#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 "sharedwhittaker.h"
+
//**********************************************************************************************************************
fileNameRoot = getRootName(globaldata->inputFileName);
format = globaldata->getFormat();
validCalculator = new ValidCalculators();
+ util = new SharedUtil();
int i;
for (i=0; i<globaldata->Estimators.size(); i++) {
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] == "sharedjabund") {
- cDisplays.push_back(new CollectDisplay(new SharedJAbund(), new SharedOneColumnFile(fileNameRoot+"shared.jabund")));
- }else if (globaldata->Estimators[i] == "sharedsorensonabund") {
- cDisplays.push_back(new CollectDisplay(new SharedSorAbund(), new SharedOneColumnFile(fileNameRoot+"shared.sorabund")));
- }else if (globaldata->Estimators[i] == "sharedjclass") {
- cDisplays.push_back(new CollectDisplay(new SharedJclass(), new SharedOneColumnFile(fileNameRoot+"shared.jclass")));
- }else if (globaldata->Estimators[i] == "sharedsorclass") {
- cDisplays.push_back(new CollectDisplay(new SharedSorClass(), new SharedOneColumnFile(fileNameRoot+"shared.sorclass")));
- }else if (globaldata->Estimators[i] == "sharedjest") {
- cDisplays.push_back(new CollectDisplay(new SharedJest(), new SharedOneColumnFile(fileNameRoot+"shared.jest")));
- }else if (globaldata->Estimators[i] == "sharedsorest") {
- cDisplays.push_back(new CollectDisplay(new SharedSorEst(), new SharedOneColumnFile(fileNameRoot+"shared.sorest")));
- }else if (globaldata->Estimators[i] == "sharedthetayc") {
- cDisplays.push_back(new CollectDisplay(new SharedThetaYC(), new SharedOneColumnFile(fileNameRoot+"shared.thetayc")));
- }else if (globaldata->Estimators[i] == "sharedthetan") {
- cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"shared.thetan")));
+ }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")));
}
}
}
delete input;
delete cCurve;
delete read;
+ delete util;
}
//**********************************************************************************************************************
//if the users entered no valid calculators don't execute command
if (cDisplays.size() == 0) { return 0; }
- if (format == "sharedfile") {
- read = new ReadPhilFile(globaldata->inputFileName);
- read->read(&*globaldata);
+ read = new ReadOTUFile(globaldata->inputFileName);
+ read->read(&*globaldata);
- input = globaldata->ginput;
- order = input->getSharedOrderVector();
- }else {
- //you are using a list and a groupfile
- read = new ReadPhilFile(globaldata->inputFileName);
- read->read(&*globaldata);
+ input = globaldata->ginput;
+ order = input->getSharedOrderVector();
- input = globaldata->ginput;
- SharedList = globaldata->gSharedList;
- order = SharedList->getSharedOrderVector();
- }
+ set<string> orderList;
+ //set users groups
+ util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "collect");
+ util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex);
+
while(order != NULL){
-
+ orderList.insert(order->getLabel());
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
//create collectors curve
cCurve = new Collect(order, cDisplays);
}
//get next line to process
- if (format == "sharedfile") {
- order = input->getSharedOrderVector();
- }else {
- //you are using a list and a groupfile
- SharedList = input->getSharedListVector(); //get new list vector to process
- if (SharedList != NULL) {
- order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
- }else {
- break;
- }
- }
-
+ order = input->getSharedOrderVector();
count++;
}
-
+ set<string>::iterator i;
+ for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
+ if(orderList.count(*i) == 0)
+ cout << "'" << *i << "'" << " is not a valid label.\n";
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