MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
-
- //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if(processors == 1){
- numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
- }else{
- numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames);
- }
- //#else
- // numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
- //#endif
- if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; }
+ if(processors == 1){ numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames); }
+ else{ numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames); }
+
+ if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; }
#endif
#ifdef USE_MPI
string extension = "";
if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
// Allocate memory for thread data.
- seqSumData* tempSum = new seqSumData(&startPosition, &endPosition, &seqLength, &ambigBases, &longHomoPolymer, filename, (sumFile+extension), m, lines[i]->start, lines[i]->end, namefile, nameMap);
+ seqSumData* tempSum = new seqSumData(filename, (sumFile+extension), m, lines[i]->start, lines[i]->end, namefile, nameMap);
pDataArray.push_back(tempSum);
//MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
num += pDataArray[i]->count;
+ for (int k = 0; k < pDataArray[i]->startPosition.size(); k++) { startPosition.push_back(pDataArray[i]->startPosition[k]); }
+ for (int k = 0; k < pDataArray[i]->endPosition.size(); k++) { endPosition.push_back(pDataArray[i]->endPosition[k]); }
+ for (int k = 0; k < pDataArray[i]->seqLength.size(); k++) { seqLength.push_back(pDataArray[i]->seqLength[k]); }
+ for (int k = 0; k < pDataArray[i]->ambigBases.size(); k++) { ambigBases.push_back(pDataArray[i]->ambigBases[k]); }
+ for (int k = 0; k < pDataArray[i]->longHomoPolymer.size(); k++) { longHomoPolymer.push_back(pDataArray[i]->longHomoPolymer[k]); }
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
}
// This is passed by void pointer so it can be any data type
// that can be passed using a single void pointer (LPVOID).
struct seqSumData {
- vector<int>* startPosition;
- vector<int>* endPosition;
- vector<int>* seqLength;
- vector<int>* ambigBases;
- vector<int>* longHomoPolymer;
+ vector<int> startPosition;
+ vector<int> endPosition;
+ vector<int> seqLength;
+ vector<int> ambigBases;
+ vector<int> longHomoPolymer;
string filename;
string sumFile;
unsigned long long start;
seqSumData(){}
- seqSumData(vector<int>* s, vector<int>* e, vector<int>* l, vector<int>* a, vector<int>* h, string f, string sf, MothurOut* mout, unsigned long long st, unsigned long long en, string na, map<string, int> nam) {
- startPosition = s;
- endPosition = e;
- seqLength = l;
- ambigBases = a;
- longHomoPolymer = h;
+ seqSumData(string f, string sf, MothurOut* mout, unsigned long long st, unsigned long long en, string na, map<string, int> nam) {
filename = f;
sumFile = sf;
m = mout;
//for each sequence this sequence represents
for (int i = 0; i < num; i++) {
- pDataArray->startPosition->push_back(current.getStartPos());
- pDataArray->endPosition->push_back(current.getEndPos());
- pDataArray->seqLength->push_back(current.getNumBases());
- pDataArray->ambigBases->push_back(current.getAmbigBases());
- pDataArray->longHomoPolymer->push_back(current.getLongHomoPolymer());
+ pDataArray->startPosition.push_back(current.getStartPos());
+ pDataArray->endPosition.push_back(current.getEndPos());
+ pDataArray->seqLength.push_back(current.getNumBases());
+ pDataArray->ambigBases.push_back(current.getAmbigBases());
+ pDataArray->longHomoPolymer.push_back(current.getLongHomoPolymer());
}
outSummary << current.getName() << '\t';
//////////////////////////////////////////////////////////////////////////////////////////////////////
//Windows version shared memory, so be careful when passing variables through the seqSumQualData struct.
//Above fork() will clone, so memory is separate, but that's not the case with windows,
- //Taking advantage of shared memory to allow both threads to add info to vectors.
+ //Taking advantage of shared memory to pass results vectors.
//////////////////////////////////////////////////////////////////////////////////////////////////////
vector<seqSumQualData*> pDataArray;
for( int i=0; i<processors; i++ ){
// Allocate memory for thread data.
- seqSumQualData* tempSum = new seqSumQualData(&position, &averageQ, &scores, filename, m, lines[i].start, lines[i].end, namefile, nameMap);
+ seqSumQualData* tempSum = new seqSumQualData(filename, m, lines[i].start, lines[i].end, namefile, nameMap);
pDataArray.push_back(tempSum);
processIDS.push_back(i);
-
- //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
- //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
+
hThreadArray[i] = CreateThread(NULL, 0, MySeqSumQualThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
}
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
numSeqs += pDataArray[i]->count;
+ int tempNum = pDataArray[i]->position.size();
+ if (position.size() < tempNum) { position.resize(tempNum, 0); }
+ if (averageQ.size() < tempNum) { averageQ.resize(tempNum, 0); }
+ if (scores.size() < tempNum) {
+ scores.resize(tempNum);
+ for (int i = 0; i < scores.size(); i++) { scores[i].resize(41, 0); }
+ }
+
+ for (int k = 0; k < tempNum; k++) { position[k] += pDataArray[i]->position[k]; }
+ for (int k = 0; k < tempNum; k++) { averageQ[k] += pDataArray[i]->averageQ[k]; }
+ for (int k = 0; k < tempNum; k++) { for (int j = 0; j < 41; j++) { scores[k][j] += pDataArray[i]->scores[k][j]; } }
+
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
}
// This is passed by void pointer so it can be any data type
// that can be passed using a single void pointer (LPVOID).
struct seqSumQualData {
- vector<int>* position;
- vector<int>* averageQ;
- vector< vector<int> >* scores;
+ vector<int> position;
+ vector<int> averageQ;
+ vector< vector<int> > scores;
string filename, namefile;
unsigned long long start;
unsigned long long end;
map<string, int> nameMap;
~seqSumQualData(){}
- seqSumQualData(vector<int>* p, vector<int>* a, vector< vector<int> >* s, string f, MothurOut* mout, unsigned long long st, unsigned long long en, string n, map<string, int> nam) {
- position = p;
- averageQ = a;
- scores = s;
+ seqSumQualData(string f, MothurOut* mout, unsigned long long st, unsigned long long en, string n, map<string, int> nam) {
filename = f;
m = mout;
start = st;
vector<int> thisScores = current.getQualityScores();
//resize to num of positions setting number of seqs with that size to 1
- if (pDataArray->position->size() < thisScores.size()) { pDataArray->position->resize(thisScores.size(), 0); }
- if (pDataArray->averageQ->size() < thisScores.size()) { pDataArray->averageQ->resize(thisScores.size(), 0); }
- if (pDataArray->scores->size() < thisScores.size()) {
- pDataArray->scores->resize(thisScores.size());
- for (int i = 0; i < pDataArray->scores->size(); i++) { pDataArray->scores->at(i).resize(41, 0); }
+ if (pDataArray->position.size() < thisScores.size()) { pDataArray->position.resize(thisScores.size(), 0); }
+ if (pDataArray->averageQ.size() < thisScores.size()) { pDataArray->averageQ.resize(thisScores.size(), 0); }
+ if (pDataArray->scores.size() < thisScores.size()) {
+ pDataArray->scores.resize(thisScores.size());
+ for (int i = 0; i < pDataArray->scores.size(); i++) { pDataArray->scores.at(i).resize(41, 0); }
}
//increase counts of number of seqs with this position
//average is really the total, we will average in execute
for (int i = 0; i < thisScores.size(); i++) {
- pDataArray->position->at(i) += num;
- pDataArray->averageQ->at(i) += (thisScores[i] * num); //weighting for namesfile
+ pDataArray->position.at(i) += num;
+ pDataArray->averageQ.at(i) += (thisScores[i] * num); //weighting for namesfile
if (thisScores[i] > 40) { pDataArray->m->mothurOut("[ERROR]: " + current.getName() + " has a quality scores of " + toString(thisScores[i]) + ", expecting values to be less than 40."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true; }
- else { pDataArray->scores->at(i)[thisScores[i]] += num; }
+ else { pDataArray->scores.at(i)[thisScores[i]] += num; }
}
count += num;
*/
#include "summarysharedcommand.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"
//**********************************************************************************************************************
vector<string> SummarySharedCommand::setParameters(){
/***********************************************************/
int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string sumFileName, string sumAllFileName) {
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
-
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- 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;
-
- //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, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists);
-
- //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 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, 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);
-
- 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);
- }
- }
+ 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
+
+
+ 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)
+ //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, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists);
+
+ //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 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, 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);
+
+ 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 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.
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
- }
- #else
- 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"));
- }
- #endif
-
- if (createPhylip) {
- for (int i = 0; i < calcDists.size(); i++) {
- if (m->control_pressed) { break; }
+ 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]);
+ }
+
+ //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
+ }
+
+ if (createPhylip) {
+ 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
- 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(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
+ 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;
+ }
+
+ //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 += " "; }
+ }
+ outDist << name << '\t';
- //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 += " "; }
- }
- outDist << name << '\t';
-
- //output distances
- for (int l = 0; l < r; l++) { outDist << matrix[r][l] << '\t'; }
- outDist << endl;
- }
-
- outDist.close();
- }
- }
+ //output distances
+ for (int l = 0; l < r; l++) { outDist << matrix[r][l] << '\t'; }
+ outDist << endl;
+ }
+
+ outDist.close();
+ }
+ }
return 0;
}
catch(exception& e) {
#include "inputdata.h"
#include "calculator.h"
#include "validcalculator.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"
class SummarySharedCommand : public Command {
};
+/**************************************************************************************************/
+//custom data structure for threads to use.
+//main process handling the calcs that can do more than 2 groups
+// This is passed by void pointer so it can be any data type
+// that can be passed using a single void pointer (LPVOID).
+struct summarySharedData {
+ vector<SharedRAbundVector*> thisLookup;
+ vector< vector<seqDist> > calcDists;
+ vector<string> Estimators;
+ unsigned long long start;
+ unsigned long long end;
+ MothurOut* m;
+ string sumFile;
+
+ summarySharedData(){}
+ summarySharedData(string sf, MothurOut* mout, unsigned long long st, unsigned long long en, vector<string> est, vector<SharedRAbundVector*> lu) {
+ sumFile = sf;
+ m = mout;
+ start = st;
+ end = en;
+ Estimators = est;
+ thisLookup = lu;
+ }
+};
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
+static DWORD WINAPI MySummarySharedThreadFunction(LPVOID lpParam){
+ summarySharedData* pDataArray;
+ pDataArray = (summarySharedData*)lpParam;
+
+ try {
+
+ vector<Calculator*> sumCalculators;
+ ValidCalculators validCalculator;
+ for (int i=0; i<pDataArray->Estimators.size(); i++) {
+ if (validCalculator.isValidCalculator("sharedsummary", pDataArray->Estimators[i]) == true) {
+ if (pDataArray->Estimators[i] == "sharedsobs") {
+ sumCalculators.push_back(new SharedSobsCS());
+ }else if (pDataArray->Estimators[i] == "sharedchao") {
+ sumCalculators.push_back(new SharedChao1());
+ }else if (pDataArray->Estimators[i] == "sharedace") {
+ sumCalculators.push_back(new SharedAce());
+ }else if (pDataArray->Estimators[i] == "jabund") {
+ sumCalculators.push_back(new JAbund());
+ }else if (pDataArray->Estimators[i] == "sorabund") {
+ sumCalculators.push_back(new SorAbund());
+ }else if (pDataArray->Estimators[i] == "jclass") {
+ sumCalculators.push_back(new Jclass());
+ }else if (pDataArray->Estimators[i] == "sorclass") {
+ sumCalculators.push_back(new SorClass());
+ }else if (pDataArray->Estimators[i] == "jest") {
+ sumCalculators.push_back(new Jest());
+ }else if (pDataArray->Estimators[i] == "sorest") {
+ sumCalculators.push_back(new SorEst());
+ }else if (pDataArray->Estimators[i] == "thetayc") {
+ sumCalculators.push_back(new ThetaYC());
+ }else if (pDataArray->Estimators[i] == "thetan") {
+ sumCalculators.push_back(new ThetaN());
+ }else if (pDataArray->Estimators[i] == "kstest") {
+ sumCalculators.push_back(new KSTest());
+ }else if (pDataArray->Estimators[i] == "sharednseqs") {
+ sumCalculators.push_back(new SharedNSeqs());
+ }else if (pDataArray->Estimators[i] == "ochiai") {
+ sumCalculators.push_back(new Ochiai());
+ }else if (pDataArray->Estimators[i] == "anderberg") {
+ sumCalculators.push_back(new Anderberg());
+ }else if (pDataArray->Estimators[i] == "kulczynski") {
+ sumCalculators.push_back(new Kulczynski());
+ }else if (pDataArray->Estimators[i] == "kulczynskicody") {
+ sumCalculators.push_back(new KulczynskiCody());
