*/
#include "summarysharedcommand.h"
+#include "subsample.h"
//**********************************************************************************************************************
vector<string> SummarySharedCommand::setParameters(){
try {
CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter psubsample("subsample", "String", "", "", "", "", "",false,false); parameters.push_back(psubsample);
CommandParameter pdistance("distance", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pdistance);
CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "",true,false); parameters.push_back(pcalc);
+ CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
CommandParameter pall("all", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pall);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
try {
string helpString = "";
ValidCalculators validCalculator;
- helpString += "The summary.shared command parameters are shared, label, calc, distance, processors and all. shared is required if there is no current sharedfile.\n";
+ helpString += "The summary.shared command parameters are shared, label, calc, distance, processors, subsample, iters and all. shared is required if there is no current sharedfile.\n";
helpString += "The summary.shared command should be in the following format: \n";
helpString += "summary.shared(label=yourLabel, calc=yourEstimators, groups=yourGroups).\n";
helpString += "Example summary.shared(label=unique-.01-.03, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n";
helpString += validCalculator.printCalc("sharedsummary");
+ helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
+ helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group.\n";
+ helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n";
helpString += "The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan\n";
helpString += "The default value for groups is all the groups in your groupfile.\n";
helpString += "The distance parameter allows you to indicate you would like a distance file created for each calculator for each label, default=f.\n";
temp = validParameter.validFile(parameters, "distance", false); if (temp == "not found") { temp = "false"; }
createPhylip = m->isTrue(temp);
+ temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
+ m->mothurConvert(temp, iters);
+
+ output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "lt"; }
+ if ((output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are lt and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
+
+ temp = validParameter.validFile(parameters, "subsample", false); if (temp == "not found") { temp = "F"; }
+ if (m->isNumeric1(temp)) { m->mothurConvert(temp, subsampleSize); subsample = true; }
+ else {
+ if (m->isTrue(temp)) { subsample = true; subsampleSize = -1; } //we will set it to smallest group later
+ else { subsample = false; }
+ }
+
+ if (subsample == false) { iters = 1; }
+
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
exit(1);
}
}
-
/***********************************************************/
-int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string sumFileName, string sumAllFileName) {
+int SummarySharedCommand::printSims(ostream& out, vector< vector<double> >& simMatrix) {
try {
- vector< vector<seqDist> > calcDists; //vector containing vectors that contains the summary results for each group compare
- calcDists.resize(sumCalculators.size()); //one for each calc, this will be used to make .dist files
+
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ //output num seqs
+ out << simMatrix.size() << endl;
+
+ if (output == "lt") {
+ for (int b = 0; b < simMatrix.size(); b++) {
+ out << lookup[b]->getGroup() << '\t';
+ for (int n = 0; n < b; n++) {
+ if (m->control_pressed) { return 0; }
+ out << simMatrix[b][n] << '\t';
+ }
+ out << endl;
+ }
+ }else{
+ for (int b = 0; b < simMatrix.size(); m++) {
+ out << lookup[b]->getGroup() << '\t';
+ for (int n = 0; n < simMatrix[b].size(); n++) {
+ if (m->control_pressed) { return 0; }
+ out << simMatrix[b][n] << '\t';
+ }
+ out << endl;
+ }
+ }
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummarySharedCommand", "printSims");
+ exit(1);
+ }
+}
+/***********************************************************/
+int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string sumFileName, string sumAllFileName) {
+ try {
