X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=collect.cpp;h=9a89020efe91f8bdd2733a3de553611e86ee6da3;hp=7397d24ab30cbb968d4c02ae5522aa3d111ca05a;hb=615301e57c25e241356a9c2380648d117709458d;hpb=7e0cf6431e287072c40b2c10c9e08199fce29ef4 diff --git a/collect.cpp b/collect.cpp index 7397d24..9a89020 100644 --- a/collect.cpp +++ b/collect.cpp @@ -9,10 +9,9 @@ #include "collect.h" - /***********************************************************************/ -void Collect::getCurve(int increment = 1){ +int Collect::getCurve(float percentFreq = 0.01){ try { RAbundVector* lookup = new RAbundVector(order->getNumBins()); SAbundVector* rank = new SAbundVector(order->getMaxRank()+1); @@ -22,9 +21,17 @@ void Collect::getCurve(int increment = 1){ for(int i=0;iregisterDisplay(displays[i]); //adds a display[i] to cdd displays[i]->init(label); //sets displays label - } + } + + //convert freq percentage to number + int increment = 1; + if (percentFreq < 1.0) { increment = numSeqs * percentFreq; } + else { increment = percentFreq; } + for(int i=0;icontrol_pressed) { delete lookup; delete rank; delete ccd; return 1; } + int binNumber = order->get(i); int abundance = lookup->get(binNumber); @@ -47,54 +54,68 @@ void Collect::getCurve(int increment = 1){ for(int i=0;ireset(); } + + delete lookup; + delete rank; + delete ccd; + + return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the Collect class Function getCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); + m->errorOut(e, "Collect", "getCurve"); + exit(1); } - catch(...) { - cout << "An unknown error has occurred in the Collect class function getCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - } /***********************************************************************/ -void Collect::getSharedCurve(int increment = 1){ +int Collect::getSharedCurve(float percentFreq = 0.01){ try { - globaldata = GlobalData::getInstance(); vector lookup; + vector subset; //create and initialize vector of sharedvectors, one for each group - for (int i = 0; i < globaldata->Groups.size(); i++) { + vector mGroups = m->getGroups(); + for (int i = 0; i < mGroups.size(); i++) { SharedRAbundVector* temp = new SharedRAbundVector(sharedorder->getNumBins()); temp->setLabel(sharedorder->getLabel()); - temp->setGroup(globaldata->Groups[i]); - temp->setGroupIndex(globaldata->gGroupmap->groupIndex[globaldata->Groups[i]]); - lookup.push_back(temp); + temp->setGroup(mGroups[i]); + lookup.push_back(temp); } - + SharedCollectorsCurveData* ccd = new SharedCollectorsCurveData(); //initialize labels for output //makes 'uniqueAB uniqueAC uniqueBC' if your groups are A, B, C getGroupComb(); - groupLabel = ""; - for (int s = 0; s < groupComb.size(); s++) { - groupLabel = groupLabel + label + groupComb[s] + "\t"; - } - + for(int i=0;iregisterDisplay(displays[i]); //adds a display[i] to cdd - displays[i]->init(groupLabel); + bool hasLciHci = displays[i]->hasLciHci(); + groupLabel = ""; + for (int s = 0; s < groupComb.size(); s++) { + if (hasLciHci) { groupLabel = groupLabel + label + groupComb[s] + "\t" + label + groupComb[s] + "lci\t" + label + groupComb[s] + "hci\t"; } + else{ groupLabel = groupLabel + label + groupComb[s] + "\t"; } + } + + string groupLabelAll = groupLabel + label + "all\t"; + if ((displays[i]->isCalcMultiple() == true) && (displays[i]->getAll() == true)) { displays[i]->init(groupLabelAll); } + else { displays[i]->init(groupLabel); } } + //convert freq percentage to number + int increment = 1; + if (percentFreq < 1.0) { increment = numSeqs * percentFreq; } + else { increment = percentFreq; } + //sample all the members for(int i=0;icontrol_pressed) { for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; } delete ccd; return 1; } + //get first sample individual chosen = sharedorder->get(i); int abundance; - + //set info for sharedvector in chosens group for (int j = 0; j < lookup.size(); j++) { if (chosen.group == lookup[j]->getGroup()) { @@ -103,50 +124,81 @@ try { break; } } - //calculate at 0 and the given increment if((i == 0) || (i+1) % increment == 0){ - //randomize group order - if (globaldata->getJumble() == "1") { random_shuffle(lookup.begin(), lookup.end()); } - //how many comparisons to make i.e. for group a, b, c = ab, ac, bc. + + //how many comparisons to make i.e. for group a, b, c = ab, ac, bc. + int n = 1; + bool pair = true; for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare for (int l = n; l < lookup.size(); l++) { - ccd->updateSharedData(lookup[k], lookup[l], i+1, globaldata->Groups.size()); + subset.clear(); //clear out old pair of sharedrabunds + //add new pair of sharedrabund vectors + subset.push_back(lookup[k]); subset.push_back(lookup[l]); + + //load subset with rest of lookup for those calcs that need everyone to calc for a pair + for (int w = 0; w < lookup.size(); w++) { + if ((w != k) && (w != l)) { subset.push_back(lookup[w]); } + } + + ccd->updateSharedData(subset, i+1, m->getNumGroups(), pair); } n++; } + + //if this is a calculator that can do multiples then do them + pair = false; + ccd->updateSharedData(lookup, i+1, m->getNumGroups(), pair); + } totalNumSeq = i+1; } - //calculate last line if you haven't already + //calculate last label if you haven't already if(numSeqs % increment != 0){ //how many comparisons to make i.e. for group a, b, c = ab, ac, bc. int n = 1; + bool pair = true; for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare for (int l = n; l < lookup.size(); l++) { - ccd->updateSharedData(lookup[k], lookup[l], totalNumSeq, globaldata->Groups.size()); + subset.clear(); //clear out old pair of sharedrabunds + //add new pair of sharedrabund vectors + subset.push_back(lookup[k]); subset.push_back(lookup[l]); + + //load subset with rest of lookup for those calcs that need everyone to calc for a pair + for (int w = 0; w < lookup.size(); w++) { + if ((w != k) && (w != l)) { subset.push_back(lookup[w]); } + } + + ccd->updateSharedData(subset, totalNumSeq, m->getNumGroups(), pair); } n++; } + //if this is a calculator that can do multiples then do them + pair = false; + ccd->updateSharedData(lookup, totalNumSeq, m->getNumGroups(), pair); } - + //resets output files for(int i=0;ireset(); } + + //memory cleanup + delete ccd; + for (int i = 0; i < lookup.size(); i++) { + delete lookup[i]; + } + + return 0; + } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the Collect class Function getSharedCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); + m->errorOut(e, "Collect", "getSharedCurve"); + exit(1); } - catch(...) { - cout << "An unknown error has occurred in the Collect class function getSharedCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - } /**************************************************************************************/ @@ -157,9 +209,10 @@ void Collect::getGroupComb() { numGroupComb = 0; int n = 1; - for (int i = 0; i < (globaldata->Groups.size() - 1); i++) { - for (int l = n; l < globaldata->Groups.size(); l++) { - group = globaldata->Groups[i] + globaldata->Groups[l]; + vector mGroups = m->getGroups(); + for (int i = 0; i < (m->getNumGroups() - 1); i++) { + for (int l = n; l < m->getNumGroups(); l++) { + group = mGroups[i] + mGroups[l]; groupComb.push_back(group); numGroupComb++; } @@ -168,4 +221,4 @@ void Collect::getGroupComb() { } -/**************************************************************************************/ \ No newline at end of file +/**************************************************************************************/