+ }else if (pDataArray->Estimators[i] == "lennon") {
+ sumCalculators.push_back(new Lennon());
+ }else if (pDataArray->Estimators[i] == "morisitahorn") {
+ sumCalculators.push_back(new MorHorn());
+ }else if (pDataArray->Estimators[i] == "braycurtis") {
+ sumCalculators.push_back(new BrayCurtis());
+ }else if (pDataArray->Estimators[i] == "whittaker") {
+ sumCalculators.push_back(new Whittaker());
+ }else if (pDataArray->Estimators[i] == "odum") {
+ sumCalculators.push_back(new Odum());
+ }else if (pDataArray->Estimators[i] == "canberra") {
+ sumCalculators.push_back(new Canberra());
+ }else if (pDataArray->Estimators[i] == "structeuclidean") {
+ sumCalculators.push_back(new StructEuclidean());
+ }else if (pDataArray->Estimators[i] == "structchord") {
+ sumCalculators.push_back(new StructChord());
+ }else if (pDataArray->Estimators[i] == "hellinger") {
+ sumCalculators.push_back(new Hellinger());
+ }else if (pDataArray->Estimators[i] == "manhattan") {
+ sumCalculators.push_back(new Manhattan());
+ }else if (pDataArray->Estimators[i] == "structpearson") {
+ sumCalculators.push_back(new StructPearson());
+ }else if (pDataArray->Estimators[i] == "soergel") {
+ sumCalculators.push_back(new Soergel());
+ }else if (pDataArray->Estimators[i] == "spearman") {
+ sumCalculators.push_back(new Spearman());
+ }else if (pDataArray->Estimators[i] == "structkulczynski") {
+ sumCalculators.push_back(new StructKulczynski());
+ }else if (pDataArray->Estimators[i] == "speciesprofile") {
+ sumCalculators.push_back(new SpeciesProfile());
+ }else if (pDataArray->Estimators[i] == "hamming") {
+ sumCalculators.push_back(new Hamming());
+ }else if (pDataArray->Estimators[i] == "structchi2") {
+ sumCalculators.push_back(new StructChi2());
+ }else if (pDataArray->Estimators[i] == "gower") {
+ sumCalculators.push_back(new Gower());
+ }else if (pDataArray->Estimators[i] == "memchi2") {
+ sumCalculators.push_back(new MemChi2());
+ }else if (pDataArray->Estimators[i] == "memchord") {
+ sumCalculators.push_back(new MemChord());
+ }else if (pDataArray->Estimators[i] == "memeuclidean") {
+ sumCalculators.push_back(new MemEuclidean());
+ }else if (pDataArray->Estimators[i] == "mempearson") {
+ sumCalculators.push_back(new MemPearson());
+ }
+ }
+ }
+
+ pDataArray->calcDists.resize(sumCalculators.size());
+
+ ofstream outputFileHandle;
+ pDataArray->m->openOutputFile(pDataArray->sumFile, outputFileHandle);
+
+ vector<SharedRAbundVector*> subset;
+ for (int k = pDataArray->start; k < pDataArray->end; k++) { // pass cdd each set of groups to compare
+
+ for (int l = 0; l < k; l++) {
+
+ outputFileHandle << pDataArray->thisLookup[0]->getLabel() << '\t';
+
+ subset.clear(); //clear out old pair of sharedrabunds
+ //add new pair of sharedrabunds
+ subset.push_back(pDataArray->thisLookup[k]); subset.push_back(pDataArray->thisLookup[l]);
+
+ //sort groups to be alphanumeric
+ if (pDataArray->thisLookup[k]->getGroup() > pDataArray->thisLookup[l]->getGroup()) {
+ outputFileHandle << (pDataArray->thisLookup[l]->getGroup() +'\t' + pDataArray->thisLookup[k]->getGroup()) << '\t'; //print out groups
+ }else{
+ outputFileHandle << (pDataArray->thisLookup[k]->getGroup() +'\t' + pDataArray->thisLookup[l]->getGroup()) << '\t'; //print out groups
+ }
+
+ for(int i=0;i<sumCalculators.size();i++) {
+
+ //if this calc needs all groups to calculate the pair load all groups
+ if (sumCalculators[i]->getNeedsAll()) {
+ //load subset with rest of lookup for those calcs that need everyone to calc for a pair
+ for (int w = 0; w < pDataArray->thisLookup.size(); w++) {
+ if ((w != k) && (w != l)) { subset.push_back(pDataArray->thisLookup[w]); }
+ }
+ }
+
+ vector<double> tempdata = sumCalculators[i]->getValues(subset); //saves the calculator outputs
+
+ if (pDataArray->m->control_pressed) { for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } outputFileHandle.close(); return 1; }
+
+ outputFileHandle << '\t';
+ sumCalculators[i]->print(outputFileHandle);
+
+ seqDist temp(l, k, tempdata[0]);
+ pDataArray->calcDists[i].push_back(temp);
+ }
+ outputFileHandle << endl;
+ }
+ }
+
+ outputFileHandle.close();
+ for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "SummarySharedCommand", "MySummarySharedThreadFunction");
+ exit(1);
+ }
+}
+#endif
+
+
#endif
projects / mothur.git / commitdiff