+ vector< vector< vector<seqDist> > > calcDistsTotals; //each iter, one for each calc, then each groupCombos dists. this will be used to make .dist files
+ vector< vector<seqDist> > calcDists; calcDists.resize(sumCalculators.size());
- if(processors == 1){
- driver(thisLookup, 0, numGroups, sumFileName+".temp", sumAllFileName+".temp", calcDists);
- m->appendFiles((sumFileName + ".temp"), sumFileName);
- m->mothurRemove((sumFileName + ".temp"));
- if (mult) {
- m->appendFiles((sumAllFileName + ".temp"), sumAllFileName);
- m->mothurRemove((sumAllFileName + ".temp"));
- }
- }else{
+ for (int thisIter = 0; thisIter < iters; thisIter++) {
- int process = 1;
- vector<int> processIDS;
+ vector<SharedRAbundVector*> thisItersLookup = thisLookup;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- //loop through and create all the processes you want
- while (process != processors) {
- int pid = fork();
+ if (subsample) {
+ SubSample sample;
+ vector<string> tempLabels; //dont need since we arent printing the sampled sharedRabunds
+
+ //make copy of lookup so we don't get access violations
+ vector<SharedRAbundVector*> newLookup;
+ for (int k = 0; k < thisItersLookup.size(); k++) {
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ temp->setLabel(thisItersLookup[k]->getLabel());
+ temp->setGroup(thisItersLookup[k]->getGroup());
+ newLookup.push_back(temp);
+ }
- if (pid > 0) {
- processIDS.push_back(pid);
- process++;
- }else if (pid == 0){
- driver(thisLookup, lines[process].start, lines[process].end, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists);
+ //for each bin
+ for (int k = 0; k < thisItersLookup[0]->getNumBins(); k++) {
+ if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
+ for (int j = 0; j < thisItersLookup.size(); j++) { newLookup[j]->push_back(thisItersLookup[j]->getAbundance(k), thisItersLookup[j]->getGroup()); }
+ }
+
+ tempLabels = sample.getSample(newLookup, subsampleSize);
+ thisItersLookup = newLookup;
+ }
+
+
+ if(processors == 1){
+ driver(thisLookup, 0, numGroups, sumFileName+".temp", sumAllFileName+".temp", calcDists);
+ m->appendFiles((sumFileName + ".temp"), sumFileName);
+ m->mothurRemove((sumFileName + ".temp"));
+ if (mult) {
+ m->appendFiles((sumAllFileName + ".temp"), sumAllFileName);
+ m->mothurRemove((sumAllFileName + ".temp"));
+ }
+ }else{
+
+ int process = 1;
+ vector<int> processIDS;
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
- //only do this if you want a distance file
- if (createPhylip) {
- string tempdistFileName = m->getRootName(m->getSimpleName(sumFileName)) + toString(getpid()) + ".dist";
- ofstream outtemp;
- m->openOutputFile(tempdistFileName, outtemp);
+ if (pid > 0) {
+ processIDS.push_back(pid);
+ process++;
+ }else if (pid == 0){
+ driver(thisLookup, lines[process].start, lines[process].end, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists);
- for (int i = 0; i < calcDists.size(); i++) {
- outtemp << calcDists[i].size() << endl;
+ //only do this if you want a distance file
+ if (createPhylip) {
+ string tempdistFileName = m->getRootName(m->getSimpleName(sumFileName)) + toString(getpid()) + ".dist";
+ ofstream outtemp;
+ m->openOutputFile(tempdistFileName, outtemp);
- for (int j = 0; j < calcDists[i].size(); j++) {
- outtemp << calcDists[i][j].seq1 << '\t' << calcDists[i][j].seq2 << '\t' << calcDists[i][j].dist << endl;
+ for (int i = 0; i < calcDists.size(); i++) {
+ outtemp << calcDists[i].size() << endl;
+
+ for (int j = 0; j < calcDists[i].size(); j++) {
+ outtemp << calcDists[i][j].seq1 << '\t' << calcDists[i][j].seq2 << '\t' << calcDists[i][j].dist << endl;
+ }
}
+ outtemp.close();
}
- outtemp.close();
+
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
}
-
- exit(0);
- }else {
- m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
- for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
- exit(0);
}
- }
-
- //parent do your part
- driver(thisLookup, lines[0].start, lines[0].end, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists);
- m->appendFiles((sumFileName + toString(getpid()) + ".temp"), sumFileName);
- m->mothurRemove((sumFileName + toString(getpid()) + ".temp"));
- if (mult) { m->appendFiles((sumAllFileName + toString(getpid()) + ".temp"), sumAllFileName); }
-
- //force parent to wait until all the processes are done
- for (int i = 0; i < processIDS.size(); i++) {
