X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readotu.cpp;h=286a2be271a4a7bb2225a71c7081b1a5c8eb4571;hb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;hp=0bcfd320cade47901ac89cbf9e86c7b8ad142b29;hpb=154e089bcd37c2c2f773e53ffb88a20170b27037;p=mothur.git

diff --git a/readotu.cpp b/readotu.cpp
index 0bcfd32..286a2be 100644
--- a/readotu.cpp
+++ b/readotu.cpp
@@ -20,29 +20,37 @@ ReadOTUFile::ReadOTUFile(string pf): philFile(pf){
 //This function reads the list, rabund or sabund files to be used by collect and rarefact command.
 void ReadOTUFile::read(GlobalData* globaldata){
 	try {
+
 		if (globaldata->getOrderFile() == "") {
 			//you have two inputs because in the next if statement if you only have one then it moves ahead in the same file.  
 			//So when you run the collect or summary commands you miss a line.
 			input = new InputData(philFile, globaldata->getFormat()); //format tells you whether philFile is list, rabund, sabund.
 			inputList = new InputData(philFile, globaldata->getFormat()); //format tells you whether philFile is list, rabund, sabund.
 			inputSabund = new InputData(philFile, globaldata->getFormat()); //format tells you whether philFile is list, rabund, sabund or shared.
+			inputRabund = new InputData(philFile, globaldata->getFormat());
 		}else {//there is an orderfile
 			input = new InputData(philFile, globaldata->getOrderFile(), globaldata->getFormat());
 		}
-		
+//cout << "made it here"	<< endl;	
 		//memory leak prevention
 		//if (globaldata->ginput != NULL) { delete globaldata->ginput;  }
 		globaldata->ginput = input;	//saving to be used by collector and rarefact commands.
-		
+//cout << "after input" << endl;		
 		if ((globaldata->getFormat() == "list") || (globaldata->getFormat() == "rabund") || (globaldata->getFormat() == "sabund")) {//you are reading a list, rabund or sabund file for collect, rarefaction or summary.
 			order = input->getOrderVector();
 			//memory leak prevention
 			//if (globaldata->gorder != NULL) { delete globaldata->gorder;  }
 			globaldata->gorder = order;	//saving to be used by collect and rarefact commands.
 			sabund = inputSabund->getSAbundVector(); 
+			//if (globaldata->sabund != NULL) { delete globaldata->sabund;  }
 			globaldata->sabund = sabund; //saving to be used by summary command.
+			rabund = inputRabund->getRAbundVector(); 
+			//if (globaldata->rabund != NULL) { delete globaldata->rabund;  }
+			globaldata->rabund = rabund; //saving to be used by heatmap.bin command.
 			list = inputList->getListVector();
+			//if (globaldata->gListVector != NULL) { delete globaldata->gListVector;  }
 			globaldata->gListVector = list;
+
 		}else if (globaldata->getFormat() == "shared") {
 			SharedList = input->getSharedListVector(); //you are reading for collect.shared, rarefaction.shared, summary.shared, parselist command, or shared commands.
 			//memory leak prevention