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BaseComposition.cpp
/*
* Copyright (C) 2010 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include <iomanip>
#include "BaseComposition.h"
// Constructor
// Initialize the base to ascii map based on the specified maptype.
BaseComposition::BaseComposition():
myBaseAsciiMap()
{
}
// Update the composition for the specified index with the specified character.
// Return false if the character is not a valid raw sequence character.
// Return true if it is valid.
bool BaseComposition::updateComposition(unsigned int rawSequenceCharIndex,
char baseChar)
{
bool validIndex = true;
// Each time we return to index 0, reset the primer count in the base/ascii
// map.
if(rawSequenceCharIndex == 0)
{
myBaseAsciiMap.resetPrimerCount();
}
// Check to see if the vector size is already sized to include this
// index. If it is not sized appropriately, add entries until it contains
// the rawSequenceCharIndex.
while(rawSequenceCharIndex >= myBaseCountVector.size())
{
// Add an entry of the base count array object to the vector.
BaseCount baseCountEntry;
myBaseCountVector.push_back(baseCountEntry);
}
// Get the base info for the specified character.
int baseIndex = myBaseAsciiMap.getBaseIndex(baseChar);
// Increment the count for the given character. This method returns false
// if the character's index falls outside the range of the base array.
// This relies on the myBaseAsciiMap indexes and the BaseCOunt object array
// to use the same indexing values for valid bases.
validIndex =
myBaseCountVector[rawSequenceCharIndex].incrementCount(baseIndex);
// Return whether or not the specified character was valid.
return(validIndex);
}
// Print the composition.
void BaseComposition::print()
{
std::cout << std::endl << "Base Composition Statistics:" << std::endl;
std::cout.precision(2);
// This assumes the relationship between indexes that are printed
// by a BaseCount object to be in a specific order based on ATGCN.
std::cout << std::fixed << "Read Index"
<< "\t%A" << "\t%C" << "\t%G" << "\t%T" << "\t%N" << "\tTotal Reads At Index"
<< std::endl;
for(unsigned int i = 0; i < myBaseCountVector.size(); i++)
{
std::cout << std::setw(10) << i << " ";
myBaseCountVector[i].printPercent();
}
std::cout << std::endl;
}
// Clear the vector.
void BaseComposition::clear()
{
myBaseCountVector.clear();
}
BaseComposition::updateComposition
bool updateComposition(unsigned int rawSequenceCharIndex, char baseChar)
Update the composition for the specified index with the specified character.
Definition BaseComposition.cpp:32
BaseComposition::clear
void clear()
Clear the composition stored in the base count vector.
Definition BaseComposition.cpp:89
BaseComposition::BaseComposition
BaseComposition()
Constructor.
Definition BaseComposition.cpp:23
BaseComposition::print
void print()
Print the composition.
Definition BaseComposition.cpp:70
BaseCount
This class is a wrapper around an array that has one index per base and an extra index for a total co...
Definition BaseCount.h:28