BaseComposition Class Reference

Class that tracks the composition of base by read location. More...

#include <BaseComposition.h>

Public Member Functions
	BaseComposition ()
	Constructor.
bool	updateComposition (unsigned int rawSequenceCharIndex, char baseChar)
	Update the composition for the specified index with the specified character.
BaseAsciiMap::SPACE_TYPE	getSpaceType ()
	Get the space type for this composition.
void	resetBaseMapType ()
	Reset the base map type for this composition.
void	setBaseMapType (BaseAsciiMap::SPACE_TYPE spaceType)
	Set the base map type for this composition.
void	print ()
	Print the composition.
void	clear ()
	Clear the composition stored in the base count vector.

Detailed Description

Class that tracks the composition of base by read location.

Definition at line 27 of file BaseComposition.h.

Constructor & Destructor Documentation

BaseComposition()

BaseComposition::BaseComposition

(

)

Constructor.

Definition at line 23 of file BaseComposition.cpp.

                                :
   myBaseAsciiMap()
{
}

Member Function Documentation

clear()

void BaseComposition::clear

(

)

Clear the composition stored in the base count vector.

Definition at line 89 of file BaseComposition.cpp.

{
   myBaseCountVector.clear();
}

getSpaceType()

BaseAsciiMap::SPACE_TYPE BaseComposition::getSpaceType ( )

inline

Get the space type for this composition.

Definition at line 40 of file BaseComposition.h.

    {
        return(myBaseAsciiMap.getSpaceType());
    }

References BaseAsciiMap::getSpaceType().

Referenced by FastQFile::getSpaceType().

print()

void BaseComposition::print

(

)

Print the composition.

Definition at line 70 of file BaseComposition.cpp.

{
   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;
}

Referenced by FastQFile::validateFastQFile().

resetBaseMapType()

void BaseComposition::resetBaseMapType ( )

inline

Reset the base map type for this composition.

Definition at line 46 of file BaseComposition.h.

    {
        myBaseAsciiMap.resetBaseMapType();
    };

References BaseAsciiMap::resetBaseMapType().

Referenced by FastQFile::openFile().

setBaseMapType()

void BaseComposition::setBaseMapType ( BaseAsciiMap::SPACE_TYPE  spaceType )

inline

Set the base map type for this composition.

Definition at line 52 of file BaseComposition.h.

    {
        myBaseAsciiMap.setBaseMapType(spaceType);
    }

References BaseAsciiMap::setBaseMapType().

Referenced by FastQFile::openFile().

updateComposition()

bool BaseComposition::updateComposition	(	unsigned int	rawSequenceCharIndex,
		char	baseChar
	)

Update the composition for the specified index with the specified character.

Returns

false if the character is not a valid raw sequence character, true if it is valid.

Definition at line 32 of file BaseComposition.cpp.

{
   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);
}

References BaseAsciiMap::getBaseIndex(), and BaseAsciiMap::resetPrimerCount().

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The documentation for this class was generated from the following files:

• fastq/BaseComposition.h
• fastq/BaseComposition.cpp