--- /dev/null
+#ifndef SHHHSEQSCOMMAND_H
+#define SHHHSEQSCOMMAND_H
+
+/*
+ * shhhseqscommand.h
+ * Mothur
+ *
+ * Created by westcott on 11/8/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "myseqdist.h"
+#include "seqnoise.h"
+#include "sequenceparser.h"
+#include "deconvolutecommand.h"
+#include "clustercommand.h"
+
+//**********************************************************************************************************************
+
+class ShhhSeqsCommand : public Command {
+
+public:
+ ShhhSeqsCommand(string);
+ ShhhSeqsCommand();
+ ~ShhhSeqsCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "shhh.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Shhh.seqs"; }
+ string getDescription() { return "shhh.seqs"; }
+
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
+private:
+
+ struct linePair {
+ int start;
+ int end;
+ linePair(int i, int j) : start(i), end(j) {}
+ };
+
+ bool abort;
+ string outputDir, fastafile, namefile, groupfile;
+ int processors;
+ double sigma;
+ vector<string> outputNames;
+
+ int readData(correctDist*, seqNoise&, vector<string>&, vector<string>&, vector<string>&, vector<int>&);
+ int loadData(correctDist*, seqNoise&, vector<string>&, vector<string>&, vector<string>&, vector<int>&, map<string, string>&, vector<Sequence>&);
+
+ int driver(seqNoise&, vector<string>&, vector<string>&, vector<string>&, vector<int>&, string, string, string, string);
+ vector<string> driverGroups(SequenceParser&, string, string, string, int, int, vector<string>);
+ vector<string> createProcessesGroups(SequenceParser&, string, string, string, vector<string>);
+ int deconvoluteResults(string, string);
+
+
+
+};
+
+/**************************************************************************************************/
+//custom data structure for threads to use.
+// This is passed by void pointer so it can be any data type
+// that can be passed using a single void pointer (LPVOID).
+struct shhhseqsData {
+ string fastafile;
+ string namefile;
+ string groupfile;
+ string newFName, newNName, newMName;
+ MothurOut* m;
+ int start;
+ int end;
+ int sigma, threadID;
+ vector<string> groups;
+ vector<string> mapfileNames;
+
+ shhhseqsData(){}
+ shhhseqsData(string f, string n, string g, string nff, string nnf, string nmf, vector<string> gr, MothurOut* mout, int st, int en, int s, int tid) {
+ fastafile = f;
+ namefile = n;
+ groupfile = g;
+ newFName = nff;
+ newNName = nnf;
+ newMName = nmf;
+ m = mout;
+ start = st;
+ end = en;
+ sigma = s;
+ threadID = tid;
+ groups = gr;
+ }
+};
+
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+static DWORD WINAPI MyShhhSeqsThreadFunction(LPVOID lpParam){
+ shhhseqsData* pDataArray;
+ pDataArray = (shhhseqsData*)lpParam;
+
+ try {
+
+ //parse fasta and name file by group
+ SequenceParser parser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile);
+
+ //precluster each group
+ for (int k = pDataArray->start; k < pDataArray->end; k++) {
+
+ int start = time(NULL);
+
+ if (pDataArray->m->control_pressed) { return 0; }
+
+ pDataArray->m->mothurOutEndLine(); pDataArray->m->mothurOut("Processing group " + pDataArray->groups[k] + ":"); pDataArray->m->mothurOutEndLine();
+
+ map<string, string> thisNameMap;
+ thisNameMap = parser.getNameMap(pDataArray->groups[k]);
+ vector<Sequence> thisSeqs = parser.getSeqs(pDataArray->groups[k]);
+
+ if (pDataArray->m->control_pressed) { return 0; }
+
+ vector<string> sequences;
+ vector<string> uniqueNames;
+ vector<string> redundantNames;
+ vector<int> seqFreq;
+
+ seqNoise noise;
+ correctDist* correct = new correctDist(1); //we use one processor since we already split up the work load.
+
+ //load this groups info in order
+ //loadData(correct, noise, sequences, uniqueNames, redundantNames, seqFreq, thisNameMap, thisSeqs);
+ //////////////////////////////////////////////////////////////////////////////////////////////////
+ bool error = false;
+ map<string, string>::iterator it;
+
+ for (int i = 0; i < thisSeqs.size(); i++) {
+
+ if (pDataArray->m->control_pressed) { return 0; }
+
+ if (thisSeqs[i].getName() != "") {
+ correct->addSeq(thisSeqs[i].getName(), thisSeqs[i].getAligned());
+
+ it = thisNameMap.find(thisSeqs[i].getName());
+ if (it != thisNameMap.end()) {
+ noise.addSeq(thisSeqs[i].getAligned(), sequences);
+ noise.addRedundantName(it->first, it->second, uniqueNames, redundantNames, seqFreq);
+ }else {
+ pDataArray->m->mothurOut("[ERROR]: " + thisSeqs[i].getName() + " is in your fasta file and not in your namefile, please correct.");
+ error = true;
+ }
+ }
+ }
+
+ if (error) { return 0; }
+ //////////////////////////////////////////////////////////////////////////////////////////////////
+
+ if (pDataArray->m->control_pressed) { return 0; }
+
+ //calc distances for cluster
+ string distFileName = pDataArray->m->getRootName(pDataArray->m->getSimpleName(pDataArray->fastafile)) + pDataArray->groups[k] + ".shhh.dist";
+ correct->execute(distFileName);
+ delete correct;
+
+ if (pDataArray->m->control_pressed) { pDataArray->m->mothurRemove(distFileName); return 0; }
+
+ //driver(noise, sequences, uniqueNames, redundantNames, seqFreq, distFileName, newFFile+groups[i], newNFile+groups[i], newMFile+groups[i]+".map");
+ ///////////////////////////////////////////////////////////////////////////////////////////////////
+ double cutOff = 0.08;
+ int minIter = 10;
+ int maxIter = 1000;
+ double minDelta = 1e-6;
+ int numIters = 0;
+ double maxDelta = 1e6;
+ int numSeqs = sequences.size();
+
+ //run cluster command
+ string inputString = "phylip=" + distFileName + ", method=furthest, cutoff=0.08";
+ pDataArray->m->mothurOut("/******************************************/"); pDataArray->m->mothurOutEndLine();
+ pDataArray->m->mothurOut("Running command: cluster(" + inputString + ")"); pDataArray->m->mothurOutEndLine();
+
+ Command* clusterCommand = new ClusterCommand(inputString);
+ clusterCommand->execute();
+
+ map<string, vector<string> > filenames = clusterCommand->getOutputFiles();
+ string listFileName = filenames["list"][0];
+ string rabundFileName = filenames["rabund"][0]; pDataArray->m->mothurRemove(rabundFileName);
+ string sabundFileName = filenames["sabund"][0]; pDataArray->m->mothurRemove(sabundFileName);
+
+ delete clusterCommand;
+ pDataArray->m->mothurOut("/******************************************/"); pDataArray->m->mothurOutEndLine();
+
+ if (pDataArray->m->control_pressed) { pDataArray->m->mothurRemove(distFileName); pDataArray->m->mothurRemove(listFileName); return 0; }
+
+ vector<double> distances(numSeqs * numSeqs);
+ noise.getDistanceData(distFileName, distances);
+ pDataArray->m->mothurRemove(distFileName);
+ if (pDataArray->m->control_pressed) { pDataArray->m->mothurRemove(listFileName); return 0; }
+
+ vector<int> otuData(numSeqs);
+ vector<int> otuFreq;
+ vector<vector<int> > otuBySeqLookUp;
+ noise.getListData(listFileName, cutOff, otuData, otuFreq, otuBySeqLookUp);
+ pDataArray->m->mothurRemove(listFileName);
+ if (pDataArray->m->control_pressed) { return 0; }
+
+ int numOTUs = otuFreq.size();
+
+ vector<double> weights(numOTUs, 0);
+ vector<int> change(numOTUs, 1);
+ vector<int> centroids(numOTUs, -1);
+ vector<int> cumCount(numOTUs, 0);
+
+ vector<double> tau(numSeqs, 1);
+ vector<int> anP(numSeqs, 0);
+ vector<int> anI(numSeqs, 0);
+ vector<int> anN(numSeqs, 0);
+ vector<vector<int> > aanI = otuBySeqLookUp;
+
+ while(numIters < minIter || ((maxDelta > minDelta) && (numIters < maxIter))){
+
+ if (pDataArray->m->control_pressed) { return 0; }
