+/**************************************************************************************************/
+
+double ShhherCommand::getNewWeights(){
+ try{
+
+ double maxChange = 0;
+
+ for(int i=0;i<numOTUs;i++){
+
+ if (m->control_pressed) { break; }
+
+ double difference = weight[i];
+ weight[i] = 0;
+
+ for(int j=0;j<nSeqsPerOTU[i];j++){
+ int index = cumNumSeqs[i] + j;
+ double tauValue = singleTau[seqNumber[index]];
+ weight[i] += tauValue;
+ }
+
+ difference = fabs(weight[i] - difference);
+ if(difference > maxChange){ maxChange = difference; }
+ }
+ return maxChange;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ShhherCommand", "getNewWeights");
+ exit(1);
+ }
+}
+
+ /**************************************************************************************************/
+
+double ShhherCommand::getLikelihood(){
+
+ try{
+
+ vector<long double> P(numSeqs, 0);
+ int effNumOTUs = 0;
+
+ for(int i=0;i<numOTUs;i++){
+ if(weight[i] > MIN_WEIGHT){
+ effNumOTUs++;
+ }
+ }
+
+ string hold;
+ for(int i=0;i<numOTUs;i++){
+
+ if (m->control_pressed) { break; }
+
+ for(int j=0;j<nSeqsPerOTU[i];j++){
+ int index = cumNumSeqs[i] + j;
+ int nI = seqIndex[index];
+ double singleDist = dist[seqNumber[index]];
+
+ P[nI] += weight[i] * exp(-singleDist * sigma);
+ }
+ }
+ double nLL = 0.00;
+ for(int i=0;i<numSeqs;i++){
+ if(P[i] == 0){ P[i] = DBL_EPSILON; }
+
+ nLL += -log(P[i]);
+ }
+
+ nLL = nLL -(double)numSeqs * log(sigma);
+
+ return nLL;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ShhherCommand", "getNewWeights");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+void ShhherCommand::checkCentroids(){
+ try{
+ vector<int> unique(numOTUs, 1);
+
+ for(int i=0;i<numOTUs;i++){
+ if(centroids[i] == -1 || weight[i] < MIN_WEIGHT){
+ unique[i] = -1;
+ }
+ }
+
+ for(int i=0;i<numOTUs;i++){
+
+ if (m->control_pressed) { break; }
+
+ if(unique[i] == 1){
+ for(int j=i+1;j<numOTUs;j++){
+ if(unique[j] == 1){
+
+ if(centroids[j] == centroids[i]){
+ unique[j] = 0;
+ centroids[j] = -1;
+
+ weight[i] += weight[j];
+ weight[j] = 0.0;
+ }
+ }
+ }
+ }
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ShhherCommand", "checkCentroids");
+ exit(1);
+ }
+}
+ /**************************************************************************************************/
+
+
+
+void ShhherCommand::writeQualities(vector<int> otuCounts){
+
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); }
+ string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.qual";
+
+ ofstream qualityFile;
+ m->openOutputFile(qualityFileName, qualityFile);
+
+ qualityFile.setf(ios::fixed, ios::floatfield);
+ qualityFile.setf(ios::showpoint);
+ qualityFile << setprecision(6);
+
+ vector<vector<int> > qualities(numOTUs);
+ vector<double> pr(HOMOPS, 0);
+
+
+ for(int i=0;i<numOTUs;i++){
+
+ if (m->control_pressed) { break; }
+
+ int index = 0;
+ int base = 0;
+
+ if(nSeqsPerOTU[i] > 0){
+ qualities[i].assign(1024, -1);
+
+ while(index < numFlowCells){
+ double maxPrValue = 1e8;
+ short maxPrIndex = -1;
+ double count = 0.0000;
+
+ pr.assign(HOMOPS, 0);
+
+ for(int j=0;j<nSeqsPerOTU[i];j++){
+ int lIndex = cumNumSeqs[i] + j;
+ double tauValue = singleTau[seqNumber[lIndex]];
+ int sequenceIndex = aaI[i][j];
+ short intensity = flowDataIntI[sequenceIndex * numFlowCells + index];
+
+ count += tauValue;
+
+ for(int s=0;s<HOMOPS;s++){
+ pr[s] += tauValue * singleLookUp[s * NUMBINS + intensity];
+ }
+ }
+
+ maxPrIndex = uniqueFlowgrams[centroids[i] * numFlowCells + index];
+ maxPrValue = pr[maxPrIndex];
+
+ if(count > MIN_COUNT){
+ double U = 0.0000;
+ double norm = 0.0000;
+
+ for(int s=0;s<HOMOPS;s++){
+ norm += exp(-(pr[s] - maxPrValue));
+ }
+
+ for(int s=1;s<=maxPrIndex;s++){
+ int value = 0;
+ double temp = 0.0000;
+
+ U += exp(-(pr[s-1]-maxPrValue))/norm;
+
+ if(U>0.00){
+ temp = log10(U);
+ }
+ else{
+ temp = -10.1;
+ }
+ temp = floor(-10 * temp);
+ value = (int)floor(temp);
+ if(value > 100){ value = 100; }
+
+ qualities[i][base] = (int)value;
+ base++;
+ }
+ }
+
+ index++;
+ }
+ }
+
+
+ if(otuCounts[i] > 0){
+ qualityFile << '>' << seqNameVector[mapUniqueToSeq[i]] << endl;
+
+ int j=4; //need to get past the first four bases
+ while(qualities[i][j] != -1){
+ qualityFile << qualities[i][j] << ' ';
+ j++;
+ }
+ qualityFile << endl;
+ }
+ }
+ qualityFile.close();
+ outputNames.push_back(qualityFileName);
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ShhherCommand", "writeQualities");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+void ShhherCommand::writeSequences(vector<int> otuCounts){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); }
+ string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.fasta";
+ ofstream fastaFile;
+ m->openOutputFile(fastaFileName, fastaFile);
+
+ vector<string> names(numOTUs, "");
+
+ for(int i=0;i<numOTUs;i++){
+
+ if (m->control_pressed) { break; }
+
+ int index = centroids[i];
+
+ if(otuCounts[i] > 0){
+ fastaFile << '>' << seqNameVector[aaI[i][0]] << endl;
+
+ string newSeq = "";
+
+ for(int j=0;j<numFlowCells;j++){
+
+ char base = flowOrder[j % 4];
+ for(int k=0;k<uniqueFlowgrams[index * numFlowCells + j];k++){
+ newSeq += base;
+ }
+ }
+
+ fastaFile << newSeq.substr(4) << endl;
+ }
+ }
+ fastaFile.close();
+
+ outputNames.push_back(fastaFileName);
+
+ if(compositeFASTAFileName != ""){
+ m->appendFiles(fastaFileName, compositeFASTAFileName);
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ShhherCommand", "writeSequences");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/