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 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);
}
}
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;
}
