X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.cpp;h=ce3de379d05d5eca8c991d2e93e64060377a2304;hb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;hp=e138121661f19f77d1c8603036793f86a95dfe67;hpb=51cf89e90eef8b300c2786eb1560dd89e6e83445;p=mothur.git diff --git a/tree.cpp b/tree.cpp index e138121..ce3de37 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; } + 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 @@ -194,13 +176,9 @@ 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 @@ -259,13 +237,9 @@ 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 +260,9 @@ 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 +302,9 @@ 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 +332,9 @@ 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 +348,9 @@ 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) { @@ -445,30 +403,35 @@ 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"; - exit(1); - } } /*****************************************************************/ void Tree::print(ostream& out) { try { int root = findRoot(); - printBranch(root, out); + 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"; + errorOut(e, "Tree", "print"); 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"; +} +/*****************************************************************/ +void Tree::printForBoot(ostream& out) { + try { + int root = findRoot(); + printBranch(root, out, "boot"); + out << ";" << endl; + } + catch(exception& e) { + errorOut(e, "Tree", "printForBoot"); exit(1); - } + } } + /*****************************************************************/ // This prints out the tree in Newick form. void Tree::createNewickFile(string f) { @@ -476,22 +439,19 @@ void Tree::createNewickFile(string f) { int root = findRoot(); //filename = getRootName(globaldata->getTreeFile()) + "newick"; filename = f; + openOutputFile(filename, out); - printBranch(root, out); + 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); - } } /*****************************************************************/ @@ -501,52 +461,60 @@ 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, ostream& out) { +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); + printBranch(tree[node].getLChild(), out, mode); out << ","; - printBranch(tree[node].getRChild(), out); + 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); - } } /*****************************************************************/ @@ -562,4 +530,145 @@ void Tree::printTree() { /*****************************************************************/ +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; + + //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(); + } + + readTreeString(filehandle); + } + //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; + + //ifthere 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. + readTreeString(filehandle); + 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); + } +} +/*******************************************************/ + +/*******************************************************/ +void 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 == ';') { break; } + //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(); + if(c == ';') { break; } + if(c == ')') { filehandle.putback(c); } + // k = c; +//cout << k << endl; + + } + } + catch(exception& e) { + errorOut(e, "Tree", "readTreeString"); + exit(1); + } +} + +/*******************************************************/ + +/*******************************************************/