X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=pairwiseseqscommand.cpp;h=c9e5ecfdfda727427793e98aaed0270cdcd6e046;hp=1aa133f38c379fd40c495d2c2a844de292c17f51;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=86c838c428a9e7d26f902f5492738241fa72c4e7 diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp index 1aa133f..c9e5ecf 100644 --- a/pairwiseseqscommand.cpp +++ b/pairwiseseqscommand.cpp @@ -8,37 +8,24 @@ */ #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 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 myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -77,7 +64,22 @@ string PairwiseSeqsCommand::getHelpString(){ 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 { @@ -99,6 +101,7 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option) { //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { vector myArray = setParameters(); @@ -197,6 +200,8 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option) { //erase from file list fastaFileNames.erase(fastaFileNames.begin()+i); i--; + }else { + m->setFastaFile(fastaFileNames[i]); } } } @@ -209,23 +214,26 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option) { // ...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); @@ -236,6 +244,7 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option) { 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); @@ -244,25 +253,6 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option) { if (calc == "default") { calc = "onegap"; } } m->splitAtDash(calc, Estimators); - - ValidCalculators validCalculator; - if (countends) { - for (int i=0; imothurOut(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; @@ -306,17 +286,21 @@ int PairwiseSeqsCommand::execute(){ int numSeqs = alignDB.getNumSeqs(); int startTime = time(NULL); string outputFile = ""; - + + map 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); } @@ -354,11 +338,11 @@ int PairwiseSeqsCommand::execute(){ 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); @@ -367,7 +351,7 @@ int PairwiseSeqsCommand::execute(){ //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"); @@ -382,12 +366,12 @@ int PairwiseSeqsCommand::execute(){ //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; @@ -400,9 +384,9 @@ int PairwiseSeqsCommand::execute(){ //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); @@ -428,11 +412,11 @@ int PairwiseSeqsCommand::execute(){ 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); @@ -441,7 +425,7 @@ int PairwiseSeqsCommand::execute(){ 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); } @@ -462,14 +446,14 @@ int PairwiseSeqsCommand::execute(){ 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); @@ -497,10 +481,8 @@ int PairwiseSeqsCommand::execute(){ 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 = ""; @@ -516,7 +498,7 @@ int PairwiseSeqsCommand::execute(){ } 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(); @@ -532,9 +514,11 @@ int PairwiseSeqsCommand::execute(){ /**************************************************************************************************/ 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) { @@ -564,13 +548,54 @@ void PairwiseSeqsCommand::createProcesses(string filename) { 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 pDataArray; //[processors-1]; + DWORD dwThreadIdArray[processors-1]; + HANDLE hThreadArray[processors-1]; + + //Create processor-1 worker threads. + for( int i=0; icount != (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;iappendFiles((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"); @@ -584,6 +609,33 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, fl 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); @@ -603,7 +655,7 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, fl for(int j=0;jcontrol_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); @@ -620,10 +672,14 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, fl 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; } } @@ -640,6 +696,8 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, fl m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine(); outFile.close(); + delete alignment; + delete distCalculator; return 1; } @@ -654,7 +712,34 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, st 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); @@ -672,7 +757,7 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, st for(int j=0;jcontrol_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); @@ -705,6 +790,8 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, st m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine(); outFile.close(); + delete alignment; + delete distCalculator; return 1; } @@ -720,14 +807,41 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, 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;icontrol_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); @@ -769,7 +883,8 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, delete buf; } - + delete alignment; + delete distCalculator; return 1; } catch(exception& e) { @@ -779,7 +894,7 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, } /**************************************************************************************************/ /////// 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; @@ -791,7 +906,33 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi 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; @@ -808,7 +949,7 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi for(int j=0;jcontrol_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); @@ -845,6 +986,8 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi } MPI_File_close(&outMPI); + delete alignment; + delete distCalculator; return 1; } @@ -855,7 +998,7 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi } /**************************************************************************************************/ /////// 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; @@ -867,8 +1010,33 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi 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; @@ -884,7 +1052,7 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi for(int j=0;jcontrol_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); @@ -922,6 +1090,7 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi MPI_File_close(&outMPI); + delete alignment; return 1; } catch(exception& e) {