//------------------------------------------------------------------------------------------------------------------------------
void ImplTreetorDistance::calculateTree(
HTree & tree,
const HMultipleAlignment & mali ) const
{
debug_func_cerr( 5 );
startUp( tree, mali );
DistanceMatrixSize swap_temp; // for swapping indices
#define SWAP(x,y) { swap_temp = x; x = y; y = swap_temp; }
//------------------------------------------------------------------------------------------
// start up
DistanceMatrixSize width = mWorkMatrix->getWidth();
DistanceMatrixSize i;
/* in this algorithm I assume that the matrix I use is only a half-matrix using the lower diagonal */
tree->setNumLeaves( width ); // allocate memory for tree
mIndices = new Node[width]; /* allocate array to keep track of indices */
for (i = 0; i < width; i++) mIndices[i] = i;
//----------------------------------------------------------------------------------------------------
// Perform hierarchical clustering
DistanceMatrixSize last_row = width - 1;
/* shrink distance matrix, until it contains only a single cluster */
while (last_row > 0)
{
debug_cerr( 6, "Last row " << last_row );
debug_cerr( 6, "Work matrix " << endl << *mWorkMatrix );
// find minimum distance in matrix
/*
-
--
---
----
-x---
------
-------
--------
*/
calculateMinimumDistance();
DistanceMatrixSize min_row = mMinimumCoord.row;
DistanceMatrixSize min_col = mMinimumCoord.col;
debug_cerr( 5, "Joining nodes -> "
<< "minimum distance :" << mMinimumValue << " "
<< "node 1: " << mIndices[min_row] << " (" << min_row << ") "
<< "node 2: " << mIndices[min_col] << " (" << min_col << ") " );
//------------------------------------------------------------------------------------------------------
// move rows around, so that the last two joined cluster are in the two last rows
/*
- -
y- --
-y- ---
-y-- -> ----
xOxx- -----
-y--x- ------
-y--x-- xxxxxxx
-y--x--- yyyyyyyy
*/
DistanceMatrixSize second_row = last_row - 1; // second to last row
// exchange row with last row
mWorkMatrix->swap( min_row, last_row);
SWAP( mIndices[min_row], mIndices[last_row]);
swapHelpers( min_row, last_row);
// exchange col with second to last row
mWorkMatrix->swap( min_col, second_row);
SWAP( mIndices[min_col], mIndices[second_row]);
swapHelpers( min_col, second_row);
//------------------------------------------------------------------------------------------------------
// join the two nodes in the tree giving the correct edge weights
Node new_node = joinNodes( tree, second_row, last_row );
debug_cerr( 6, "-> new node " << new_node );
//------------------------------------------------------------------------------------------------------
// calculate distance to new cluster and put them in second to last row
updateDistanceMatrix( tree, second_row, last_row);
/* delete last row, update mIndices, so that the last row now
contains the number of the new cluster id */
/*
- -
-- --
--- ---
---- -> ----
----- -----
------ ------
xxxxxxx xxxxxxx
yyyyyyyy
*/
mWorkMatrix->shrink();
mIndices[last_row - 1] = new_node;
last_row = mWorkMatrix->getWidth() - 1;
}
delete [] mIndices;
cleanUp(); // cleans up mWorkMatrix
}
void pn::Init() {
PNFactory* instance = PNFactory::GetInstance();
instance->Init();
//Input Node Queue
Node* p1 = instance->createNode("p1", PlaceObjectType, SingleToken);
Node* p2 = instance->createNode("p2", PlaceObjectType, SingleToken);
Node* p3 = instance->createNode("p3", PlaceObjectType, SingleToken);
//Input Node
Node* t1 = instance->createNode("t1", TransitionObjectType, SingleToken);
Node* t2 = instance->createNode("t2", TransitionObjectType, SingleToken);
Node* t3 = instance->createNode("t3", TransitionObjectType, SingleToken);
//Routing Queue
Node* p4 = instance->createNode("p4 (routing queue)", PlaceObjectType, SingleToken);
//Routing
Node* t4 = instance->createNode("t4 (routing)", TransitionObjectType, SingleToken);
//Output Node Queue
Node* p5 = instance->createNode("p5", PlaceObjectType, SingleToken);
Node* p6 = instance->createNode("p6", PlaceObjectType, SingleToken);
Node* p7 = instance->createNode("p7", PlaceObjectType, SingleToken);
//Output Node
Node* t5 = instance->createNode("t5", TransitionObjectType, SingleToken);
Node* t6 = instance->createNode("t6", TransitionObjectType, SingleToken);
Node* t7 = instance->createNode("t7", TransitionObjectType, SingleToken);
//Output
Node* p8 = instance->createNode("p8", PlaceObjectType, SingleToken);
Node* p9 = instance->createNode("p9", PlaceObjectType, SingleToken);
Node* p10 = instance->createNode("p10", PlaceObjectType, SingleToken);
//Input Node Queue & Input Node
joinNodes(p1, t1);
joinNodes(p2, t2);
joinNodes(p3, t3);
//Input Node & Routing Queue
joinNodes(t1, p4);
joinNodes(t2, p4);
joinNodes(t3, p4);
//Routing Queue & Routing
joinNodes(p4, t4);
//Routing & Output Node Queue
joinNodes(t4, p5);
joinNodes(t4, p6);
joinNodes(t4, p7);
//Output Node Queue & Output
joinNodes(p5, t5);
joinNodes(p6, t6);
joinNodes(p7, t7);
//Output & Final Place
joinNodes(t5, p8);
joinNodes(t6, p9);
joinNodes(t7, p10);
//Connect Generator
gm::addNewGenerator(p1, 1, 250);
gm::addNewGenerator(p2, 2, 250);
gm::addNewGenerator(p3, 3, 250);
}
