X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=unifracweightedcommand.cpp;h=1df79888eb8bdacb442b9dc2c89c51a7d4fa75ff;hb=36a6b02cf7f09d2bc34376b588944a9ca73429c5;hp=e596db230ee24d80597cfa903a49ed9ee6a7f25b;hpb=03dca3b32a903c3f29fbcf5b410b19d6ab6dae63;p=mothur.git diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp index e596db2..1df7988 100644 --- a/unifracweightedcommand.cpp +++ b/unifracweightedcommand.cpp @@ -10,6 +10,7 @@ #include "unifracweightedcommand.h" #include "consensus.h" #include "subsample.h" +#include "treereader.h" //********************************************************************************************************************** vector UnifracWeightedCommand::setParameters(){ @@ -141,12 +142,6 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) { } } - m->runParse = true; - m->clearGroups(); - m->clearAllGroups(); - m->Treenames.clear(); - m->names.clear(); - //check for required parameters treefile = validParameter.validFile(parameters, "tree", true); if (treefile == "not open") { treefile = ""; abort = true; } @@ -238,7 +233,14 @@ int UnifracWeightedCommand::execute() { m->setTreeFile(treefile); - readTrees(); if (m->control_pressed) { delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; } return 0; } + TreeReader* reader = new TreeReader(treefile, groupfile, namefile); + T = reader->getTrees(); + tmap = T[0]->getTreeMap(); + map nameMap = reader->getNames(); + map unique2Dup = reader->getNameMap(); + delete reader; + + if (m->control_pressed) { delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; } return 0; } sumFile = outputDir + m->getSimpleName(treefile) + ".wsummary"; m->openOutputFile(sumFile, outSum); @@ -253,7 +255,7 @@ int UnifracWeightedCommand::execute() { if (m->control_pressed) { delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; } return 0; } - Weighted weighted(tmap, includeRoot); + Weighted weighted(includeRoot); int start = time(NULL); @@ -333,16 +335,20 @@ int UnifracWeightedCommand::execute() { if (m->control_pressed) { break; } - //copy to preserve old one - would do this in subsample but tree needs it and memory cleanup becomes messy. + //copy to preserve old one - would do this in subsample but memory cleanup becomes messy. TreeMap* newTmap = new TreeMap(); - newTmap->getCopy(tmap); + //newTmap->getCopy(*tmap); + + //SubSample sample; + //Tree* subSampleTree = sample.getSample(T[i], newTmap, nameMap, subsampleSize); + //uses method of setting groups to doNotIncludeMe SubSample sample; - Tree* subSampleTree = sample.getSample(T[i], newTmap, nameMap, subsampleSize); - + Tree* subSampleTree = sample.getSample(T[i], tmap, newTmap, subsampleSize, unique2Dup); + //call new weighted function vector iterData; iterData.resize(numComp,0); - Weighted thisWeighted(newTmap, includeRoot); + Weighted thisWeighted(includeRoot); iterData = thisWeighted.getValues(subSampleTree, processors, outputDir); //userData[0] = weightedscore //save data to make ave dist, std dist @@ -350,6 +356,8 @@ int UnifracWeightedCommand::execute() { delete newTmap; delete subSampleTree; + + if((thisIter+1) % 100 == 0){ m->mothurOut(toString(thisIter+1)); m->mothurOutEndLine(); } } if (m->control_pressed) { delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; } if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } @@ -525,8 +533,8 @@ int UnifracWeightedCommand::getConsensusTrees(vector< vector >& dists, i m->runParse = false; //create treemap class from groupmap for tree class to use - TreeMap* newTmap = new TreeMap(); - newTmap->makeSim(m->getGroups()); + TreeMap newTmap; + newTmap.makeSim(m->getGroups()); //clear old tree names if any m->Treenames.clear(); @@ -536,10 +544,10 @@ int UnifracWeightedCommand::getConsensusTrees(vector< vector >& dists, i vector newTrees = buildTrees(dists, treeNum, newTmap); //also creates .all.tre file containing the trees created - if (m->control_pressed) { delete newTmap; return 0; } + if (m->control_pressed) { return 0; } Consensus con; - Tree* conTree = con.getTree(newTrees, newTmap); + Tree* conTree = con.getTree(newTrees); //create a new filename string conFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(treeNum+1) + ".weighted.cons.tre"; @@ -549,7 +557,6 @@ int UnifracWeightedCommand::getConsensusTrees(vector< vector >& dists, i if (conTree != NULL) { conTree->print(outTree, "boot"); delete conTree; } outTree.close(); - delete newTmap; return 0; @@ -561,7 +568,7 @@ int UnifracWeightedCommand::getConsensusTrees(vector< vector >& dists, i } /**************************************************************************************************/ -vector UnifracWeightedCommand::buildTrees(vector< vector >& dists, int treeNum, TreeMap* mytmap) { +vector UnifracWeightedCommand::buildTrees(vector< vector >& dists, int treeNum, TreeMap& mytmap) { try { vector trees; @@ -595,8 +602,9 @@ vector UnifracWeightedCommand::buildTrees(vector< vector >& dists } //create tree - Tree* tempTree = new Tree(mytmap, sims); - tempTree->assembleTree(); + Tree* tempTree = new Tree(&mytmap, sims); + map empty; + tempTree->assembleTree(empty); trees.push_back(tempTree); @@ -617,80 +625,6 @@ vector UnifracWeightedCommand::buildTrees(vector< vector >& dists } /**************************************************************************************************/ -int UnifracWeightedCommand::readTrees() { - try { - - if (groupfile != "") { - //read in group map info. - tmap = new TreeMap(groupfile); - tmap->readMap(); - }else{ //fake out by putting everyone in one group - Tree* tree = new Tree(treefile); delete tree; //extracts names from tree to make faked out groupmap - tmap = new TreeMap(); - - for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); } - } - - if (namefile != "") { readNamesFile(); } - - read = new ReadNewickTree(treefile); - int readOk = read->read(tmap); - - if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete tmap; delete read; return 0; } - - read->AssembleTrees(); - T = read->getTrees(); - delete read; - - //make sure all files match - //if you provide a namefile we will use the numNames in the namefile as long as the number of unique match the tree names size. - int numNamesInTree; - if (namefile != "") { - if (numUniquesInName == m->Treenames.size()) { numNamesInTree = nameMap.size(); } - else { numNamesInTree = m->Treenames.size(); } - }else { numNamesInTree = m->Treenames.size(); } - - - //output any names that are in group file but not in tree - if (numNamesInTree < tmap->getNumSeqs()) { - for (int i = 0; i < tmap->namesOfSeqs.size(); i++) { - //is that name in the tree? - int count = 0; - for (int j = 0; j < m->Treenames.size(); j++) { - if (tmap->namesOfSeqs[i] == m->Treenames[j]) { break; } //found it - count++; - } - - if (m->control_pressed) { - delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; } - for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); - m->clearGroups(); - return 0; - } - - //then you did not find it so report it - if (count == m->Treenames.size()) { - //if it is in your namefile then don't remove - map::iterator it = nameMap.find(tmap->namesOfSeqs[i]); - - if (it == nameMap.end()) { - m->mothurOut(tmap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine(); - tmap->removeSeq(tmap->namesOfSeqs[i]); - i--; //need this because removeSeq removes name from namesOfSeqs - } - } - } - } - - return 0; - } - catch(exception& e) { - m->errorOut(e, "UnifracWeightedCommand", "readTrees"); - exit(1); - } -} -/**************************************************************************************************/ - int UnifracWeightedCommand::runRandomCalcs(Tree* thisTree, vector usersScores) { try { @@ -731,7 +665,7 @@ int UnifracWeightedCommand::runRandomCalcs(Tree* thisTree, vector usersS createProcesses(thisTree, namesOfGroupCombos, rScores); } #else - driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), rScores); + driver(thisTree, namesOfGroupCombos, 0, namesOfGroupCombos.size(), rScores); #endif if (m->control_pressed) { delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; } delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } @@ -839,7 +773,7 @@ int UnifracWeightedCommand::driver(Tree* t, vector< vector > namesOfGrou try { Tree* randT = new Tree(tmap); - Weighted weighted(tmap, includeRoot); + Weighted weighted(includeRoot); for (int h = start; h < (start+num); h++) { @@ -1079,46 +1013,6 @@ void UnifracWeightedCommand::calculateFreqsCumuls() { exit(1); } } -/*****************************************************************/ -int UnifracWeightedCommand::readNamesFile() { - try { - m->names.clear(); - numUniquesInName = 0; - - ifstream in; - m->openInputFile(namefile, in); - - string first, second; - map::iterator itNames; - - while(!in.eof()) { - in >> first >> second; m->gobble(in); - - numUniquesInName++; - - itNames = m->names.find(first); - if (itNames == m->names.end()) { - m->names[first] = second; - - //we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them - vector dupNames; - m->splitAtComma(second, dupNames); - - for (int i = 0; i < dupNames.size(); i++) { - nameMap[dupNames[i]] = first; - if ((groupfile == "") && (i != 0)) { tmap->addSeq(dupNames[i], "Group1"); } - } - }else { m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); m->names.clear(); namefile = ""; return 1; } - } - in.close(); - - return 0; - } - catch(exception& e) { - m->errorOut(e, "UnifracWeightedCommand", "readNamesFile"); - exit(1); - } -} /***********************************************************/