X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.cpp;h=50e1bfa7e590d6e2fa47b4c184700b440cdb9621;hb=791f42d21a85f794529fd4c912dcc27d873c25e8;hp=403b2b86d9addf1f9291e7f87fac63ef1755c002;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp index 403b2b8..50e1bfa 100644 --- a/parsimonycommand.cpp +++ b/parsimonycommand.cpp @@ -8,6 +8,7 @@ */ #include "parsimonycommand.h" +#include "treereader.h" //********************************************************************************************************************** vector ParsimonyCommand::setParameters(){ @@ -125,12 +126,6 @@ ParsimonyCommand::ParsimonyCommand(string option) { } } - m->runParse = true; - m->Groups.clear(); - m->namesOfGroups.clear(); - m->Treenames.clear(); - m->names.clear(); - outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; } randomtree = validParameter.validFile(parameters, "random", false); if (randomtree == "not found") { randomtree = ""; } @@ -139,21 +134,23 @@ ParsimonyCommand::ParsimonyCommand(string option) { if (randomtree == "") { //check for required parameters treefile = validParameter.validFile(parameters, "tree", true); - if (treefile == "not open") { abort = true; } + if (treefile == "not open") { treefile = ""; abort = true; } else if (treefile == "not found") { //if there is a current design file, use it treefile = m->getTreeFile(); if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); } else { m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; } - } + }else { m->setTreeFile(treefile); } //check for required parameters groupfile = validParameter.validFile(parameters, "group", true); if (groupfile == "not open") { abort = true; } else if (groupfile == "not found") { groupfile = ""; } + else { m->setGroupFile(groupfile); } namefile = validParameter.validFile(parameters, "name", true); - if (namefile == "not open") { abort = true; } + if (namefile == "not open") { namefile = ""; abort = true; } else if (namefile == "not found") { namefile = ""; } + else { m->setNameFile(namefile); } } //if the user changes the output directory command factory will send this info to us in the output parameter @@ -162,18 +159,23 @@ ParsimonyCommand::ParsimonyCommand(string option) { //check for optional parameter and set defaults // ...at some point should added some additional type checking... groups = validParameter.validFile(parameters, "groups", false); - if (groups == "not found") { groups = ""; m->Groups.clear(); } + if (groups == "not found") { groups = ""; m->clearGroups(); } else { m->splitAtDash(groups, Groups); - m->Groups = Groups; + m->setGroups(Groups); } itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; } - convert(itersString, iters); + m->mothurConvert(itersString, iters); string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } m->setProcessors(temp); - convert(temp, processors); + m->mothurConvert(temp, processors); + + if (namefile == "") { + vector files; files.push_back(treefile); + parser.getNameFile(files); + } } @@ -196,68 +198,11 @@ int ParsimonyCommand::execute() { m->setTreeFile(treefile); - 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++) { remove(outputNames[i].c_str()); } outputTypes.clear(); - m->Groups.clear(); - 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 - } - } - } - } - + TreeReader* reader = new TreeReader(treefile, groupfile, namefile); + T = reader->getTrees(); + tmap = T[0]->getTreeMap(); + delete reader; + if(outputDir == "") { outputDir += m->hasPath(treefile); } output = new ColumnFile(outputDir + m->getSimpleName(treefile) + ".parsimony", itersString); outputNames.push_back(outputDir + m->getSimpleName(treefile) + ".parsimony"); @@ -277,25 +222,27 @@ int ParsimonyCommand::execute() { } //set users groups to analyze - util = new SharedUtil(); - util->setGroups(m->Groups, tmap->namesOfGroups, allGroups, numGroups, "parsimony"); //sets the groups the user wants to analyze - util->getCombos(groupComb, m->Groups, numComp); - delete util; + SharedUtil util; + vector mGroups = m->getGroups(); + vector tGroups = tmap->getNamesOfGroups(); + util.setGroups(mGroups, tGroups, allGroups, numGroups, "parsimony"); //sets the groups the user wants to analyze + util.getCombos(groupComb, mGroups, numComp); + m->setGroups(mGroups); if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); } - pars = new Parsimony(tmap); + Parsimony pars; counter = 0; Progress* reading; reading = new Progress("Comparing to random:", iters); if (m->control_pressed) { - delete reading; delete pars; delete output; + delete reading; delete output; delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; } if (randomtree == "") { outSum.close(); } - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); - m->Groups.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); + m->clearGroups(); return 0; } @@ -313,14 +260,14 @@ int ParsimonyCommand::execute() { if (randomtree == "") { //get pscores for users trees for (int i = 0; i < T.size(); i++) { - userData = pars->getValues(T[i], processors, outputDir); //data = AB, AC, BC, ABC. + userData = pars.getValues(T[i], processors, outputDir); //data = AB, AC, BC, ABC. if (m->control_pressed) { - delete reading; delete pars; delete output; + delete reading; delete output; delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; } if (randomtree == "") { outSum.close(); } - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); - m->Groups.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); + m->clearGroups(); return 0; } @@ -352,14 +299,14 @@ int ParsimonyCommand::execute() { randT->assembleRandomTree(); //get pscore of random tree - randomData = pars->getValues(randT, processors, outputDir); + randomData = pars.getValues(randT, processors, outputDir); if (m->control_pressed) { - delete reading; delete pars; delete output; delete randT; + delete reading; delete output; delete randT; if (randomtree == "") { outSum.close(); } - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; } - m->Groups.clear(); + m->clearGroups(); return 0; } @@ -393,23 +340,17 @@ int ParsimonyCommand::execute() { randT->assembleRandomTree(); if (m->control_pressed) { - delete reading; delete pars; delete output; delete randT; - delete tmap; - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); - m->Groups.clear(); - return 0; + delete reading; delete output; delete randT; delete tmap; + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } //get pscore of random tree - randomData = pars->getValues(randT, processors, outputDir); + randomData = pars.getValues(randT, processors, outputDir); if (m->control_pressed) { - delete reading; delete pars; delete output; delete randT; - delete tmap; - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); - m->Groups.clear(); - return 0; + delete reading; delete output; delete randT; delete tmap; + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } for(int r = 0; r < numComp; r++) { @@ -461,29 +402,23 @@ int ParsimonyCommand::execute() { } if (m->control_pressed) { - delete reading; delete pars; delete output; + delete reading; delete output; delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; } if (randomtree == "") { outSum.close(); } - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); - m->Groups.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } //finish progress bar reading->finish(); delete reading; - printParsimonyFile(); if (randomtree == "") { printUSummaryFile(); } + + delete output; delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; } - //reset groups parameter - m->Groups.clear(); - - delete pars; delete output; - delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; } - - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); return 0;} + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;} m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); @@ -583,6 +518,7 @@ void ParsimonyCommand::getUserInput() { count = 1; numEachGroup.resize(numGroups, 0); + for (int i = 1; i <= numGroups; i++) { m->mothurOut("Please enter the number of sequences in group " + toString(i) + ": "); cin >> num; @@ -590,7 +526,7 @@ void ParsimonyCommand::getUserInput() { //set tmaps seqsPerGroup tmap->seqsPerGroup[toString(i)] = num; - tmap->namesOfGroups.push_back(toString(i)); + tmap->addGroup(toString(i)); //set tmaps namesOfSeqs for (int j = 0; j < num; j++) { @@ -612,46 +548,6 @@ void ParsimonyCommand::getUserInput() { exit(1); } } -/*****************************************************************/ -int ParsimonyCommand::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]] = dupNames[i]; - 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, "ParsimonyCommand", "readNamesFile"); - exit(1); - } -} /***********************************************************/