X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedrabundvector.cpp;h=a050ab3fe71998b5a8a6abf2b34b0e67f0083808;hb=002421a439168e2610a2b62f1318f21c7202fe6d;hp=cb20accf9f93819a45d8492ca9176cd8537b8a0c;hpb=ac1da2a793271cb67f2a2155c5558e1fabdd6aba;p=mothur.git diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp index cb20acc..a050ab3 100644 --- a/sharedrabundvector.cpp +++ b/sharedrabundvector.cpp @@ -51,7 +51,7 @@ SharedRAbundVector::SharedRAbundVector(string id, vector rav) : Data } } catch(exception& e) { - errorOut(e, "SharedRAbundVector", "SharedRAbundVector"); + m->errorOut(e, "SharedRAbundVector", "SharedRAbundVector"); exit(1); } } @@ -70,11 +70,14 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), string holdLabel, nextLabel, groupN; individual newguy; - for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } - lookup.clear(); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } lookup.clear(); + + if (globaldata->saveNextLabel == "") { f >> label; } + else { label = globaldata->saveNextLabel; } //read in first row since you know there is at least 1 group. - f >> label >> groupN >> num; + f >> groupN >> num; + holdLabel = label; //add new vector to lookup @@ -93,16 +96,17 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), for(int i=0;i> inputData; - lookup[0]->push_back(inputData, i, groupN); //abundance, bin, group - push_back(inputData, i, groupN); - numSeqs += inputData; - numBins++; + lookup[0]->push_back(inputData, groupN); //abundance, bin, group + push_back(inputData, groupN); + //numSeqs += inputData; + //numBins++; if (inputData > maxRank) { maxRank = inputData; } - } - if (f.eof() != true) { f >> nextLabel; } + m->gobble(f); + if (!(f.eof())) { f >> nextLabel; } + //read the rest of the groups info in while ((nextLabel == holdLabel) && (f.eof() != true)) { f >> groupN >> num; @@ -110,6 +114,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), if (globaldata->gGroupmap == NULL) { //save group in groupmap + groupmap->namesOfGroups.push_back(groupN); groupmap->groupIndex[groupN] = count; } @@ -123,21 +128,21 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), //fill vector. for(int i=0;i> inputData; - lookup[count]->push_back(inputData, i, groupN); //abundance, bin, group + lookup[count]->push_back(inputData, groupN); //abundance, bin, group } + m->gobble(f); if (f.eof() != true) { f >> nextLabel; } } - - //put file pointer back since you are now at a new distance label - for (int i = 0; i < nextLabel.length(); i++) { f.unget(); } + + globaldata->saveNextLabel = nextLabel; if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap; } } catch(exception& e) { - errorOut(e, "SharedRAbundVector", "SharedRAbundVector"); + m->errorOut(e, "SharedRAbundVector", "SharedRAbundVector"); exit(1); } } @@ -155,7 +160,7 @@ void SharedRAbundVector::set(int binNumber, int newBinSize, string groupname){ numSeqs += (newBinSize - oldBinSize); } catch(exception& e) { - errorOut(e, "SharedRAbundVector", "set"); + m->errorOut(e, "SharedRAbundVector", "set"); exit(1); } } @@ -199,12 +204,22 @@ vector SharedRAbundVector::getData(){ } /***********************************************************************/ -void SharedRAbundVector::push_back(int binSize, int otu, string groupName){ +void SharedRAbundVector::clear(){ + numBins = 0; + maxRank = 0; + numSeqs = 0; + data.clear(); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } + lookup.clear(); +} +/***********************************************************************/ + +void SharedRAbundVector::push_back(int binSize, string groupName){ try { individual newGuy; newGuy.abundance = binSize; newGuy.group = groupName; - newGuy.bin = otu; + newGuy.bin = data.size(); data.push_back(newGuy); numBins++; @@ -216,7 +231,7 @@ void SharedRAbundVector::push_back(int binSize, int otu, string groupName){ numSeqs += binSize; } catch(exception& e) { - errorOut(e, "SharedRAbundVector", "push_back"); + m->errorOut(e, "SharedRAbundVector", "push_back"); exit(1); } } @@ -240,7 +255,7 @@ void SharedRAbundVector::insert(int binSize, int otu, string groupName){ numSeqs += binSize; } catch(exception& e) { - errorOut(e, "SharedRAbundVector", "insert"); + m->errorOut(e, "SharedRAbundVector", "insert"); exit(1); } } @@ -264,7 +279,7 @@ void SharedRAbundVector::push_front(int binSize, int otu, string groupName){ numSeqs += binSize; } catch(exception& e) { - errorOut(e, "SharedRAbundVector", "push_front"); + m->errorOut(e, "SharedRAbundVector", "push_front"); exit(1); } } @@ -310,7 +325,7 @@ void