*/
#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(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign);
- CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
- CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
- CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
- CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter poutput("output", "Multiple", "column-lt-square", "column", "", "", "",false,false); parameters.push_back(poutput);
- CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "",false,false); parameters.push_back(pcalc);
- CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcountends);
- CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcompress);
- CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","phylip-column",false,true,true); parameters.push_back(pfasta);
+ CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "","",false,false); parameters.push_back(palign);
+ CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
+ CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
+ CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen);
+ CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter poutput("output", "Multiple", "column-lt-square-phylip", "column", "", "", "","phylip-column",false,false,true); parameters.push_back(poutput);
+ CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "","",false,false); parameters.push_back(pcalc);
+ CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pcountends);
+ CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pcompress);
+ CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "","",false,false,true); parameters.push_back(pcutoff);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
exit(1);
}
}
-
+//**********************************************************************************************************************
+string PairwiseSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "phylip") { pattern = "[filename],[outputtag],dist"; }
+ else if (type == "column") { pattern = "[filename],dist"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PairwiseSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
PairwiseSeqsCommand::PairwiseSeqsCommand(){
try {
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
+ }else {
+ m->setFastaFile(fastaFileNames[i]);
}
}
}
// ...at some point should added some additional type checking...
string temp;
temp = validParameter.validFile(parameters, "match", false); if (temp == "not found"){ temp = "1.0"; }
- convert(temp, match);
+ m->mothurConvert(temp, match);
temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; }
- convert(temp, misMatch);
+ m->mothurConvert(temp, misMatch);
+ if (misMatch > 0) { m->mothurOut("[ERROR]: mismatch must be negative.\n"); abort=true; }
temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-2.0"; }
- convert(temp, gapOpen);
+ m->mothurConvert(temp, gapOpen);
+ if (gapOpen > 0) { m->mothurOut("[ERROR]: gapopen must be negative.\n"); abort=true; }
temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; }
- convert(temp, gapExtend);
+ m->mothurConvert(temp, gapExtend);
+ if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "cutoff", false); if(temp == "not found"){ temp = "1.0"; }
- convert(temp, cutoff);
+ m->mothurConvert(temp, cutoff);
temp = validParameter.validFile(parameters, "countends", false); if(temp == "not found"){ temp = "T"; }
countends = m->isTrue(temp);
align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; }
output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "column"; }
+ if (output=="phylip") { output = "lt"; }
if ((output != "column") && (output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are column, lt and square. I will use column."); m->mothurOutEndLine(); output = "column"; }
calc = validParameter.validFile(parameters, "calc", false);
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;
int numSeqs = alignDB.getNumSeqs();
int startTime = time(NULL);
string outputFile = "";
-
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
if (output == "lt") { //does the user want lower triangle phylip formatted file
- outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "phylip.dist";
- remove(outputFile.c_str()); outputTypes["phylip"].push_back(outputFile);
+ variables["[outputtag]"] = "phylip";
+ outputFile = getOutputFileName("phylip", variables);
+ m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
}else if (output == "column") { //user wants column format
- outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "dist";
+ outputFile = getOutputFileName("column", variables);
outputTypes["column"].push_back(outputFile);
- remove(outputFile.c_str());
+ m->mothurRemove(outputFile);
}else { //assume square
- outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "square.dist";
- remove(outputFile.c_str());
+ variables["[outputtag]"] = "square";
+ outputFile = getOutputFileName("phylip", variables);
+ m->mothurRemove(outputFile);
outputTypes["phylip"].push_back(outputFile);
}
driverMPI(start, end, outMPI, cutoff);
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); remove(outputFile.c_str()); 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); remove(outputFile.c_str()); 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); remove(outputFile.c_str()); 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");
//do your part
string outputMyPart;
- unsigned long int mySize;
+ unsigned long long mySize;
if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
else { driverMPI(start, end, outputFile, mySize, output); }
- if (m->control_pressed) { outputTypes.clear(); remove(outputFile.c_str()); 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;
//wait on chidren
for(int b = 1; b < processors; b++) {
- unsigned long int fileSize;
+ unsigned long long fileSize;
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); remove(outputFile.c_str()); 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_File_close(&outMPI);
}else { //you are a child process
//do your part
- unsigned long int size;
+ unsigned long long size;
if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
- if (m->control_pressed) { delete distCalculator; return 0; }
+ if (m->control_pressed) { return 0; }
//tell parent you are done.
MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//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; remove(outputFile.c_str()); 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; remove(outputFile.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFile); return 0; }
}
-
- delete distCalculator;
//set phylip file as new current phylipfile
string current = "";
}
m->mothurOutEndLine();
- m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
/**************************************************************************************************/
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) || (__linux__) || (__unix__) || (__unix)
+
//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, cutoff, 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"); }
- //append and remove temp files
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ if (pDataArray[i]->count != (pDataArray[i]->end-pDataArray[i]->start)) {
+ m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " sequences assigned to it, quitting. \n"); m->control_pressed = true;
+ }
+ 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);
- remove((filename + toString(processIDS[i]) + ".temp").c_str());
+ 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);
seqI.setAligned(alignment->getSeqAAln());
seqJ.setAligned(alignment->getSeqBAln());
-
+ //cout << seqI.getName() << '\t' << seqJ.getName() << endl;
+ //cout << alignment->getSeqAAln() << endl << alignment->getSeqBAln() << endl;
+
distCalculator->calcDist(seqI, seqJ);
double dist = distCalculator->getDist();
-
+
+ //cout << "dist = " << dist << endl;
+
if(dist <= cutoff){
if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
}
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) {
}
/**************************************************************************************************/
/////// need to fix to work with calcs and sequencedb
-int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size){
+int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size){
try {
MPI_Status status;
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;
}
}
/**************************************************************************************************/
/////// need to fix to work with calcs and sequencedb
-int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size, string square){
+int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size, string square){
try {
MPI_Status status;
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<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) {
projects / mothur.git / blobdiff