X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=tree.cpp;h=745893471e065abee12e7752b91c71bb37c1a635;hp=cd3d7a6789c9179066899ac62f0db115f14e295b;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=4de093e3b92bdab1579565cb2873553412f6671e diff --git a/tree.cpp b/tree.cpp index cd3d7a6..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->namesOfGroups.size(); i++) { - groupNodeInfo[tmap->namesOfGroups[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(""); @@ -89,11 +101,138 @@ Tree::Tree(TreeMap* t) : tmap(t) { exit(1); } } +/*****************************************************************/ +Tree::Tree(CountTable* t, vector< vector >& sims) : ct(t) { + try { + m = MothurOut::getInstance(); + + if (m->runParse == true) { parseTreeFile(); m->runParse = false; } + numLeaves = m->Treenames.size(); + numNodes = 2*numLeaves - 1; + + tree.resize(numNodes); + + //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(m->Treenames[i]); + + //save group info + 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(""); + vector tempGroups; + tree[i].setGroup(tempGroups); + } + } + + //build tree from matrix + //initialize indexes + 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 < (numLeaves - 1); i++) { + float largest = -1000.0; + + if (m->control_pressed) { break; } + + int row, column; + //find largest value in sims matrix by searching lower triangle + for (int j = 1; j < sims.size(); j++) { + for (int k = 0; k < j; k++) { + if (sims[j][k] > largest) { largest = sims[j][k]; row = j; column = k; } + } + } + + //set non-leaf node info and update leaves to know their parents + //non-leaf + tree[numLeaves + i].setChildren(thisIndexes[row], thisIndexes[column]); + + //parents + tree[thisIndexes[row]].setParent(numLeaves + i); + tree[thisIndexes[column]].setParent(numLeaves + i); + + //blength = distance / 2; + float blength = ((1.0 - largest) / 2); + + //branchlengths + 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[numLeaves + i].setLengthToLeaves(tree[thisIndexes[row]].getLengthToLeaves() + tree[thisIndexes[row]].getBranchLength()); + + + //update index + thisIndexes[row] = numLeaves+i; + thisIndexes[column] = numLeaves+i; + + //remove highest value that caused the merge. + sims[row][column] = -1000.0; + sims[column][row] = -1000.0; + + //merge values in simsMatrix + for (int n = 0; n < sims.size(); n++) { + //row becomes merge of 2 groups + sims[row][n] = (sims[row][n] + sims[column][n]) / 2; + sims[n][row] = sims[row][n]; + //delete column + sims[column][n] = -1000.0; + sims[n][column] = -1000.0; + } + } + + //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); + } +} /*****************************************************************/ Tree::~Tree() {} -/*****************************************************************/ -void Tree::addNamesToCounts() { +/***************************************************************** +void Tree::addNamesToCounts(map nameMap) { try { //ex. seq1 seq2,seq3,se4 // seq1 = pasture @@ -116,12 +255,12 @@ void Tree::addNamesToCounts() { string name = tree[i].getName(); - map::iterator itNames = m->names.find(name); + map::iterator itNames = nameMap.find(name); - if (itNames == m->names.end()) { m->mothurOut(name + " is not in your name file, please correct."); m->mothurOutEndLine(); exit(1); } + if (itNames == nameMap.end()) { m->mothurOut(name + " is not in your name file, please correct."); m->mothurOutEndLine(); exit(1); } else { vector dupNames; - m->splitAtComma(m->names[name], dupNames); + m->splitAtComma(nameMap[name], dupNames); map::iterator itCounts; int maxPars = 1; @@ -189,15 +328,15 @@ void Tree::addNamesToCounts() { 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"); @@ -208,8 +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"); @@ -218,12 +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(); } - + 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; } @@ -231,28 +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) { @@ -261,38 +376,65 @@ int Tree::assembleTree(string n) { } } /*****************************************************************/ -void Tree::getSubTree(Tree* copy, vector Groups) { +//assumes leaf node names are in groups and no names file - used by indicator command +void Tree::getSubTree(Tree* Ctree, vector Groups) { try { - + + //copy Tree since we are going to destroy it + Tree* copy = new Tree(ct); + copy->getCopy(Ctree); + 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++) { @@ -408,12 +550,40 @@ void Tree::getSubTree(Tree* copy, vector Groups) { //you found the root if (copy->tree[i].getParent() == -1) { root = i; break; } } - + int nextSpot = numLeaves; populateNewTree(copy->tree, root, nextSpot); + + delete copy; } catch(exception& e) { - m->errorOut(e, "Tree", "getCopy"); + m->errorOut(e, "Tree", "getSubTree"); + 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) { + try { + + if (numLeaves != seqsToInclude.size()) { m->mothurOut("[ERROR]: numLeaves does not equal numUniques, cannot create subtree.\n"); m->control_pressed = true; return 0; } + + getSubTree(copy, seqsToInclude); + 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) { return 1; } + + tree[i].pGroups = (mergeGroups(i)); + tree[i].pcount = (mergeGcounts(i)); + } + + return 0; + } + catch(exception& e) { + m->errorOut(e, "Tree", "getSubTree"); exit(1); } } @@ -435,7 +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; } } @@ -445,6 +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 { @@ -466,8 +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; @@ -627,13 +826,12 @@ map Tree::mergeGcounts(int position) { } } /**************************************************************************************************/ - void Tree::randomLabels(vector g) { try { //initialize groupNodeInfo - for (int i = 0; i < tmap->namesOfGroups.size(); i++) { - groupNodeInfo[tmap->namesOfGroups[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++){ @@ -676,36 +874,6 @@ void Tree::randomLabels(vector g) { exit(1); } } -/************************************************************************************************** - -void Tree::randomLabels(string groupA, string groupB) { - try { - int numSeqsA = globaldata->gTreemap->seqsPerGroup[groupA]; - int numSeqsB = globaldata->gTreemap->seqsPerGroup[groupB]; - - vector randomGroups(numSeqsA+numSeqsB, groupA); - for(int i=numSeqsA;ierrorOut(e, "Tree", "randomLabels"); - exit(1); - } -} /**************************************************************************************************/ void Tree::randomBlengths() { try { @@ -725,14 +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(); } /*************************************************************************************************/ @@ -792,6 +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(); @@ -844,10 +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); @@ -874,16 +1125,16 @@ try { } } }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(); @@ -937,16 +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(); @@ -982,7 +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 { @@ -995,8 +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; @@ -1016,7 +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; } @@ -1045,7 +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; @@ -1058,7 +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; @@ -1076,7 +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 == ')') { @@ -1093,7 +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; @@ -1101,7 +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;