*/
#include "pairwiseseqscommand.h"
-#include "sequence.hpp"
-
-#include "gotohoverlap.hpp"
-#include "needlemanoverlap.hpp"
-#include "blastalign.hpp"
-#include "noalign.hpp"
-
-#include "ignoregaps.h"
-#include "eachgapdist.h"
-#include "eachgapignore.h"
-#include "onegapdist.h"
-#include "onegapignore.h"
-
//**********************************************************************************************************************
vector<string> PairwiseSeqsCommand::setParameters(){
if (calc == "default") { calc = "onegap"; }
}
m->splitAtDash(calc, Estimators);
-
- ValidCalculators validCalculator;
- if (countends) {
- for (int i=0; i<Estimators.size(); i++) {
- if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
- if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
- else if (Estimators[i] == "eachgap") { distCalculator = new eachGapDist(); }
- else if (Estimators[i] == "onegap") { distCalculator = new oneGapDist(); }
- }
- }
- }else {
- for (int i=0; i<Estimators.size(); i++) {
- if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
- if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
- else if (Estimators[i] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
- else if (Estimators[i] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
- }
- }
- }
}
}
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- int longestBase = 2000; //will need to update this in driver if we find sequences with more bases. hardcoded so we don't have the pre-read user fasta file.
-
- if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
- else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
- else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
- else if(align == "noalign") { alignment = new NoAlign(); }
- else {
- m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
- m->mothurOutEndLine();
- alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
- }
+ longestBase = 2000; //will need to update this in driver if we find sequences with more bases. hardcoded so we don't have the pre-read user fasta file.
cutoff += 0.005;
driverMPI(start, end, outMPI, cutoff);
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); return 0; }
//wait on chidren
for(int i = 1; i < processors; i++) {
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); return 0; }
char buf[5];
MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
//do your part
driverMPI(start, end, outMPI, cutoff);
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); return 0; }
char buf[5];
strcpy(buf, "done");
if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
else { driverMPI(start, end, outputFile, mySize, output); }
- if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFile); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFile); return 0; }
int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
MPI_File outMPI;
for(int b = 1; b < processors; b++) {
unsigned long long fileSize;
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); return 0; }
MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
//if you don't need to fork anything
if(processors == 1){
if (output != "square") { driver(0, numSeqs, outputFile, cutoff); }
createProcesses(outputFile);
}
- #else
+ //#else
//ifstream inFASTA;
- if (output != "square") { driver(0, numSeqs, outputFile, cutoff); }
- else { driver(0, numSeqs, outputFile, "square"); }
- #endif
+ //if (output != "square") { driver(0, numSeqs, outputFile, cutoff); }
+ //else { driver(0, numSeqs, outputFile, "square"); }
+ //#endif
#endif
- if (m->control_pressed) { outputTypes.clear(); delete distCalculator; m->mothurRemove(outputFile); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFile); return 0; }
#ifdef USE_MPI
MPI_Comm_rank(MPI_COMM_WORLD, &pid);
m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
- if (m->control_pressed) { outputTypes.clear(); delete distCalculator; m->mothurRemove(outputFile); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFile); return 0; }
}
-
- delete distCalculator;
//set phylip file as new current phylipfile
string current = "";
/**************************************************************************************************/
void PairwiseSeqsCommand::createProcesses(string filename) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- int process = 1;
+ int process = 1;
processIDS.clear();
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+
//loop through and create all the processes you want
while (process != processors) {
int temp = processIDS[i];
wait(&temp);
}
+#else
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the distanceData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //that's why the distance calculator was moved inside of the driver to make separate copies.
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<pairwiseData*> pDataArray; //[processors-1];
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor-1 worker threads.
+ for( int i=0; i<processors-1; i++ ){
+ string extension = toString(i) + ".temp";
+
+ // Allocate memory for thread data.
