vector<SharedRAbundVector*> lookup;
//create and initialize vector of sharedvectors, one for each group
- for (int i = 0; i < globaldata->gGroupmap->getNumGroups(); i++) {
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
SharedRAbundVector* temp = new SharedRAbundVector(sharedorder->getNumBins());
temp->setLabel(sharedorder->getLabel());
- temp->setGroup(globaldata->gGroupmap->namesOfGroups[i]);
- temp->setGroupIndex(globaldata->gGroupmap->groupIndex[globaldata->gGroupmap->namesOfGroups[i]]);
+ temp->setGroup(globaldata->Groups[i]);
+ temp->setGroupIndex(globaldata->gGroupmap->groupIndex[globaldata->Groups[i]]);
lookup.push_back(temp);
}
//set info for sharedvector in chosens group
for (int j = 0; j < lookup.size(); j++) {
- if (chosen.group == lookup[j]->getGroup()) {
- abundance = lookup[j]->getAbundance(chosen.bin);
- lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
- break;
- }
+ if (chosen.group == lookup[j]->getGroup()) {
+ abundance = lookup[j]->getAbundance(chosen.bin);
+ lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
+ break;
+ }
}
+
//calculate at 0 and the given increment
if((i == 0) || (i+1) % increment == 0){
//randomize group order
int n = 1;
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->gGroupmap->namesOfGroups.size());
+ ccd->updateSharedData(lookup[k], lookup[l], i+1, globaldata->Groups.size());
}
n++;
}
int n = 1;
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->gGroupmap->namesOfGroups.size());
+ ccd->updateSharedData(lookup[k], lookup[l], totalNumSeq, globaldata->Groups.size());
}
n++;
}
/**************************************************************************************/
void Collect::getGroupComb() {
- string group;
+ string group;
- numGroupComb = 0;
+ numGroupComb = 0;
- int n = 1;
- for (int i = 0; i < (globaldata->gGroupmap->getNumGroups() - 1); i++) {
- for (int l = n; l < globaldata->gGroupmap->getNumGroups(); l++) {
- group = globaldata->gGroupmap->namesOfGroups[i] + globaldata->gGroupmap->namesOfGroups[l];
- groupComb.push_back(group);
- numGroupComb++;
- }
- n++;
- }
+ 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];
+ groupComb.push_back(group);
+ numGroupComb++;
+ }
+ n++;
+ }
}
format = globaldata->getFormat();
validCalculator = new ValidCalculators();
+ //set users groups
+ setGroups();
+
int i;
for (i=0; i<globaldata->Estimators.size(); i++) {
if (validCalculator->isValidCalculator("shared", globaldata->Estimators[i]) == true) {
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);
+ }
+
+}
+/***********************************************************/
+
vector<Display*> cDisplays;
int freq;
string format;
+ void setGroups();
};
index++;
}
}
+/************************************************************/
+bool GroupMap::isValidGroup(string groupname) {
+ try {
+ for (int i = 0; i < namesOfGroups.size(); i++) {
+ if (groupname == namesOfGroups[i]) { return true; }
+ }
+
+ return false;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the GroupMap class Function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the GroupMap class function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
~GroupMap();
void readMap();
int getNumGroups();
+ bool isValidGroup(string); //return true if string is a valid group
string getGroup(string);
void setGroup(string, string);
vector<string> namesOfGroups;
lookup.clear();
//create and initialize vector of sharedvectors, one for each group
- for (int i = 0; i < globaldata->gGroupmap->getNumGroups(); i++) {
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
SharedRAbundVector* temp = new SharedRAbundVector(sharedorder->getNumBins());
temp->setLabel(sharedorder->getLabel());
- temp->setGroup(globaldata->gGroupmap->namesOfGroups[i]);
+ temp->setGroup(globaldata->Groups[i]);
lookup.push_back(temp);
}
fileNameRoot = getRootName(globaldata->inputFileName);
format = globaldata->getFormat();
validCalculator = new ValidCalculators();
+
+ setGroups();
int i;
for (i=0; i<globaldata->Estimators.size(); i++) {
}
for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
+
+ //reset groups parameter
+ globaldata->Groups.clear(); globaldata->setGroups("");
+
return 0;
}
catch(exception& e) {
//**********************************************************************************************************************
+
+void RareFactSharedCommand::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 RareFactSharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the RareFactSharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+/***********************************************************/
+
int execute();
private:
+ void setGroups();
GlobalData* globaldata;
SharedListVector* SharedList;
ReadMatrix* read;
#include "sharedthetayc.h"
#include "sharedthetan.h"
+
//**********************************************************************************************************************
SummarySharedCommand::SummarySharedCommand(){
format = globaldata->getFormat();
validCalculator = new ValidCalculators();
+ //set users groups
+ setGroups();
+
int i;
for (i=0; i<globaldata->Estimators.size(); i++) {
if (validCalculator->isValidCalculator("sharedsummary", globaldata->Estimators[i]) == true) {
}
count++;
}
-
+
+ //reset groups parameter
+ globaldata->Groups.clear(); globaldata->setGroups("");
+
return 0;
}
catch(exception& e) {
break;
}
}
-
}
+
+ //get rid of vectors from groups you don't want to analyze
+ for (int r = 0; r < lookup.size(); r++) {
+ if (inUsersGroups(lookup[r]->getGroup(), globaldata->Groups) != true) {
+ lookup.erase(lookup.begin()+r);
+ }
+ }
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
}
//**********************************************************************************************************************
+void SummarySharedCommand::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 SummarySharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SummarySharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+/***********************************************************/
private:
void getSharedVectors();
+ void setGroups();
GlobalData* globaldata;
ReadMatrix* read;