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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/phylo__tree__ps_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/widgets/phylo_tree/phylo_tree_ps.cpp Source File

: m_ElectricalRepulsion(100.0f)

, m_RepulsionDist(350.0f)

, m_VelocityThresholdK(0.002f)

sub_menu->

(

,

std::vector<Edge>::iterator eiter;

std::vector<int>& neighbor_nodes =

.

(adjacent_idx);

(

=0;

<cell_nodes.size(); ++

) {

(

j=0; j<neighbor_nodes.size(); ++j) {

idx1 = cell_nodes[

];

idx2 = neighbor_nodes[j];

dist2 =

.Length2();

(dist2 < m_RepulsionDist2 && dist2 >

) {

dist = sqrtf(dist2);

(

x = min_pos.

(); x <= max_pos.

(); ++x) {

(

y = min_pos.

(); y <= max_pos.

(); ++y) {

(cell_nodes.size() > 0) {

(

=0;

<cell_nodes.size(); ++

) {

(

j=

+1; j<cell_nodes.size(); ++j) {

idx1 = cell_nodes[

];

idx2 = cell_nodes[j];

dist2 =

.Length2();

(dist2 < m_RepulsionDist2 && dist2 >

) {

dist = sqrtf(dist2);

x_ApplyNeighborCellForces(cell_nodes, CVect2<int>(x+1,y));

if (y+1 < m_NodeGrid.GetHeight())

x_ApplyNeighborCellForces(cell_nodes, CVect2<int>(x+1,y+1));

x_ApplyNeighborCellForces(cell_nodes, CVect2<int>(x,y+1));

x_ApplyNeighborCellForces(cell_nodes, CVect2<int>(x-1,y+1));

(

=0;

<

.size(); ++

) {

(

j=

+1; j<

.size(); ++j) {

dist2 =

.Length2();

std::vector<Edge>::iterator eiter;

dist =

.Length();

ldist = logf(dist*(*eiter).rest_len_inv);

#ifdef NUMERIC_ERROR_CHECK

std::vector<Node>::iterator niter1, niter2;

(niter1=

.begin(); niter1!=

.end(); ++niter1) {

p1 = (*niter1).pos;

(niter2=niter1+1; niter2!=

.end(); ++niter2) {

p2 = (*niter2).pos;

dist2 =

.Length2();

idx1 = niter1-

.begin();

idx2 = niter2-

.begin();

std::vector<Node>::iterator niter;

prev_offset((*niter).pos - (*niter).prev_pos);

(*niter).prev_pos = (*niter).pos;

(*niter).accel.X()*step)*(*niter).constrained;

(*niter).accel.Y()*step)*(*niter).constrained;

#ifdef NUMERIC_ERROR_CHECK

(

<< (*niter).pos.X() <<

<< (*niter).pos.Y());

max_velocity_squared = 0.0f;

std::vector<Node>::iterator niter;

prev_offset((*niter).pos - (*niter).prev_pos);

(*niter).prev_pos = (*niter).pos;

(*niter).accel.X()*step)*(*niter).constrained;

(*niter).accel.Y()*step)*(*niter).constrained;

max_velocity_squared =

(max_velocity_squared, xoff*xoff + yoff*yoff);

(*niter).pos.X() += xoff;

(*niter).pos.Y() += yoff;

(*m_Tree)[(*niter).tree_node_idx]->XY() = (*niter).pos;

(*m_Tree)[(*niter).tree_node_idx]->SetAngle(

((*niter).pos.X()-ppos.

() >= 0.0f) ? 0.0f : 3.1415927f);

node_count = (float)

.size();

threshold =

(10.0f, threshold);

std::vector<Edge>::iterator eiter;

dist =

.Length();

ldist = logf(dist*(*eiter).rest_len_inv);

glColor3f(1.0f, 1.0f, 0.0f);

std::vector<Node>::iterator niter;

(

j=0; j<

.size(); ++j) {

.pos = tnode->XY();

.prev_pos =

.pos;

.constrained = 1.0f;

.tree_node_idx = node_idx;

.constrained = 1.0f;

= (

.pos-ppos).Length();

(

== -1) {

CInitPSNodes(CPhyloTreePS *ps)

CPhyloTree::TTreeIdx TTreeIdx

ETreeTraverseCode operator()(CPhyloTree &tree, TTreeIdx node_idx, int delta)

float m_RepulsionDist2

Square of current effective repulsion distance.

float m_RepulsionInv_x_ElectricalRepulsion

Inverse of repulsion dist * electrical repulsion factor.

void Init(CPhyloTreeDataSource &ds)

void x_ApplyNeighborCellForces(std::vector< int > &cell_nodes, const CVect2< int > &adjacent_idx)

Called compute forces between nodes in 2 cells.

