X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedrabundvector.cpp;h=b41c5fafa40255b1535526f79c2ce1c5dc637a43;hb=82bf18e3ef0a52345519f91a682e64cc385b56bb;hp=0a69e4c37849171e01544da40f2c09bbd86d40b0;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;p=mothur.git diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp index 0a69e4c..b41c5fa 100644 --- a/sharedrabundvector.cpp +++ b/sharedrabundvector.cpp @@ -14,8 +14,7 @@ /***********************************************************************/ - -SharedRAbundVector::SharedRAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {globaldata = GlobalData::getInstance();} +SharedRAbundVector::SharedRAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {} /***********************************************************************/ SharedRAbundVector::~SharedRAbundVector() { @@ -26,7 +25,6 @@ SharedRAbundVector::~SharedRAbundVector() { /***********************************************************************/ SharedRAbundVector::SharedRAbundVector(int n) : DataVector(), maxRank(0), numBins(n), numSeqs(0) { - globaldata = GlobalData::getInstance(); individual newGuy; //initialize data for (int i=0; i< n; i++) { @@ -51,7 +49,7 @@ SharedRAbundVector::SharedRAbundVector(string id, vector rav) : Data } } catch(exception& e) { - errorOut(e, "SharedRAbundVector", "SharedRAbundVector"); + m->errorOut(e, "SharedRAbundVector", "SharedRAbundVector"); exit(1); } } @@ -61,20 +59,21 @@ SharedRAbundVector::SharedRAbundVector(string id, vector rav) : Data //reads a shared file SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) { try { - globaldata = GlobalData::getInstance(); - - if (globaldata->gGroupmap == NULL) { groupmap = new GroupMap(); } - + m->namesOfGroups.clear(); + int num, inputData, count; count = 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 (m->saveNextLabel == "") { f >> label; } + else { label = m->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 @@ -83,36 +82,29 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), lookup[0]->setLabel(label); lookup[0]->setGroup(groupN); - if (globaldata->gGroupmap == NULL) { - //save group in groupmap - groupmap->namesOfGroups.push_back(groupN); - groupmap->groupIndex[groupN] = 0; - } + m->namesOfGroups.push_back(groupN); //fill vector. data = first sharedrabund in file 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; count++; - if (globaldata->gGroupmap == NULL) { - //save group in groupmap - groupmap->namesOfGroups.push_back(groupN); - groupmap->groupIndex[groupN] = count; - } + m->namesOfGroups.push_back(groupN); //add new vector to lookup temp = new SharedRAbundVector(); @@ -123,21 +115,18 @@ 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(); } - - if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap; } + m->saveNextLabel = nextLabel; } catch(exception& e) { - errorOut(e, "SharedRAbundVector", "SharedRAbundVector"); + m->errorOut(e, "SharedRAbundVector", "SharedRAbundVector"); exit(1); } } @@ -155,7 +144,7 @@ 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 +188,22 @@ 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 +215,7 @@ 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 +239,7 @@ 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 +263,7 @@ 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 +309,7 @@ void SharedRAbundVector::print(ostream& output){ output << endl; } catch(exception& e) { - errorOut(e, "SharedRAbundVector", "print"); + m->errorOut(e, "SharedRAbundVector", "print"); exit(1); } } @@ -355,23 +354,102 @@ vector SharedRAbundVector::getSharedRAbundVectors(){ SharedUtil* util; util = new SharedUtil(); - util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups); - + util->setGroups(m->Groups, m->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]; + if (util->isValidGroup(lookup[i]->getGroup(), m->Groups) == false) { + 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); } } @@ -379,16 +457,19 @@ vector SharedRAbundVector::getSharedRAbundVectors(){ RAbundVector SharedRAbundVector::getRAbundVector() { try { - RAbundVector rav(data.size()); + RAbundVector rav; for (int i = 0; i < data.size(); i++) { - rav.set(i, data[i].abundance); + if(data[i].abundance != 0) { + rav.push_back(data[i].abundance); + } } - + + rav.setLabel(label); return rav; } catch(exception& e) { - errorOut(e, "SharedRAbundVector", "getRAbundVector"); + m->errorOut(e, "SharedRAbundVector", "getRAbundVector"); exit(1); } } @@ -403,7 +484,7 @@ RAbundVector SharedRAbundVector::getRAbundVector2() { return rav; } catch(exception& e) { - errorOut(e, "SharedRAbundVector", "getRAbundVector2"); + m->errorOut(e, "SharedRAbundVector", "getRAbundVector2"); exit(1); } } @@ -425,7 +506,7 @@ SharedSAbundVector SharedRAbundVector::getSharedSAbundVector(){ return sav; } catch(exception& e) { - errorOut(e, "SharedRAbundVector", "getSharedSAbundVector"); + m->errorOut(e, "SharedRAbundVector", "getSharedSAbundVector"); exit(1); } } @@ -444,7 +525,7 @@ SAbundVector SharedRAbundVector::getSAbundVector() { return sav; } catch(exception& e) { - errorOut(e, "SharedRAbundVector", "getSAbundVector"); + m->errorOut(e, "SharedRAbundVector", "getSAbundVector"); exit(1); } } @@ -468,7 +549,7 @@ SharedOrderVector SharedRAbundVector::getSharedOrderVector() { return ov; } catch(exception& e) { - errorOut(e, "SharedRAbundVector", "getSharedOrderVector"); + m->errorOut(e, "SharedRAbundVector", "getSharedOrderVector"); exit(1); } } @@ -477,19 +558,19 @@ SharedOrderVector SharedRAbundVector::getSharedOrderVector() { OrderVector SharedRAbundVector::getOrderVector(map* nameMap = NULL) { try { OrderVector ov; - - for(int i=0;ierrorOut(e, "SharedRAbundVector", "getOrderVector"); exit(1); } }