ppALIGN API documentation

DriverLocalBound Class Reference

#include <localbound.hpp>

Inheritance diagram for DriverLocalBound:
PartitionDriverBase

List of all members.

Public Member Functions

 DriverLocalBound ()
void SetStart (Pair pstart, Pair pend, long offset)
virtual bool NeedForward ()
virtual bool NeedBackward ()
void BeforeComputation ()
void AfterComputation ()
void OnForward (long i, const PartitionWorkspace::RowInfo &last_row, const PartitionWorkspace::RowInfo &curr_row, const PartitionWorkspace::const_iterator last, const PartitionWorkspace::const_iterator curr)
void OnBackward (long i, const PartitionWorkspace::RowInfo &last_row, const PartitionWorkspace::RowInfo &curr_row, const PartitionWorkspace::const_iterator last, const PartitionWorkspace::const_iterator curr)
void StreamOut (std::ostream &ost, Sequence &seq1, Sequence &seq2, Pair seq_offset, bool shortcut=false)

Detailed Description

Compute the start and end probabilities for local alignment.

Definition at line 27 of file localbound.hpp.

Constructor & Destructor Documentation

DriverLocalBound::DriverLocalBound (  ) 

constructor

Member Function Documentation

void DriverLocalBound::AfterComputation (  )  [virtual]

An event that is thrown when the complete computation has been finished, forward and evtl. backward if required.

Reimplemented from PartitionDriverBase.

void DriverLocalBound::BeforeComputation (  )  [virtual]

An event that is thrown before the acutal computation begins.

Reimplemented from PartitionDriverBase.

virtual bool DriverLocalBound::NeedBackward (  )  [inline, virtual]

Tell the main algorithm that a callback of OnBackward() for each row is needed. The algorithm provides the current and the last row of the backward computation. These events are emitted as soon as the current and the last row are available for the first time

Returns:
true / false

Reimplemented from PartitionDriverBase.

Definition at line 44 of file localbound.hpp.

virtual bool DriverLocalBound::NeedForward (  )  [inline, virtual]

Tell the main algorithm that a callback of OnForward() for each row is needed.

Returns:
true if the OnForward method is to be called for each row every time the row is (re-)computed

Reimplemented from PartitionDriverBase.

Definition at line 43 of file localbound.hpp.

void DriverLocalBound::OnBackward ( long  i,
const PartitionWorkspace::RowInfo &  last_row,
const PartitionWorkspace::RowInfo &  curr_row,
const PartitionWorkspace::const_iterator  last,
const PartitionWorkspace::const_iterator  curr 
) [virtual]

An event that is emitted whenever the backward partition functions are availiable for row i and row i+1

To obtain the partition functions for row i and column j on has to access the memory via the iterator curr

Parameters:
i row that has been computed (i=-1 ... (length1-1))
last_row information about the last row (the row before the current row)
curr_row information (i.e. the strip layout) about the current row (the one that has just be computed)
last iterator that points on the begin of the last row (i+1)
curr iterator that points on the begin of the current row in the workspace (in the strip layout)

Reimplemented from PartitionDriverBase.

void DriverLocalBound::OnForward ( long  i,
const PartitionWorkspace::RowInfo &  last_row,
const PartitionWorkspace::RowInfo &  curr_row,
const PartitionWorkspace::const_iterator  last,
const PartitionWorkspace::const_iterator  curr 
) [virtual]

An event that is emitted whenever the forward partition functions are availiable

To obtain the partition functions for row i and column j on has to access the memory via the iterator curr

    xdouble Z_ij = curr[j]
Parameters:
i row that has been computed (i=0 ... (length1-1))
last_row information about the last row (the row before the current row)
curr_row information (i.e. the strip layout) about the current row (the one that has just be computed)
last iterator that points on the begin of the last row (i-1)
curr iterator that points on the begin of the current row in the workspace (in the strip layout)

Reimplemented from PartitionDriverBase.

void DriverLocalBound::SetStart ( Pair  pstart,
Pair  pend,
long  offset 
)

Set positions around which the probability is to be computed.

Parameters:
pstart start position of a given alignment
pend end position of a given alignment
offset offset arround the start and end position
The documentation for this class was generated from the following file: