X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedcommand.cpp;h=c252b4fecc9cebad935e0970fa88aaf5d43e7ac0;hb=191ae1be0679d5cf4eda950b3b1bf26fb7dd503d;hp=213fd49588bbf8a9278bc04c14d474bd11ccb278;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git diff --git a/sharedcommand.cpp b/sharedcommand.cpp index 213fd49..c252b4f 100644 --- a/sharedcommand.cpp +++ b/sharedcommand.cpp @@ -8,21 +8,78 @@ */ #include "sharedcommand.h" +//******************************************************************************************************************** +//sorts lowest to highest +inline bool compareSharedRabunds(SharedRAbundVector* left, SharedRAbundVector* right){ + return (left->getGroup() < right->getGroup()); +} +//********************************************************************************************************************** +vector SharedCommand::getValidParameters(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "SharedCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +SharedCommand::SharedCommand(){ + try { + //initialize outputTypes + vector tempOutNames; + outputTypes["rabund"] = tempOutNames; + outputTypes["shared"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "SharedCommand", "SharedCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector SharedCommand::getRequiredParameters(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "SharedCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector SharedCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "SharedCommand", "getRequiredFiles"); + exit(1); + } +} //********************************************************************************************************************** SharedCommand::SharedCommand(string o) : outputDir(o) { try { globaldata = GlobalData::getInstance(); + //initialize outputTypes + vector tempOutNames; + outputTypes["rabund"] = tempOutNames; + outputTypes["shared"] = tempOutNames; + //getting output filename filename = globaldata->inputFileName; - if (outputDir == "") { outputDir += hasPath(filename); } + if (outputDir == "") { outputDir += m->hasPath(filename); } - filename = outputDir + getRootName(getSimpleName(filename)); + filename = outputDir + m->getRootName(m->getSimpleName(filename)); filename = filename + "shared"; + outputTypes["shared"].push_back(filename); - openOutputFile(filename, out); + m->openOutputFile(filename, out); pickedGroups = false; groupMap = globaldata->gGroupmap; @@ -44,12 +101,13 @@ SharedCommand::SharedCommand(string o) : outputDir(o) { } //set fileroot - fileroot = outputDir + getRootName(getSimpleName(globaldata->getListFile())); + fileroot = outputDir + m->getRootName(m->getSimpleName(globaldata->getListFile())); //clears file before we start to write to it below for (int i=0; igetOrderGroupFile() != "") { readOrderFile(); } + //read in listfile read = new ReadOTUFile(globaldata->inputFileName); read->read(&*globaldata); @@ -112,9 +173,9 @@ int SharedCommand::execute(){ groups += globaldata->Groups[i] + "."; } - string newGroupFile = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + groups + "groups"; + string newGroupFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + groups + "groups"; ofstream outGroups; - openOutputFile(newGroupFile, outGroups); + m->openOutputFile(newGroupFile, outGroups); vector names = groupMap->getNamesSeqs(); string groupName; @@ -143,6 +204,7 @@ int SharedCommand::execute(){ if(globaldata->allLines == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){ lookup = SharedList->getSharedRAbundVector(); + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); if (pickedGroups) { //check for otus with no seqs in them eliminateZeroOTUS(lookup); @@ -164,7 +226,7 @@ int SharedCommand::execute(){ userLabels.erase(SharedList->getLabel()); } - if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) { + if ((m->anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) { string saveLabel = SharedList->getLabel(); delete SharedList; @@ -251,6 +313,7 @@ int SharedCommand::execute(){ globaldata->setGroupFile(""); globaldata->setSharedFile(filename); + if (m->control_pressed) { delete input; globaldata->ginput = NULL; remove(filename.c_str()); @@ -275,16 +338,53 @@ int SharedCommand::execute(){ void SharedCommand::printSharedData(vector thislookup) { try { - //initialize bin values - for (int i = 0; i < thislookup.size(); i++) { -//cout << "in printData " << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << endl; - out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t'; - thislookup[i]->print(out); + if (order.size() == 0) { //user has not specified an order so do aplabetically + sort(thislookup.begin(), thislookup.end(), compareSharedRabunds); + + globaldata->Groups.clear(); + + //initialize bin values + for (int i = 0; i < thislookup.size(); i++) { + out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t'; + thislookup[i]->print(out); + + globaldata->Groups.push_back(thislookup[i]->getGroup()); + + RAbundVector rav = thislookup[i]->getRAbundVector(); + m->openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()])); + rav.print(*(filehandles[thislookup[i]->getGroup()])); + (*(filehandles[thislookup[i]->getGroup()])).close(); + } + }else{ + //create a map from groupName to each sharedrabund + map myMap; + map::iterator myIt; - RAbundVector rav = thislookup[i]->getRAbundVector(); - openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()])); - rav.print(*(filehandles[thislookup[i]->getGroup()])); - (*(filehandles[thislookup[i]->getGroup()])).close(); + for (int i = 0; i < thislookup.size(); i++) { + myMap[thislookup[i]->getGroup()] = thislookup[i]; + } + + globaldata->Groups.clear(); + + //loop through ordered list and print the rabund + for (int i = 0; i < order.size(); i++) { + myIt = myMap.find(order[i]); + + if(myIt != myMap.end()) { //we found it + out << (myIt->second)->getLabel() << '\t' << (myIt->second)->getGroup() << '\t'; + (myIt->second)->print(out); + + globaldata->Groups.push_back((myIt->second)->getGroup()); + + RAbundVector rav = (myIt->second)->getRAbundVector(); + m->openOutputFileAppend(fileroot + (myIt->second)->getGroup() + ".rabund", *(filehandles[(myIt->second)->getGroup()])); + rav.print(*(filehandles[(myIt->second)->getGroup()])); + (*(filehandles[(myIt->second)->getGroup()])).close(); + }else{ + m->mothurOut("Can't find shared info for " + order[i] + ", skipping."); m->mothurOutEndLine(); + } + } + } } @@ -339,14 +439,14 @@ int SharedCommand::eliminateZeroOTUS(vector& thislookup) { int SharedCommand::createMisMatchFile() { try { ofstream outMisMatch; - string outputMisMatchName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)); + string outputMisMatchName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)); //you have sequences in your list file that are not in your group file if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) { outputMisMatchName += "missing.group"; m->mothurOut("For a list of names that are in your list file and not in your group file, please refer to " + outputMisMatchName + "."); m->mothurOutEndLine(); - openOutputFile(outputMisMatchName, outMisMatch); + m->openOutputFile(outputMisMatchName, outMisMatch); map listNames; map::iterator itList; @@ -420,7 +520,7 @@ int SharedCommand::createMisMatchFile() { map::iterator itMatch; - openOutputFile(outputMisMatchName, outMisMatch); + m->openOutputFile(outputMisMatchName, outMisMatch); //loop through names in seqNames and if they aren't in namesIn list output them for (int i = 0; i < seqNames.size(); i++) { @@ -451,7 +551,32 @@ SharedCommand::~SharedCommand(){ } - +//********************************************************************************************************************** +int SharedCommand::readOrderFile() { + try { + //remove old names + order.clear(); + + ifstream in; + m->openInputFile(globaldata->getOrderGroupFile(), in); + string thisGroup; + + while(!in.eof()){ + in >> thisGroup; m->gobble(in); + + order.push_back(thisGroup); + + if (m->control_pressed) { order.clear(); break; } + } + in.close(); + + return 0; + } + catch(exception& e) { + m->errorOut(e, "SharedCommand", "readOrderFile"); + exit(1); + } +} //********************************************************************************************************************** bool SharedCommand::isValidGroup(string groupname, vector groups) {