void Tree::Trichotomise() {
double lengthbefore = GetLength();
PolyNode* node = mRoot->down;
if (node->next->next == node) {
if (!node->IsLeaf()) {
node = node->next;
}
else {
if (node->next->IsLeaf()) {
cerr << "error : cannot trichotomise a two species tree\n";
exit(1);
}
}
PolyNode* temp = node->next;
node->Detach();
// PolyNode* temp = mRoot->down;
mRoot->down = 0;
// delete mRoot;
mRoot = temp;
mRoot->up = 0;
node->branchLength += mRoot->branchLength;
mRoot->branchLength = 0;
node->AttachTo(mRoot);
}
double lengthafter = GetLength();
if (fabs(lengthafter - lengthbefore) > 1e-8) {
cerr << "error in trichotomise: length not conserved\n";
cerr << "length before : " << lengthbefore << '\n';
cerr << "length after : " << lengthafter << '\n';
cerr << lengthbefore - lengthafter << '\n';
exit(1);
}
}
void
Tree::RootAt(PolyNode* inNode) {
double lengthbefore = GetLength();
// inNode should not be root
if (inNode->IsRoot()) {
cerr << "error in PolyNode::RootAt : inNode is root\n";
exit(1);
}
if (inNode) {
PolyNode* theUp = inNode->Up();
PolyNode* newRoot = 0;
if (theUp->IsRoot()) {
inNode->Detach();
if (theUp->down->next != theUp->down) {
newRoot = new PolyNode();
newRoot->SetTree(this);
theUp->AttachTo(newRoot);
theUp->mProb = inNode->mProb;
}
else {
newRoot = theUp;
}
}
else {
newRoot = theUp->FlipFlop();
if ( ! newRoot) {
newRoot = new PolyNode();
newRoot->SetTree(this);
}
inNode->Detach();
theUp->AttachTo(newRoot);
theUp->mProb = inNode->mProb;
}
inNode->AttachTo(newRoot);
mRoot = newRoot;
}
double lengthafter = GetLength();
if (fabs(lengthafter - lengthbefore) > 1e-8) {
cerr << "error in rerooting: length not conserved\n";
cerr << "length before : " << lengthbefore << '\n';
cerr << "length after : " << lengthafter << '\n';
cerr << lengthbefore - lengthafter << '\n';
// exit(1);
}
double totallength = mRoot->down->branchLength + mRoot->down->next->branchLength;
mRoot->down->branchLength = totallength / 2;
mRoot->down->next->branchLength = totallength / 2;
}
void SHAPE_POLY_SET::importTree( PolyTree* tree)
{
m_polys.clear();
for( PolyNode* n = tree->GetFirst(); n; n = n->GetNext() )
{
if( !n->IsHole() )
{
POLYGON paths;
paths.push_back( convertFromClipper( n->Contour ) );
for( unsigned int i = 0; i < n->Childs.size(); i++ )
paths.push_back( convertFromClipper( n->Childs[i]->Contour ) );
m_polys.push_back(paths);
}
}
}
int Tree::ReadPhylip(istream& is, PolyNode* currentNode) {
// int verbose = 1;
PolyNode* node = 0;
double d;
int END = 0;
char c = is.peek();
while ((c == ' ') || (c == '\n') || (c == '\t')) {
is.get();
c = is.peek();
}
while( (! is.eof()) && (! END) ) {
string s;
char c = is.peek();
// cerr << c ;
switch (c) {
case '\n' :
case ' ' :
case '\t' :
is >> c;
if (verbose) {
cerr << c;
}
break;
case '(' :
is >> c;
if (verbose) {
cerr << c;
}
// make a new polynode
node = new PolyNode();
node->AttachTo(currentNode);
currentNode = node;
break;
case ',' :
is >> c;
if (verbose) {
cerr << c;
}
node = new PolyNode();
if (currentNode->IsRoot()) {
cerr << "error in reading tree file : found a coma not within brackets\n";
exit(1);
}
node->AttachTo(currentNode->Up());
currentNode = node;
break;
case ')' :
is >> c;
if (verbose) {
cerr << c;
}
if (currentNode->IsRoot()) {
cerr << "error in reading tree file: found more closing than opening brackets\n";
exit(1);
}
currentNode = currentNode->Up();
// check whether is followed by a digit, a ':', a ')' or a ',' (anything else will throw exception)
c = is.peek();
switch(c) {
case '0':
case '1':
case '2':
case '3':
case '4':
case '5':
case '6':
case '7':
case '8':
case '9':
// probability
is >> d;
if (verbose) {
cerr << d;
}
currentNode->SetProb(d);
// then check whether is further followed by ':' or ',' or ')' (anything else exits)
c = is.peek();
switch(c) {
case ':' :
is >> c;
if (verbose) {
cerr << c;
}
// read branchLength
// and check that it is followed either by ',' or by ')'
is >> d;
if (verbose) {
cerr << "BL" << d;
}
currentNode->SetBranchLength(d);
c = is.peek();
if ((c != ',') && (c != ')') && (c != ';')) {
cerr << "error\n";
cerr << c << '\n';
exit(1);
}
break;
case ',' :
case ')' :
break;
default :
cerr << "error in reading tree file : after reading a branchlength of an internal node\n";
cerr << c << '\n';
double d;
is >> d;
cerr << d << '\n';
exit(1);
break;
}
break;
case ':' :
is >> c;
if (verbose) {
cerr << c;
}
// read branchLength
// and check that it is followed either by ',' or by ')'
is >> d;
if (verbose) {
cerr << "BL" << d;
}
currentNode->SetBranchLength(d);
c = is.peek();
if ((c != ',') && (c != ')') && (c != ';')) {
