X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.cpp;h=44ecadd534b60d60b602d9e052259ac69709f9d3;hb=28bcfc4a41b8b82f66636587e0d4d355d07cbdd1;hp=432811ecaabf1e50161061e291985ca080ed7773;hpb=03dca3b32a903c3f29fbcf5b410b19d6ab6dae63;p=mothur.git diff --git a/tree.cpp b/tree.cpp index 432811e..44ecadd 100644 --- a/tree.cpp +++ b/tree.cpp @@ -16,7 +16,7 @@ Tree::Tree(int num, TreeMap* t) : tmap(t) { numLeaves = num; numNodes = 2*numLeaves - 1; - + tree.resize(numNodes); } catch(exception& e) { @@ -28,9 +28,6 @@ Tree::Tree(int num, TreeMap* t) : tmap(t) { Tree::Tree(string g) { //do not use tree generated by this its just to extract the treenames, its a chicken before the egg thing that needs to be revisited. try { m = MothurOut::getInstance(); - - tmap = NULL; - parseTreeFile(); m->runParse = false; } catch(exception& e) { @@ -95,7 +92,6 @@ Tree::Tree(TreeMap* t, vector< vector >& sims) : tmap(t) { m = MothurOut::getInstance(); if (m->runParse == true) { parseTreeFile(); m->runParse = false; } - //for(int i = 0; i < globaldata->Treenames.size(); i++) { cout << i << '\t' << globaldata->Treenames[i] << endl; } numLeaves = m->Treenames.size(); numNodes = 2*numLeaves - 1; @@ -137,12 +133,11 @@ Tree::Tree(TreeMap* t, vector< vector >& sims) : tmap(t) { //build tree from matrix //initialize indexes map indexes; //maps row in simMatrix to vector index in the tree - int numGroups = (tmap->getNamesOfGroups()).size(); - for (int g = 0; g < numGroups; g++) { indexes[g] = g; } + for (int g = 0; g < numLeaves; g++) { indexes[g] = g; } //do merges and create tree structure by setting parents and children //there are numGroups - 1 merges to do - for (int i = 0; i < (numGroups - 1); i++) { + for (int i = 0; i < (numLeaves - 1); i++) { float largest = -1000.0; if (m->control_pressed) { break; } @@ -157,11 +152,11 @@ Tree::Tree(TreeMap* t, vector< vector >& sims) : tmap(t) { //set non-leaf node info and update leaves to know their parents //non-leaf - tree[numGroups + i].setChildren(indexes[row], indexes[column]); + tree[numLeaves + i].setChildren(indexes[row], indexes[column]); //parents - tree[indexes[row]].setParent(numGroups + i); - tree[indexes[column]].setParent(numGroups + i); + tree[indexes[row]].setParent(numLeaves + i); + tree[indexes[column]].setParent(numLeaves + i); //blength = distance / 2; float blength = ((1.0 - largest) / 2); @@ -171,12 +166,12 @@ Tree::Tree(TreeMap* t, vector< vector >& sims) : tmap(t) { tree[indexes[column]].setBranchLength(blength - tree[indexes[column]].getLengthToLeaves()); //set your length to leaves to your childs length plus branchlength - tree[numGroups + i].setLengthToLeaves(tree[indexes[row]].getLengthToLeaves() + tree[indexes[row]].getBranchLength()); + tree[numLeaves + i].setLengthToLeaves(tree[indexes[row]].getLengthToLeaves() + tree[indexes[row]].getBranchLength()); //update index - indexes[row] = numGroups+i; - indexes[column] = numGroups+i; + indexes[row] = numLeaves+i; + indexes[column] = numLeaves+i; //remove highest value that caused the merge. sims[row][column] = -1000.0; @@ -196,7 +191,8 @@ Tree::Tree(TreeMap* t, vector< vector >& sims) : tmap(t) { //adjust tree to make sure root to tip length is .5 int root = findRoot(); tree[root].setBranchLength((0.5 - tree[root].getLengthToLeaves())); - } + + } catch(exception& e) { m->errorOut(e, "Tree", "Tree"); exit(1); @@ -329,12 +325,13 @@ void Tree::setIndex(string searchName, int index) { } } /*****************************************************************/ -int Tree::assembleTree() { +int Tree::assembleTree(map nameMap) { try { - //float A = clock(); + //save for later + names = nameMap; //if user has given a names file we want to include that info in the pgroups and pcount info. - if(m->names.size() != 