*/
#include "matrixoutputcommand.h"
-#include "sharedsobscollectsummary.h"
-#include "sharedchao1.h"
-#include "sharedace.h"
-#include "sharednseqs.h"
-#include "sharedjabund.h"
-#include "sharedsorabund.h"
-#include "sharedjclass.h"
-#include "sharedsorclass.h"
-#include "sharedjest.h"
-#include "sharedsorest.h"
-#include "sharedthetayc.h"
-#include "sharedthetan.h"
-#include "sharedkstest.h"
-#include "whittaker.h"
-#include "sharedochiai.h"
-#include "sharedanderbergs.h"
-#include "sharedkulczynski.h"
-#include "sharedkulczynskicody.h"
-#include "sharedlennon.h"
-#include "sharedmorisitahorn.h"
-#include "sharedbraycurtis.h"
-#include "sharedjackknife.h"
-#include "whittaker.h"
-#include "odum.h"
-#include "canberra.h"
-#include "structeuclidean.h"
-#include "structchord.h"
-#include "hellinger.h"
-#include "manhattan.h"
-#include "structpearson.h"
-#include "soergel.h"
-#include "spearman.h"
-#include "structkulczynski.h"
-#include "structchi2.h"
-#include "speciesprofile.h"
-#include "hamming.h"
-#include "gower.h"
-#include "memchi2.h"
-#include "memchord.h"
-#include "memeuclidean.h"
-#include "mempearson.h"
+#include "subsample.h"
//**********************************************************************************************************************
vector<string> MatrixOutputCommand::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 pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
- CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","phylip",false,true,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 pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "","",true,false,true); parameters.push_back(pcalc);
+ CommandParameter poutput("output", "Multiple", "lt-square-column", "lt", "", "", "","",false,false); parameters.push_back(poutput);
+ CommandParameter pmode("mode", "Multiple", "average-median", "average", "", "", "","",false,false); parameters.push_back(pmode);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
try {
string helpString = "";
ValidCalculators validCalculator;
- helpString += "The dist.shared command parameters are shared, groups, calc, output, processors and label. shared is a required, unless you have a valid current file.\n";
+ helpString += "The dist.shared command parameters are shared, groups, calc, output, processors, subsample, iters, mode, and label. shared is a required, unless you have a valid current file.\n";
helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
helpString += "The group names are separated by dashes. The label parameter allows you to select what distance levels you would like distance matrices created for, and is also separated by dashes.\n";
+ 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 dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\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 output parameter allows you to specify format of your distance matrix. Options are lt, column and square. The default is lt.\n";
+ helpString += "The mode parameter allows you to specify if you want the average or the median values reported when subsampling. Options are average, and median. The default is average.\n";
helpString += "Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n";
helpString += "The default value for groups is all the groups in your groupfile.\n";
helpString += "The default value for calc is jclass and thetayc.\n";
}
}
//**********************************************************************************************************************
+string MatrixOutputCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "phylip") { pattern = "[filename],[calc],[distance],[outputtag],dist-[filename],[calc],[distance],[outputtag],[tag2],dist"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MatrixOutputCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
MatrixOutputCommand::MatrixOutputCommand(){
try {
abort = true; calledHelp = true;
if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
}else if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else { m->setSharedFile(sharedfile); }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
}
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"; }
+ if ((output != "lt") && (output != "square") && (output != "column")) { m->mothurOut(output + " is not a valid output form. Options are lt, column and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
+
+ mode = validParameter.validFile(parameters, "mode", false); if(mode == "not found"){ mode = "average"; }
+ if ((mode != "average") && (mode != "median")) { m->mothurOut(mode + " is not a valid mode. Options are average and medina. I will use average."); m->mothurOutEndLine(); output = "average"; }
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
}
string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
calc = validParameter.validFile(parameters, "calc", false);
if (calc == "not found") { calc = "jclass-thetayc"; }
//remove citation from list of calcs
for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
}
-
+
+ temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
+ m->mothurConvert(temp, iters);
+
+ 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 = 0; }
+
if (abort == false) {
ValidCalculators validCalculator;
set<string> userLabels = labels;
if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0;}
-
+
+ if (subsample) {
+ if (subsampleSize == -1) { //user has not set size, set size = smallest samples size
+ subsampleSize = lookup[0]->getNumSeqs();
+ for (int i = 1; i < lookup.size(); i++) {
+ int thisSize = lookup[i]->getNumSeqs();
+
+ if (thisSize < subsampleSize) { subsampleSize = thisSize; }
+ }
+ }else {
+ m->clearGroups();
+ Groups.clear();
+ vector<SharedRAbundVector*> temp;
+ for (int i = 0; i < lookup.size(); i++) {
+ if (lookup[i]->getNumSeqs() < subsampleSize) {
+ m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
+ delete lookup[i];
+ }else {
+ Groups.push_back(lookup[i]->getGroup());
+ temp.push_back(lookup[i]);
+ }
+ }
+ lookup = temp;
+ m->setGroups(Groups);
+ }
+
+ if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; delete input; return 0; }
+ }
+
numGroups = lookup.size();
- lines.resize(processors);
+ lines.resize(processors);
for (int i = 0; i < processors; i++) {
lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
}
-
- if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); return 0; }
+
+ if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; }
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } m->Groups.clear(); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
lookup = input->getSharedRAbundVectors();
}
- if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } m->Groups.clear(); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
}
}
- if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } m->Groups.clear(); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0; }
//run last label if you need to
if (needToRun == true) {
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } m->Groups.clear(); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0; }
//reset groups parameter
- m->Groups.clear();
+ m->clearGroups();
//set phylip file as new current phylipfile
string current = "";
}
}
/***********************************************************/
-void MatrixOutputCommand::printSims(ostream& out, vector< vector<float> >& simMatrix) {
+void MatrixOutputCommand::printSims(ostream& out, vector< vector<double> >& simMatrix) {
try {
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-
- //output num seqs
- out << simMatrix.size() << endl;
-
+
if (output == "lt") {
- for (int m = 0; m < simMatrix.size(); m++) {
- out << lookup[m]->getGroup() << '\t';
- for (int n = 0; n < m; n++) {
- out << simMatrix[m][n] << '\t';
+ out << simMatrix.size() << endl;
+ for (int b = 0; b < simMatrix.size(); b++) {
+ out << lookup[b]->getGroup() << '\t';
+ for (int n = 0; n < b; n++) {
+ out << simMatrix[b][n] << '\t';
}
out << endl;
}
+ }else if (output == "column") {
+ for (int b = 0; b < simMatrix.size(); b++) {
+ for (int n = 0; n < b; n++) {
+ out << lookup[b]->getGroup() << '\t' << lookup[n]->getGroup() << '\t' << simMatrix[b][n] << endl;
+ }
+ }
}else{
- for (int m = 0; m < simMatrix.size(); m++) {
- out << lookup[m]->getGroup() << '\t';
- for (int n = 0; n < simMatrix[m].size(); n++) {
- out << simMatrix[m][n] << '\t';
+ out << simMatrix.size() << endl;
+ for (int b = 0; b < simMatrix.size(); b++) {
+ out << lookup[b]->getGroup() << '\t';
+ for (int n = 0; n < simMatrix[b].size(); n++) {
+ out << simMatrix[b][n] << '\t';
}
out << endl;
}
/***********************************************************/
int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
try {
- EstOutput data;
- vector<SharedRAbundVector*> subset;
- vector< vector<seqDist> > calcDists; calcDists.resize(matrixCalculators.size()); //one for each calc, this will be used to make .dist files
-
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if(processors == 1){
- driver(thisLookup, 0, numGroups, calcDists);
- }else{
- int process = 1;
- vector<int> processIDS;
-
- //loop through and create all the processes you want
- while (process != processors) {
- int pid = fork();
-
- if (pid > 0) {
- processIDS.push_back(pid);
- process++;
- }else if (pid == 0){
- driver(thisLookup, lines[process].start, lines[process].end, calcDists);
-
- string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(getpid()) + ".dist";
- ofstream outtemp;
- m->openOutputFile(tempdistFileName, outtemp);
-
- 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();
-
- 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, calcDists);
-
- //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++) {
- string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(processIDS[i]) + ".dist";
- ifstream intemp;
- m->openInputFile(tempdistFileName, intemp);
-
- for (int k = 0; k < calcDists.size(); k++) {
- int size = 0;
- intemp >> size; m->gobble(intemp);
-
- 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();
- remove(tempdistFileName.c_str());
- }
-
+ 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(matrixCalculators.size());
+
+ for (int thisIter = 0; thisIter < iters+1; thisIter++) {
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[distance]"] = thisLookup[0]->getLabel();
+ variables["[tag2]"] = "";
+
+ vector<SharedRAbundVector*> thisItersLookup = thisLookup;
+
+ if (subsample && (thisIter != 0)) {
+ 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);
+ }
+
+ //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(thisItersLookup, 0, numGroups, calcDists);
+ }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();
+
+ if (pid > 0) {
+ processIDS.push_back(pid);
+ process++;
+ }else if (pid == 0){
+
+ driver(thisItersLookup, lines[process].start, lines[process].end, calcDists);
+
+ string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(getpid()) + ".dist";
+ ofstream outtemp;
+ m->openOutputFile(tempdistFileName, outtemp);
+
+ 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();
+
+ 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(thisItersLookup, lines[0].start, lines[0].end, calcDists);
+
+ //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++) {
+ string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(processIDS[i]) + ".dist";
+ ifstream intemp;
+ m->openInputFile(tempdistFileName, intemp);
+
+ for (int k = 0; k < calcDists.size(); k++) {
+ int size = 0;
+ intemp >> size; m->gobble(intemp);
+
+ 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);
+ }
+ #else
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the distSharedData 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<distSharedData*> 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 < thisItersLookup.size(); k++) {
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ temp->setLabel(thisItersLookup[k]->getLabel());
+ temp->setGroup(thisItersLookup[k]->getGroup());
+ newLookup.push_back(temp);
+ }
+
+ //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()); }
+ }
+
+ // Allocate memory for thread data.