+ pairwiseData* tempDist = new pairwiseData((filename+extension), align, "square", Estimators[0], countends, output, alignDB, m, lines[i+1].start, lines[i+1].end, match, misMatch, gapOpen, gapExtend, longestBase, i);
+ pDataArray.push_back(tempDist);
+ processIDS.push_back(i);
+
+ if (output != "square") { hThreadArray[i] = CreateThread(NULL, 0, MyPairwiseThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]); }
+ else { hThreadArray[i] = CreateThread(NULL, 0, MyPairwiseSquareThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]); }
+ }
+
+ //do your part
+ if (output != "square") { driver(lines[0].start, lines[0].end, filename, cutoff); }
+ else { driver(lines[0].start, lines[0].end, filename, "square"); }
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
- //append and remove temp files
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+
+#endif
+
+ //append and remove temp files
for (int i=0;i<processIDS.size();i++) {
m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
m->mothurRemove((filename + toString(processIDS[i]) + ".temp"));
}
-#endif
+
}
catch(exception& e) {
m->errorOut(e, "PairwiseSeqsCommand", "createProcesses");
try {
int startTime = time(NULL);
+
+ Alignment* alignment;
+ if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
+ else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
+ else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
+ else if(align == "noalign") { alignment = new NoAlign(); }
+ else {
+ m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
+ m->mothurOutEndLine();
+ alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
+ }
+
+ ValidCalculators validCalculator;
+ Dist* distCalculator;
+ if (countends) {
+ if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
+ if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (Estimators[0] == "eachgap") { distCalculator = new eachGapDist(); }
+ else if (Estimators[0] == "onegap") { distCalculator = new oneGapDist(); }
+ }
+ }else {
+ if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
+ if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (Estimators[0] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
+ else if (Estimators[0] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
+ }
+ }
//column file
ofstream outFile(dFileName.c_str(), ios::trunc);
for(int j=0;j<i;j++){
- if (m->control_pressed) { outFile.close(); return 0; }
+ if (m->control_pressed) { outFile.close(); delete alignment; delete distCalculator; return 0; }
if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
alignment->resize(alignDB.get(i).getUnaligned().length()+1);
m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
outFile.close();
+ delete alignment;
+ delete distCalculator;
return 1;
}
try {
int startTime = time(NULL);
+
+ Alignment* alignment;
+ if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
+ else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
+ else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
+ else if(align == "noalign") { alignment = new NoAlign(); }
+ else {
+ m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
+ m->mothurOutEndLine();
+ alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
+ }
+ ValidCalculators validCalculator;
+ Dist* distCalculator;
+ if (countends) {
+ if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
+ if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (Estimators[0] == "eachgap") { distCalculator = new eachGapDist(); }
+ else if (Estimators[0] == "onegap") { distCalculator = new oneGapDist(); }
+ }
+ }else {
+ if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
+ if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (Estimators[0] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
+ else if (Estimators[0] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
+ }
+ }
+
//column file
ofstream outFile(dFileName.c_str(), ios::trunc);
outFile.setf(ios::fixed, ios::showpoint);
for(int j=0;j<alignDB.getNumSeqs();j++){
- if (m->control_pressed) { outFile.close(); return 0; }
+ if (m->control_pressed) { outFile.close(); delete alignment; delete distCalculator; return 0; }
if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
alignment->resize(alignDB.get(i).getUnaligned().length()+1);
m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
outFile.close();
+ delete alignment;
+ delete distCalculator;
return 1;
}
try {
MPI_Status status;
int startTime = time(NULL);
+
+ Alignment* alignment;
+ if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
+ else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
+ else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
+ else if(align == "noalign") { alignment = new NoAlign(); }
+ else {
+ m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
+ m->mothurOutEndLine();
+ alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
+ }
+ ValidCalculators validCalculator;
+ Dist* distCalculator;
+ if (countends) {
+ if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
+ if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (Estimators[0] == "eachgap") { distCalculator = new eachGapDist(); }
+ else if (Estimators[0] == "onegap") { distCalculator = new oneGapDist(); }
+ }
+ }else {
+ if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
+ if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (Estimators[0] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
+ else if (Estimators[0] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
+ }
+ }
+
string outputString = "";
