ofstream out;
m->openOutputFile(outputFileName, out);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
- out << "Node\tOTU#\tIndVal" << endl;
-
+
string treeOutputDir = outputDir;
if (outputDir == "") { treeOutputDir += m->hasPath(treefile); }
string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + "indicator.tre";
//you need the distances to leaf to decide grouping below
//this will also set branch lengths if the tree does not include them
- map<int, float> distToLeaf = getLengthToLeaf(T);
+ map<int, float> distToRoot = getDistToRoot(T);
//for each node
for (int i = T->getNumLeaves(); i < T->getNumNodes(); i++) {
if (sharedfile != "") {
vector< vector<SharedRAbundVector*> > groupings;
- /*groupings.resize(1);
- groupings[0].push_back(lookup[0]);
- groupings[0].push_back(lookup[1]);
- groupings[0].push_back(lookup[2]);
- groupings[0].push_back(lookup[3]);
- groupings[0].push_back(lookup[4]);*/
-
//get nodes that will be a valid grouping
//you are valid if you are not one of my descendants
- //AND your distToLeaf is <= mine
- //AND your distToLeaf is >= my smallest childs
- //AND you were not added as part of a larger groupings
+ //AND your distToRoot is >= mine
+ //AND you were not added as part of a larger grouping. Largest nodes are added first.
set<string> groupsAlreadyAdded;
//create a grouping with my grouping
for (int j = (T->getNumNodes()-1); j >= 0; j--) {
- if ((descendantNodes[i].count(j) == 0) && (distToLeaf[j] <= distToLeaf[i]) && ((distToLeaf[j] >= distToLeaf[T->tree[i].getLChild()]) || (distToLeaf[j] >= distToLeaf[T->tree[i].getRChild()]))) {
+
+
+ if ((descendantNodes[i].count(j) == 0) && (distToRoot[j] >= distToRoot[i])) {
vector<SharedRAbundVector*> subset;
int count = 0;
int doneCount = nodeToDescendants[j].size();
}
}
- if (groupsAlreadyAdded.size() != lookup.size()) { cout << i << '\t' << groupsAlreadyAdded.size() << '\t' << lookup.size() << endl; m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
- for (int k = 0; k < lookup.size(); k++) {
- if (groupsAlreadyAdded.count(lookup[k]->getGroup()) == 0) { cout << lookup[k]->getGroup() << endl; }
- }
+ if (groupsAlreadyAdded.size() != lookup.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
+ //for (int k = 0; k < lookup.size(); k++) {
+ // if (groupsAlreadyAdded.count(lookup[k]->getGroup()) == 0) { cout << lookup[k]->getGroup() << endl; }
+ //}
indicatorValues = getValues(groupings);
//get nodes that will be a valid grouping
//you are valid if you are not one of my descendants
- //AND your distToLeaf is <= mine
- //AND your distToLeaf is >= my smallest childs
- //AND you were not added as part of a larger grouping
+ //AND your distToRoot is >= mine
+ //AND you were not added as part of a larger grouping. Largest nodes are added first.
set<string> groupsAlreadyAdded;
//create a grouping with my grouping
if (subset.size() != 0) { groupings.push_back(subset); }
for (int j = (T->getNumNodes()-1); j >= 0; j--) {
- if ((descendantNodes[i].count(j) == 0) && (distToLeaf[j] <= distToLeaf[i]) && ((distToLeaf[j] >= distToLeaf[T->tree[i].getLChild()]) || (distToLeaf[j] >= distToLeaf[T->tree[i].getRChild()]))) {
+ if ((descendantNodes[i].count(j) == 0) && (distToRoot[j] >= distToRoot[i])) {
vector<SharedRAbundFloatVector*> subset;
int count = 0;
int doneCount = nodeToDescendants[j].size();
if (m->control_pressed) { out.close(); return 0; }
+
/******************************************************/
//output indicator values to table form + label tree //
/*****************************************************/
+ out << (i+1) << '\t';
for (int j = 0; j < indicatorValues.size(); j++) {
if (m->control_pressed) { out.close(); return 0; }
- out << (i+1) << '\t' << (j+1) << '\t' << indicatorValues[j] << endl;
+ out << indicatorValues[j] << '\t';
}
+ out << endl;
T->tree[i].setLabel((i+1));
}
}
//**********************************************************************************************************************
-//you need the distances to leaf to decide groupings
+//you need the distances to root to decide groupings
//this will also set branch lengths if the tree does not include them
-map<int, float> IndicatorCommand::getLengthToLeaf(Tree*& T){
+map<int, float> IndicatorCommand::getDistToRoot(Tree*& T){
try {
map<int, float> dists;
- for (int i = 0; i < T->getNumNodes(); i++) {
-
- int lc = T->tree[i].getLChild();
- int rc = T->tree[i].getRChild();
-
- //if you have no branch length, set it then calc
- if (T->tree[i].getBranchLength() <= 0.0) {
+ bool hasBranchLengths = false;
+ for (int i = 0; i < T->getNumNodes(); i++) {
+ if (T->tree[i].getBranchLength() > 0.0) { hasBranchLengths = true; break; }
+ }
+
+ //set branchlengths if needed
+ if (!hasBranchLengths) {
+ for (int i = 0; i < T->getNumNodes(); i++) {
+
+ int lc = T->tree[i].getLChild();
+ int rc = T->tree[i].getRChild();
if (lc == -1) { // you are a leaf
//if you are a leaf set you priliminary length to 1.0, this may adjust later
float rdist = dists[rc];
float greater = ldist;
- if (rdist > greater) { greater = rdist; dists[i] = ldist; }
- else { dists[i] = rdist; }
+ if (rdist > greater) { greater = rdist; dists[i] = ldist + 1.0;}
+ else { dists[i] = rdist + 1.0; }
+
//branch length = difference + 1
T->tree[lc].setBranchLength((abs(ldist-greater) + 1.0));
T->tree[rc].setBranchLength((abs(rdist-greater) + 1.0));
}
-
- }else{
- if (lc == -1) { dists[i] = T->tree[i].getBranchLength(); }
- else { //smaller of my two children distances plus my branch length
- //look at your children's length to leaf
- float ldist = dists[lc];
- float rdist = dists[rc];
-
- float smaller = ldist;
- if (rdist < smaller) { smaller = rdist; }
-
- dists[i] = smaller + T->tree[i].getBranchLength();
+ }
+ }
+
+ dists.clear();
+
+ for (int i = 0; i < T->getNumNodes(); i++) {
+
+ double sum = 0.0;
+ int index = i;
+
+ while(T->tree[index].getParent() != -1){
+ if (T->tree[index].getBranchLength() != -1) {
+ sum += abs(T->tree[index].getBranchLength());
}
+ index = T->tree[index].getParent();
}
+ dists[i] = sum;
}
return dists;
projects / mothur.git / blobdiff