X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.cpp;h=f124b6002ee2c247db14716b4be81cb9ec10d8f2;hb=dc383fb61b6d165a8d36e6108df8bc7129243ae6;hp=2d46efc9efebcfbe7807292cb814cf58686f9ac4;hpb=16abd6271c455bd01b34ff89a2e3641bef0fa128;p=mothur.git diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp index 2d46efc..f124b60 100644 --- a/parsimonycommand.cpp +++ b/parsimonycommand.cpp @@ -8,6 +8,7 @@ */ #include "parsimonycommand.h" +#include "treereader.h" //********************************************************************************************************************** vector ParsimonyCommand::setParameters(){ @@ -51,6 +52,27 @@ string ParsimonyCommand::getHelpString(){ exit(1); } } +//********************************************************************************************************************** +string ParsimonyCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + string outputFileName = ""; + map >::iterator it; + + //is this a type this command creates + it = outputTypes.find(type); + if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } + else { + if (type == "parsimony") { outputFileName = "parsimony"; } + else if (type == "psummary") { outputFileName = "psummary"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } + } + return outputFileName; + } + catch(exception& e) { + m->errorOut(e, "ParsimonyCommand", "getOutputFileNameTag"); + exit(1); + } +} //********************************************************************************************************************** ParsimonyCommand::ParsimonyCommand(){ @@ -125,12 +147,6 @@ ParsimonyCommand::ParsimonyCommand(string option) { } } - m->runParse = true; - m->clearGroups(); - m->clearAllGroups(); - 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 = ""; } @@ -203,74 +219,17 @@ 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++) { 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 - } - } - } - } - + 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"); - outputTypes["parsimony"].push_back(outputDir + m->getSimpleName(treefile) + ".parsimony"); + output = new ColumnFile(outputDir + m->getSimpleName(treefile) + "." + getOutputFileNameTag("parsimony"), itersString); + outputNames.push_back(outputDir + m->getSimpleName(treefile) + "." + getOutputFileNameTag("parsimony")); + outputTypes["parsimony"].push_back(outputDir + m->getSimpleName(treefile) + "." + getOutputFileNameTag("parsimony")); - sumFile = outputDir + m->getSimpleName(treefile) + ".psummary"; + sumFile = outputDir + m->getSimpleName(treefile) + "." + getOutputFileNameTag("psummary"); m->openOutputFile(sumFile, outSum); outputNames.push_back(sumFile); outputTypes["psummary"].push_back(sumFile); @@ -284,24 +243,23 @@ int ParsimonyCommand::execute() { } //set users groups to analyze - util = new SharedUtil(); + 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); + util.setGroups(mGroups, tGroups, allGroups, numGroups, "parsimony"); //sets the groups the user wants to analyze + util.getCombos(groupComb, mGroups, numComp); m->setGroups(mGroups); - delete util; 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++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); @@ -323,10 +281,10 @@ 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++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); @@ -362,10 +320,10 @@ 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++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; } @@ -403,23 +361,17 @@ 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++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); - m->clearGroups(); - 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++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); - m->clearGroups(); - 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++) { @@ -471,27 +423,21 @@ 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++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); - m->clearGroups(); return 0; } //finish progress bar reading->finish(); delete reading; - printParsimonyFile(); if (randomtree == "") { printUSummaryFile(); } - - //reset groups parameter - m->clearGroups(); - - delete pars; delete output; - delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; } + + 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++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;} @@ -623,46 +569,6 @@ 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); - } -} /***********************************************************/