#include "sharedthetayc.h"
#include "sharedthetan.h"
#include "sharedkstest.h"
-#include "sharedbdiversity.h"
+#include "whittaker.h"
#include "sharednseqs.h"
#include "sharedochiai.h"
#include "sharedanderbergs.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] == "sharedkstest") {
- cDisplays.push_back(new CollectDisplay(new SharedKSTest(), new SharedOneColumnFile(fileNameRoot+"shared.kstest")));
- }else if (globaldata->Estimators[i] == "sharedbdiversity") {
- cDisplays.push_back(new CollectDisplay(new SharedBDiversity(), new SharedOneColumnFile(fileNameRoot+"shared.bdiversity")));
+ }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] == "sharedochiai") {
- cDisplays.push_back(new CollectDisplay(new SharedOchiai(), new SharedOneColumnFile(fileNameRoot+"shared.ochiai")));
- }else if (globaldata->Estimators[i] == "sharedanderberg") {
- cDisplays.push_back(new CollectDisplay(new SharedAnderberg(), new SharedOneColumnFile(fileNameRoot+"shared.anderberg")));
- }else if (globaldata->Estimators[i] == "sharedkulczynski") {
- cDisplays.push_back(new CollectDisplay(new SharedKulczynski(), new SharedOneColumnFile(fileNameRoot+"shared.kulczynski")));
- }else if (globaldata->Estimators[i] == "sharedkulczynskicody") {
- cDisplays.push_back(new CollectDisplay(new SharedKulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"shared.kulczynskicody")));
- }else if (globaldata->Estimators[i] == "sharedlennon") {
- cDisplays.push_back(new CollectDisplay(new SharedLennon(), new SharedOneColumnFile(fileNameRoot+"shared.lennon")));
- }else if (globaldata->Estimators[i] == "sharedmorisitahorn") {
- cDisplays.push_back(new CollectDisplay(new SharedMorHorn(), new SharedOneColumnFile(fileNameRoot+"shared.morisitahorn")));
- }else if (globaldata->Estimators[i] == "sharedbraycurtis") {
- cDisplays.push_back(new CollectDisplay(new SharedBrayCurtis(), new SharedOneColumnFile(fileNameRoot+"shared.braycurtis")));
+
+ }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
- setGroups();
+ 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);
convert(globaldata->getFreq(), freq);
}
//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;
- }
- }
-
+ delete order;
+ 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
}
}
-
-//**********************************************************************************************************************
-void CollectSharedCommand::setGroups() {
- try {
- //if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() != 0) {
- if (globaldata->Groups[0] != "all") {
- //check that groups are valid
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
- cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
- // erase the invalid group from globaldata->Groups
- globaldata->Groups.erase(globaldata->Groups.begin()+i);
- }
- }
-
- //if the user only entered invalid groups
- if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) {
- cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
- for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
- }
- }
- }else{//user has enter "all" and wants the default groups
- globaldata->Groups.clear();
- for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
- }
- globaldata->setGroups("");
- }
- }else {
- for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
- }
- }
-
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the CollectSharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
-}
/***********************************************************/
projects / mothur.git / blobdiff