X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=splitmatrix.cpp;fp=splitmatrix.cpp;h=a4e1f98581b9ce947dd53ad016dc347c71c99ffe;hb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;hp=6e40e97a10b0fd2af75b09c97ae43a26095016b8;hpb=d84bb41d7dadcfa2c67ce5edb9b94060e5659fa7;p=mothur.git diff --git a/splitmatrix.cpp b/splitmatrix.cpp index 6e40e97..a4e1f98 100644 --- a/splitmatrix.cpp +++ b/splitmatrix.cpp @@ -87,12 +87,12 @@ int SplitMatrix::splitClassify(){ PhyloTree* phylo = new PhyloTree(); ifstream in; - openInputFile(taxFile, in); + m->openInputFile(taxFile, in); //read in users taxonomy file and add sequences to tree string seqname, tax; while(!in.eof()){ - in >> seqname >> tax; gobble(in); + in >> seqname >> tax; m->gobble(in); phylo->addSeqToTree(seqname, tax); } in.close(); @@ -146,12 +146,12 @@ int SplitMatrix::createDistanceFilesFromTax(map& seqGroup, int numG } ifstream in; - openInputFile(fastafile, in); + m->openInputFile(fastafile, in); //parse fastafile ofstream outFile; while (!in.eof()) { - Sequence query(in); gobble(in); + Sequence query(in); m->gobble(in); if (query.getName() != "") { it = seqGroup.find(query.getName()); @@ -160,7 +160,7 @@ int SplitMatrix::createDistanceFilesFromTax(map& seqGroup, int numG if (namefile == "") { names.insert(query.getName()); } if (it != seqGroup.end()) { //not singleton - openOutputFileAppend((fastafile + "." + toString(it->second) + ".temp"), outFile); + m->openOutputFileAppend((fastafile + "." + toString(it->second) + ".temp"), outFile); query.printSequence(outFile); outFile.close(); @@ -195,22 +195,22 @@ int SplitMatrix::createDistanceFilesFromTax(map& seqGroup, int numG singleton = namefile + ".extra.temp"; ofstream remainingNames; - openOutputFile(singleton, remainingNames); + m->openOutputFile(singleton, remainingNames); bool wroteExtra = false; ifstream bigNameFile; - openInputFile(namefile, bigNameFile); + m->openInputFile(namefile, bigNameFile); string name, nameList; while(!bigNameFile.eof()){ - bigNameFile >> name >> nameList; gobble(bigNameFile); + bigNameFile >> name >> nameList; m->gobble(bigNameFile); //did this sequence get assigned a group it = seqGroup.find(name); if (it != seqGroup.end()) { - openOutputFileAppend((namefile + "." + toString(it->second) + ".temp"), outFile); + m->openOutputFileAppend((namefile + "." + toString(it->second) + ".temp"), outFile); outFile << name << '\t' << nameList << endl; outFile.close(); }else{ @@ -222,23 +222,23 @@ int SplitMatrix::createDistanceFilesFromTax(map& seqGroup, int numG for(int i=0;igetRootName(m->getSimpleName((fastafile + "." + toString(i) + ".temp"))) + "dist"; //if there are valid distances ifstream fileHandle; fileHandle.open(tempDistFile.c_str()); if(fileHandle) { - gobble(fileHandle); + m->gobble(fileHandle); if (!fileHandle.eof()) { //check for blank file - this could occur if all dists in group are above cutoff map temp; temp[tempDistFile] = tempNameFile; dists.push_back(temp); }else { ifstream in; - openInputFile(tempNameFile, in); + m->openInputFile(tempNameFile, in); while(!in.eof()) { - in >> name >> nameList; gobble(in); + in >> name >> nameList; m->gobble(in); wroteExtra = true; remainingNames << name << '\t' << nameList << endl; } @@ -271,7 +271,7 @@ int SplitMatrix::splitDistanceFileByTax(map& seqGroup, int numGroup map::iterator it2; ifstream dFile; - openInputFile(distFile, dFile); + m->openInputFile(distFile, dFile); ofstream outFile; for (int i = 0; i < numGroups; i++) { //remove old temp