+++ /dev/null
-#ifndef CLUSTERSPLITCOMMAND_H
-#define CLUSTERSPLITCOMMAND_H
-
-/*
- * clustersplitcommand.h
- * Mothur
- *
- * Created by westcott on 5/19/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "command.hpp"
-#include "rabundvector.hpp"
-#include "sabundvector.hpp"
-#include "listvector.hpp"
-#include "cluster.hpp"
-#include "sparsematrix.hpp"
-#include "readcluster.h"
-#include "splitmatrix.h"
-#include "readphylip.h"
-#include "readcolumn.h"
-#include "readmatrix.hpp"
-#include "inputdata.h"
-#include "clustercommand.h"
-
-class ClusterSplitCommand : public Command {
-
-public:
- ClusterSplitCommand(string);
- ClusterSplitCommand();
- ~ClusterSplitCommand() {}
-
- vector<string> setParameters();
- string getCommandName() { return "cluster.split"; }
- string getCommandCategory() { return "Clustering"; }
- string getHelpString();
- string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Cluster.split"; }
- string getDescription() { return "splits your sequences by distance or taxonomy then clusters into OTUs"; }
-
- int execute();
- void help() { m->mothurOut(getHelpString()); }
-
-private:
- vector<int> processIDS; //processid
- vector<string> outputNames;
-
- string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
- double cutoff, splitcutoff;
- int precision, length, processors, taxLevelCutoff;
- bool print_start, abort, hard, large;
- time_t start;
- ofstream outList, outRabund, outSabund;
-
- void printData(ListVector*);
- vector<string> createProcesses(vector< map<string, string> >, set<string>&);
- vector<string> cluster(vector< map<string, string> >, set<string>&);
- int mergeLists(vector<string>, map<float, int>, ListVector*);
- map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
- int createMergedDistanceFile(vector< map<string, string> >);
-};
-
-/////////////////not working for Windows////////////////////////////////////////////////////////////
-// getting an access violation error. This is most likely caused by the
-// threads stepping on eachother's structures, as I can run the thread function and the cluster fuction
-// in separately without errors occuring. I suspect it may be in the use of the
-// static class mothurOut, but I can't pinpoint the problem. All other objects are made new
-// within the thread. MothurOut is used by almost all the classes in mothur, so if this was
-// really the cause I would expect to see all the windows threaded commands to have issues, but not
-// all do. So far, shhh.flows and trim.flows have similiar problems. Other thoughts, could it have
-// anything to do with mothur's use of copy constructors in many of our data structures. ie. listvector
-// is copied by nameassignment and passed to read which passes to the thread? -westcott 2-8-12
-////////////////////////////////////////////////////////////////////////////////////////////////////
-/**************************************************************************************************/
-//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 clusterData {
- set<string> labels;
- vector < map<string, string> > distNames;
- string method;
- MothurOut* m;
- double cutoff, precision;
- string tag, outputDir;
- vector<string> listFiles;
- bool hard;
- int length, threadID;
-
-
- clusterData(){}
- clusterData(vector < map<string, string> > dv, MothurOut* mout, double cu, string me, string ou, bool hd, double pre, int len, int th) {
- distNames = dv;
- m = mout;
- cutoff = cu;
- method = me;
- outputDir = ou;
- hard = hd;
- precision = pre;
- length = len;
- threadID = th;
- }
-};
-
-/**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-#else
-static DWORD WINAPI MyClusterThreadFunction(LPVOID lpParam){
- clusterData* pDataArray;
- pDataArray = (clusterData*)lpParam;
-
- try {
- cout << "starting " << endl;
-
- double smallestCutoff = pDataArray->cutoff;
-
- //cluster each distance file
- for (int i = 0; i < pDataArray->distNames.size(); i++) {
-
- Cluster* mycluster = NULL;
- SparseMatrix* mymatrix = NULL;
- ListVector* mylist = NULL;
- ListVector myoldList;
- RAbundVector* myrabund = NULL;
-
- if (pDataArray->m->control_pressed) { break; }
-
- string thisNamefile = pDataArray->distNames[i].begin()->second;
- string thisDistFile = pDataArray->distNames[i].begin()->first;
- cout << thisNamefile << '\t' << thisDistFile << endl;
- pDataArray->m->mothurOutEndLine(); pDataArray->m->mothurOut("Reading " + thisDistFile); pDataArray->m->mothurOutEndLine();
-
- ReadMatrix* myread = new ReadColumnMatrix(thisDistFile);
- myread->setCutoff(pDataArray->cutoff);
- NameAssignment* mynameMap = new NameAssignment(thisNamefile);
- mynameMap->readMap();
- cout << "done reading " << thisNamefile << endl;
- myread->read(mynameMap);
- cout << "done reading " << thisDistFile << endl;
- if (pDataArray->m->control_pressed) { delete myread; delete mynameMap; break; }
-
- mylist = myread->getListVector();
- myoldList = *mylist;
- mymatrix = myread->getMatrix();
- cout << "here" << endl;
- delete myread; myread = NULL;
- delete mynameMap; mynameMap = NULL;
-
- pDataArray->m->mothurOutEndLine(); pDataArray->m->mothurOut("Clustering " + thisDistFile); pDataArray->m->mothurOutEndLine();
-
- myrabund = new RAbundVector(mylist->getRAbundVector());
- cout << "here" << endl;
- //create cluster
- if (pDataArray->method == "furthest") { mycluster = new CompleteLinkage(myrabund, mylist, mymatrix, pDataArray->cutoff, pDataArray->method); }
- else if(pDataArray->method == "nearest"){ mycluster = new SingleLinkage(myrabund, mylist, mymatrix, pDataArray->cutoff, pDataArray->method); }
- else if(pDataArray->method == "average"){ mycluster = new AverageLinkage(myrabund, mylist, mymatrix, pDataArray->cutoff, pDataArray->method); }
- pDataArray->tag = mycluster->getTag();
- cout << "here" << endl;
- if (pDataArray->outputDir == "") { pDataArray->outputDir += pDataArray->m->hasPath(thisDistFile); }
- string fileroot = pDataArray->outputDir + pDataArray->m->getRootName(pDataArray->m->getSimpleName(thisDistFile));
- cout << "here" << endl;
- ofstream listFile;
- pDataArray->m->openOutputFile(fileroot+ pDataArray->tag + ".list", listFile);
- cout << "here" << endl;
- pDataArray->listFiles.push_back(fileroot+ pDataArray->tag + ".list");
-
- float previousDist = 0.00000;
- float rndPreviousDist = 0.00000;
-
- myoldList = *mylist;
-
- bool print_start = true;
- int start = time(NULL);
- double saveCutoff = pDataArray->cutoff;
-
- while (mymatrix->getSmallDist() < pDataArray->cutoff && mymatrix->getNNodes() > 0){
-
- if (pDataArray->m->control_pressed) { //clean up
- delete mymatrix; delete mylist; delete mycluster; delete myrabund;
- listFile.close();
- for (int i = 0; i < pDataArray->listFiles.size(); i++) { pDataArray->m->mothurRemove(pDataArray->listFiles[i]); }
- pDataArray->listFiles.clear(); break;
- }
-
- mycluster->update(saveCutoff);
-
- float dist = mymatrix->getSmallDist();
- float rndDist;
- if (pDataArray->hard) {
- rndDist = pDataArray->m->ceilDist(dist, pDataArray->precision);
- }else{
- rndDist = pDataArray->m->roundDist(dist, pDataArray->precision);
- }
-
- if(previousDist <= 0.0000 && dist != previousDist){
- myoldList.setLabel("unique");
- myoldList.print(listFile);
- if (pDataArray->labels.count("unique") == 0) { pDataArray->labels.insert("unique"); }
- }
- else if(rndDist != rndPreviousDist){
- myoldList.setLabel(toString(rndPreviousDist, pDataArray->length-1));
- myoldList.print(listFile);
- if (pDataArray->labels.count(toString(rndPreviousDist, pDataArray->length-1)) == 0) { pDataArray->labels.insert(toString(rndPreviousDist, pDataArray->length-1)); }
- }
-
- previousDist = dist;
- rndPreviousDist = rndDist;
- myoldList = *mylist;
- }
-
- cout << "here2" << endl;
- if(previousDist <= 0.0000){
- myoldList.setLabel("unique");
- myoldList.print(listFile);
- if (pDataArray->labels.count("unique") == 0) { pDataArray->labels.insert("unique"); }
- }
- else if(rndPreviousDist<pDataArray->cutoff){
- myoldList.setLabel(toString(rndPreviousDist, pDataArray->length-1));
- myoldList.print(listFile);
- if (pDataArray->labels.count(toString(rndPreviousDist, pDataArray->length-1)) == 0) { pDataArray->labels.insert(toString(rndPreviousDist, pDataArray->length-1)); }
- }
-
- delete mymatrix; delete mylist; delete mycluster; delete myrabund;
- mymatrix = NULL; mylist = NULL; mycluster = NULL; myrabund = NULL;
- listFile.close();
-
- if (pDataArray->m->control_pressed) { //clean up
- for (int i = 0; i < pDataArray->listFiles.size(); i++) { pDataArray->m->mothurRemove(pDataArray->listFiles[i]); }
- pDataArray->listFiles.clear(); break;
- }
- cout << "here3" << endl;
- pDataArray->m->mothurRemove(thisDistFile);
- pDataArray->m->mothurRemove(thisNamefile);
- cout << "here4" << endl;
- if (saveCutoff != pDataArray->cutoff) {
- if (pDataArray->hard) { saveCutoff = pDataArray->m->ceilDist(saveCutoff, pDataArray->precision); }
- else { saveCutoff = pDataArray->m->roundDist(saveCutoff, pDataArray->precision); }
-
- pDataArray->m->mothurOut("Cutoff was " + toString(pDataArray->cutoff) + " changed cutoff to " + toString(saveCutoff)); pDataArray->m->mothurOutEndLine();
- }
- cout << "here5" << endl;
- if (saveCutoff < smallestCutoff) { smallestCutoff = saveCutoff; }
- }
-
- pDataArray->cutoff = smallestCutoff;
-
- return 0;
-
- }
- catch(exception& e) {
- pDataArray->m->errorOut(e, "ClusterSplitCommand", "MyClusterThreadFunction");
- exit(1);
- }
-}
-#endif
-
-
-
-
-#endif
-
projects / mothur.git / blobdiff