0) { addNamesToCounts(m->names); } + if(nameMap.size() != 0) { addNamesToCounts(nameMap); } //build the pGroups in non leaf nodes to be used in the parsimony calcs. for (int i = numLeaves; i < numNodes; i++) { @@ -343,8 +340,7 @@ int Tree::assembleTree() { tree[i].pGroups = (mergeGroups(i)); tree[i].pcount = (mergeGcounts(i)); } - //float B = clock(); - //cout << "assembleTree\t" << (B-A) / CLOCKS_PER_SEC << endl; + return 0; } catch(exception& e) { @@ -352,7 +348,7 @@ int Tree::assembleTree() { exit(1); } } -/*****************************************************************/ +/***************************************************************** int Tree::assembleTree(string n) { try { @@ -380,7 +376,8 @@ void Tree::getSubTree(Tree* Ctree, vector Groups) { //copy Tree since we are going to destroy it Tree* copy = new Tree(tmap); copy->getCopy(Ctree); - copy->assembleTree("nonames"); + map empty; + copy->assembleTree(empty); //we want to select some of the leaf nodes to create the output tree //go through the input Tree starting at parents of leaves @@ -591,6 +588,37 @@ int Tree::populateNewTree(vector& oldtree, int node, int& index) { } } /*****************************************************************/ +void Tree::getCopy(Tree* copy, map nameMap) { + try { + + //for each node in the tree copy its info + for (int i = 0; i < numNodes; i++) { + //copy branch length + tree[i].setBranchLength(copy->tree[i].getBranchLength()); + + //copy parent + tree[i].setParent(copy->tree[i].getParent()); + + //copy children + tree[i].setChildren(copy->tree[i].getLChild(), copy->tree[i].getRChild()); + } + + if (nameMap.size() != 0) { addNamesToCounts(nameMap); } + + //build the pGroups in non leaf nodes to be used in the parsimony calcs. + for (int i = numLeaves; i < numNodes; i++) { + if (m->control_pressed) { break; } + + tree[i].pGroups = (mergeGroups(i)); + tree[i].pcount = (mergeGcounts(i)); + } + } + catch(exception& e) { + m->errorOut(e, "Tree", "getCopy"); + exit(1); + } +} +/*****************************************************************/ void Tree::getCopy(Tree* copy) { try { @@ -840,21 +868,23 @@ void Tree::randomBlengths() { /*************************************************************************************************/ void Tree::assembleRandomUnifracTree(vector g) { randomLabels(g); - assembleTree("noNameCounts"); + map empty; + assembleTree(empty); } /*************************************************************************************************/ void Tree::assembleRandomUnifracTree(string groupA, string groupB) { - vector temp; temp.push_back(groupA); temp.push_back(groupB); randomLabels(temp); - assembleTree("noNameCounts"); + map empty; + assembleTree(empty); } /*************************************************************************************************/ //for now it's just random topology but may become random labels as well later that why this is such a simple function now... void Tree::assembleRandomTree() { randomTopology(); - assembleTree(); + map empty; + assembleTree(empty); } /**************************************************************************************************/ @@ -907,6 +937,18 @@ void Tree::print(ostream& out) { } } /*****************************************************************/ +void Tree::print(ostream& out, map nameMap) { + try { + int root = findRoot(); + printBranch(root, out, nameMap); + out << ";" << endl; + } + catch(exception& e) { + m->errorOut(e, "Tree", "print"); + exit(1); + } +} +/*****************************************************************/ void Tree::print(ostream& out, string mode) { try { int root = findRoot(); @@ -959,10 +1001,82 @@ int Tree::findRoot() { } } /*****************************************************************/ -void Tree::printBranch(int node, ostream& out, string