*/
#include "venncommand.h"
+#include "ace.h"
+#include "sobs.h"
+#include "chao1.h"
+//#include "jackknife.h"
+#include "sharedsobscollectsummary.h"
+#include "sharedchao1.h"
+#include "sharedace.h"
+
//**********************************************************************************************************************
VennCommand::VennCommand(){
try {
globaldata = GlobalData::getInstance();
- venn = new Venn();
format = globaldata->getFormat();
+ validCalculator = new ValidCalculators();
+ util = new SharedUtil();
+
+ int i;
+
+ if (format == "list") {
+ for (i=0; i<globaldata->Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("vennsingle", globaldata->Estimators[i]) == true) {
+ if (globaldata->Estimators[i] == "sobs") {
+ vennCalculators.push_back(new Sobs());
+ }else if (globaldata->Estimators[i] == "chao") {
+ vennCalculators.push_back(new Chao1());
+ }else if (globaldata->Estimators[i] == "ace") {
+ convert(globaldata->getAbund(), abund);
+ if(abund < 5)
+ abund = 10;
+ vennCalculators.push_back(new Ace(abund));
+ //}else if (globaldata->Estimators[i] == "jack") {
+ //vennCalculators.push_back(new Jackknife());
+ }
+ }
+ }
+ }else {
+ for (i=0; i<globaldata->Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("vennshared", globaldata->Estimators[i]) == true) {
+ if (globaldata->Estimators[i] == "sharedsobs") {
+ vennCalculators.push_back(new SharedSobsCS());
+ }else if (globaldata->Estimators[i] == "sharedchao") {
+ vennCalculators.push_back(new SharedChao1());
+ }else if (globaldata->Estimators[i] == "sharedace") {
+ vennCalculators.push_back(new SharedAce());
+ }
+ }
+ }
+ }
+
+ venn = new Venn();
+
+ //reset calc for next command
+ globaldata->setCalc("");
+
}
catch(exception& e) {
delete input;
delete read;
delete venn;
+ delete util;
}
//**********************************************************************************************************************
try {
int count = 1;
+ //if the users entered no valid calculators don't execute command
+ if (vennCalculators.size() == 0) { return 0; }
+
if (format == "sharedfile") {
//you have groups
read = new ReadPhilFile(globaldata->inputFileName);
if (format != "list") {
- setGroups();
+ util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "venn");
+ globaldata->setGroups("");
while(order != NULL){
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
cout << order->getLabel() << '\t' << count << endl;
- venn->getPic(order);
+ venn->getPic(order, vennCalculators);
}
}
//reset groups parameter
- globaldata->Groups.clear(); globaldata->setGroups("");
+ globaldata->Groups.clear();
}else{
while(ordersingle != NULL){
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(ordersingle->getLabel()) == 1){
cout << ordersingle->getLabel() << '\t' << count << endl;
- venn->getPic(ordersingle);
+ venn->getPic(ordersingle, vennCalculators);
}
}
//**********************************************************************************************************************
-void VennCommand::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) {
- if (globaldata->gGroupmap->namesOfGroups.size() > 4) {
- cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using the first four groups in your groupfile." << endl;
- for (int i = 0; i < 4; i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
- }
- }else {
- cout << "When using the groups parameter you must have at least 1 valid group. 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]);
- }
- }
-
-
- //check to make sure their are only 3 groups
- if (globaldata->Groups.size() > 4) {
- cout << "You may only use up to 4 groups at a time with this command. I will choose the first four and disregard the rest." << endl;
- for (int i = 4; i < globaldata->Groups.size(); i++) {
- globaldata->Groups.erase(globaldata->Groups.begin()+i);
- }
- }
-
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the VennCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
-}
-/***********************************************************/
projects / mothur.git / blobdiff