cerr << "error\n";
cerr << c << '\n';
exit(1);
}
break;
case ';' :
case ',' :
case ')' :
break;
default :
cerr << "error in reading tree file\n";
cerr << "character : " << c << '\n';
exit(1);
break;
}
break;
case ';' :
is >> c;
if (verbose) {
cerr << "END" << c;
}
// close the tree
// current node should be root
if (! currentNode->IsRoot()) {
cerr << "error in reading tree file : lacking closing brackets overall\n";
exit(1);
}
END = 1;
break;
case '0':
case '1':
case '2':
case '3':
case '4':
case '5':
case '6':
case '7':
case '8':
case '9':
// species label
s == "";
do {
s += c;
is >> c;
if (is.eof()) {
cerr << "error in reading treefile : unexpected end of file in string\n";
exit(1);
}
c = is.peek();
} while ((c != ',') && (c != ':') && (c != ')'));
if (IsInt(s)) {
int i = Int(s);
// is >> i;
if (verbose) {
cerr << i;
}
node->SetLabel(i);
}
else {
node->SetName(s);
}
// check whether is followed by : or , or ) (anything else will throw exception)
c = is.peek();
switch(c) {
case ':' :
is >> c;
if (verbose) {
cerr << c;
}
// branchlength
double d;
is >> d;
if (verbose) {
cerr << "BL" << d;
}
node->SetBranchLength(d);
c = is.peek();
if ((c != ',') && (c != ')')) {
cerr << "error\n";
cerr << c << '\n';
exit(1);
}
break;
case ',' :
case ')' :
break;
default :
cerr << "error in reading tree file\n";
cerr << "character : " << c << '\n';
exit(1);
break;
}
break;
default :
// assume this is a species name
s == "";
do {
s += c;
is >> c;
if (is.eof()) {
return 0;
}
c = is.peek();
} while ((c != ',') && (c != ':') && (c != ')'));
currentNode->SetName(s);
if (verbose) {
cerr << '\"' << s << '\"';
}
// check whether is followed by : or , (anything else will throw exception)
c = is.peek();
switch(c) {
case ':' :
is >> c;
if (verbose) {
cerr << c;
}
// branchlength
double d;
is >> d;
if (verbose) {
cerr << "BL" << d;
}
node->SetBranchLength(d);
break;
case ',' :
case ')':
break;
default :
cerr << "error in reading tree file : after reading species name\n";
exit(1);
break;
}
break;
}
}
if (verbose) {
cerr << "tree read : ok " << '\n' << '\n';
cerr.flush();
}
return 1;
}
void triangulate(const Polygon& inputPoly, std::vector<Mesh>& outputMeshes)
{
// Use Clipper to ensure strictly simple polygons
using namespace ClipperLib;
Clipper clipper;
clipper.StrictlySimple(true);
try
{
clipper.AddPaths(polyToClipperPaths(inputPoly), ptSubject, true);
}
catch (...)
{
std::cerr << "Error in Clipper::AddPaths" << std::endl;
return;
}
PolyTree polyTree;
clipper.Execute(ctUnion, polyTree, pftNonZero, pftNonZero);
// Traverse the PolyTree nodes and triangulate them with only their children holes
PolyNode *currentNode = polyTree.GetFirst();
while(currentNode != NULL)
{
// The holes are only used as the children of the contours
if (currentNode->IsHole())
{
currentNode = currentNode->GetNext();
continue;
}
// Convert to poly2tri's format
std::vector<p2t::Point> allPoints;
std::vector<size_t> linesSizes;
// Contour
for (const auto& pt : currentNode->Contour)
allPoints.emplace_back(static_cast<double>(pt.X), static_cast<double>(pt.Y));
linesSizes.push_back(allPoints.size());
// Holes
for(const auto childNode : currentNode->Childs)
{
// Slightly modify the polygon to guarantee no duplicate points
edgeShrink(childNode->Contour);
for (const auto& pt : childNode->Contour)
allPoints.emplace_back(static_cast<double>(pt.X), static_cast<double>(pt.Y));
linesSizes.push_back(allPoints.size());
}
// Poly2Tri uses pointers to points
std::vector<p2t::Point*> contourLine;
std::vector<std::vector<p2t::Point*>> holes;
auto nbLines = linesSizes.size();
size_t start = 0;
for (size_t i = 0; i < nbLines; ++i)
{
size_t end = linesSizes[i];
std::vector<p2t::Point*> line;
line.reserve(end - start);
for (size_t j = start; j < end; ++j)
line.push_back(&allPoints[j]);
start = end;
if (!i) contourLine = std::move(line);
else holes.push_back(std::move(line));
}
// Set the contour in poly2tri
p2t::CDT cdt(contourLine);
// Add the holes
for(auto& hole : holes)
cdt.AddHole(hole);
// Do the actual triangulation
cdt.Triangulate();
// Downscale the points and add them to the mesh
Mesh mesh;
for (const auto pt : allPoints)
mesh.addPoint(convert(pt));
// Convert the triangles
auto triangles = cdt.GetTriangles();
auto firstPt = allPoints.data();
for (const auto triangle : triangles)
{
int ptId1 = std::distance(firstPt, triangle->GetPoint(0));
int ptId2 = std::distance(firstPt, triangle->GetPoint(1));
int ptId3 = std::distance(firstPt, triangle->GetPoint(2));
mesh.addTriangle(ptId1, ptId2, ptId3);
}
outputMeshes.push_back(mesh);
currentNode = currentNode->GetNext();
}
}