files, just in case @@ -294,7 +294,7 @@ int SplitMatrix::splitDistanceFileByTax(map& seqGroup, int numGroup if (m->control_pressed) { dFile.close(); for (int i = 0; i < numGroups; i++) { remove((distFile + "." + toString(i) + ".temp").c_str()); } } - dFile >> seqA >> seqB >> dist; gobble(dFile); + dFile >> seqA >> seqB >> dist; m->gobble(dFile); //if both sequences are in the same group then they are within the cutoff it = seqGroup.find(seqA); @@ -303,7 +303,7 @@ int SplitMatrix::splitDistanceFileByTax(map& seqGroup, int numGroup if ((it != seqGroup.end()) && (it2 != seqGroup.end())) { //they are both not singletons if (it->second == it2->second) { //they are from the same group so add the distance if (numOutputs[it->second] > 30) { - openOutputFileAppend((distFile + "." + toString(it->second) + ".temp"), outFile); + m->openOutputFileAppend((distFile + "." + toString(it->second) + ".temp"), outFile); outFile << outputs[it->second] << seqA << '\t' << seqB << '\t' << dist << endl; outFile.close(); outputs[it->second] = ""; @@ -323,7 +323,7 @@ int SplitMatrix::splitDistanceFileByTax(map& seqGroup, int numGroup //write out any remaining buffers if (numOutputs[i] > 0) { - openOutputFileAppend((distFile + "." + toString(i) + ".temp"), outFile); + m->openOutputFileAppend((distFile + "." + toString(i) + ".temp"), outFile); outFile << outputs[i]; outFile.close(); outputs[i] = ""; @@ -333,23 +333,23 @@ int SplitMatrix::splitDistanceFileByTax(map& seqGroup, int numGroup } ifstream bigNameFile; - openInputFile(namefile, bigNameFile); + m->openInputFile(namefile, bigNameFile); singleton = namefile + ".extra.temp"; ofstream remainingNames; - openOutputFile(singleton, remainingNames); + m->openOutputFile(singleton, remainingNames); bool wroteExtra = false; string name, nameList; while(!bigNameFile.eof()){ - bigNameFile >> name >> nameList; gobble(bigNameFile); + bigNameFile >> name >> nameList; m->gobble(bigNameFile); //did this sequence get assigned a group it = seqGroup.find(name); if (it != seqGroup.end()) { - openOutputFileAppend((namefile + "." + toString(it->second) + ".temp"), outFile); + m->openOutputFileAppend((namefile + "." + toString(it->second) + ".temp"), outFile); outFile << name << '\t' << nameList << endl; outFile.close(); }else{ @@ -370,10 +370,10 @@ int SplitMatrix::splitDistanceFileByTax(map& seqGroup, int numGroup dists.push_back(temp); }else{ ifstream in; - openInputFile(tempNameFile, in); + m->openInputFile(tempNameFile, in); while(!in.eof()) { - in >> name >> nameList; gobble(in); + in >> name >> nameList; m->gobble(in); wroteExtra = true; remainingNames << name << '\t' << nameList << endl; } @@ -419,7 +419,7 @@ int SplitMatrix::splitDistanceLarge(){ ofstream outFile; ifstream dFile; - openInputFile(distFile, dFile); + m->openInputFile(distFile, dFile); while(dFile){ string seqA, seqB; @@ -633,7 +633,7 @@ int SplitMatrix::splitDistanceLarge(){ } } } - gobble(dFile); + m->gobble(dFile); } dFile.close(); @@ -671,7 +671,7 @@ int SplitMatrix::splitNames(vector >& groups){ while(bigNameFile){ bigNameFile >> name >> nameList; nameMap[name] = nameList; - gobble(bigNameFile); + m->gobble(bigNameFile); } bigNameFile.close(); @@ -740,7 +740,7 @@ int SplitMatrix::splitDistanceRAM(){ int numGroups = 0; ifstream dFile; - openInputFile(distFile, dFile); + m->openInputFile(distFile, dFile); while(dFile){ string seqA, seqB; @@ -823,7 +823,7 @@ int SplitMatrix::splitDistanceRAM(){ } } } - gobble(dFile); + m->gobble(dFile); } dFile.close();