- int temp = processIDS[i];
- wait(&temp);
- }
-
- for (int i = 0; i < processIDS.size(); i++) {
- m->appendFiles((sumFileName + toString(processIDS[i]) + ".temp"), sumFileName);
- m->mothurRemove((sumFileName + toString(processIDS[i]) + ".temp"));
- if (mult) { m->mothurRemove((sumAllFileName + toString(processIDS[i]) + ".temp")); }
- if (createPhylip) {
- string tempdistFileName = m->getRootName(m->getSimpleName(sumFileName)) + toString(processIDS[i]) + ".dist";
- ifstream intemp;
- m->openInputFile(tempdistFileName, intemp);
+ //parent do your part
+ driver(thisLookup, lines[0].start, lines[0].end, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists);
+ m->appendFiles((sumFileName + toString(getpid()) + ".temp"), sumFileName);
+ m->mothurRemove((sumFileName + toString(getpid()) + ".temp"));
+ if (mult) { m->appendFiles((sumAllFileName + toString(getpid()) + ".temp"), sumAllFileName); }
+
+ //force parent to wait until all the processes are done
+ for (int i = 0; i < processIDS.size(); i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ for (int i = 0; i < processIDS.size(); i++) {
+ m->appendFiles((sumFileName + toString(processIDS[i]) + ".temp"), sumFileName);
+ m->mothurRemove((sumFileName + toString(processIDS[i]) + ".temp"));
+ if (mult) { m->mothurRemove((sumAllFileName + toString(processIDS[i]) + ".temp")); }
- for (int k = 0; k < calcDists.size(); k++) {
- int size = 0;
- intemp >> size; m->gobble(intemp);
+ if (createPhylip) {
+ string tempdistFileName = m->getRootName(m->getSimpleName(sumFileName)) + toString(processIDS[i]) + ".dist";
+ ifstream intemp;
+ m->openInputFile(tempdistFileName, intemp);
- for (int j = 0; j < size; j++) {
- int seq1 = 0;
- int seq2 = 0;
- float dist = 1.0;
+ for (int k = 0; k < calcDists.size(); k++) {
+ int size = 0;
+ intemp >> size; m->gobble(intemp);
- intemp >> seq1 >> seq2 >> dist; m->gobble(intemp);
-
- seqDist tempDist(seq1, seq2, dist);
- calcDists[k].push_back(tempDist);
+ for (int j = 0; j < size; j++) {
+ int seq1 = 0;
+ int seq2 = 0;
+ float dist = 1.0;
+
+ intemp >> seq1 >> seq2 >> dist; m->gobble(intemp);
+
+ seqDist tempDist(seq1, seq2, dist);
+ calcDists[k].push_back(tempDist);
+ }
}
+ intemp.close();
+ m->mothurRemove(tempdistFileName);
}
- intemp.close();
- m->mothurRemove(tempdistFileName);
}
- }
#else
- //////////////////////////////////////////////////////////////////////////////////////////////////////
- //Windows version shared memory, so be careful when passing variables through the summarySharedData struct.
- //Above fork() will clone, so memory is separate, but that's not the case with windows,
- //Taking advantage of shared memory to pass results vectors.
- //////////////////////////////////////////////////////////////////////////////////////////////////////
-
- vector<summarySharedData*> pDataArray;
- DWORD dwThreadIdArray[processors-1];
- HANDLE hThreadArray[processors-1];
-
- //Create processor worker threads.
- for( int i=1; i<processors; i++ ){
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the summarySharedData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //Taking advantage of shared memory to pass results vectors.
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
- //make copy of lookup so we don't get access violations
- vector<SharedRAbundVector*> newLookup;
- for (int k = 0; k < thisLookup.size(); k++) {
- SharedRAbundVector* temp = new SharedRAbundVector();
- temp->setLabel(thisLookup[k]->getLabel());
- temp->setGroup(thisLookup[k]->getGroup());
- newLookup.push_back(temp);
+ vector<summarySharedData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor worker threads.
+ for( int i=1; i<processors; i++ ){
+
+ //make copy of lookup so we don't get access violations
+ vector<SharedRAbundVector*> newLookup;
+ for (int k = 0; k < thisLookup.size(); k++) {
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ temp->setLabel(thisLookup[k]->getLabel());
+ temp->setGroup(thisLookup[k]->getGroup());
+ newLookup.push_back(temp);
+ }
+
+ //for each bin
+ for (int k = 0; k < thisLookup[0]->getNumBins(); k++) {
+ if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
+ for (int j = 0; j < thisLookup.size(); j++) { newLookup[j]->push_back(thisLookup[j]->getAbundance(k), thisLookup[j]->getGroup()); }
+ }
+
+ // Allocate memory for thread data.
