X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.cpp;h=a6c9c07a0714fb850498a3d6f4439d4247602468;hb=fb01d5df390a98313ca095a812fc240dc079d084;hp=642c6658739dd5252b2d61083ce6af2b872785ec;hpb=38922fcff5a03abfedffda3e06a45fad2270a044;p=mothur.git diff --git a/tree.cpp b/tree.cpp index 642c665..a6c9c07 100644 --- a/tree.cpp +++ b/tree.cpp @@ -13,9 +13,9 @@ /*****************************************************************/ Tree::Tree() { try { - globaldata = GlobalData::getInstance(); - numLeaves = globaldata->gTreemap->getNumSeqs(); + + numLeaves = globaldata->Treenames.size(); numNodes = 2*numLeaves - 1; tree.resize(numNodes); @@ -24,22 +24,18 @@ Tree::Tree() { for (int i = 0; i < numNodes; i++) { //initialize leaf nodes if (i <= (numLeaves-1)) { - tree[i].setName(globaldata->gTreemap->namesOfSeqs[i]); - tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])); - //the node knows its index - tree[i].setIndex(i); + tree[i].setName(globaldata->Treenames[i]); + tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->Treenames[i])); //set pcount and pGroup for groupname to 1. - tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1; - tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1; + tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1; + tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1; //Treemap knows name, group and index to speed up search - globaldata->gTreemap->setIndex(globaldata->gTreemap->namesOfSeqs[i], i); + globaldata->gTreemap->setIndex(globaldata->Treenames[i], i); //intialize non leaf nodes }else if (i > (numLeaves-1)) { tree[i].setName(""); tree[i].setGroup(""); - //the node knows its index - tree[i].setIndex(i); } } } @@ -54,7 +50,8 @@ Tree::Tree() { } /*****************************************************************/ - +Tree::~Tree() {} +/*****************************************************************/ int Tree::getIndex(string searchName) { try { //Treemap knows name, group and index to speed up search @@ -157,7 +154,7 @@ map Tree::mergeGroups(int i) { try { int lc = tree[i].getLChild(); int rc = tree[i].getRChild(); - + //set parsimony groups to left child map parsimony = tree[lc].pGroups; @@ -183,7 +180,7 @@ map Tree::mergeGroups(int i) { for(it=parsimony.begin();it!=parsimony.end();it++){ if(it->second == 1){ parsimony.erase(it->first); - it--; +// it--; } } //set one remaining groups to 1 @@ -245,24 +242,20 @@ map Tree::mergeUserGroups(int i, vector g) { maxPars = parsimony[it->first]; } } - + // this is true if right child had a greater parsimony for a certain group if(maxPars > 1){ //erase all the groups that are only 1 because you found something with 2. for(it=parsimony.begin();it!=parsimony.end();it++){ if(it->second == 1){ parsimony.erase(it->first); - it--; } } - //set one remaining groups to 1 - //so with our above example p[white] = 2 would be left and it would become p[white] = 1 for(it=parsimony.begin();it!=parsimony.end();it++){ parsimony[it->first] = 1; } + } - } - return parsimony; } catch(exception& e) { @@ -460,6 +453,38 @@ void Tree::randomTopology() { exit(1); } } +/*****************************************************************/ +void Tree::print(ostream& out) { + try { + int root = findRoot(); + printBranch(root, out, "branch"); + out << ";" << endl; + } + catch(exception& e) { + cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } + catch(...) { + cout << "An unknown error has occurred in the Tree class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } +} +/*****************************************************************/ +void Tree::printForBoot(ostream& out) { + try { + int root = findRoot(); + printBranch(root, out, "boot"); + out << ";" << endl; + } + catch(exception& e) { + cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function printForBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } + catch(...) { + cout << "An unknown error has occurred in the Tree class function printForBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } +} /*****************************************************************/ // This prints out the tree in Newick form. @@ -470,7 +495,7 @@ void Tree::createNewickFile(string f) { filename = f; openOutputFile(filename, out); - printBranch(root); + printBranch(root, out, "branch"); // you are at the end of the tree out << ";" << endl; @@ -493,7 +518,7 @@ int Tree::findRoot() { try { for (int i = 0; i < numNodes; i++) { //you found the root - if (tree[i].getParent() == -1) { return i; } + if (tree[i].getParent() == -1) { return i; } } return -1; } @@ -508,18 +533,40 @@ int Tree::findRoot() { } /*****************************************************************/ -void Tree::printBranch(int node) { +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()); + printBranch(tree[node].getLChild(), out, mode); out << ","; - printBranch(tree[node].getRChild()); + printBranch(tree[node].getRChild(), out, mode); out << ")"; + if (mode == "branch") { + //if there is a branch length then print it + if (tree[node].getBranchLength() != -1) { + out << ":" << tree[node].getBranchLength(); + } + }else if (mode == "boot") { + //if there is a label then print it + if (tree[node].getLabel() != -1) { + out << tree[node].getLabel(); + } + } }else { //you are a leaf - out << tree[node].getGroup() << ":" << tree[node].getBranchLength(); + out << tree[node].getGroup(); + if (mode == "branch") { + //if there is a branch length then print it + if (tree[node].getBranchLength() != -1) { + out << ":" << tree[node].getBranchLength(); + } + }else if (mode == "boot") { + //if there is a label then print it + if (tree[node].getLabel() != -1) { + out << tree[node].getLabel(); + } + } } }