mode) { +void Tree::printBranch(int node, ostream& out, map names) { try { // you are not a leaf + if (tree[node].getLChild() != -1) { + out << "("; + printBranch(tree[node].getLChild(), out, names); + out << ","; + printBranch(tree[node].getRChild(), out, names); + out << ")"; + + //if there is a branch length then print it + if (tree[node].getBranchLength() != -1) { + out << ":" << tree[node].getBranchLength(); + } + + }else { //you are a leaf + map::iterator itNames = names.find(tree[node].getName()); + + string outputString = ""; + if (itNames != names.end()) { + + vector dupNames; + m->splitAtComma((itNames->second), dupNames); + + if (dupNames.size() == 1) { + outputString += tree[node].getName(); + if (tree[node].getBranchLength() != -1) { + outputString += ":" + toString(tree[node].getBranchLength()); + } + }else { + outputString += "("; + + for (int u = 0; u < dupNames.size()-1; u++) { + outputString += dupNames[u]; + + if (tree[node].getBranchLength() != -1) { + outputString += ":" + toString(0.0); + } + outputString += ","; + } + + outputString += dupNames[dupNames.size()-1]; + if (tree[node].getBranchLength() != -1) { + outputString += ":" + toString(0.0); + } + + outputString += ")"; + if (tree[node].getBranchLength() != -1) { + outputString += ":" + toString(tree[node].getBranchLength()); + } + } + }else { + outputString = tree[node].getName(); + //if there is a branch length then print it + if (tree[node].getBranchLength() != -1) { + outputString += ":" + toString(tree[node].getBranchLength()); + } + + m->mothurOut("[ERROR]: " + tree[node].getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); + } + + out << outputString; + } + + } + catch(exception& e) { + m->errorOut(e, "Tree", "printBranch"); + exit(1); + } +} +/*****************************************************************/ +void Tree::printBranch(int node, ostream& out, string mode) { + try { + + // you are not a leaf if (tree[node].getLChild() != -1) { out << "("; printBranch(tree[node].getLChild(), out, mode); @@ -987,11 +1101,6 @@ try { if (tree[node].getBranchLength() != -1) { out << ":" << tree[node].getBranchLength(); } - }else if (mode == "deunique") { - //if there is a branch length then print it - if (tree[node].getBranchLength() != -1) { - out << ":" << tree[node].getBranchLength(); - } } }else { //you are a leaf string leafGroup = tmap->getGroup(tree[node].getName()); @@ -1017,53 +1126,6 @@ try { if (tree[node].getBranchLength() != -1) { out << ":" << tree[node].getBranchLength(); } - }else if (mode == "deunique") { - map::iterator itNames = m->names.find(tree[node].getName()); - - string outputString = ""; - if (itNames != m->names.end()) { - - vector dupNames; - m->splitAtComma((itNames->second), dupNames); - - if (dupNames.size() == 1) { - outputString += tree[node].getName(); - if (tree[node].getBranchLength() != -1) { - outputString += ":" + toString(tree[node].getBranchLength()); - } - }else { - outputString += "("; - - for (int u = 0; u < dupNames.size()-1; u++) { - outputString += dupNames[u]; - - if (tree[node].getBranchLength() != -1) { - outputString += ":" + toString(0.0); - } - outputString += ","; - } - - outputString += dupNames[dupNames.size()-1]; - if (tree[node].getBranchLength() != -1) { - outputString += ":" + toString(0.0); - } - - outputString += ")"; - if (tree[node].getBranchLength() != -1) { - outputString += ":" + toString(tree[node].getBranchLength()); - } - } - }else { - outputString = tree[node].getName(); - //if there is a branch length then print it - if (tree[node].getBranchLength() != -1) { - outputString += ":" + toString(tree[node].getBranchLength()); - } - - m->mothurOut("[ERROR]: " + tree[node].getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); - } - - out << outputString; } }