X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=listvector.cpp;h=2758c94264a1ba527e8d7c3970e0bac53254579b;hp=9005dc0ad450161c580a2ed2dc5074afb8e53912;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=bfbc55964f1977da72c2cea984288a427d370a59 diff --git a/listvector.cpp b/listvector.cpp index 9005dc0..2758c94 100644 --- a/listvector.cpp +++ b/listvector.cpp @@ -7,23 +7,41 @@ * */ -using namespace std; - #include "sabundvector.hpp" #include "rabundvector.hpp" #include "ordervector.hpp" -#include "utilities.hpp" #include "listvector.hpp" +//sorts highest to lowest +/***********************************************************************/ +inline bool abundNamesSort(string left, string right){ + + int countLeft = 0; + if(left != ""){ + countLeft = 1; + for(int i=0;i countRight) { + return true; + } + return false; +} /***********************************************************************/ -ListVector::ListVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){}; +ListVector::ListVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){} /***********************************************************************/ -ListVector::ListVector(int n): DataVector(), data(n, "") , maxRank(0), numBins(0), numSeqs(0){}; +ListVector::ListVector(int n): DataVector(), data(n, "") , maxRank(0), numBins(0), numSeqs(0){} /***********************************************************************/ @@ -31,7 +49,7 @@ ListVector::ListVector(string id, vector lv) : DataVector(id), data(lv){ try { for(int i=0;igetNumNames(data[i]); numBins = i+1; if(binSize > maxRank) { maxRank = binSize; } numSeqs += binSize; @@ -39,11 +57,7 @@ ListVector::ListVector(string id, vector lv) : DataVector(id), data(lv){ } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function ListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ListVector class function ListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ListVector", "ListVector"); exit(1); } } @@ -62,13 +76,10 @@ ListVector::ListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numS f >> inputData; set(i, inputData); } + m->gobble(f); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function ListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ListVector class function ListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ListVector", "ListVector"); exit(1); } } @@ -77,9 +88,9 @@ ListVector::ListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numS void ListVector::set(int binNumber, string seqNames){ try { - int nNames_old = getNumNames(data[binNumber]); + int nNames_old = m->getNumNames(data[binNumber]); data[binNumber] = seqNames; - int nNames_new = getNumNames(seqNames); + int nNames_new = m->getNumNames(seqNames); if(nNames_old == 0) { numBins++; } if(nNames_new == 0) { numBins--; } @@ -88,11 +99,7 @@ void ListVector::set(int binNumber, string seqNames){ numSeqs += (nNames_new - nNames_old); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ListVector class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ListVector", "set"); exit(1); } } @@ -108,7 +115,7 @@ string ListVector::get(int index){ void ListVector::push_back(string seqNames){ try { data.push_back(seqNames); - int nNames = getNumNames(seqNames); + int nNames = m->getNumNames(seqNames); numBins++; @@ -117,11 +124,7 @@ void ListVector::push_back(string seqNames){ numSeqs += nNames; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ListVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ListVector", "push_back"); exit(1); } } @@ -153,19 +156,18 @@ void ListVector::print(ostream& output){ try { output << label << '\t' << numBins << '\t'; - for(int i=0;i hold = data; + sort(hold.begin(), hold.end(), abundNamesSort); + + for(int i=0;ierrorOut(e, "ListVector", "print"); exit(1); } } @@ -178,7 +180,7 @@ RAbundVector ListVector::getRAbundVector(){ RAbundVector rav; for(int i=0;igetNumNames(data[i]); rav.push_back(binSize); } @@ -196,11 +198,7 @@ RAbundVector ListVector::getRAbundVector(){ return rav; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ListVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ListVector", "getRAbundVector"); exit(1); } } @@ -212,7 +210,7 @@ SAbundVector ListVector::getSAbundVector(){ SAbundVector sav(maxRank+1); for(int i=0;igetNumNames(data[i]); sav.set(binSize, sav.get(binSize) + 1); } sav.set(0, 0); @@ -221,11 +219,7 @@ SAbundVector ListVector::getSAbundVector(){ return sav; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ListVector class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ListVector", "getSAbundVector"); exit(1); } } @@ -239,7 +233,7 @@ OrderVector ListVector::getOrderVector(map* orderMap = NULL){ OrderVector ov; for(int i=0;igetNumNames(data[i]); for(int j=0;j* orderMap = NULL){ } else{ if(orderMap->count(seqName) == 0){ - cerr << seqName << " not found, check *.names file\n"; + m->mothurOut(seqName + " not found, check *.names file\n"); exit(1); } @@ -277,7 +271,7 @@ OrderVector ListVector::getOrderVector(map* orderMap = NULL){ } if(orderMap->count(seqName) == 0){ - cerr << seqName << " not found, check *.names file\n"; + m->mothurOut(seqName + " not found, check *.names file\n"); exit(1); } ov.set((*orderMap)[seqName], i); @@ -290,11 +284,7 @@ OrderVector ListVector::getOrderVector(map* orderMap = NULL){ } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ListVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ListVector", "getOrderVector"); exit(1); } }