HOG2
Public Member Functions | Private Attributes | List of all members
SequenceAlignment Class Reference

#include <SequenceAlignment.h>

Inheritance diagram for SequenceAlignment:
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Collaboration diagram for SequenceAlignment:
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Public Member Functions

 SequenceAlignment (int length)
 
virtual void GetSuccessors (const SequenceAlignmentState &nodeID, std::vector< SequenceAlignmentState > &neighbors) const
 
virtual void GetActions (const SequenceAlignmentState &nodeID, std::vector< SequenceAlignmentAction > &actions) const
 
virtual SequenceAlignmentAction GetAction (const SequenceAlignmentState &s1, const SequenceAlignmentState &s2) const
 
virtual void ApplyAction (SequenceAlignmentState &s, SequenceAlignmentAction a) const
 
virtual void GetNextState (const SequenceAlignmentState &, SequenceAlignmentAction, SequenceAlignmentState &) const
 
virtual bool InvertAction (SequenceAlignmentAction &a) const
 
virtual double HCost (const SequenceAlignmentState &node1, const SequenceAlignmentState &node2) const
 Heuristic value between two arbitrary nodes. More...
 
virtual double HCost (const SequenceAlignmentState &node) const
 Heuristic value between node and the stored goal. More...
 
virtual double GCost (const SequenceAlignmentState &node1, const SequenceAlignmentState &node2) const
 
virtual double GCost (const SequenceAlignmentState &node, const SequenceAlignmentAction &act) const
 
virtual bool GoalTest (const SequenceAlignmentState &node, const SequenceAlignmentState &goal) const
 
virtual bool GoalTest (const SequenceAlignmentState &node) const
 Goal Test if the goal is stored. More...
 
virtual uint64_t GetStateHash (const SequenceAlignmentState &node) const
 
virtual uint64_t GetActionHash (SequenceAlignmentAction act) const
 
virtual void OpenGLDraw () const
 
virtual void OpenGLDraw (const SequenceAlignmentState &) const
 
virtual void OpenGLDraw (const SequenceAlignmentState &, const SequenceAlignmentState &, float) const
 Draw the transition at some percentage 0...1 between two states. More...
 
virtual void OpenGLDraw (const SequenceAlignmentState &, const SequenceAlignmentAction &) const
 
- Public Member Functions inherited from SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >
virtual ~SearchEnvironment ()
 
virtual int GetNumSuccessors (const SequenceAlignmentState &stateID) const
 
virtual void UndoAction (SequenceAlignmentState &s, SequenceAlignmentAction a) const
 
virtual void StoreGoal (SequenceAlignmentState &s)
 Stores the goal for use by single-state HCost. More...
 
virtual void ClearGoal ()
 Clears the goal from memory. More...
 
virtual bool IsGoalStored () const
 Returns true if the goal is stored and false otherwise. More...
 
virtual double HCost (const SequenceAlignmentState &node1, const SequenceAlignmentState &node2, double parentHCost) const
 
virtual uint64_t GetMaxHash () const
 
virtual void GetStateFromHash (uint64_t parent, SequenceAlignmentState &s) const
 
virtual double GetPathLength (std::vector< SequenceAlignmentState > &neighbors)
 
virtual double GetPathLength (const SequenceAlignmentState &start, std::vector< SequenceAlignmentAction > &neighbors)
 
virtual OccupancyInterface< SequenceAlignmentState, SequenceAlignmentAction > * GetOccupancyInfo ()
 
virtual void SetOccupancyInfo (OccupancyInterface< SequenceAlignmentState, SequenceAlignmentAction > *)
 
virtual void OpenGLDraw () const
 
virtual void GLLabelState (const SequenceAlignmentState &, const char *) const
 
virtual void GLDrawLine (const SequenceAlignmentState &x, const SequenceAlignmentState &y) const
 
virtual void GLDrawPath (const std::vector< SequenceAlignmentState > &x) const
 
virtual void SetColor (const rgbColor &r) const
 
virtual void SetColor (GLfloat rr, GLfloat g, GLfloat b, GLfloat t=1.0) const
 
virtual void GetColor (GLfloat &rr, GLfloat &g, GLfloat &b, GLfloat &t) const
 
virtual rgbColor GetColor () const
 
virtual void Draw (Graphics::Display &display) const
 
virtual void Draw (Graphics::Display &display, const SequenceAlignmentState &) const
 
virtual void DrawLine (Graphics::Display &display, const SequenceAlignmentState &x, const SequenceAlignmentState &y, float width=1.0) const
 
- Public Member Functions inherited from Heuristic< SequenceAlignmentState >
 Heuristic ()
 
virtual ~Heuristic ()
 

Private Attributes

int d
 

Additional Inherited Members

- Public Attributes inherited from Heuristic< SequenceAlignmentState >
std::vector< HeuristicTreeNode > lookups
 
std::vector< Heuristic * > heuristics
 
uint64_t histogram [256]
 
- Protected Attributes inherited from SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >
bool bValidSearchGoal
 
SequenceAlignmentState searchGoal
 
rgbColor color
 
GLfloat transparency
 

Detailed Description

Definition at line 20 of file SequenceAlignment.h.

Constructor & Destructor Documentation

◆ SequenceAlignment()

SequenceAlignment::SequenceAlignment ( int  length)
inline

Definition at line 23 of file SequenceAlignment.h.

