*/
#include "collectsharedcommand.h"
+#include "sharedsobscollectsummary.h"
#include "sharedchao1.h"
#include "sharedace.h"
#include "sharedjabund.h"
#include "sharedsorest.h"
#include "sharedthetayc.h"
#include "sharedthetan.h"
+<<<<<<< collectsharedcommand.cpp
+#include "sharedkstest.h"
+#include "sharedbdiversity.h"
+=======
+#include "sharednseqs.h"
+#include "sharedochiai.h"
+#include "sharedanderberg.h"
+#include "sharedkulczynski.h"
+#include "sharedkulczynskicody.h"
+#include "sharedlennon.h"
+#include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
+>>>>>>> 1.13
//**********************************************************************************************************************
globaldata = GlobalData::getInstance();
string fileNameRoot;
fileNameRoot = getRootName(globaldata->inputFileName);
- groupmap = globaldata->gGroupmap;
+ format = globaldata->getFormat();
+ validCalculator = new ValidCalculators();
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+"sharedChao", groupmap->namesOfGroups)));
- }else if (globaldata->sharedEstimators[i] == "sharedAce") {
- cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"sharedAce", groupmap->namesOfGroups)));
- }else if (globaldata->sharedEstimators[i] == "sharedJabund") {
- cDisplays.push_back(new CollectDisplay(new SharedJAbund(), new SharedOneColumnFile(fileNameRoot+"SharedJabund", groupmap->namesOfGroups)));
- }else if (globaldata->sharedEstimators[i] == "sharedSorensonAbund") {
- cDisplays.push_back(new CollectDisplay(new SharedSorAbund(), new SharedOneColumnFile(fileNameRoot+"SharedSorensonAbund", groupmap->namesOfGroups)));
- }else if (globaldata->sharedEstimators[i] == "sharedJclass") {
- cDisplays.push_back(new CollectDisplay(new SharedJclass(), new SharedOneColumnFile(fileNameRoot+"SharedJclass", groupmap->namesOfGroups)));
- }else if (globaldata->sharedEstimators[i] == "sharedSorClass") {
- cDisplays.push_back(new CollectDisplay(new SharedSorClass(), new SharedOneColumnFile(fileNameRoot+"SharedSorClass", groupmap->namesOfGroups)));
- }else if (globaldata->sharedEstimators[i] == "sharedJest") {
- cDisplays.push_back(new CollectDisplay(new SharedJest(), new SharedOneColumnFile(fileNameRoot+"SharedJest", groupmap->namesOfGroups)));
- }else if (globaldata->sharedEstimators[i] == "sharedSorEst") {
- cDisplays.push_back(new CollectDisplay(new SharedSorEst(), new SharedOneColumnFile(fileNameRoot+"SharedSorEst", groupmap->namesOfGroups)));
- }else if (globaldata->sharedEstimators[i] == "SharedThetaYC") {
- cDisplays.push_back(new CollectDisplay(new SharedThetaYC(), new SharedOneColumnFile(fileNameRoot+"SharedThetaYC", groupmap->namesOfGroups)));
- }else if (globaldata->sharedEstimators[i] == "SharedThetaN") {
- cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"SharedThetaN", 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] == "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] == "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")));
+ }
}
}
+
+ //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";
int CollectSharedCommand::execute(){
try {
int count = 1;
- read = new ReadPhilFile(globaldata->inputFileName);
- read->read(&*globaldata);
- input = globaldata->ginput;
- list = globaldata->glist;
- order = list->getSharedOrderVector();
+ //if the users entered no valid calculators don't execute command
+ if (cDisplays.size() == 0) { return 0; }
- while(order != NULL){
+ if (format == "sharedfile") {
+ read = new ReadPhilFile(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;
+ SharedList = globaldata->gSharedList;
+ order = SharedList->getSharedOrderVector();
+ }
+ set<string> orderList;
+
+ //set users groups
+ setGroups();
+
+ 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);
cout << order->getLabel() << '\t' << count << endl;
}
- list = input->getListVector(); //get new list vector to process
- if (list != NULL) {
- order = list->getSharedOrderVector(); //gets new order vector with group info.
- count++;
+ //get next line to process
+ if (format == "sharedfile") {
+ order = input->getSharedOrderVector();
}else {
- break;
+ //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;
+ }
}
-
+
+ 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) {
//**********************************************************************************************************************
+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