#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, count;
+ 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);
+ pDataArray->count = 0;
+
+ 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->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); }
+ pDataArray->count++;
+ }
+ pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)+"\n");
+ }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->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
+ }
+ pDataArray->count++;
+ }
+ pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)+"\n");
+ }
+
+ 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();
- int execute();
- void help();
+ DistanceCommand();
+ ~DistanceCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "dist.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+
+ string getHelpString();
+ string getOutputPattern(string);
+ 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 linePair {
+ struct distlinePair {
int start;
int end;
+
};
- Dist* distCalculator;
+ //Dist* distCalculator;
SequenceDB alignDB;
- string countends, output, fastafile, calc, outputDir, oldfastafile, column;
+ string countends, output, fastafile, calc, outputDir, oldfastafile, column, compress;
+
int processors, numNewFasta;
float cutoff;
- map<int, int> processIDS; //end line, processid
- vector<linePair*> lines;
+ vector<int> processIDS; //end line, processid
+ vector<distlinePair> lines;
bool abort;
- vector<string> Estimators; //holds estimators to be used
+ 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, long&);
+ int driverMPI(int, int, string, unsigned long long&);
+ int driverMPI(int, int, string, unsigned long long&, string);
#endif
- int convertMatrix(string);
+ //int convertMatrix(string);
bool sanityCheck();
- int convertToLowerTriangle(string);
+ //int convertToLowerTriangle(string);
};
#endif
+/**************************************************************************************************/
+
projects / mothur.git / blobdiff