BaseComposition Class Reference

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

#include <BaseComposition.h>

Collaboration diagram for BaseComposition:

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List of all members.

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.

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Detailed Description

Class that tracks the composition of base by read location.

Definition at line 27 of file BaseComposition.h.

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Member Function Documentation

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.

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

{
   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);
}

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

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