for(int i=startLine;i<endLine;i++){
for(int j=0;j<i;j++){
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { delete alignment; delete distCalculator; return 0; }
if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
alignment->resize(alignDB.get(i).getUnaligned().length()+1);
delete buf;
}
-
+ delete alignment;
+ delete distCalculator;
return 1;
}
catch(exception& e) {
MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
-
+ Alignment* alignment;
+ if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
+ else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
+ else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
+ else if(align == "noalign") { alignment = new NoAlign(); }
+ else {
+ m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
+ m->mothurOutEndLine();
+ alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
+ }
+
+ ValidCalculators validCalculator;
+ Dist* distCalculator;
+ if (countends) {
+ if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
+ if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (Estimators[0] == "eachgap") { distCalculator = new eachGapDist(); }
+ else if (Estimators[0] == "onegap") { distCalculator = new oneGapDist(); }
+ }
+ }else {
+ if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
+ if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (Estimators[0] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
+ else if (Estimators[0] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
+ }
+ }
+
string outputString = "";
size = 0;
for(int j=0;j<i;j++){
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { delete alignment; delete distCalculator; return 0; }
if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
alignment->resize(alignDB.get(i).getUnaligned().length()+1);
}
MPI_File_close(&outMPI);
+ delete alignment;
+ delete distCalculator;
return 1;
}
MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
-
+ Alignment* alignment;
+ if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
+ else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
+ else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
+ else if(align == "noalign") { alignment = new NoAlign(); }
+ else {
+ m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
+ m->mothurOutEndLine();
+ alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
+ }
string outputString = "";
size = 0;
for(int j=0;j<alignDB.getNumSeqs();j++){
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { delete alignment; return 0; }
if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
alignment->resize(alignDB.get(i).getUnaligned().length()+1);
MPI_File_close(&outMPI);
+ delete alignment;
return 1;
}
catch(exception& e) {
#include "validcalculator.h"
#include "dist.h"
#include "sequencedb.h"
+#include "sequence.hpp"
+
+#include "gotohoverlap.hpp"
+#include "needlemanoverlap.hpp"
+#include "blastalign.hpp"
+#include "noalign.hpp"
+
+#include "ignoregaps.h"
+#include "eachgapdist.h"
+#include "eachgapignore.h"
+#include "onegapdist.h"
+#include "onegapignore.h"
class PairwiseSeqsCommand : public Command {
vector<int> processIDS; //end line, processid
vector<distlinePair> lines;
- Alignment* alignment;
- Dist* distCalculator;
SequenceDB alignDB;
void createProcesses(string);
string fastaFileName, align, calc, outputDir, output;
float match, misMatch, gapOpen, gapExtend, cutoff;
- int processors;
+ int processors, longestBase;
vector<string> fastaFileNames, Estimators;
vector<string> outputNames;
bool abort, countends, compress;
};
+/**************************************************************************************************/
+//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 pairwiseData {
+ string outputFileName;
+ string align, square, distcalcType, output;
+ unsigned long long start;
+ unsigned long long end;
+ MothurOut* m;
+ float match, misMatch, gapOpen, gapExtend, cutoff;
+ int count, threadID, longestBase;
+ bool countends;
+ SequenceDB alignDB;
+
+ pairwiseData(){}
+ pairwiseData(string ofn, string al, string sq, string di, bool co, string op, SequenceDB DB, MothurOut* mout, unsigned long long st, unsigned long long en, float ma, float misMa, float gapO, float gapE, int thr, int tid) {
+ outputFileName = ofn;
+ m = mout;
+ start = st;
+ end = en;
+ match = ma;
+ misMatch = misMa;
+ gapOpen = gapO;
+ gapExtend = gapE;
+ longestBase = thr;
+ align = al;
+ square = sq;
+ distcalcType = di;
+ countends = co;
+ alignDB = DB;
+ count = 0;
+ output = op;
+ threadID = tid;
+ }
+};
+
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
+static DWORD WINAPI MyPairwiseSquareThreadFunction(LPVOID lpParam){
+ pairwiseData* pDataArray;
+ pDataArray = (pairwiseData*)lpParam;
+
+ try {
+ ofstream outFile((pDataArray->outputFileName).c_str(), ios::trunc);
+ outFile.setf(ios::fixed, ios::showpoint);
+ outFile << setprecision(4);
+
+ pDataArray->count = pDataArray->end;
+
+ int startTime = time(NULL);
+
+ Alignment* alignment;
+ if(pDataArray->align == "gotoh") { alignment = new GotohOverlap(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase); }
+ else if(pDataArray->align == "needleman") { alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase); }
+ else if(pDataArray->align == "blast") { alignment = new BlastAlignment(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch); }
+ else if(pDataArray->align == "noalign") { alignment = new NoAlign(); }
+ else {
+ pDataArray->m->mothurOut(pDataArray->align + " is not a valid alignment option. I will run the command using needleman.");
