CLU::CLUESTData Class Reference
Container for CLU's hash maps for ESTs. More...
#include <CLU.h>
Public Member Functions | |
| CLUESTData () | |
| The default constructor. | |
| virtual | ~CLUESTData () |
| The destructor. | |
Public Attributes | |
| int * | referenceHashMap |
| Hash table to accelerate the comparison of all words in a sequence. | |
| int * | complementHashMap |
| Hash table to accelerate the comparison of all words in a complement (reverse) sequence. | |
Detailed Description
Container for CLU's hash maps for ESTs.
This class is used to encapsulate the reference and complement hash maps needed by CLU to compare ESTs. This class extends ESTCustomData so that the hash maps can be directly associated with the EST they refer to. New instances of this object are created in the initialize method. The place holder objects are automatically deleted once analysis is complete.
Definition at line 342 of file CLU.h.
Constructor & Destructor Documentation
| CLU::CLUESTData::CLUESTData | ( | ) | [inline] |
| CLU::CLUESTData::~CLUESTData | ( | ) | [virtual] |
The destructor.
The destructor deletes the reference and complement hash map in this class if they are not NULL.
Definition at line 383 of file CLU.cpp.
References complementHashMap, and referenceHashMap.
Member Data Documentation
Hash table to accelerate the comparison of all words in a complement (reverse) sequence.
Quotation from CLU paper: To accelerate the comparison all words found in sequence Sq are presented in a table (H). The table H is a linear array, where the offset itself is a hash value of certain oligonucleotide. Each element of this array contains a number, associated with a corresponding oligonucleotide.
This vector has a size 4^wordSize (for example, if wordSize is 6, this table has 4096 entries). These entries are populated in the setReferenceEST() method using the reverse of a given EST sequence.
Definition at line 391 of file CLU.h.
Referenced by CLU::getMetric(), and ~CLUESTData().
Hash table to accelerate the comparison of all words in a sequence.
Quotation from CLU paper: To accelerate the comparison all words found in sequence Sq are presented in a table (H). The table H is a linear array, where the offset itself is a hash value of certain oligonucleotide. Each element of this array contains a number, associated with a corresponding oligonucleotide.
This vector has a size 4^wordSize (for example, if wordSize is 6, this table has 4096 entries). These entries are populated in the setReferenceEST() method.
Definition at line 373 of file CLU.h.
Referenced by CLU::getMetric(), and ~CLUESTData().
The documentation for this class was generated from the following files:
