X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=tree.cpp;h=745893471e065abee12e7752b91c71bb37c1a635;hp=432811ecaabf1e50161061e291985ca080ed7773;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=03dca3b32a903c3f29fbcf5b410b19d6ab6dae63 diff --git a/tree.cpp b/tree.cpp index 432811e..7458934 100644 --- a/tree.cpp +++ b/tree.cpp @@ -10,13 +10,13 @@ #include "tree.h" /*****************************************************************/ -Tree::Tree(int num, TreeMap* t) : tmap(t) { +Tree::Tree(int num, CountTable* t) : ct(t) { try { m = MothurOut::getInstance(); 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) { @@ -39,21 +36,20 @@ Tree::Tree(string g) { //do not use tree generated by this its just to extract t } } /*****************************************************************/ -Tree::Tree(TreeMap* t) : tmap(t) { +Tree::Tree(CountTable* t) : ct(t) { try { 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; tree.resize(numNodes); //initialize groupNodeInfo - for (int i = 0; i < (tmap->getNamesOfGroups()).size(); i++) { - groupNodeInfo[(tmap->getNamesOfGroups())[i]].resize(0); - } + vector namesOfGroups = ct->getNamesOfGroups(); + for (int i = 0; i < namesOfGroups.size(); i++) { groupNodeInfo[namesOfGroups[i]].resize(0); } //initialize tree with correct number of nodes, name and group info. for (int i = 0; i < numNodes; i++) { @@ -62,19 +58,35 @@ Tree::Tree(TreeMap* t) : tmap(t) { tree[i].setName(m->Treenames[i]); //save group info - string group = tmap->getGroup(m->Treenames[i]); - - vector tempGroups; tempGroups.push_back(group); - tree[i].setGroup(tempGroups); - groupNodeInfo[group].push_back(i); - - //set pcount and pGroup for groupname to 1. - tree[i].pcount[group] = 1; - tree[i].pGroups[group] = 1; - - //Treemap knows name, group and index to speed up search - tmap->setIndex(m->Treenames[i], i); - + int maxPars = 1; + vector group; + vector counts = ct->getGroupCounts(m->Treenames[i]); + for (int j = 0; j < namesOfGroups.size(); j++) { + if (counts[j] != 0) { //you have seqs from this group + groupNodeInfo[namesOfGroups[j]].push_back(i); + group.push_back(namesOfGroups[j]); + tree[i].pGroups[namesOfGroups[j]] = counts[j]; + tree[i].pcount[namesOfGroups[j]] = counts[j]; + //keep highest group + if(counts[j] > maxPars){ maxPars = counts[j]; } + } + } + tree[i].setGroup(group); + setIndex(m->Treenames[i], i); + + if (maxPars > 1) { //then we have some more dominant groups + //erase all the groups that are less than maxPars because you found a more dominant group. + for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();){ + if(it->second < maxPars){ + tree[i].pGroups.erase(it++); + }else { it++; } + } + //set one remaining groups to 1 + for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();it++){ + tree[i].pGroups[it->first] = 1; + } + }//end if + //intialize non leaf nodes }else if (i > (numLeaves-1)) { tree[i].setName(""); @@ -90,21 +102,19 @@ Tree::Tree(TreeMap* t) : tmap(t) { } } /*****************************************************************/ -Tree::Tree(TreeMap* t, vector< vector >& sims) : tmap(t) { +Tree::Tree(CountTable* t, vector< vector >& sims) : ct(t) { try { 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; tree.resize(numNodes); //initialize groupNodeInfo - for (int i = 0; i < (tmap->getNamesOfGroups()).size(); i++) { - groupNodeInfo[(tmap->getNamesOfGroups())[i]].resize(0); - } + vector namesOfGroups = ct->getNamesOfGroups(); + for (int i = 0; i < namesOfGroups.size(); i++) { groupNodeInfo[namesOfGroups[i]].resize(0); } //initialize tree with correct number of nodes, name and group info. for (int i = 0; i < numNodes; i++) { @@ -113,18 +123,34 @@ Tree::Tree(TreeMap* t, vector< vector >& sims) : tmap(t) { tree[i].setName(m->Treenames[i]); //save group info - string group = tmap->getGroup(m->Treenames[i]); - - vector tempGroups; tempGroups.push_back(group); - tree[i].setGroup(tempGroups); - groupNodeInfo[group].push_back(i); - - //set pcount and pGroup for groupname to 1. - tree[i].pcount[group] = 1; - tree[i].pGroups[group] = 1; - - //Treemap knows name, group and index to speed up search - tmap->setIndex(m->Treenames[i], i); + int maxPars = 1; + vector group; + vector counts = ct->getGroupCounts(m->Treenames[i]); + for (int j = 0; j < namesOfGroups.size(); j++) { + if (counts[j] != 0) { //you have seqs from this group + groupNodeInfo[namesOfGroups[j]].push_back(i); + group.push_back(namesOfGroups[j]); + tree[i].pGroups[namesOfGroups[j]] = counts[j]; + tree[i].pcount[namesOfGroups[j]] = counts[j]; + //keep highest group + if(counts[j] > maxPars){ maxPars = counts[j]; } + } + } + tree[i].setGroup(group); + setIndex(m->Treenames[i], i); + + if (maxPars > 1) { //then we have some more dominant groups + //erase all the groups that are less than maxPars because you found a more dominant group. + for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();){ + if(it->second < maxPars){ + tree[i].pGroups.erase(it++); + }else { it++; } + } + //set one remaining groups to 1 + for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();it++){ + tree[i].pGroups[it->first] = 1; + } + }//end if //intialize non leaf nodes }else if (i > (numLeaves-1)) { @@ -133,16 +159,16 @@ Tree::Tree(TreeMap* t, vector< vector >& sims) : tmap(t) { tree[i].setGroup(tempGroups); } } + //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; } + map thisIndexes; //maps row in simMatrix to vector index in the tree + for (int g = 0; g < numLeaves; g++) { thisIndexes[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; } @@ -157,26 +183,26 @@ 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(thisIndexes[row], thisIndexes[column]); //parents - tree[indexes[row]].setParent(numGroups + i); - tree[indexes[column]].setParent(numGroups + i); + tree[thisIndexes[row]].setParent(numLeaves + i); + tree[thisIndexes[column]].setParent(numLeaves + i); //blength = distance / 2; float blength = ((1.0 - largest) / 2); //branchlengths - tree[indexes[row]].setBranchLength(blength - tree[indexes[row]].getLengthToLeaves()); - tree[indexes[column]].setBranchLength(blength - tree[indexes[column]].getLengthToLeaves()); + tree[thisIndexes[row]].setBranchLength(blength - tree[thisIndexes[row]].getLengthToLeaves()); + tree[thisIndexes[column]].setBranchLength(blength - tree[thisIndexes[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[thisIndexes[row]].getLengthToLeaves() + tree[thisIndexes[row]].getBranchLength()); //update index - indexes[row] = numGroups+i; - indexes[column] = numGroups+i; + thisIndexes[row] = numLeaves+i; + thisIndexes[column] = numLeaves+i; //remove highest value that caused the merge. sims[row][column] = -1000.0; @@ -196,7 +222,8 @@ 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); @@ -204,7 +231,7 @@ Tree::Tree(TreeMap* t, vector< vector >& sims) : tmap(t) { } /*****************************************************************/ Tree::~Tree() {} -/*****************************************************************/ +/***************************************************************** void Tree::addNamesToCounts(map nameMap) { try { //ex. seq1 seq2,seq3,se4 @@ -301,15 +328,15 @@ void Tree::addNamesToCounts(map nameMap) { m->errorOut(e, "Tree", "addNamesToCounts"); exit(1); } -} +}*/ /*****************************************************************/ int Tree::getIndex(string searchName) { try { - //Treemap knows name, group and index to speed up search - // getIndex function will return the vector index or -1 if seq is not found. - int index = tmap->getIndex(searchName); - return index; - + map::iterator itIndex = indexes.find(searchName); + if (itIndex != indexes.end()) { + return itIndex->second; + } + return -1; } catch(exception& e) { m->errorOut(e, "Tree", "getIndex"); @@ -320,8 +347,10 @@ int Tree::getIndex(string searchName) { void Tree::setIndex(string searchName, int index) { try { - //set index in treemap - tmap->setIndex(searchName, index); + map::iterator itIndex = indexes.find(searchName); + if (itIndex == indexes.end()) { + indexes[searchName] = index; + } } catch(exception& e) { m->errorOut(e, "Tree", "setIndex"); @@ -330,12 +359,7 @@ void Tree::setIndex(string searchName, int index) { } /*****************************************************************/ int Tree::assembleTree() { - try { - //float A = clock(); - - //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); } - + try { //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) { return 1; } @@ -343,28 +367,7 @@ 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) { - m->errorOut(e, "Tree", "assembleTree"); - exit(1); - } -} -/*****************************************************************/ -int Tree::assembleTree(string n) { - try { - //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) { return 1; } - - 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) { @@ -378,39 +381,60 @@ void Tree::getSubTree(Tree* Ctree, vector Groups) { try { //copy Tree since we are going to destroy it - Tree* copy = new Tree(tmap); + Tree* copy = new Tree(ct); copy->getCopy(Ctree); - copy->assembleTree("nonames"); + copy->assembleTree(); //we want to select some of the leaf nodes to create the output tree //go through the input Tree starting at parents of leaves + //initialize groupNodeInfo + vector namesOfGroups = ct->getNamesOfGroups(); + for (int i = 0; i < namesOfGroups.size(); i++) { groupNodeInfo[namesOfGroups[i]].resize(0); } + + //initialize tree with correct number of nodes, name and group info. for (int i = 0; i < numNodes; i++) { - //initialize leaf nodes if (i <= (numLeaves-1)) { tree[i].setName(Groups[i]); //save group info - string group = tmap->getGroup(Groups[i]); - vector tempGroups; tempGroups.push_back(group); - tree[i].setGroup(tempGroups); - groupNodeInfo[group].push_back(i); - - //set pcount and pGroup for groupname to 1. - tree[i].pcount[group] = 1; - tree[i].pGroups[group] = 1; - - //Treemap knows name, group and index to speed up search - tmap->setIndex(Groups[i], i); - - //intialize non leaf nodes + int maxPars = 1; + vector group; + vector counts = ct->getGroupCounts(Groups[i]); + for (int j = 0; j < namesOfGroups.size(); j++) { + if (counts[j] != 0) { //you have seqs from this group + groupNodeInfo[namesOfGroups[j]].push_back(i); + group.push_back(namesOfGroups[j]); + tree[i].pGroups[namesOfGroups[j]] = counts[j]; + tree[i].pcount[namesOfGroups[j]] = counts[j]; + //keep highest group + if(counts[j] > maxPars){ maxPars = counts[j]; } + } + } + tree[i].setGroup(group); + setIndex(Groups[i], i); + + if (maxPars > 1) { //then we have some more dominant groups + //erase all the groups that are less than maxPars because you found a more dominant group. + for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();){ + if(it->second < maxPars){ + tree[i].pGroups.erase(it++); + }else { it++; } + } + //set one remaining groups to 1 + for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();it++){ + tree[i].pGroups[it->first] = 1; + } + }//end if + + //intialize non leaf nodes }else if (i > (numLeaves-1)) { tree[i].setName(""); vector tempGroups; tree[i].setGroup(tempGroups); } } - + set removedLeaves; for (int i = 0; i < copy->getNumLeaves(); i++) { @@ -537,7 +561,7 @@ void Tree::getSubTree(Tree* Ctree, vector Groups) { exit(1); } } -/*****************************************************************/ +/***************************************************************** //assumes nameMap contains unique names as key or is empty. //assumes numLeaves defined in tree constructor equals size of seqsToInclude and seqsToInclude only contains unique seqs. int Tree::getSubTree(Tree* copy, vector seqsToInclude, map nameMap) { @@ -581,7 +605,7 @@ int Tree::populateNewTree(vector& oldtree, int node, int& index) { return (index++); }else { //you are a leaf - int indexInNewTree = tmap->getIndex(oldtree[node].getName()); + int indexInNewTree = getIndex(oldtree[node].getName()); return indexInNewTree; } } @@ -591,6 +615,35 @@ int Tree::populateNewTree(vector& oldtree, int node, int& index) { } } /*****************************************************************/ +void Tree::getCopy(Tree* copy, bool subsample) { + 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()); + } + + //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 { @@ -612,8 +665,8 @@ void Tree::getCopy(Tree* copy) { tree[i].setChildren(copy->tree[i].getLChild(), copy->tree[i].getRChild()); //copy index in node and tmap + setIndex(copy->tree[i].getName(), getIndex(copy->tree[i].getName())); tree[i].setIndex(copy->tree[i].getIndex()); - setIndex(copy->tree[i].getName(), getIndex(copy->tree[i].getName())); //copy pGroups tree[i].pGroups = copy->tree[i].pGroups; @@ -777,8 +830,8 @@ void Tree::randomLabels(vector g) { try { //initialize groupNodeInfo - for (int i = 0; i < (tmap->getNamesOfGroups()).size(); i++) { - groupNodeInfo[(tmap->getNamesOfGroups())[i]].resize(0); + for (int i = 0; i < (ct->getNamesOfGroups()).size(); i++) { + groupNodeInfo[(ct->getNamesOfGroups())[i]].resize(0); } for(int i = 0; i < numLeaves; i++){ @@ -840,14 +893,13 @@ void Tree::randomBlengths() { /*************************************************************************************************/ void Tree::assembleRandomUnifracTree(vector g) { randomLabels(g); - assembleTree("noNameCounts"); + assembleTree(); } /*************************************************************************************************/ void Tree::assembleRandomUnifracTree(string groupA, string groupB) { - vector temp; temp.push_back(groupA); temp.push_back(groupB); randomLabels(temp); - assembleTree("noNameCounts"); + assembleTree(); } /*************************************************************************************************/ @@ -907,6 +959,18 @@ 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 +1023,82 @@ 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); @@ -987,23 +1123,18 @@ 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()); + vector leafGroup = ct->getGroups(tree[node].getName()); if (mode == "branch") { - out << leafGroup; + out << leafGroup[0]; //if there is a branch length then print it if (tree[node].getBranchLength() != -1) { out << ":" << tree[node].getBranchLength(); } }else if (mode == "boot") { - out << leafGroup; + out << leafGroup[0]; //if there is a label then print it if (tree[node].getLabel() != -1) { out << tree[node].getLabel(); @@ -1017,53 +1148,6 @@ 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; } } @@ -1104,16 +1188,16 @@ void Tree::printBranch(int node, ostream& out, string mode, vector& theseN } } }else { //you are a leaf - string leafGroup = tmap->getGroup(theseNodes[node].getName()); + vector leafGroup = ct->getGroups(theseNodes[node].getName()); if (mode == "branch") { - out << leafGroup; + out << leafGroup[0]; //if there is a branch length then print it if (theseNodes[node].getBranchLength() != -1) { out << ":" << theseNodes[node].getBranchLength(); } }else if (mode == "boot") { - out << leafGroup; + out << leafGroup[0]; //if there is a label then print it if (theseNodes[node].getLabel() != -1) { out << theseNodes[node].getLabel(); @@ -1149,7 +1233,7 @@ void Tree::printTree() { /*****************************************************************/ //this code is a mess and should be rethought...-slw -void Tree::parseTreeFile() { +int Tree::parseTreeFile() { //only takes names from the first tree and assumes that all trees use the same names. try { @@ -1162,8 +1246,10 @@ void Tree::parseTreeFile() { //ifyou are not a nexus file if((c = filehandle.peek()) != '#') { - while((c = filehandle.peek()) != ';') { + while((c = filehandle.peek()) != ';') { + if (m->control_pressed) { filehandle.close(); return 0; } while ((c = filehandle.peek()) != ';') { + if (m->control_pressed) { filehandle.close(); return 0; } // get past comments if(c == '[') { comment = 1; @@ -1183,7 +1269,8 @@ void Tree::parseTreeFile() { string holder = ""; // get past comments - while(holder != "translate" && holder != "Translate"){ + while(holder != "translate" && holder != "Translate"){ + if (m->control_pressed) { filehandle.close(); return 0; } if(holder == "[" || holder == "[!"){ comment = 1; } @@ -1212,7 +1299,8 @@ void Tree::parseTreeFile() { string number, name, h; h = ""; // so it enters the loop the first time - while((h != ";") && (number != ";")) { + while((h != ";") && (number != ";")) { + if (m->control_pressed) { filehandle.close(); return 0; } filehandle >> number; filehandle >> name; @@ -1225,7 +1313,7 @@ void Tree::parseTreeFile() { } } filehandle.close(); - + return 0; //for (int i = 0; i < globaldata->Treenames.size(); i++) { //cout << globaldata->Treenames[i] << endl; } //cout << globaldata->Treenames.size() << endl; @@ -1243,7 +1331,8 @@ int Tree::readTreeString(ifstream& filehandle) { int c; string name; //, k - while((c = filehandle.peek()) != ';') { + while((c = filehandle.peek()) != ';') { + if (m->control_pressed) { return 0; } //k = c; //cout << " at beginning of while " << k << endl; if(c == ')') { @@ -1260,7 +1349,7 @@ int Tree::readTreeString(ifstream& filehandle) { c = filehandle.get(); //k = c; //cout << k << endl; - while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) { + while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) { name += c; c = filehandle.get(); //k = c; @@ -1268,7 +1357,9 @@ int Tree::readTreeString(ifstream& filehandle) { } //cout << "name = " << name << endl; - m->Treenames.push_back(name); + if (name != "\r" ) { + m->Treenames.push_back(name); } //cout << m->Treenames.size() << '\t' << name << endl; + filehandle.putback(c); //k = c; //cout << " after putback" << k << endl;