+ distSharedData* tempSum = new distSharedData(m, lines[i].start, lines[i].end, Estimators, newLookup);
+ pDataArray.push_back(tempSum);
+ processIDS.push_back(i);
+
+ hThreadArray[i-1] = CreateThread(NULL, 0, MyDistSharedThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
+ }
+
+ //parent do your part
+ driver(thisItersLookup, lines[0].start, lines[0].end, calcDists);
+
+ //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++){
+ if (pDataArray[i]->count != (pDataArray[i]->end-pDataArray[i]->start)) {
+ m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " groups assigned to it, quitting. \n"); m->control_pressed = true;
+ }
+ for (int j = 0; j < pDataArray[i]->thisLookup.size(); j++) { delete pDataArray[i]->thisLookup[j]; }
+
+ 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
+ }
+
+ if (subsample && (thisIter != 0)) {
+ if((thisIter) % 100 == 0){ m->mothurOut(toString(thisIter)); m->mothurOutEndLine(); }
+ calcDistsTotals.push_back(calcDists);
+ for (int i = 0; i < calcDists.size(); i++) {
+ for (int j = 0; j < calcDists[i].size(); j++) {
+ if (m->debug) { m->mothurOut("[DEBUG]: Results: iter = " + toString(thisIter) + ", " + thisLookup[calcDists[i][j].seq1]->getGroup() + " - " + thisLookup[calcDists[i][j].seq2]->getGroup() + " distance = " + toString(calcDists[i][j].dist) + ".\n"); }
+ }
+ }
+ //clean up memory
+ for (int i = 0; i < thisItersLookup.size(); i++) { delete thisItersLookup[i]; }
+ thisItersLookup.clear();
+ }else { //print results for whole dataset
+ 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;
+ }
+
+ variables["[outputtag]"] = output;
+ variables["[calc]"] = matrixCalculators[i]->getName();
+ string distFileName = getOutputFileName("phylip",variables);
+ 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();
+ }
+ }
+ for (int i = 0; i < calcDists.size(); i++) { calcDists[i].clear(); }
}
-#else
- driver(thisLookup, 0, numGroups, calcDists);
-#endif
- for (int i = 0; i < calcDists.size(); i++) {
- if (m->control_pressed) { break; }
-
- //initialize matrix
- vector< vector<float> > 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;
- float dist = calcDists[i][j].dist;
-
- matrix[row][column] = dist;
- matrix[column][row] = dist;
- }
-
- string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[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();
- }
+ if (iters != 0) {
+ //we need to find the average distance and standard deviation for each groups distance
+ vector< vector<seqDist> > calcAverages = m->getAverages(calcDistsTotals, mode);
+
+ //find standard deviation
+ vector< vector<seqDist> > stdDev = m->getStandardDeviation(calcDistsTotals, calcAverages);
+
+ //print results
+ for (int i = 0; i < calcDists.size(); i++) {
+ 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 < 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;
+ }
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[distance]"] = thisLookup[0]->getLabel();
+ variables["[outputtag]"] = output;
+ variables["[tag2]"] = "ave";
+ variables["[calc]"] = matrixCalculators[i]->getName();
+ string distFileName = getOutputFileName("phylip",variables);
+ 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();
+
+ variables["[tag2]"] = "std";
+ distFileName = getOutputFileName("phylip",variables);
+ 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();
+
+ }
+ }
return 0;
}
/**************************************************************************************************/
int MatrixOutputCommand::driver(vector<SharedRAbundVector*> thisLookup, int start, int end, vector< vector<seqDist> >& calcDists) {
try {
-
vector<SharedRAbundVector*> subset;
+
for (int k = start; k < end; k++) { // pass cdd each set of groups to compare
for (int l = 0; l < k; l++) {
if (m->control_pressed) { return 1; }
- seqDist temp(l, k, (1.0 - tempdata[0]));
+ seqDist temp(l, k, tempdata[0]);
calcDists[i].push_back(temp);
}
}
projects / mothur.git / blobdiff