucleotide histogram' file='" << fileName << "'>\n";
// Base Counts
int baseCounts[5] = {0};
countBases(baseCounts);
ss << " ";
ss << "A=" << baseCounts[0];
ss << ",C=" << baseCounts[1];
ss << ",G=" << baseCounts[2];
ss << ",T=" << baseCounts[3];
if (baseCounts[4] > 0)
ss << ",N=" << baseCounts[4];
ss << "\n";
// Footer
ss << " </result>\n";
return ss.str();
}
// Public Accessors
// =============================================
const int FastaFile::getSequenceLength() {
return dnaSequence.length();
}
string& FastaFile::getFileName() {
return fileName;
}
string& FastaFile::getDnaSequence() {
return dnaSequence;
}
// Private Methods
// =============================================
// populate()
// Purpose:
// Reads in the Fasta File specified by filePath and fileName and populates
// the object with its contents
// Preconditions:
// fileName and filePath have been set
// Postconditions:
// firstLine - populated with first line from file
// dnaSequence - populated with dnaSequence from file
// reverseComplement - populated with reverse complement of dnaSequence
void FastaFile::populate() {
ifstream inputFile(filePath + fileName);
stringstream ss;
string line;
getline(inputFile, firstLine);
while(getline(inputFile, line)) {
ss << line;
}
dnaSequence = ss.str();
inputFile.close();
createReverseComplement();
}
// createReverseComplment()
// Purpose:
// populates the reverseComplement attribute with the reverse comlpement
// of the dnaSequence
// Preconditions:
// dnaSequence has been set
// Postconditions:
// reverseComplement - populated with reverse complement of dnaSequence
void FastaFile::createReverseComplement() {
stringstream ss;
// Append the complements in order
for (string::size_type i = 0; i < dnaSequence.length(); i++) {
ss << complement(dnaSequence[i]);
}
// Reverse the string and set it to the reverseComplement attribute
string complement = ss.str();
reverseComplement = string(complement.rbegin(), complement.rend());
}
// char complement(char aChar)
// Purpose: returns the dna complement of aChar
char FastaFile::complement(char aChar) {
if (aChar == 'A')
return 'T';
if (aChar == 'T')
return 'A';
if (aChar == 'G')
return 'C';
if (aChar == 'C')
return 'G';
return aChar;
}
// countBases(int counts[])
// Purpose:
// populates the counts array with the counts for base occurrences
// in dnaSequence. The array is populated with the folllowing
// scheme:
// counts[0] = counts for A
// counts[1] = counts for C
// counts[2] = counts for G
// counts[3] = counts for T
// counts[4] = counts for other characters encountered
void FastaFile::countBases(int counts[]) {
for (string::size_type i=0; i < dnaSequence.length(); i++) {
char currentChar = dnaSequence[i];
if (currentChar == 'A')
counts[0]++;
else if (currentChar == 'C')
counts[1]++;
else if (currentChar == 'G')
counts[2]++;
else if (currentChar == 'T')
counts[3]++;
else
counts[4]++;
}
}