HalfAlignPile Class Reference
#include <Interval.h>
Public Member Functions | |
| HalfAlignPile () | |
| HalfAlignPile (const HalfAlignPile &p) | |
| HalfAlignPile (HalfAlignInterval *hp) | |
| float | getIdentity () const |
| float | getCov () const |
| float | getQcov () const |
| float | getTcov () const |
| string | toDelimitedString (const string &dl="\t") const |
Private Member Functions | |
| void | computeIntermediateResult () const |
Private Attributes | |
| float | identity |
| float | qcov |
| float | tcov |
Detailed Description
This is more at application level class. Represents all alignments clusterd together.Constructor & Destructor Documentation
| HalfAlignPile::HalfAlignPile | ( | ) | [inline] |
| HalfAlignPile::HalfAlignPile | ( | const HalfAlignPile & | p | ) | [inline] |
| HalfAlignPile::HalfAlignPile | ( | HalfAlignInterval * | hp | ) | [inline] |
Member Function Documentation
| float HalfAlignPile::getIdentity | ( | ) | const |
return the average identity over the covered regions It is simply computed by sum(identical)/sum(alnlen)
this method will only be called once for each object It will also compute the coverage.
References computeIntermediateResult(), and identity.
Referenced by toDelimitedString().
| float HalfAlignPile::getCov | ( | ) | const [inline] |
return the average target coverage for this pile's
Simple average of all, with respect to target sequence.
References getTcov().
| float HalfAlignPile::getQcov | ( | ) | const |
computed by the sum of all intervals divided by the outer most interval length of this pile divided again by the number of intervals in this pile This is called the local_qcov in the context of the chain.
References computeIntermediateResult(), and qcov.
Referenced by toDelimitedString().
| float HalfAlignPile::getTcov | ( | ) | const |
| string HalfAlignPile::toDelimitedString | ( | const string & | dl = "\t" |
) | const [virtual] |
print the information in tabular format. The columns: aln_begin, aln_end, pile_size, avg_identity, local_qcov, avg_tcov
- Parameters:
-
dl is the field separator
Reimplemented from IntervalPile.
References getIdentity(), getQcov(), getTcov(), and IntervalPile::toDelimitedString().
| void HalfAlignPile::computeIntermediateResult | ( | ) | const [private] |
helper function used by this object to compute identity, qcov, and tcov It only changes mutable variables and looks like a const function.
References HalfAlignInterval::getAlnlen(), HalfAlignInterval::getCov(), HalfAlignInterval::getIdentical(), identity, Interval::length(), IntervalPile::members, qcov, IntervalPile::size(), and tcov.
Referenced by getIdentity(), getQcov(), and getTcov().
Member Data Documentation
float HalfAlignPile::identity [mutable, private] |
for repeated calls of getting the average identity This is a tmp variable for getIdentity()
Referenced by computeIntermediateResult(), and getIdentity().
float HalfAlignPile::qcov [mutable, private] |
tmp variable for getCov() Average query coverage on this pile
Referenced by computeIntermediateResult(), and getQcov().
float HalfAlignPile::tcov [mutable, private] |
average tcov
Referenced by computeIntermediateResult(), and getTcov().
The documentation for this class was generated from the following files:
- range/Interval.h
- range/Interval.cpp
