X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.cpp;h=6a09ada5d3e8e4141c56a0c0ef4943beae6ef815;hb=4f4070ac3fbb5da75f834b48062e9123364b006e;hp=486e6c4982b885c82a39e5387b0b987e54f843ec;hpb=ee27b6e01a979fdf832668eb87412b029f77e4d7;p=mothur.git diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp index 486e6c4..6a09ada 100644 --- a/summarysharedcommand.cpp +++ b/summarysharedcommand.cpp @@ -30,7 +30,7 @@ #include "sharedmorisitahorn.h" #include "sharedbraycurtis.h" #include "sharedjackknife.h" -#include "sharedwhittaker.h" +#include "whittaker.h" //********************************************************************************************************************** @@ -42,7 +42,6 @@ SummarySharedCommand::SummarySharedCommand(){ openOutputFile(outputFileName, outputFileHandle); format = globaldata->getFormat(); validCalculator = new ValidCalculators(); - util = new SharedUtil(); mult = false; int i; @@ -111,7 +110,6 @@ SummarySharedCommand::SummarySharedCommand(){ SummarySharedCommand::~SummarySharedCommand(){ delete input; delete read; - delete util; } //********************************************************************************************************************** @@ -119,7 +117,7 @@ SummarySharedCommand::~SummarySharedCommand(){ int SummarySharedCommand::execute(){ try { int count = 1; - + //if the users entered no valid calculators don't execute command if (sumCalculators.size() == 0) { return 0; } //check if any calcs can do multiples @@ -129,14 +127,13 @@ int SummarySharedCommand::execute(){ } } + //read first line read = new ReadOTUFile(globaldata->inputFileName); read->read(&*globaldata); input = globaldata->ginput; - order = input->getSharedOrderVector(); - - //set users groups - util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "summary"); + lookup = input->getSharedRAbundVectors(); + vector lastLookup = lookup; //output estimator names as column headers outputFileHandle << "label" <<'\t' << "comparison" << '\t'; @@ -146,7 +143,7 @@ int SummarySharedCommand::execute(){ outputFileHandle << endl; //create file and put column headers for multiple groups file - if (mult = true) { + if (mult == true) { outAllFileName = ((getRootName(globaldata->inputFileName)) + "sharedmultiple.summary"); openOutputFile(outAllFileName, outAll); @@ -159,55 +156,142 @@ int SummarySharedCommand::execute(){ outAll << endl; } - while(order != NULL){ + if (lookup.size() < 2) { + cout << "I cannot run the command without at least 2 valid groups."; + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + + //close files and clean up + outputFileHandle.close(); remove(outputFileName.c_str()); + if (mult == true) { outAll.close(); remove(outAllFileName.c_str()); } + return 0; + //if you only have 2 groups you don't need a .sharedmultiple file + }else if ((lookup.size() == 2) && (mult == true)) { + mult = false; + outAll.close(); + remove(outAllFileName.c_str()); + } + + //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. + set processedLabels; + set userLabels = globaldata->labels; + set userLines = globaldata->lines; - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){ - - cout << order->getLabel() << '\t' << count << endl; - util->getSharedVectors(globaldata->Groups, lookup, order); //fills group vectors from order vector. //fills group vectors from order vector. + //as long as you are not at the end of the file or done wih the lines you want + while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { + + if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){ + cout << lookup[0]->getLabel() << '\t' << count << endl; + process(lookup); + + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + userLines.erase(count); + } + + if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) { + cout << lastLookup[0]->getLabel() << '\t' << count << endl; + process(lastLookup); + + processedLabels.insert(lastLookup[0]->getLabel()); + userLabels.erase(lastLookup[0]->getLabel()); + } + + + //prevent memory leak + if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } } + lastLookup = lookup; + //get next line to process + lookup = input->getSharedRAbundVectors(); + count++; + } + + //output error messages about any remaining user labels + set::iterator it; + bool needToRun = false; + for (it = userLabels.begin(); it != userLabels.end(); it++) { + cout << "Your file does not include the label "<< *it; + if (processedLabels.count(lastLookup[0]->getLabel()) != 1) { + cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl; + needToRun = true; + }else { + cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl; + } + } + + //run last line if you need to + if (needToRun == true) { + cout << lastLookup[0]->getLabel() << '\t' << count << endl; + process(lastLookup); + } + + for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } + + //reset groups parameter + globaldata->Groups.clear(); globaldata->setGroups(""); + + //close files + outputFileHandle.close(); + if (mult == true) { outAll.close(); } + + return 0; + } + catch(exception& e) { + cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } + catch(...) { + cout << "An unknown error has occurred in the SummarySharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } +} + +/***********************************************************/ +void SummarySharedCommand::process(vector thisLookup) { + try { //loop through calculators and add to file all for all calcs that can do mutiple groups - if (mult = true) { + if (mult == true) { //output label - outAll << order->getLabel() << '\t'; + outAll << thisLookup[0]->getLabel() << '\t'; //output groups names string outNames = ""; - for (int j = 0; j < lookup.size(); j++) { - outNames += lookup[j]->getGroup() + "-"; + for (int j = 0; j < thisLookup.size(); j++) { + outNames += thisLookup[j]->getGroup() + "-"; } outNames = outNames.substr(0, outNames.length()-1); //rip off extra '-'; outAll << outNames << '\t'; for(int i=0;igetMultiple() == true) { - sumCalculators[i]->getValues(lookup); + sumCalculators[i]->getValues(thisLookup); outAll << '\t'; sumCalculators[i]->print(outAll); } } outAll << endl; } - + int n = 1; vector subset; - for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare - for (int l = n; l < lookup.size(); l++) { + for (int k = 0; k < (thisLookup.size() - 1); k++) { // pass cdd each set of groups to commpare + for (int l = n; l < thisLookup.size(); l++) { - outputFileHandle << order->getLabel() << '\t'; + outputFileHandle << thisLookup[0]->getLabel() << '\t'; subset.clear(); //clear out old pair of sharedrabunds //add new pair of sharedrabunds - subset.push_back(lookup[k]); subset.push_back(lookup[l]); + subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]); //sort groups to be alphanumeric - if (lookup[k]->getGroup() > lookup[l]->getGroup()) { - outputFileHandle << (lookup[l]->getGroup() +'\t' + lookup[k]->getGroup()) << '\t'; //print out groups + if (thisLookup[k]->getGroup() > thisLookup[l]->getGroup()) { + outputFileHandle << (thisLookup[l]->getGroup() +'\t' + thisLookup[k]->getGroup()) << '\t'; //print out groups }else{ - outputFileHandle << (lookup[k]->getGroup() +'\t' + lookup[l]->getGroup()) << '\t'; //print out groups + outputFileHandle << (thisLookup[k]->getGroup() +'\t' + thisLookup[l]->getGroup()) << '\t'; //print out groups } for(int i=0;igetValues(subset); //saves the calculator outputs outputFileHandle << '\t'; sumCalculators[i]->print(outputFileHandle); @@ -216,26 +300,16 @@ int SummarySharedCommand::execute(){ } n++; } - } - - //get next line to process - order = input->getSharedOrderVector(); - count++; - } - - //reset groups parameter - globaldata->Groups.clear(); globaldata->setGroups(""); - return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; exit(1); } catch(...) { - cout << "An unknown error has occurred in the SummarySharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + cout << "An unknown error has occurred in the SummarySharedCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; exit(1); } } -/***********************************************************/ +/***********************************************************/ \ No newline at end of file