From: westcott Date: Tue, 1 Sep 2009 19:16:29 +0000 (+0000) Subject: changed raredisplay to use vectors instead of files X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=30b3ffcd1cfd08e7144ae721bb53e27eb3f7a5d1 changed raredisplay to use vectors instead of files --- diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index a0ba7c2..75ef0d5 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -199,9 +199,9 @@ 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getoturepcommand.cpp; sourceTree = SOURCE_ROOT; }; 371B30B20FD7EE67000414CA /* screenseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = screenseqscommand.cpp; sourceTree = SOURCE_ROOT; }; 371B30B30FD7EE67000414CA /* screenseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; 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fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bergerparker.cpp; sourceTree = SOURCE_ROOT; }; diff --git a/listvector.cpp b/listvector.cpp index 6e00807..e123298 100644 --- a/listvector.cpp +++ b/listvector.cpp @@ -55,6 +55,8 @@ ListVector::ListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numS f >> inputData; set(i, inputData); } + + gobble(f); } catch(exception& e) { errorOut(e, "ListVector", "ListVector"); diff --git a/raredisplay.cpp b/raredisplay.cpp index b86312b..6c5a5e5 100644 --- a/raredisplay.cpp +++ b/raredisplay.cpp @@ -14,14 +14,6 @@ void RareDisplay::init(string label){ try { this->label = label; - if(nIters != 1){ - tempInFile.clear(); - openOutputFile(tempOutName, tempOutFile); - openInputFile(tempInName, tempInFile); - } - else{ - openOutputFile(tempOutName, tempOutFile); - } } catch(exception& e) { errorOut(e, "RareDisplay", "init"); @@ -38,20 +30,22 @@ void RareDisplay::update(SAbundVector* rank){ if(nIters != 1){ - double oldNSeqs, oldMean, oldVar; - - tempInFile >> oldNSeqs >> oldMean >> oldVar; - - double oldS = oldVar * ( nIters - 2 ); - double delta = data[0] - oldMean; - double newMean = oldMean + delta / nIters; + double oldS = var[index] * ( nIters - 2 ); + double delta = data[0] - results[index]; + double newMean = results[index] + delta / nIters; double newS = oldS + delta * ( data[0] - newMean ); double newVar = newS / ( nIters - 1 ); - tempOutFile << newNSeqs << '\t' << newMean << '\t' << newVar << endl; + seqs[index] = newNSeqs; + results[index] = newMean; + var[index] = newVar; + + index++; } else{ - tempOutFile << newNSeqs << '\t' << data[0] << '\t' << 0 << endl; + seqs.push_back(newNSeqs); + results.push_back(data[0]); + var.push_back(0.0); } } catch(exception& e) { @@ -67,20 +61,24 @@ void RareDisplay::update(vector shared, int numSeqs, int nu double newNSeqs = data[0]; if(nIters != 1){ - double oldNSeqs, oldMean, oldVar; - tempInFile >> oldNSeqs >> oldMean >> oldVar; - - double oldS = oldVar * ( nIters - 2 ); - double delta = data[0] - oldMean; - double newMean = oldMean + delta / nIters; + double oldS = var[index] * ( nIters - 2 ); + double delta = data[0] - results[index]; + double newMean = results[index] + delta / nIters; double newS = oldS + delta * ( data[0] - newMean ); double newVar = newS / ( nIters - 1 ); - - tempOutFile << newNSeqs << '\t' << newMean << '\t' << newVar << endl; + seqs[index] = newNSeqs; + results[index] = newMean; + var[index] = newVar; + + index++; } else{ - tempOutFile << newNSeqs << '\t' << data[0] << '\t' << 0 << endl; + + seqs.push_back(newNSeqs); + results.push_back(data[0]); + var.push_back(0.0); + } } catch(exception& e) { @@ -93,21 +91,8 @@ void RareDisplay::update(vector shared, int numSeqs, int nu void RareDisplay::reset(){ try { - if(nIters != 1){ - tempOutFile.close(); - tempInFile.close(); - } - else{ - tempOutFile.close(); - } - nIters++; - - remove(tempInName.c_str()); - renameOk = rename(tempOutName.c_str(), tempInName.c_str()); - - //checks to make sure user was able to rename and remove successfully - if (renameOk != 0) { mothurOut("Unable to rename the necessary temp files."); mothurOutEndLine(); } + index = 0; } catch(exception& e) { errorOut(e, "RareDisplay", "reset"); @@ -122,32 +107,27 @@ void RareDisplay::close(){ output->initFile(label); - openInputFile(tempInName, tempInFile); - - while(!tempInFile.eof()){ - int nSeqs; - tempInFile >> nSeqs; + for (int i = 0; i < seqs.size(); i++) { vector data(3,0); - double variance = 0; - - tempInFile >> data[0]; - tempInFile >> variance; - + double variance = var[i]; + + data[0] = results[i]; + double ci = 1.96 * pow(variance, 0.5); data[1] = data[0] - ci; data[2] = data[0] + ci; - output->output(nSeqs, data); - - gobble(tempInFile); + output->output(seqs[i], data); } - tempInFile.close(); - - remove(tempInName.c_str()); - remove(tempOutName.c_str()); nIters = 1; + index = 0; + + seqs.clear(); + results.clear(); + var.clear(); + output->resetFile(); } catch(exception& e) { diff --git a/raredisplay.h b/raredisplay.h index c906706..72147ad 100644 --- a/raredisplay.h +++ b/raredisplay.h @@ -11,8 +11,7 @@ class RareDisplay : public Display { public: - RareDisplay(Calculator* calc, FileOutput* file) : estimate(calc), output(file), nIters(1), - tempInName(getPathName(output->getFileName()) + ".tempin"), tempOutName(getPathName(output->getFileName()) + ".tempout") {}; + RareDisplay(Calculator* calc, FileOutput* file) : estimate(calc), output(file), nIters(1), index(0) {}; ~RareDisplay() { delete estimate; delete output; }; void init(string); void reset(); @@ -25,12 +24,10 @@ private: Calculator* estimate; FileOutput* output; string label; - int nIters; - string tempInName, tempOutName; - ifstream tempInFile; - ofstream tempOutFile; - int renameOk; - + vector seqs; + vector results; + vector var; + int index, nIters; }; #endif