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eXpress “1.5”
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eXpress “1.5”
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The Fragment class stores information for all alignments of a single fragment. More...
#include <fragments.h>
Public Member Functions | |
| Fragment (Library *lib) | |
| Fragment Constructor. | |
| ~Fragment () | |
| Fragment destructor deletes all FragHit and ReadHit objects pointed to by the Fragment. | |
| const Library * | lib () |
| Accessor for the global variables associated with the library this fragment is from. | |
| bool | add_map_end (ReadHit *r) |
| A member function that adds a new ReadHit to the Fragment. | |
| const std::string & | name () const |
| A member function that returns a reference to the "Query Template Name". | |
| size_t | num_hits () const |
| An accessor for the number of valid alignments of the fragment. | |
| FragHit * | operator[] (size_t i) const |
| An accessor for a pointer to the FragHit at the given index. | |
| const std::vector< FragHit * > & | hits () const |
| Accessor for the FragHit objects associated with the fragment. | |
| const FragHit * | sample_hit () const |
| A member function that returns a single FragHit of the fragment sampled at random based on the probabalistic assignments. | |
| void | mass (double m) |
| Mutator for the mass of the fragment according to the forgetting factor. | |
| double | mass () const |
| An accessor for the mass of the fragment according to the forgetting factor. | |
| void | sort_hits () |
| A member function that sorts the FragHits by the TargID of the targets they are aligned to. | |
| bool | paired () const |
| An accessor that returns true iff the Fragment has paired alignments. | |
The Fragment class stores information for all alignments of a single fragment.
By design, only paired-end mappings of paired-end reads will be accepted. All mappings of single-end reads will be accepted.
Definition at line 384 of file fragments.h.
| bool Fragment::add_map_end | ( | ReadHit * | r | ) |
A member function that adds a new ReadHit to the Fragment.
If it is the first ReadHit, it sets the Fragment name. If the fragment is not paired, a FragHit is created and added to _frag_hits. Otherwise, add_open_mate is called.
| r | a pointer to the ReadHit to be added. |
Definition at line 28 of file fragments.cpp.
| const std::vector<FragHit*>& Fragment::hits | ( | ) | const [inline] |
Accessor for the FragHit objects associated with the fragment.
Returned value does not outlive this.
Definition at line 464 of file fragments.h.
| const Library* Fragment::lib | ( | ) | [inline] |
Accessor for the global variables associated with the library this fragment is from.
Pointer outlives this.
Definition at line 432 of file fragments.h.
| void Fragment::mass | ( | double | m | ) | [inline] |
Mutator for the mass of the fragment according to the forgetting factor.
| m | a double representing the value to set to the mass to. |
Definition at line 476 of file fragments.h.
| double Fragment::mass | ( | ) | const [inline] |
An accessor for the mass of the fragment according to the forgetting factor.
Definition at line 482 of file fragments.h.
| const std::string& Fragment::name | ( | ) | const [inline] |
A member function that returns a reference to the "Query Template Name".
Definition at line 447 of file fragments.h.
| size_t Fragment::num_hits | ( | ) | const [inline] |
An accessor for the number of valid alignments of the fragment.
Definition at line 452 of file fragments.h.
| FragHit* Fragment::operator[] | ( | size_t | i | ) | const [inline] |
An accessor for a pointer to the FragHit at the given index.
| i | index of the FragHit requested. |
Definition at line 458 of file fragments.h.
| bool Fragment::paired | ( | ) | const [inline] |
An accessor that returns true iff the Fragment has paired alignments.
Definition at line 492 of file fragments.h.
| const FragHit * Fragment::sample_hit | ( | ) | const |
A member function that returns a single FragHit of the fragment sampled at random based on the probabalistic assignments.
Returned value does not outlive this.
Definition at line 75 of file fragments.cpp.
1.7.3 