+
+ noise.updateOTUCountData(otuFreq, otuBySeqLookUp, aanI, anP, anI, cumCount); if (pDataArray->m->control_pressed) { return 0; }
+ maxDelta = noise.calcNewWeights(weights, seqFreq, anI, cumCount, anP, otuFreq, tau); if (pDataArray->m->control_pressed) { return 0; }
+
+ noise.calcCentroids(anI, anP, change, centroids, cumCount, distances, seqFreq, otuFreq, tau); if (pDataArray->m->control_pressed) { return 0; }
+ noise.checkCentroids(weights, centroids); if (pDataArray->m->control_pressed) { return 0; }
+
+ otuFreq.assign(numOTUs, 0);
+
+ int total = 0;
+
+ for(int i=0;i<numSeqs;i++){
+ if (pDataArray->m->control_pressed) { return 0; }
+
+ double offset = 1e6;
+ double norm = 0.0000;
+ double minWeight = 0.1;
+ vector<double> currentTau(numOTUs);
+
+ for(int j=0;j<numOTUs;j++){
+ if (pDataArray->m->control_pressed) { return 0; }
+ if(weights[j] > minWeight && distances[i * numSeqs+centroids[j]] < offset){
+ offset = distances[i * numSeqs+centroids[j]];
+ }
+ }
+
+ for(int j=0;j<numOTUs;j++){
+ if (pDataArray->m->control_pressed) { return 0; }
+ if(weights[j] > minWeight){
+ currentTau[j] = exp(pDataArray->sigma * (-distances[(i * numSeqs + centroids[j])] + offset)) * weights[j];
+ norm += currentTau[j];
+ }
+ else{
+ currentTau[j] = 0.0000;
+ }
+ }
+
+ for(int j=0;j<numOTUs;j++){
+ if (pDataArray->m->control_pressed) { return 0; }
+ currentTau[j] /= norm;
+ }
+
+ for(int j=0;j<numOTUs;j++){
+ if (pDataArray->m->control_pressed) { return 0; }
+
+ if(currentTau[j] > 1.0e-4){
+ int oldTotal = total;
+ total++;
+
+ tau.resize(oldTotal+1);
+ tau[oldTotal] = currentTau[j];
+ otuBySeqLookUp[j][otuFreq[j]] = oldTotal;
+ aanI[j][otuFreq[j]] = i;
+ otuFreq[j]++;
+
+ }
+ }
+
+ anP.resize(total);
+ anI.resize(total);
+ }
+
+ numIters++;
+ }
+
+ noise.updateOTUCountData(otuFreq, otuBySeqLookUp, aanI, anP, anI, cumCount); if (pDataArray->m->control_pressed) { return 0; }
+
+ vector<double> percentage(numSeqs);
+ noise.setUpOTUData(otuData, percentage, cumCount, tau, otuFreq, anP, anI); if (pDataArray->m->control_pressed) { return 0; }
+ noise.finishOTUData(otuData, otuFreq, anP, anI, cumCount, otuBySeqLookUp, aanI, tau); if (pDataArray->m->control_pressed) { return 0; }
+
+ change.assign(numOTUs, 1);
+ noise.calcCentroids(anI, anP, change, centroids, cumCount, distances, seqFreq, otuFreq, tau); if (pDataArray->m->control_pressed) { return 0; }
+
+
+ vector<int> finalTau(numOTUs, 0);
+ for(int i=0;i<numSeqs;i++){
+ if (pDataArray->m->control_pressed) { return 0; }
+ finalTau[otuData[i]] += int(seqFreq[i]);
+ }
+
+ noise.writeOutput(pDataArray->newFName+pDataArray->groups[k], pDataArray->newNName+pDataArray->groups[k], pDataArray->newMName+pDataArray->groups[k]+".map", finalTau, centroids, otuData, sequences, uniqueNames, redundantNames, seqFreq, distances);
+
+ ///////////////////////////////////////////////////////////////////////////////////////////////////
+
+ if (pDataArray->m->control_pressed) { return 0; }
+
+ pDataArray->m->appendFiles(pDataArray->newFName+pDataArray->groups[k], pDataArray->newFName); pDataArray->m->mothurRemove(pDataArray->newFName+pDataArray->groups[k]);
+ pDataArray->m->appendFiles(pDataArray->newNName+pDataArray->groups[k], pDataArray->newNName); pDataArray->m->mothurRemove(pDataArray->newNName+pDataArray->groups[k]);
+ pDataArray->mapfileNames.push_back(pDataArray->newMName+pDataArray->groups[k]+".map");
+
+ pDataArray->m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process group " + pDataArray->groups[k] + "."); pDataArray->m->mothurOutEndLine();
+ }
+
+ return 0;
+
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "ShhhSeqsCommand", "MyShhhSeqsThreadFunction");
+ exit(1);
+ }
+}
+#endif
+/**************************************************************************************************/
+
+#endif
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