X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.cpp;h=902b9a253b0aa7e5515b74adf464b7fe17a65e2c;hb=cd7040a22ae19c86a13c2c10ed90a64b77a0c482;hp=5d7df3440439c469f3311073d2237b87272e79e6;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 5d7df34..902b9a2 100644
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -125,6 +125,7 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -178,21 +179,22 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
 			phylipfile = validParameter.validFile(parameters, "phylip", true);
 			if (phylipfile == "not open") { phylipfile = ""; abort = true; }
 			else if (phylipfile == "not found") { phylipfile = ""; }	
-			else {  inputfile = phylipfile;  format = "phylip"; 	}
+			else {  inputfile = phylipfile;  format = "phylip"; m->setPhylipFile(phylipfile);	}
 			
 			columnfile = validParameter.validFile(parameters, "column", true);
 			if (columnfile == "not open") { columnfile = ""; abort = true; }	
 			else if (columnfile == "not found") { columnfile = ""; }
-			else {  inputfile = columnfile; format = "column";	}
+			else {  inputfile = columnfile; format = "column";	m->setColumnFile(columnfile); }
 			
 			sharedfile = validParameter.validFile(parameters, "shared", true);
 			if (sharedfile == "not open") { sharedfile = ""; abort = true; }	
 			else if (sharedfile == "not found") { sharedfile = ""; }
-			else {  inputfile = sharedfile; format = "sharedfile";	}
+			else {  inputfile = sharedfile; format = "sharedfile";	m->setSharedFile(sharedfile); }
 			
 			namefile = validParameter.validFile(parameters, "name", true);
 			if (namefile == "not open") { abort = true; }	
 			else if (namefile == "not found") { namefile = ""; }
+			else { m->setNameFile(namefile); }
 			
 			if ((phylipfile == "") && (columnfile == "") && (sharedfile == "")) { 
 				//is there are current file available for either of these?
@@ -247,6 +249,11 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
 				 if (calc == "default")  {  calc = "jclass-thetayc";  }
 			}
 			m->splitAtDash(calc, Estimators);
+			if (m->inUsersGroups("citation", Estimators)) { 
+				ValidCalculators validCalc; validCalc.printCitations(Estimators); 
+				//remove citation from list of calcs
+				for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
+			}
 
 			string temp;
 			temp = validParameter.validFile(parameters, "precision", false);			if (temp == "not found") { temp = "100"; }
@@ -752,8 +759,8 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
 								if (m->control_pressed) { return 1; }
 								
 								//save values in similarity matrix
-								simMatrix[k][l] = data[0];
-								simMatrix[l][k] = data[0];
+								simMatrix[k][l] = -(data[0]-1.0);
+								simMatrix[l][k] = -(data[0]-1.0);
 							}
 						}
 					}