X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectsharedcommand.cpp;h=8c04545d61fc321382122526bc53e4c2892321eb;hb=ec43347d04dbb2a7d9d9ecfb5fc556e21ad8c2bc;hp=434d4a44311f57300c42623c0b052cff012d9e10;hpb=4761e165b4a196fefa57755d3176d9ced19df6b1;p=mothur.git

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 434d4a4..8c04545 100644
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -8,7 +8,7 @@
  */
 
 #include "collectsharedcommand.h"
-#include "sharedsobs.h"
+#include "sharedsobscollectsummary.h"
 #include "sharedchao1.h"
 #include "sharedace.h"
 #include "sharedjabund.h"
@@ -28,34 +28,41 @@ CollectSharedCommand::CollectSharedCommand(){
 		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+"shared.chao", groupmap->namesOfGroups)));
-			}else if (globaldata->sharedEstimators[i] == "sharedSobs") { 
-				cDisplays.push_back(new CollectDisplay(new SharedSobs(), new SharedOneColumnFile(fileNameRoot+"shared.sobs", groupmap->namesOfGroups)));
-			}else if (globaldata->sharedEstimators[i] == "sharedAce") { 
-				cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace", groupmap->namesOfGroups)));
-			}else if (globaldata->sharedEstimators[i] == "sharedJabund") { 	
-				cDisplays.push_back(new CollectDisplay(new SharedJAbund(), new SharedOneColumnFile(fileNameRoot+"shared.jabund", groupmap->namesOfGroups)));
-			}else if (globaldata->sharedEstimators[i] == "sharedSorensonAbund") { 
-				cDisplays.push_back(new CollectDisplay(new SharedSorAbund(), new SharedOneColumnFile(fileNameRoot+"shared.sorabund", groupmap->namesOfGroups)));
-			}else if (globaldata->sharedEstimators[i] == "sharedJclass") { 
-				cDisplays.push_back(new CollectDisplay(new SharedJclass(), new SharedOneColumnFile(fileNameRoot+"shared.jclass", groupmap->namesOfGroups)));
-			}else if (globaldata->sharedEstimators[i] == "sharedSorClass") { 
-				cDisplays.push_back(new CollectDisplay(new SharedSorClass(), new SharedOneColumnFile(fileNameRoot+"shared.sorclass", groupmap->namesOfGroups)));
-			}else if (globaldata->sharedEstimators[i] == "sharedJest") { 
-				cDisplays.push_back(new CollectDisplay(new SharedJest(), new SharedOneColumnFile(fileNameRoot+"shared.jest", groupmap->namesOfGroups)));
-			}else if (globaldata->sharedEstimators[i] == "sharedSorEst") { 
-				cDisplays.push_back(new CollectDisplay(new SharedSorEst(), new SharedOneColumnFile(fileNameRoot+"shared.sorest", groupmap->namesOfGroups)));
-			}else if (globaldata->sharedEstimators[i] == "SharedThetaYC") { 
-				cDisplays.push_back(new CollectDisplay(new SharedThetaYC(), new SharedOneColumnFile(fileNameRoot+"shared.thetayc", groupmap->namesOfGroups)));
-			}else if (globaldata->sharedEstimators[i] == "SharedThetaN") { 
-				cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"shared.thetan", 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")));
+				}
 			}
 		}
+		
+		//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";
@@ -82,15 +89,29 @@ CollectSharedCommand::~CollectSharedCommand(){
 int CollectSharedCommand::execute(){
 	try {
 		int count = 1;
-		read = new ReadPhilFile(globaldata->inputFileName);	
-		read->read(&*globaldata); 
 		
-		input = globaldata->ginput;
-		SharedList = globaldata->gSharedList;
-		order = SharedList->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;
+
+		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);
@@ -102,16 +123,25 @@ int CollectSharedCommand::execute(){
 				cout << order->getLabel() << '\t' << count << endl;
 			}
 			
-			SharedList = input->getSharedListVector(); //get new list vector to process
-			if (SharedList != NULL) {
-				order = SharedList->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];	}	
 		return 0;
 	}