X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=libshuffcommand.cpp;h=74acd841b676acc429df6df4e303210d82ae92ba;hb=c82900be3ceed3d9bc491bdc98b1819ef85c1af7;hp=9a71a038cd4d0bd29d7eaeeeaae96d9847d81fa8;hpb=cd37904452dc95b183ff313ff05720c562902487;p=mothur.git diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp index 9a71a03..74acd84 100644 --- a/libshuffcommand.cpp +++ b/libshuffcommand.cpp @@ -22,8 +22,6 @@ LibShuffCommand::LibShuffCommand(string option){ try { - srand( (unsigned)time( NULL ) ); - globaldata = GlobalData::getInstance(); abort = false; Groups.clear(); @@ -49,7 +47,7 @@ LibShuffCommand::LibShuffCommand(string option){ //make sure the user has already run the read.dist command if ((globaldata->gMatrix == NULL) || (globaldata->gGroupmap == NULL)) { - cout << "You must read in a matrix and groupfile using the read.dist command, before you use the libshuff command. " << endl; abort = true;; + mothurOut("You must read in a matrix and groupfile using the read.dist command, before you use the libshuff command. "); mothurOutEndLine(); abort = true;; } //check for optional parameter and set defaults @@ -75,9 +73,19 @@ LibShuffCommand::LibShuffCommand(string option){ userform = validParameter.validFile(parameters, "form", false); if (userform == "not found") { userform = "integral"; } if (abort == false) { - + matrix = globaldata->gMatrix; //get the distance matrix - setGroups(); //set the groups to be analyzed + setGroups(); //set the groups to be analyzed and sorts them + + /********************************************************************************************/ + //this is needed because when we read the matrix we sort it into groups in alphabetical order + //the rest of the command and the classes used in this command assume specific order + /********************************************************************************************/ + matrix->setGroups(globaldata->gGroupmap->namesOfGroups); + vector sizes; + for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) { sizes.push_back(globaldata->gGroupmap->getNumSeqs(globaldata->gGroupmap->namesOfGroups[i])); } + matrix->setSizes(sizes); + if(userform == "discrete"){ form = new DLibshuff(matrix, iters, step, cutOff); @@ -91,39 +99,30 @@ LibShuffCommand::LibShuffCommand(string option){ } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function LibShuffCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "LibShuffCommand", "LibShuffCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the LibShuffCommand class function LibShuffCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - } //********************************************************************************************************************** void LibShuffCommand::help(){ try { - cout << "The libshuff command can only be executed after a successful read.dist command including a groupfile." << "\n"; - cout << "The libshuff command parameters are groups, iters, step, form and cutoff. No parameters are required." << "\n"; - cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups." << "\n"; - cout << "The group names are separated by dashes. The iters parameter allows you to specify how many random matrices you would like compared to your matrix." << "\n"; - cout << "The step parameter allows you to specify change in distance you would like between each output if you are using the discrete form." << "\n"; - cout << "The form parameter allows you to specify if you would like to analyze your matrix using the discrete or integral form. Your options are integral or discrete." << "\n"; - cout << "The libshuff command should be in the following format: libshuff(groups=yourGroups, iters=yourIters, cutOff=yourCutOff, form=yourForm, step=yourStep)." << "\n"; - cout << "Example libshuff(groups=A-B-C, iters=500, form=discrete, step=0.01, cutOff=2.0)." << "\n"; - cout << "The default value for groups is all the groups in your groupfile, iters is 10000, cutoff is 1.0, form is integral and step is 0.01." << "\n"; - cout << "The libshuff command output two files: .coverage and .slsummary their descriptions are in the manual." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e.yourIters)." << "\n" << "\n"; + mothurOut("The libshuff command can only be executed after a successful read.dist command including a groupfile.\n"); + mothurOut("The libshuff command parameters are groups, iters, step, form and cutoff. No parameters are required.\n"); + mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups.\n"); + mothurOut("The group names are separated by dashes. The iters parameter allows you to specify how many random matrices you would like compared to your matrix.\n"); + mothurOut("The step parameter allows you to specify change in distance you would like between each output if you are using the discrete form.\n"); + mothurOut("The form parameter allows you to specify if you would like to analyze your matrix using the discrete or integral form. Your options are integral or discrete.\n"); + mothurOut("The libshuff command should be in the following format: libshuff(groups=yourGroups, iters=yourIters, cutOff=yourCutOff, form=yourForm, step=yourStep).\n"); + mothurOut("Example libshuff(groups=A-B-C, iters=500, form=discrete, step=0.01, cutOff=2.0).\n"); + mothurOut("The default value for groups is all the groups in your groupfile, iters is 10000, cutoff is 1.0, form is integral and step is 0.01.\n"); + mothurOut("The libshuff command output two files: .coverage and .slsummary their descriptions are in the manual.\n"); + mothurOut("Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e.yourIters).