*/
#include "collectsharedcommand.h"
-#include "sharedsobs.h"
+#include "sharedsobscollectsummary.h"
#include "sharedchao1.h"
#include "sharedace.h"
#include "sharedjabund.h"
#include "sharedsorest.h"
#include "sharedthetayc.h"
#include "sharedthetan.h"
+#include "sharedkstest.h"
+#include "whittaker.h"
+#include "sharednseqs.h"
+#include "sharedochiai.h"
+#include "sharedanderbergs.h"
+#include "sharedkulczynski.h"
+#include "sharedkulczynskicody.h"
+#include "sharedlennon.h"
+#include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
+#include "sharedjackknife.h"
+#include "whittaker.h"
+
//**********************************************************************************************************************
globaldata = GlobalData::getInstance();
string fileNameRoot;
fileNameRoot = getRootName(globaldata->inputFileName);
- groupmap = globaldata->gGroupmap;
+ format = globaldata->getFormat();
+ convert(globaldata->getFreq(), freq);
+ validCalculator = new ValidCalculators();
+ util = new SharedUtil();
int i;
- for (i=0; i<globaldata->sharedEstimators.size(); i++) {
- if (globaldata->sharedEstimators[i] == "sharedChao") {
- cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao", groupmap->namesOfGroups)));
- }else if (globaldata->sharedEstimators[i] == "sharedSobs") {
- cDisplays.push_back(new CollectDisplay(new SharedSobs(), new SharedOneColumnFile(fileNameRoot+"shared.sobs", groupmap->namesOfGroups)));
- }else if (globaldata->sharedEstimators[i] == "sharedAce") {
- cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace", groupmap->namesOfGroups)));
- }else if (globaldata->sharedEstimators[i] == "sharedJabund") {
- cDisplays.push_back(new CollectDisplay(new SharedJAbund(), new SharedOneColumnFile(fileNameRoot+"shared.jabund", groupmap->namesOfGroups)));
- }else if (globaldata->sharedEstimators[i] == "sharedSorensonAbund") {
- cDisplays.push_back(new CollectDisplay(new SharedSorAbund(), new SharedOneColumnFile(fileNameRoot+"shared.sorabund", groupmap->namesOfGroups)));
- }else if (globaldata->sharedEstimators[i] == "sharedJclass") {
- cDisplays.push_back(new CollectDisplay(new SharedJclass(), new SharedOneColumnFile(fileNameRoot+"shared.jclass", groupmap->namesOfGroups)));
- }else if (globaldata->sharedEstimators[i] == "sharedSorClass") {
- cDisplays.push_back(new CollectDisplay(new SharedSorClass(), new SharedOneColumnFile(fileNameRoot+"shared.sorclass", groupmap->namesOfGroups)));
- }else if (globaldata->sharedEstimators[i] == "sharedJest") {
- cDisplays.push_back(new CollectDisplay(new SharedJest(), new SharedOneColumnFile(fileNameRoot+"shared.jest", groupmap->namesOfGroups)));
- }else if (globaldata->sharedEstimators[i] == "sharedSorEst") {
- cDisplays.push_back(new CollectDisplay(new SharedSorEst(), new SharedOneColumnFile(fileNameRoot+"shared.sorest", groupmap->namesOfGroups)));
- }else if (globaldata->sharedEstimators[i] == "SharedThetaYC") {
- cDisplays.push_back(new CollectDisplay(new SharedThetaYC(), new SharedOneColumnFile(fileNameRoot+"shared.thetayc", groupmap->namesOfGroups)));
- }else if (globaldata->sharedEstimators[i] == "SharedThetaN") {
- cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"shared.thetan", groupmap->namesOfGroups)));
+ for (i=0; i<globaldata->Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("shared", globaldata->Estimators[i]) == true) {
+ if (globaldata->Estimators[i] == "sharedchao") {
+ cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao")));
+ }else if (globaldata->Estimators[i] == "sharedsobs") {
+ cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
+ }else if (globaldata->Estimators[i] == "sharedace") {
+ cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
+ }else if (globaldata->Estimators[i] == "jabund") {
+ cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(fileNameRoot+"jabund")));
+ }else if (globaldata->Estimators[i] == "sorabund") {
+ cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(fileNameRoot+"sorabund")));
+ }else if (globaldata->Estimators[i] == "jclass") {
+ cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(fileNameRoot+"jclass")));
+ }else if (globaldata->Estimators[i] == "sorclass") {
+ cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(fileNameRoot+"sorclass")));
+ }else if (globaldata->Estimators[i] == "jest") {
+ cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(fileNameRoot+"jest")));
+ }else if (globaldata->Estimators[i] == "sorest") {
+ cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(fileNameRoot+"sorest")));
+ }else if (globaldata->Estimators[i] == "thetayc") {
+ cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(fileNameRoot+"thetayc")));
+ }else if (globaldata->Estimators[i] == "thetan") {
+ cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(fileNameRoot+"thetan")));
+ }else if (globaldata->Estimators[i] == "kstest") {
+ cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(fileNameRoot+"kstest")));
+ }else if (globaldata->Estimators[i] == "whittaker") {
+ cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(fileNameRoot+"whittaker")));
+ }else if (globaldata->Estimators[i] == "sharednseqs") {
+ cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
+
+ }else if (globaldata->Estimators[i] == "ochiai") {
+ cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(fileNameRoot+"ochiai")));
+ }else if (globaldata->Estimators[i] == "anderberg") {
+ cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(fileNameRoot+"anderberg")));
+ }else if (globaldata->Estimators[i] == "skulczynski") {
+ cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(fileNameRoot+"kulczynski")));
+ }else if (globaldata->Estimators[i] == "kulczynskicody") {
+ cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"kulczynskicody")));
+ }else if (globaldata->Estimators[i] == "lennon") {
+ cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(fileNameRoot+"lennon")));
+ }else if (globaldata->Estimators[i] == "morisitahorn") {
+ cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(fileNameRoot+"morisitahorn")));
+ }else if (globaldata->Estimators[i] == "braycurtis") {
+ cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(fileNameRoot+"braycurtis")));
+ }
}
}
+
+ //reset calc for next command
+ globaldata->setCalc("");
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
delete input;
delete cCurve;
delete read;
+ delete util;
}
//**********************************************************************************************************************
int CollectSharedCommand::execute(){
try {
int count = 1;
- read = new ReadPhilFile(globaldata->inputFileName);
- read->read(&*globaldata);
- input = globaldata->ginput;
- SharedList = globaldata->gSharedList;
- order = SharedList->getSharedOrderVector();
+ //if the users entered no valid calculators don't execute command
+ if (cDisplays.size() == 0) { return 0; }
- while(order != NULL){
+ read = new ReadOTUFile(globaldata->inputFileName);
+ read->read(&*globaldata);
+
+ input = globaldata->ginput;
+ order = input->getSharedOrderVector();
+ SharedOrderVector* lastOrder = order;
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = globaldata->labels;
+ set<int> userLines = globaldata->lines;
+
+ //set users groups
+ util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "collect");
+ util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex);
+
+ while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
+
//create collectors curve
cCurve = new Collect(order, cDisplays);
- convert(globaldata->getFreq(), freq);
cCurve->getSharedCurve(freq);
-
delete cCurve;
cout << order->getLabel() << '\t' << count << endl;
+ processedLabels.insert(order->getLabel());
+ userLabels.erase(order->getLabel());
+ userLines.erase(count);
+
+ //you have a label the user want that is smaller than this line and the last line has not already been processed
+ }
+
+ if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
+ //create collectors curve
+ cCurve = new Collect(lastOrder, cDisplays);
+ cCurve->getSharedCurve(freq);
+ delete cCurve;
+
+ cout << lastOrder->getLabel() << '\t' << count << endl;
+ processedLabels.insert(lastOrder->getLabel());
+ userLabels.erase(lastOrder->getLabel());
}
- SharedList = input->getSharedListVector(); //get new list vector to process
- if (SharedList != NULL) {
- order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
- count++;
+ if (count != 1) { delete lastOrder; }
+ lastOrder = order;
+
+ //get next line to process
+ order = input->getSharedOrderVector();
+ count++;
+ }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ cout << "Your file does not include the label "<< *it;
+ if (processedLabels.count(lastOrder->getLabel()) != 1) {
+ cout << ". I will use " << lastOrder->getLabel() << "." << endl;
+ needToRun = true;
}else {
- break;
+ cout << ". Please refer to " << lastOrder->getLabel() << "." << endl;
}
+ }
+ //run last line if you need to
+ if (needToRun == true) {
+ cCurve = new Collect(lastOrder, cDisplays);
+ cCurve->getCurve(freq);
+ delete cCurve;
+
+ cout << lastOrder->getLabel() << '\t' << count << endl;
}
-
+
+ delete lastOrder;
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
+
+ //reset groups parameter
+ globaldata->Groups.clear(); globaldata->setGroups("");
+
return 0;
}
catch(exception& e) {
}
}
+/***********************************************************/
-//**********************************************************************************************************************
projects / mothur.git / blobdiff