+ pDataArray->m->mothurOutEndLine();
+ alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase);
+ }
+
+ ValidCalculators validCalculator;
+ Dist* distCalculator;
+ if (pDataArray->countends) {
+ if (validCalculator.isValidCalculator("distance", pDataArray->distcalcType) == true) {
+ if (pDataArray->distcalcType == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (pDataArray->distcalcType == "eachgap") { distCalculator = new eachGapDist(); }
+ else if (pDataArray->distcalcType == "onegap") { distCalculator = new oneGapDist(); }
+ }
+ }else {
+ if (validCalculator.isValidCalculator("distance", pDataArray->distcalcType) == true) {
+ if (pDataArray->distcalcType == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (pDataArray->distcalcType == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
+ else if (pDataArray->distcalcType == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
+ }
+ }
+
+ if(pDataArray->start == 0){ outFile << pDataArray->alignDB.getNumSeqs() << endl; }
+
+ for(int i=pDataArray->start;i<pDataArray->end;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) { outFile.close(); delete alignment; delete distCalculator; return 0; }
+
+ if (pDataArray->alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
+ alignment->resize(pDataArray->alignDB.get(i).getUnaligned().length()+1);
+ }
+
+ if (pDataArray->alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
+ alignment->resize(pDataArray->alignDB.get(j).getUnaligned().length()+1);
+ }
+
+ Sequence seqI(pDataArray->alignDB.get(i).getName(), pDataArray->alignDB.get(i).getAligned());
+ Sequence seqJ(pDataArray->alignDB.get(j).getName(), pDataArray->alignDB.get(j).getAligned());
+
+ alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
+ seqI.setAligned(alignment->getSeqAAln());
+ seqJ.setAligned(alignment->getSeqBAln());
+
+ distCalculator->calcDist(seqI, seqJ);
+ 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->end-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+
+ outFile.close();
+ delete alignment;
+ delete distCalculator;
+
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "PairwiseSeqsCommand", "MyPairwiseSquareThreadFunction");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+static DWORD WINAPI MyPairwiseThreadFunction(LPVOID lpParam){
+ pairwiseData* pDataArray;
+ pDataArray = (pairwiseData*)lpParam;
+
+ try {
+ ofstream outFile((pDataArray->outputFileName).c_str(), ios::trunc);
+ outFile.setf(ios::fixed, ios::showpoint);
+ outFile << setprecision(4);
+
+ pDataArray->count = pDataArray->end;
+
+ int startTime = time(NULL);
+
+ Alignment* alignment;
+ if(pDataArray->align == "gotoh") { alignment = new GotohOverlap(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase); }
+ else if(pDataArray->align == "needleman") { alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase); }
+ else if(pDataArray->align == "blast") { alignment = new BlastAlignment(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch); }
+ else if(pDataArray->align == "noalign") { alignment = new NoAlign(); }
+ else {
+ pDataArray->m->mothurOut(pDataArray->align + " is not a valid alignment option. I will run the command using needleman.");
+ pDataArray->m->mothurOutEndLine();
+ alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase);
+ }
+
+ ValidCalculators validCalculator;
+ Dist* distCalculator;
+ if (pDataArray->countends) {
+ if (validCalculator.isValidCalculator("distance", pDataArray->distcalcType) == true) {
+ if (pDataArray->distcalcType == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (pDataArray->distcalcType == "eachgap") { distCalculator = new eachGapDist(); }
+ else if (pDataArray->distcalcType == "onegap") { distCalculator = new oneGapDist(); }
+ }
+ }else {
+ if (validCalculator.isValidCalculator("distance", pDataArray->distcalcType) == true) {
+ if (pDataArray->distcalcType == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (pDataArray->distcalcType == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
+ else if (pDataArray->distcalcType == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
+ }
+ }
+
+ if((pDataArray->output == "lt") && pDataArray->start == 0){ outFile << pDataArray->alignDB.getNumSeqs() << endl; }
+
+ for(int i=pDataArray->start;i<pDataArray->end;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) { outFile.close(); delete alignment; delete distCalculator; return 0; }
+
+ if (pDataArray->alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
+ alignment->resize(pDataArray->alignDB.get(i).getUnaligned().length()+1);
+ }
+
+ if (pDataArray->alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
+ alignment->resize(pDataArray->alignDB.get(j).getUnaligned().length()+1);
+ }
+
+ Sequence seqI(pDataArray->alignDB.get(i).getName(), pDataArray->alignDB.get(i).getAligned());
+ Sequence seqJ(pDataArray->alignDB.get(j).getName(), pDataArray->alignDB.get(j).getAligned());
+
+ alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
+ seqI.setAligned(alignment->getSeqAAln());
+ seqJ.setAligned(alignment->getSeqBAln());
+
+ distCalculator->calcDist(seqI, seqJ);
+ 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->end-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+
+ outFile.close();
+ delete alignment;
+ delete distCalculator;
+
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "PairwiseSeqsCommand", "MyPairwiseThreadFunction");
+ exit(1);
+ }
+}
+
+#endif
+
+
#endif
projects / mothur.git / commitdiff