\n\n"); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "LibShuffCommand", "help"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the LibShuffCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //********************************************************************************************************************** @@ -132,10 +131,10 @@ int LibShuffCommand::execute(){ try { if (abort == true) { return 0; } - + savedDXYValues = form->evaluateAll(); savedMinValues = form->getSavedMins(); - + pValueCounts.resize(numGroups); for(int i=0;inewLine(groupNames[i]+'-'+groupNames[j], iters); + int spoti = globaldata->gGroupmap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix + int spotj = globaldata->gGroupmap->groupIndex[groupNames[j]]; + for(int p=0;prandomizeGroups(i,j); - if(form->evaluatePair(i,j) >= savedDXYValues[i][j]) { pValueCounts[i][j]++; } - if(form->evaluatePair(j,i) >= savedDXYValues[j][i]) { pValueCounts[j][i]++; } + form->randomizeGroups(spoti,spotj); + if(form->evaluatePair(spoti,spotj) >= savedDXYValues[spoti][spotj]) { pValueCounts[i][j]++; } + if(form->evaluatePair(spotj,spoti) >= savedDXYValues[spotj][spoti]) { pValueCounts[j][i]++; } reading->update(p); } - form->resetGroup(i); - form->resetGroup(j); + form->resetGroup(spoti); + form->resetGroup(spotj); } } reading->finish(); delete reading; - cout << endl; + mothurOutEndLine(); printSummaryFile(); printCoverageFile(); @@ -173,13 +175,9 @@ int LibShuffCommand::execute(){ return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "LibShuffCommand", "execute"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the LibShuffCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //********************************************************************************************************************** @@ -191,7 +189,7 @@ void LibShuffCommand::printCoverageFile() { summaryFile = getRootName(globaldata->getPhylipFile()) + "libshuff.coverage"; openOutputFile(summaryFile, outCov); outCov.setf(ios::fixed, ios::floatfield); outCov.setf(ios::showpoint); - cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint); + //cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint); map > allDistances; map >::iterator it; @@ -204,25 +202,29 @@ void LibShuffCommand::printCoverageFile() { indices[i].assign(numGroups,0); for(int j=0;jgGroupmap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix + int spotj = globaldata->gGroupmap->groupIndex[groupNames[j]]; + + for(int k=0;k prevRow = it->second; it++; - for(it;it!=allDistances.end();it++){ + for(;it!=allDistances.end();it++){ for(int i=0;isecond.size();i++){ it->second[i] += prevRow[i]; } @@ -257,16 +259,12 @@ void LibShuffCommand::printCoverageFile() { } outCov << endl; } - + outCov.close(); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function printCoverageFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "LibShuffCommand", "printCoverageFile"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the LibShuffCommand class function printCoverageFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //********************************************************************************************************************** @@ -282,40 +280,44 @@ void LibShuffCommand::printSummaryFile() { cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint); cout << setw(20) << left << "Comparison" << '\t' << setprecision(8) << "dCXYScore" << '\t' << "Significance" << endl; + mothurOutJustToLog("Comparison\tdCXYScore\tSignificance"); mothurOutEndLine(); outSum << setw(20) << left << "Comparison" << '\t' << setprecision(8) << "dCXYScore" << '\t' << "Significance" << endl; int precision = (int)log10(iters); for(int i=0;igGroupmap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix + int spotj = globaldata->gGroupmap->groupIndex[groupNames[j]]; + if(pValueCounts[i][j]){ - cout << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[i][j] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl; - outSum << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[i][j] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl; + cout << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl; + mothurOutJustToLog(groupNames[i]+"-"+groupNames[j] + "\t" + toString(savedDXYValues[spoti][spotj]) + "\t" + toString((pValueCounts[i][j]/(float)iters))); mothurOutEndLine(); + outSum << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl; } else{ - cout << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[i][j] << '\t' << '<' <Groups.size(); i++) { if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) { - cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl; + mothurOut(globaldata->Groups[i] + " is not a valid group, and will be disregarded."); mothurOutEndLine(); // erase the invalid group from globaldata->Groups globaldata->Groups.erase(globaldata->Groups.begin()+i); } @@ -345,7 +347,7 @@ void LibShuffCommand::setGroups() { for (int i=0; i < numGroups; i++) { globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]); } - cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl; + mothurOut("When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile."); mothurOutEndLine(); } else { numGroups = globaldata->Groups.size(); } } else { //users wants all groups numGroups = globaldata->gGroupmap->getNumGroups(); @@ -361,23 +363,14 @@ void LibShuffCommand::setGroups() { //sort sort(globaldata->gGroupmap->namesOfGroups.begin(), globaldata->gGroupmap->namesOfGroups.end()); + + for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) { globaldata->gGroupmap->groupIndex[globaldata->gGroupmap->namesOfGroups[i]] = i; } groupNames = globaldata->Groups; - // number of comparisons i.e. with groups A,B,C = AA, AB, AC, BA, BB, BC...; -// for (int i=0; iGroups[i] + "-" + globaldata->Groups[l]); -// } -// } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the LibShuffCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "LibShuffCommand", "setGroups"); exit(1); } }