Member Function Documentation

◆ ApplyAction()

void SequenceAlignment::ApplyAction ( SequenceAlignmentState &  s,
SequenceAlignmentAction  a 
) const
virtual

Implements SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >.

Definition at line 39 of file SequenceAlignment.cpp.

References d.

Referenced by GetNextState().

◆ GCost() [1/2]

double SequenceAlignment::GCost ( const SequenceAlignmentState &  node,
const SequenceAlignmentAction &  act 
) const
virtual

Implements SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >.

Definition at line 68 of file SequenceAlignment.cpp.

◆ GCost() [2/2]

double SequenceAlignment::GCost ( const SequenceAlignmentState &  node1,
const SequenceAlignmentState &  node2 
) const
virtual

Implements SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >.

Definition at line 66 of file SequenceAlignment.cpp.

References d.

◆ GetAction()

SequenceAlignmentAction SequenceAlignment::GetAction ( const SequenceAlignmentState &  s1,
const SequenceAlignmentState &  s2 
) const
virtual

Reimplemented from SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >.

Definition at line 33 of file SequenceAlignment.cpp.

◆ GetActionHash()

uint64_t SequenceAlignment::GetActionHash ( SequenceAlignmentAction  act) const
virtual

Implements SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >.

Definition at line 74 of file SequenceAlignment.cpp.

◆ GetActions()

void SequenceAlignment::GetActions ( const SequenceAlignmentState &  nodeID,
std::vector< SequenceAlignmentAction > &  actions 
) const
virtual

Implements SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >.

Definition at line 23 of file SequenceAlignment.cpp.

References d.

◆ GetNextState()

void SequenceAlignment::GetNextState ( const SequenceAlignmentState &  s1,
SequenceAlignmentAction  a,
SequenceAlignmentState &  s2 
) const
virtual

Reimplemented from SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >.

Definition at line 54 of file SequenceAlignment.cpp.

References ApplyAction().

◆ GetStateHash()

uint64_t SequenceAlignment::GetStateHash ( const SequenceAlignmentState &  node) const
virtual

Implements SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >.

Definition at line 73 of file SequenceAlignment.cpp.

◆ GetSuccessors()

void SequenceAlignment::GetSuccessors ( const SequenceAlignmentState &  nodeID,
std::vector< SequenceAlignmentState > &  neighbors 
) const
virtual

Implements SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >.

Definition at line 12 of file SequenceAlignment.cpp.

References d.

◆ GoalTest() [1/2]

virtual bool SequenceAlignment::GoalTest ( const SequenceAlignmentState &  node) const
inlinevirtual

Goal Test if the goal is stored.

Reimplemented from SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >.

Definition at line 47 of file SequenceAlignment.h.

References SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >::bValidSearchGoal, and SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >::searchGoal.

◆ GoalTest() [2/2]

bool SequenceAlignment::GoalTest ( const SequenceAlignmentState &  node,
const SequenceAlignmentState &  goal 
) const
virtual

Implements SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >.

Definition at line 70 of file SequenceAlignment.cpp.

◆ HCost() [1/2]

virtual double SequenceAlignment::HCost ( const SequenceAlignmentState &  node) const
inlinevirtual

Heuristic value between node and the stored goal.

Asserts that the goal is stored

Reimplemented from SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >.

Definition at line 39 of file SequenceAlignment.h.

References SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >::bValidSearchGoal, HCost(), and SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >::searchGoal.

◆ HCost() [2/2]

double SequenceAlignment::HCost ( const SequenceAlignmentState &  node1,
const SequenceAlignmentState &  node2 
) const
virtual

Heuristic value between two arbitrary nodes.

Implements SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >.

Definition at line 63 of file SequenceAlignment.cpp.

Referenced by HCost().

◆ InvertAction()

bool SequenceAlignment::InvertAction ( SequenceAlignmentAction &  a) const
virtual

Implements SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >.

Definition at line 60 of file SequenceAlignment.cpp.

◆ OpenGLDraw() [1/4]

virtual void SequenceAlignment::OpenGLDraw ( ) const
inlinevirtual

Definition at line 53 of file SequenceAlignment.h.

◆ OpenGLDraw() [2/4]

virtual void SequenceAlignment::OpenGLDraw ( const SequenceAlignmentState &  ) const
inlinevirtual

Reimplemented from SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >.

Definition at line 54 of file SequenceAlignment.h.

◆ OpenGLDraw() [3/4]

virtual void SequenceAlignment::OpenGLDraw ( const SequenceAlignmentState &  ,
const SequenceAlignmentAction &   
) const
inlinevirtual

Reimplemented from SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >.

Definition at line 56 of file SequenceAlignment.h.

◆ OpenGLDraw() [4/4]

virtual void SequenceAlignment::OpenGLDraw ( const SequenceAlignmentState &  ,
const SequenceAlignmentState &  ,
float   
) const
inlinevirtual

Draw the transition at some percentage 0...1 between two states.

Reimplemented from SearchEnvironment< SequenceAlignmentState, SequenceAlignmentAction >.

Definition at line 55 of file SequenceAlignment.h.

Member Data Documentation

◆ d

int SequenceAlignment::d
private

Definition at line 58 of file SequenceAlignment.h.

Referenced by ApplyAction(), GCost(), GetActions(), and GetSuccessors().

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