+ summarySharedData* tempSum = new summarySharedData((sumFileName+toString(i)+".temp"), m, lines[i].start, lines[i].end, Estimators, newLookup);
+ pDataArray.push_back(tempSum);
+ processIDS.push_back(i);
+
+ hThreadArray[i-1] = CreateThread(NULL, 0, MySummarySharedThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
}
- //for each bin
- for (int k = 0; k < thisLookup[0]->getNumBins(); k++) {
- if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
- for (int j = 0; j < thisLookup.size(); j++) { newLookup[j]->push_back(thisLookup[j]->getAbundance(k), thisLookup[j]->getGroup()); }
+ //parent do your part
+ driver(thisLookup, lines[0].start, lines[0].end, sumFileName +"0.temp", sumAllFileName + "0.temp", calcDists);
+ m->appendFiles((sumFileName + "0.temp"), sumFileName);
+ m->mothurRemove((sumFileName + "0.temp"));
+ if (mult) { m->appendFiles((sumAllFileName + "0.temp"), sumAllFileName); }
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ m->appendFiles((sumFileName + toString(processIDS[i]) + ".temp"), sumFileName);
+ m->mothurRemove((sumFileName + toString(processIDS[i]) + ".temp"));
+
+ for (int j = 0; j < pDataArray[i]->thisLookup.size(); j++) { delete pDataArray[i]->thisLookup[j]; }
+
+ if (createPhylip) {
+ for (int k = 0; k < calcDists.size(); k++) {
+ int size = pDataArray[i]->calcDists[k].size();
+ for (int j = 0; j < size; j++) { calcDists[k].push_back(pDataArray[i]->calcDists[k][j]); }
+ }
+ }
+
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
}
+
+#endif
+ }
+ calcDistsTotals.push_back(calcDists);
+
+ if (subsample) {
+
+ //clean up memory
+ for (int i = 0; i < thisItersLookup.size(); i++) { delete thisItersLookup[i]; }
+ thisItersLookup.clear();
+ for (int i = 0; i < calcDists.size(); i++) { calcDists[i].clear(); }
+ }
+ }
- // Allocate memory for thread data.
- summarySharedData* tempSum = new summarySharedData((sumFileName+toString(i)+".temp"), m, lines[i].start, lines[i].end, Estimators, newLookup);
- pDataArray.push_back(tempSum);
- processIDS.push_back(i);
+ if (iters != 1) {
+ //we need to find the average distance and standard deviation for each groups distance
+
+ vector< vector<seqDist> > calcAverages; calcAverages.resize(sumCalculators.size());
+ for (int i = 0; i < calcAverages.size(); i++) { //initialize sums to zero.
+ calcAverages[i].resize(calcDistsTotals[0][i].size());
- hThreadArray[i-1] = CreateThread(NULL, 0, MySummarySharedThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
+ for (int j = 0; j < calcAverages[i].size(); j++) {
+ calcAverages[i][j].seq1 = calcDists[i][j].seq1;
+ calcAverages[i][j].seq2 = calcDists[i][j].seq2;
+ calcAverages[i][j].dist = 0.0;
+ }
}
- //parent do your part
- driver(thisLookup, lines[0].start, lines[0].end, sumFileName +"0.temp", sumAllFileName + "0.temp", calcDists);
- m->appendFiles((sumFileName + "0.temp"), sumFileName);
- m->mothurRemove((sumFileName + "0.temp"));
- if (mult) { m->appendFiles((sumAllFileName + "0.temp"), sumAllFileName); }
+ for (int thisIter = 0; thisIter < iters; thisIter++) { //sum all groups dists for each calculator
+ for (int i = 0; i < calcAverages.size(); i++) { //initialize sums to zero.
+ for (int j = 0; j < calcAverages[i].size(); j++) {
+ calcAverages[i][j].dist += calcDistsTotals[thisIter][i][j].dist;
+ }
+ }
+ }
- //Wait until all threads have terminated.
- WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+ for (int i = 0; i < calcAverages.size(); i++) { //finds average.
+ for (int j = 0; j < calcAverages[i].size(); j++) {
+ calcAverages[i][j].dist /= (float) iters;
+ }
+ }
- //Close all thread handles and free memory allocations.
- for(int i=0; i < pDataArray.size(); i++){
- m->appendFiles((sumFileName + toString(processIDS[i]) + ".temp"), sumFileName);
- m->mothurRemove((sumFileName + toString(processIDS[i]) + ".temp"));
+ //find standard deviation
+ vector< vector<seqDist> > stdDev; stdDev.resize(sumCalculators.size());
+ for (int i = 0; i < stdDev.size(); i++) { //initialize sums to zero.