SharedRAbundVector::print(ostream& output){ output << endl; } catch(exception& e) { - errorOut(e, "SharedRAbundVector", "print"); + m->errorOut(e, "SharedRAbundVector", "print"); exit(1); } } @@ -356,22 +371,101 @@ vector SharedRAbundVector::getSharedRAbundVectors(){ util = new SharedUtil(); util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups); - + + bool remove = false; for (int i = 0; i < lookup.size(); i++) { //if this sharedrabund is not from a group the user wants then delete it. if (util->isValidGroup(lookup[i]->getGroup(), globaldata->Groups) == false) { - delete lookup[i]; + remove = true; + delete lookup[i]; lookup[i] = NULL; lookup.erase(lookup.begin()+i); i--; } } delete util; + + if (remove) { eliminateZeroOTUS(lookup); } return lookup; } catch(exception& e) { - errorOut(e, "SharedRAbundVector", "getSharedRAbundVectors"); + m->errorOut(e, "SharedRAbundVector", "getSharedRAbundVectors"); + exit(1); + } +} +//********************************************************************************************************************** +int SharedRAbundVector::eliminateZeroOTUS(vector& thislookup) { + try { + + vector newLookup; + for (int i = 0; i < thislookup.size(); i++) { + SharedRAbundVector* temp = new SharedRAbundVector(); + temp->setLabel(thislookup[i]->getLabel()); + temp->setGroup(thislookup[i]->getGroup()); + newLookup.push_back(temp); + } + + //for each bin + for (int i = 0; i < thislookup[0]->getNumBins(); i++) { + if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; } + + //look at each sharedRabund and make sure they are not all zero + bool allZero = true; + for (int j = 0; j < thislookup.size(); j++) { + if (thislookup[j]->getAbundance(i) != 0) { allZero = false; break; } + } + + //if they are not all zero add this bin + if (!allZero) { + for (int j = 0; j < thislookup.size(); j++) { + newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup()); + } + } + } + + for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; } + + thislookup = newLookup; + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "SharedRAbundVector", "eliminateZeroOTUS"); + exit(1); + } + } + +/***********************************************************************/ +vector SharedRAbundVector::getSharedRAbundFloatVectors(vector thislookup){ + try { + vector newLookupFloat; + for (int i = 0; i < lookup.size(); i++) { + SharedRAbundFloatVector* temp = new SharedRAbundFloatVector(); + temp->setLabel(thislookup[i]->getLabel()); + temp->setGroup(thislookup[i]->getGroup()); + newLookupFloat.push_back(temp); + } + + for (int i = 0; i < thislookup.size(); i++) { + + for (int j = 0; j < thislookup[i]->getNumBins(); j++) { + + if (m->control_pressed) { return newLookupFloat; } + + int abund = thislookup[i]->getAbundance(j); + + float relabund = abund / (float) thislookup[i]->getNumSeqs(); + + newLookupFloat[i]->push_back(relabund, thislookup[i]->getGroup()); + } + } + + return newLookupFloat; + } + catch(exception& e) { + m->errorOut(e, "SharedRAbundVector", "getSharedRAbundVectors"); exit(1); } } @@ -391,7 +485,7 @@ RAbundVector SharedRAbundVector::getRAbundVector() { return rav; } catch(exception& e) { - errorOut(e, "SharedRAbundVector", "getRAbundVector"); + m->errorOut(e, "SharedRAbundVector", "getRAbundVector"); exit(1); } } @@ -406,7 +500,7 @@ RAbundVector SharedRAbundVector::getRAbundVector2() { return rav; } catch(exception& e) { - errorOut(e, "SharedRAbundVector", "getRAbundVector2"); + m->errorOut(e, "SharedRAbundVector", "getRAbundVector2"); exit(1); } } @@ -428,7 +522,7 @@ SharedSAbundVector SharedRAbundVector::getSharedSAbundVector(){ return sav; } catch(exception& e) { - errorOut(e, "SharedRAbundVector", "getSharedSAbundVector"); + m->errorOut(e, "SharedRAbundVector", "getSharedSAbundVector"); exit(1); } } @@ -447,7 +541,7 @@ SAbundVector SharedRAbundVector::getSAbundVector() { return sav; } catch(exception& e) { - errorOut(e, "SharedRAbundVector", "getSAbundVector"); + m->errorOut(e, "SharedRAbundVector", "getSAbundVector"); exit(1); } } @@ -471,7 +565,7 @@ SharedOrderVector SharedRAbundVector::getSharedOrderVector() { return ov; } catch(exception& e) { - errorOut(e, "SharedRAbundVector", "getSharedOrderVector"); + m->errorOut(e, "SharedRAbundVector", "getSharedOrderVector"); exit(1); } } @@ -480,19 +574,19 @@ SharedOrderVector SharedRAbundVector::getSharedOrderVector() { OrderVector SharedRAbundVector::getOrderVector(map* nameMap = NULL) { try { OrderVector ov; - - for(int i=0;ierrorOut(e, "SharedRAbundVector", "getOrderVector"); exit(1); } }