X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.cpp;h=ad80b2bafe98c048fb44e8e2683aae962da08894;hb=72ebb6fa35b45b149812d47c2b1cb8acaca64659;hp=f93b9335749b4e79bb8c3e3c1be58684efc1cf65;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d;p=mothur.git diff --git a/tree.cpp b/tree.cpp index f93b933..ad80b2b 100644 --- a/tree.cpp +++ b/tree.cpp @@ -15,6 +15,8 @@ Tree::Tree() { try { globaldata = GlobalData::getInstance(); + if (globaldata->runParse == true) { parseTreeFile(); globaldata->runParse = false; } +//for(int i = 0; i < globaldata->Treenames.size(); i++) { cout << i << '\t' << globaldata->Treenames[i] << endl; } numLeaves = globaldata->Treenames.size(); numNodes = 2*numLeaves - 1; @@ -40,13 +42,9 @@ Tree::Tree() { } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function Tree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "Tree", "Tree"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the Tree class function Tree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /*****************************************************************/ @@ -61,13 +59,9 @@ int Tree::getIndex(string searchName) { } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function getIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "Tree", "getIndex"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the Tree class function getIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /*****************************************************************/ @@ -77,13 +71,9 @@ void Tree::setIndex(string searchName, int index) { globaldata->gTreemap->setIndex(searchName, index); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function setIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "Tree", "setIndex"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the Tree class function setIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /*****************************************************************/ void Tree::assembleTree() { @@ -95,13 +85,9 @@ void Tree::assembleTree() { } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function assembleTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "Tree", "assembleTree"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the Tree class function assembleTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /*****************************************************************/ void Tree::getCopy(Tree* copy) { @@ -136,13 +122,9 @@ void Tree::getCopy(Tree* copy) { } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function getCopy. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "Tree", "getCopy"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the Tree class function getCopy. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /*****************************************************************/ //returns a map with a groupname and the number of times that group was seen in the children @@ -177,11 +159,10 @@ map Tree::mergeGroups(int i) { // 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++){ + for(it=parsimony.begin();it!=parsimony.end();){ if(it->second == 1){ - parsimony.erase(it->first); -// it--; - } + parsimony.erase(it++); + }else { 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 @@ -194,13 +175,9 @@ map Tree::mergeGroups(int i) { return parsimony; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "Tree", "mergeGroups"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the Tree class function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /*****************************************************************/ //returns a map with a groupname and the number of times that group was seen in the children @@ -215,13 +192,17 @@ map Tree::mergeUserGroups(int i, vector g) { int rc = tree[i].getRChild(); //loop through nodes groups removing the ones the user doesn't want - for (it = tree[lc].pGroups.begin(); it != tree[lc].pGroups.end(); it++) { - if (inUsersGroups(it->first, g) != true) { tree[lc].pGroups.erase(it->first); } + for(it=tree[lc].pGroups.begin();it!=tree[lc].pGroups.end();){ + if (inUsersGroups(it->first, g) != true) { + tree[lc].pGroups.erase(it++); + }else { it++; } } - + //loop through nodes groups removing the ones the user doesn't want - for (it = tree[rc].pGroups.begin(); it != tree[rc].pGroups.end(); it++) { - if (inUsersGroups(it->first, g) != true) { tree[rc].pGroups.erase(it->first); } + for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();){ + if (inUsersGroups(it->first, g) != true) { + tree[rc].pGroups.erase(it++); + }else { it++; } } //set parsimony groups to left child @@ -246,11 +227,12 @@ map Tree::mergeUserGroups(int i, vector g) { // 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++){ + for(it=parsimony.begin();it!=parsimony.end();){ if(it->second == 1){ - parsimony.erase(it->first); - } + parsimony.erase(it++); + }else { it++; } } + for(it=parsimony.begin();it!=parsimony.end();it++){ parsimony[it->first] = 1; } @@ -259,13 +241,9 @@ map Tree::mergeUserGroups(int i, vector g) { return parsimony; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "Tree", "mergeUserGroups"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the Tree class function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } @@ -286,13 +264,9 @@ map Tree::mergeGcounts(int position) { return sum; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function mergeGcounts. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "Tree", "mergeGcounts"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the Tree class function mergeGcounts. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /**************************************************************************************************/ @@ -332,13 +306,9 @@ void Tree::randomLabels(vector g) { } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "Tree", "randomLabels"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the Tree class function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /**************************************************************************************************/ @@ -366,13 +336,9 @@ void Tree::randomLabels(string groupA, string groupB) { } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "Tree", "randomLabels"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the Tree class function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /**************************************************************************************************/ void Tree::randomBlengths() { @@ -386,13 +352,9 @@ void Tree::randomBlengths() { } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomBlengths. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "Tree", "randomBlengths"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the Tree class function randomBlengths. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /*************************************************************************************************/ void Tree::assembleRandomUnifracTree(vector g) { @@ -437,7 +399,7 @@ void Tree::randomTopology() { escape = 1; } } - + tree[i].setChildren(rnd_index1,rnd_index2); tree[i].setParent(-1); tree[rnd_index1].setParent(i); @@ -445,13 +407,33 @@ void Tree::randomTopology() { } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomTopology. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "Tree", "randomTopology"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the Tree class function randomTopology. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +/*****************************************************************/ +void Tree::print(ostream& out) { + try { + int root = findRoot(); + printBranch(root, out, "branch"); + out << ";" << endl; + } + catch(exception& e) { + errorOut(e, "Tree", "print"); exit(1); - } + } +} +/*****************************************************************/ +void Tree::printForBoot(ostream& out) { + try { + int root = findRoot(); + printBranch(root, out, "boot"); + out << ";" << endl; + } + catch(exception& e) { + errorOut(e, "Tree", "printForBoot"); + exit(1); + } } /*****************************************************************/ @@ -461,22 +443,19 @@ void Tree::createNewickFile(string f) { int root = findRoot(); //filename = getRootName(globaldata->getTreeFile()) + "newick"; filename = f; + openOutputFile(filename, out); - printBranch(root); + printBranch(root, out, "branch"); // you are at the end of the tree out << ";" << endl; out.close(); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function createNewickFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "Tree", "createNewickFile"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the Tree class function createNewickFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /*****************************************************************/ @@ -486,52 +465,60 @@ 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; } + //cout << "i = " << i << endl; + //cout << "i's parent = " << tree[i].getParent() << endl; } return -1; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function findRoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "Tree", "findRoot"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the Tree class function findRoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /*****************************************************************/ -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 there is a branch length then print it - if (tree[node].getBranchLength() != -1) { - out << ":" << tree[node].getBranchLength(); + 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(); - //if there is a branch length then print it - if (tree[node].getBranchLength() != -1) { - out << ":" << tree[node].getBranchLength(); + 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(); + } } } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function printBranch. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "Tree", "printBranch"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the Tree class function printBranch. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /*****************************************************************/ @@ -546,5 +533,155 @@ void Tree::printTree() { } /*****************************************************************/ +//this code is a mess and should be rethought...-slw +void Tree::parseTreeFile() { + + //only takes names from the first tree and assumes that all trees use the same names. + try { + string filename = globaldata->getTreeFile(); + ifstream filehandle; + openInputFile(filename, filehandle); + int c, comment; + comment = 0; + int done = 1; + + //ifyou are not a nexus file + if((c = filehandle.peek()) != '#') { + while((c = filehandle.peek()) != ';') { + while ((c = filehandle.peek()) != ';') { + // get past comments + if(c == '[') { + comment = 1; + } + if(c == ']'){ + comment = 0; + } + if((c == '(') && (comment != 1)){ break; } + filehandle.get(); + } + + done = readTreeString(filehandle); + if (done == 0) { break; } + } + //ifyou are a nexus file + }else if((c = filehandle.peek()) == '#') { + string holder = ""; + + // get past comments + while(holder != "translate" && holder != "Translate"){ + if(holder == "[" || holder == "[!"){ + comment = 1; + } + if(holder == "]"){ + comment = 0; + } + filehandle >> holder; + + //if there is no translate then you must read tree string otherwise use translate to get names + if((holder == "tree") && (comment != 1)){ + //pass over the "tree rep.6878900 = " + while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF)) {;} + + if(c == EOF) { break; } + filehandle.putback(c); //put back first ( of tree. + done = readTreeString(filehandle); + + break; + } + + if (done == 0) { break; } + } + + //use nexus translation rather than parsing tree to save time + if((holder == "translate") || (holder == "Translate")) { + + string number, name, h; + h = ""; // so it enters the loop the first time + while((h != ";") && (number != ";")) { + filehandle >> number; + filehandle >> name; + + //c = , until done with translation then c = ; + h = name.substr(name.length()-1, name.length()); + name.erase(name.end()-1); //erase the comma + globaldata->Treenames.push_back(number); + } + if(number == ";") { globaldata->Treenames.pop_back(); } //in case ';' from translation is on next line instead of next to last name + } + } + filehandle.close(); + } + catch(exception& e) { + errorOut(e, "Tree", "parseTreeFile"); + exit(1); + } +} +/*******************************************************/ + +/*******************************************************/ +int Tree::readTreeString(ifstream& filehandle) { + try { + int c; + string name; //, k + + while((c = filehandle.peek()) != ';') { +//k = c; +//cout << " at beginning of while " << k << endl; + if(c == ')') { + //to pass over labels in trees + c=filehandle.get(); + while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); } + filehandle.putback(c); + } + if(c == ';') { return 0; } + if(c == -1) { return 0; } + //if you are a name + if((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space + name = ""; + c = filehandle.get(); + //k = c; +//cout << k << endl; + while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) { + name += c; + c = filehandle.get(); + //k = c; +//cout << " in name while " << k << endl; + } + +//cout << "name = " << name << endl; + globaldata->Treenames.push_back(name); + filehandle.putback(c); +//k = c; +//cout << " after putback" << k << endl; + } + + if(c == ':') { //read until you reach the end of the branch length + while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) { + c = filehandle.get(); + //k = c; + //cout << " in branch while " << k << endl; + } + filehandle.putback(c); + } + + c = filehandle.get(); +//k = c; + //cout << " here after get " << k << endl; + if(c == ';') { return 0; } + if(c == ')') { filehandle.putback(c); } + //k = c; +//cout << k << endl; + + } + return 0; + } + catch(exception& e) { + errorOut(e, "Tree", "readTreeString"); + exit(1); + } +} + +/*******************************************************/ +/*******************************************************/