+ stdDev[i].resize(calcDistsTotals[0][i].size());
- for (int j = 0; j < pDataArray[i]->thisLookup.size(); j++) { delete pDataArray[i]->thisLookup[j]; }
-
- if (createPhylip) {
- for (int k = 0; k < calcDists.size(); k++) {
- int size = pDataArray[i]->calcDists[k].size();
- for (int j = 0; j < size; j++) { calcDists[k].push_back(pDataArray[i]->calcDists[k][j]); }
+ for (int j = 0; j < stdDev[i].size(); j++) {
+ stdDev[i][j].seq1 = calcDists[i][j].seq1;
+ stdDev[i][j].seq2 = calcDists[i][j].seq2;
+ stdDev[i][j].dist = 0.0;
+ }
+ }
+
+ for (int thisIter = 0; thisIter < iters; thisIter++) { //compute the difference of each dist from the mean, and square the result of each
+ for (int i = 0; i < stdDev.size(); i++) {
+ for (int j = 0; j < stdDev[i].size(); j++) {
+ stdDev[i][j].dist += ((calcDistsTotals[thisIter][i][j].dist - calcAverages[i][j].dist) * (calcDistsTotals[thisIter][i][j].dist - calcAverages[i][j].dist));
}
}
-
- CloseHandle(hThreadArray[i]);
- delete pDataArray[i];
}
-
-#endif
- }
-
- if (createPhylip) {
+
+ for (int i = 0; i < stdDev.size(); i++) { //finds average.
+ for (int j = 0; j < stdDev[i].size(); j++) {
+ stdDev[i][j].dist /= (float) iters;
+ stdDev[i][j].dist = sqrt(stdDev[i][j].dist);
+ }
+ }
+
+ //print results
for (int i = 0; i < calcDists.size(); i++) {
- if (m->control_pressed) { break; }
-
- string distFileName = outputDir + m->getRootName(m->getSimpleName(sumFileName)) + sumCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".dist";
- outputNames.push_back(distFileName);
- ofstream outDist;
- m->openOutputFile(distFileName, outDist);
- outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
-
- //initialize matrix
- vector< vector<float> > matrix; //square matrix to represent the distance
+ vector< vector<double> > matrix; //square matrix to represent the distance
matrix.resize(thisLookup.size());
for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); }
+ vector< vector<double> > stdmatrix; //square matrix to represent the stdDev
+ stdmatrix.resize(thisLookup.size());
+ for (int k = 0; k < thisLookup.size(); k++) { stdmatrix[k].resize(thisLookup.size(), 0.0); }
+
- for (int j = 0; j < calcDists[i].size(); j++) {
- int row = calcDists[i][j].seq1;
- int column = calcDists[i][j].seq2;
- float dist = calcDists[i][j].dist;
+ for (int j = 0; j < calcAverages[i].size(); j++) {
+ int row = calcAverages[i][j].seq1;
+ int column = calcAverages[i][j].seq2;
+ float dist = calcAverages[i][j].dist;
+ float stdDist = stdDev[i][j].dist;
matrix[row][column] = dist;
matrix[column][row] = dist;
+ stdmatrix[row][column] = stdDist;
+ stdmatrix[column][row] = stdDist;
}
- //output to file
- outDist << thisLookup.size() << endl;
- for (int r=0; r<thisLookup.size(); r++) {
- //output name
- string name = thisLookup[r]->getGroup();
- if (name.length() < 10) { //pad with spaces to make compatible
- while (name.length() < 10) { name += " "; }
+ string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + sumCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".ave.dist";
+ outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
+ ofstream outAve;
+ m->openOutputFile(distFileName, outAve);
+ outAve.setf(ios::fixed, ios::floatfield); outAve.setf(ios::showpoint);
+
+ printSims(outAve, matrix);
+
+ outAve.close();
+
+ distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + sumCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".std.dist";
+ outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
+ ofstream outSTD;
+ m->openOutputFile(distFileName, outSTD);
+ outSTD.setf(ios::fixed, ios::floatfield); outSTD.setf(ios::showpoint);
+
+ printSims(outSTD, stdmatrix);
+
+ outSTD.close();
+
+ }
+ }else {
+ if (createPhylip) {
+ for (int i = 0; i < calcDists.size(); i++) {
+ if (m->control_pressed) { break; }
+
+ //initialize matrix
+ vector< vector<double> > matrix; //square matrix to represent the distance
+ matrix.resize(thisLookup.size());
+ for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); }
+
+ for (int j = 0; j < calcDists[i].size(); j++) {
+ int row = calcDists[i][j].seq1;
+ int column = calcDists[i][j].seq2;
+ double dist = calcDists[i][j].dist;
+
+ matrix[row][column] = dist;
+ matrix[column][row] = dist;
}
- outDist << name << '\t';
-
- //output distances
- for (int l = 0; l < r; l++) { outDist << matrix[r][l] << '\t'; }
- outDist << endl;
+
+ string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + sumCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist";
+ outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
+ ofstream outDist;
+ m->openOutputFile(distFileName, outDist);
+ outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
+
+ printSims(outDist, matrix);
+
+ outDist.close();
}
-
- outDist.close();
}
}
- return 0;
+
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "SummarySharedCommand", "process");
projects / mothur.git / blobdiff