PhysicsParms m_PhysicsParmsSafe

Updated from m_PhysicsPamsVolatile when safe to do so.

float m_MaxVelocity

The maximum velocity is the maximum node velocity during the last call to UpdateAndSynch()

float m_edge_forces_t

For timer values.

float m_bound_update_safe_t

PhysicsParms m_PhysicsParmsVolatile

(potentially) updated from other thread(s)

int m_node_node_interactions_safe_t

std::vector< CVect2< int > > m_ValidateGrid

Only used for debugging.

float m_edge_forces_safe_t

bool m_IsDone

If true, system has slowed down to the point where continuing to update it is not necessary.

void x_Init(CPhyloTree *tree)

Create particle system from tree - ignore collapsed.

void x_ApplyRepulsiveForces()

Apply repulsive forces between all nodes.

std::vector< Node > m_Nodes

Set of all nodes.

float m_DefaultEdgeLen

Default length for all edges in system.

TVec & GetMinPos()

Tracks bounding rectangle for all nodes.

float m_AdaptiveStep

Multiplier for m_PhysicsParmsSafe.m_Step to allow step size to be adaptively lowered if system appear...

float m_node_forces_safe_t

void Draw()

Visualize graph - debug rendering.

TVec m_MinPos

Tracks bounding rectangle for all nodes.

float m_LogDistMax

For debug-drawing.

std::vector< Edge > m_Edges

Set of all edges.

void x_UpdateVoxels()

Update spatial subdivision of nodes.

int m_node_node_interactions_t

void x_ApplyRepulsiveForcesHashed()

Apply forces between nodes based on defined neighborhood size.

float & GetDefaultEdgeLen()

Default length for all edges in system.

std::vector< Node > & GetNodes()

Set of all nodes.

std::vector< Edge > & GetEdges()

Set of all edges.

void UpdateAndSynch()

Calculate forces, update positions, and update underlying tree.

void Update()

Calculate force then update positions.

float m_PrevMaxVelocity

Maximum velocity in previous update.

CSpatialHash2D< std::vector< int > > m_NodeGrid

Grid that keeps track of adjacent nodes.

CPhyloTree * m_Tree

Root node of tree.

void CalcForces()

Calculate forces for all nodes.

std::vector< CVect2< int > > m_ValidateNsq

Tree subclass also has functions and data needed for rendering and selection.

const TVeci & GetMin()

Get min/max indices for current (whole) grid.

TElemType & Get(const TVeci &item)

int GetWidth() const

Get width/height of grid.

bool HasParent() const

Check if the node has a parent.

bool IsLeaf() const

Report whether this is a leaf node.

static TTreeIdx Null()

Return the index value that represents a NULL node.

const T * GetData() const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

double Restart(void)

Return time elapsed since first Start() or last Restart() call (in seconds).

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

void Stop(void)

Suspend the timer.

void Start(void)

Start the timer.

ETreeTraverseCode

Tree traverse code returned by the traverse predicate function.

@ eTreeTraverse

Keep traversal.

unsigned int

A callback function used to compare two keys in a database.

if(yy_accept[yy_current_state])

The NCBI C++/STL use hints.

Defines: CTimeFormat - storage class for time format.

Int4 delta(size_t dimension_, const Int4 *score_)

void TreeDepthFirstEx(TTreeModel &tree_model, typename TTreeModel::TTreeIdx node_idx, Fun &func)

Depth-first tree traversal that skips collapsed nodes.

Data structure for an edge between two nodes.

Data structure for a node in the particle system.

float m_VelocityThresholdK

factor to scale final velocity threshold

float m_ElectricalRepulsion

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