+++ /dev/null
-#ifndef DISTANCECOMMAND_H
-#define DISTANCECOMMAND_H
-
-/*
- * distancecommand.h
- * Mothur
- *
- * Created by Sarah Westcott on 5/7/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "mothur.h"
-#include "command.hpp"
-#include "validcalculator.h"
-#include "dist.h"
-#include "sequencedb.h"
-#include "ignoregaps.h"
-#include "eachgapdist.h"
-#include "eachgapignore.h"
-#include "onegapdist.h"
-#include "onegapignore.h"
-
-//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 distanceData {
- int startLine;
- int endLine;
- string dFileName;
- float cutoff;
- SequenceDB alignDB;
- vector<string> Estimators;
- MothurOut* m;
- string output;
- int numNewFasta;
- string countends;
-
- distanceData(){}
- distanceData(int s, int e, string dbname, float c, SequenceDB db, vector<string> Est, MothurOut* mout, string o, int num, string count) {
- startLine = s;
- endLine = e;
- dFileName = dbname;
- cutoff = c;
- alignDB = db;
- Estimators = Est;
- m = mout;
- output = o;
- numNewFasta = num;
- countends = count;
-
- }
-};
-
-/**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-#else
-static DWORD WINAPI MyDistThreadFunction(LPVOID lpParam){
- distanceData* pDataArray;
- pDataArray = (distanceData*)lpParam;
-
- try {
- ValidCalculators validCalculator;
- Dist* distCalculator;
- if (pDataArray->m->isTrue(pDataArray->countends) == true) {
- for (int i=0; i<pDataArray->Estimators.size(); i++) {
- if (validCalculator.isValidCalculator("distance", pDataArray->Estimators[i]) == true) {
- if (pDataArray->Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
- else if (pDataArray->Estimators[i] == "eachgap") { distCalculator = new eachGapDist(); }
- else if (pDataArray->Estimators[i] == "onegap") { distCalculator = new oneGapDist(); }
- }
- }
- }else {
- for (int i=0; i<pDataArray->Estimators.size(); i++) {
- if (validCalculator.isValidCalculator("distance", pDataArray->Estimators[i]) == true) {
- if (pDataArray->Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
- else if (pDataArray->Estimators[i] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
- else if (pDataArray->Estimators[i] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
- }
- }
- }
-
- int startTime = time(NULL);
-
- //column file
- ofstream outFile(pDataArray->dFileName.c_str(), ios::trunc);
- outFile.setf(ios::fixed, ios::showpoint);
- outFile << setprecision(4);
-
-
- if (pDataArray->output != "square") {
- if((pDataArray->output == "lt") && (pDataArray->startLine == 0)){ outFile << pDataArray->alignDB.getNumSeqs() << endl; }
-
- for(int i=pDataArray->startLine;i<pDataArray->endLine;i++){
- if(pDataArray->output == "lt") {
- string name = pDataArray->alignDB.get(i).getName();
- if (name.length() < 10) { //pad with spaces to make compatible
- while (name.length() < 10) { name += " "; }
- }
- outFile << name << '\t';
- }
- for(int j=0;j<i;j++){
-
- if (pDataArray->m->control_pressed) { delete distCalculator; outFile.close(); return 0; }
-
- //if there was a column file given and we are appending, we don't want to calculate the distances that are already in the column file
- //the alignDB contains the new sequences and then the old, so if i an oldsequence and j is an old sequence then break out of this loop
- if ((i >= pDataArray->numNewFasta) && (j >= pDataArray->numNewFasta)) { break; }
-
- distCalculator->calcDist(pDataArray->alignDB.get(i), pDataArray->alignDB.get(j));
- double dist = distCalculator->getDist();
-
- if(dist <= pDataArray->cutoff){
- if (pDataArray->output == "column") { outFile << pDataArray->alignDB.get(i).getName() << ' ' << pDataArray->alignDB.get(j).getName() << ' ' << dist << endl; }
- }
- if (pDataArray->output == "lt") { outFile << dist << '\t'; }
- }
-
- if (pDataArray->output == "lt") { outFile << endl; }
-
- if(i % 100 == 0){
- pDataArray->m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
- }
-
- }
- pDataArray->m->mothurOut(toString(pDataArray->endLine-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
- }else{
- if(pDataArray->startLine == 0){ outFile << pDataArray->alignDB.getNumSeqs() << endl; }
-
- for(int i=pDataArray->startLine;i<pDataArray->endLine;i++){
-
- string name = pDataArray->alignDB.get(i).getName();
- //pad with spaces to make compatible
- if (name.length() < 10) { while (name.length() < 10) { name += " "; } }
-
- outFile << name << '\t';
-
- for(int j=0;j<pDataArray->alignDB.getNumSeqs();j++){
-
- if (pDataArray->m->control_pressed) { delete distCalculator; outFile.close(); return 0; }
-
- distCalculator->calcDist(pDataArray->alignDB.get(i), pDataArray->alignDB.get(j));
- double dist = distCalculator->getDist();
-
- outFile << dist << '\t';
- }
-
- outFile << endl;
-
- if(i % 100 == 0){
- pDataArray->m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
- }
-
- }
- pDataArray->m->mothurOut(toString(pDataArray->endLine-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
- }
-
- outFile.close();
- delete distCalculator;
-
- return 0;
- }
- catch(exception& e) {
- pDataArray->m->errorOut(e, "DistanceCommand", "MyDistThreadFunction");
- exit(1);
- }
-}
-#endif
-
-/**************************************************************************************************/
-class DistanceCommand : public Command {
-
-public:
- DistanceCommand(string);
- DistanceCommand();
- ~DistanceCommand() {}
-
- vector<string> setParameters();
- string getCommandName() { return "dist.seqs"; }
- string getCommandCategory() { return "Sequence Processing"; }
- string getHelpString();
- string getCitation() { return "Schloss PD (2010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844. \nhttp://www.mothur.org/wiki/Dist.seqs"; }
- string getDescription() { return "calculate the pairwaise distances between aligned sequences"; }
-
- int execute();
- void help() { m->mothurOut(getHelpString()); }
-
-
-private:
- struct distlinePair {
- int start;
- int end;
-
- };
-
- //Dist* distCalculator;
- SequenceDB alignDB;
-
- string countends, output, fastafile, calc, outputDir, oldfastafile, column, compress;
-
- int processors, numNewFasta;
- float cutoff;
- vector<int> processIDS; //end line, processid
- vector<distlinePair> lines;
-
- bool abort;
- vector<string> Estimators, outputNames; //holds estimators to be used
-
- //void m->appendFiles(string, string);
- void createProcesses(string);
- int driver(/*Dist*, SequenceDB, */int, int, string, float);
- int driver(int, int, string, string);
-
- #ifdef USE_MPI
- int driverMPI(int, int, MPI_File&, float);
- int driverMPI(int, int, string, unsigned long long&);
- int driverMPI(int, int, string, unsigned long long&, string);
- #endif
-
- //int convertMatrix(string);
- bool sanityCheck();
- //int convertToLowerTriangle(string);
-
-};
-
-#endif
-
-/**************************************************************************************************/
-
-
-
projects / mothur.git / blobdiff