X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readphylip.cpp;h=1c529b26f15fdfa172c8a0f7ebcf20187e87b03b;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=bc39b52ca071d126bc9adc671e8d202c9a112dd6;hpb=c196b6b4768ccb84955d773ff0f22e4994d1ba7b;p=mothur.git diff --git a/readphylip.cpp b/readphylip.cpp index bc39b52..1c529b2 100644 --- a/readphylip.cpp +++ b/readphylip.cpp @@ -14,22 +14,35 @@ ReadPhylipMatrix::ReadPhylipMatrix(string distFile){ - successOpen = openInputFile(distFile, fileHandle); + successOpen = m->openInputFile(distFile, fileHandle); + sim=false; } +/***********************************************************************/ + +ReadPhylipMatrix::ReadPhylipMatrix(string distFile, bool s){ + + successOpen = m->openInputFile(distFile, fileHandle); + sim=s; +} + /***********************************************************************/ -void ReadPhylipMatrix::read(NameAssignment* nameMap){ +int ReadPhylipMatrix::read(NameAssignment* nameMap){ try { float distance; int square, nseqs; string name; vector matrixNames; - - fileHandle >> nseqs >> name; - + + string numTest; + fileHandle >> numTest >> name; + + if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); } + else { convert(numTest, nseqs); } + matrixNames.push_back(name); if(nameMap == NULL){ @@ -38,7 +51,7 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){ } else{ list = new ListVector(nameMap->getListVector()); - if(nameMap->count(name)==0){ cout << "Error: Sequence '" << name << "' was not found in the names file, please correct" << endl; } + if(nameMap->count(name)==0){ m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); } } char d; @@ -59,25 +72,33 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){ } Progress* reading; - + if(square == 0){ reading = new Progress("Reading matrix: ", nseqs * (nseqs - 1) / 2); int index = 0; - + for(int i=1;icontrol_pressed) { fileHandle.close(); delete reading; return 0; } + fileHandle >> name; matrixNames.push_back(name); + //there's A LOT of repeated code throughout this method... if(nameMap == NULL){ list->set(i, name); for(int j=0;jcontrol_pressed) { delete reading; fileHandle.close(); return 0; } + fileHandle >> distance; + if (distance == -1) { distance = 1000000; } + else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert. if(distance < cutoff){ PCell value(i, j, distance); @@ -89,12 +110,15 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){ } else{ - if(nameMap->count(name)==0){ cout << "Error: Sequence '" << name << "' was not found in the names file, please correct" << endl; } + if(nameMap->count(name)==0){ m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); } for(int j=0;j> distance; + + if (m->control_pressed) { delete reading; fileHandle.close(); return 0; } if (distance == -1) { distance = 1000000; } + else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert. if(distance < cutoff){ PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance); @@ -115,13 +139,18 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){ for(int i=1;i> name; matrixNames.push_back(name); + + if(nameMap == NULL){ list->set(i, name); for(int j=0;j> distance; - + + if (m->control_pressed) { fileHandle.close(); delete reading; return 0; } + if (distance == -1) { distance = 1000000; } + else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert. if(distance < cutoff && j < i){ PCell value(i, j, distance); @@ -133,14 +162,17 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){ } else{ - if(nameMap->count(name)==0){ cout << "Error: Sequence '" << name << "' was not found in the names file, please correct" << endl; } + if(nameMap->count(name)==0){ m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); } for(int j=0;j> distance; - - if (distance == -1) { distance = 1000000; } + + if (m->control_pressed) { fileHandle.close(); delete reading; return 0; } + + if (distance == -1) { distance = 1000000; } + else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert. - if(distance < cutoff && j < i){ + if(distance < cutoff && j < i){ PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance); D->addCell(value); } @@ -150,36 +182,37 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){ } } } + + if (m->control_pressed) { fileHandle.close(); delete reading; return 0; } + reading->finish(); delete reading; list->setLabel("0"); fileHandle.close(); - if(nameMap != NULL){ + /* if(nameMap != NULL){ for(int i=0;ierase(matrixNames[i]); } if(nameMap->size() > 0){ //should probably tell them what is missing if we missed something - cout << "missed something" << '\t' << nameMap->size() << endl; + m->mothurOut("missed something\t" + toString(nameMap->size())); m->mothurOutEndLine(); } - } + } */ + + return 1; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ReadPhylipMatrix class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ReadPhylipMatrix class function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ReadPhylipMatrix", "read"); exit(1); } -} + } /***********************************************************************/ ReadPhylipMatrix::~ReadPhylipMatrix(){ - delete D; - delete list; + // delete D; + // delete list; }