X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mgclustercommand.cpp;h=6ef968c2248de78e304291f3c781a2baa44ad8ea;hb=ccae9eef0b44f2d63fdf4a707d0d40243aa1b990;hp=61e130647c6734ee49ba99b0bcded20804ee103d;hpb=38491018f166c7c5517518cfa64832582f20dd85;p=mothur.git

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 61e1306..6ef968c 100644
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -14,6 +14,8 @@ vector<string> MGClusterCommand::setParameters(){
 	try {
 		CommandParameter pblast("blast", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pblast);
 		CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+        CommandParameter pcount("count", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcount);
+        //CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge);
 		CommandParameter plength("length", "Number", "", "5", "", "", "",false,false); parameters.push_back(plength);
 		CommandParameter ppenalty("penalty", "Number", "", "0.10", "", "", "",false,false); parameters.push_back(ppenalty);
 		CommandParameter pcutoff("cutoff", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pcutoff);
@@ -164,11 +166,21 @@ MGClusterCommand::MGClusterCommand(string option) {
 			if (namefile == "not open") { abort = true; }	
 			else if (namefile == "not found") { namefile = ""; }
 			else { m->setNameFile(namefile); }
+            
+            countfile = validParameter.validFile(parameters, "count", true);
+			if (countfile == "not open") { abort = true; }	
+			else if (countfile == "not found") { countfile = ""; }
+            else { m->setCountTableFile(countfile); }
+            
+            if (countfile != "" && namefile != "") { m->mothurOut("[ERROR]: Cannot have both a name file and count file. Please use one or the other."); m->mothurOutEndLine(); abort = true; }
 			
 			if ((blastfile == "")) { m->mothurOut("When executing a mgcluster command you must provide a blastfile."); m->mothurOutEndLine(); abort = true; }
 			
 			//check for optional parameter and set defaults
 			string temp;
+            temp = validParameter.validFile(parameters, "large", false);			if (temp == "not found") { temp = "false"; }            
+			large = m->isTrue(temp); 
+            
 			temp = validParameter.validFile(parameters, "precision", false);		if (temp == "not found") { temp = "100"; }
 			precisionLength = temp.length();
 			m->mothurConvert(temp, precision); 
@@ -199,7 +211,7 @@ MGClusterCommand::MGClusterCommand(string option) {
 			hclusterWanted = m->isTrue(temp); 
 			
 			temp = validParameter.validFile(parameters, "hard", false);			if (temp == "not found") { temp = "T"; }
-			hard = m->isTrue(temp);
+			hard = m->isTrue(temp);            
 		}
 
 	}
@@ -211,7 +223,6 @@ MGClusterCommand::MGClusterCommand(string option) {
 //**********************************************************************************************************************
 int MGClusterCommand::execute(){
 	try {
-		
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//read names file
@@ -225,14 +236,28 @@ int MGClusterCommand::execute(){
 		time_t start;
 		float previousDist = 0.00000;
 		float rndPreviousDist = 0.00000; 
-		
+        
 		//read blastfile - creates sparsematrices for the distances and overlaps as well as a listvector
 		//must remember to delete those objects here since readBlast does not
 		read = new ReadBlast(blastfile, cutoff, penalty, length, minWanted, hclusterWanted);
 		read->read(nameMap);
-		
-		list = new ListVector(nameMap->getListVector());
-		RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
+        
+        list = new ListVector(nameMap->getListVector());
+        RAbundVector* rabund = NULL;
+        
+        if(countfile != "") {
+            //map<string, int> nameMapCounts = m->readNames(namefile);
+            ct = new CountTable();
+            ct->readTable(countfile);
+            rabund = new RAbundVector();
+            createRabund(ct, list, rabund);
+        }else {
+            rabund = new RAbundVector(list->getRAbundVector());
+        }
+        
+                
+		//list = new ListVector(nameMap->getListVector());
+		//rabund = new RAbundVector(list->getRAbundVector());
 		
 		if (m->control_pressed) { outputTypes.clear(); delete nameMap; delete read; delete list; delete rabund; return 0; }
 		
@@ -503,8 +528,8 @@ int MGClusterCommand::execute(){
 			m->mothurRemove(overlapFile);
 		}
 		
-		delete list; 
-		delete rabund;
+		delete list;
+		if (!large) {delete rabund;}
 		listFile.close();
 		sabundFile.close();
 		rabundFile.close();
@@ -699,7 +724,33 @@ void MGClusterCommand::sortHclusterFiles(string unsortedDist, string unsortedOve
 
 //**********************************************************************************************************************
 
+void MGClusterCommand::createRabund(CountTable*& ct, ListVector*& list, RAbundVector*& rabund){
+    try {
+        //vector<string> names = ct.getNamesOfSeqs();
 
+        //for ( int i; i < ct.getNumGroups(); i++ ) {    rav.push_back( ct.getNumSeqs(names[i]) );    }
+        //return rav;
+        
+        for(int i = 0; i < list->getNumBins(); i++) { 
+           vector<string> binNames;
+           string bin = list->get(i);
+           m->splitAtComma(bin, binNames);
+           int total = 0;
+           for (int j = 0; j < binNames.size(); j++) { 
+               total += ct->getNumSeqs(binNames[j]);
+           }
+           rabund->push_back(total);   
+       }
+        
+        
+    }
+    catch(exception& e) {
+		m->errorOut(e, "MGClusterCommand", "createRabund");
+		exit(1);
+	}
+    
+}
 
+//**********************************************************************************************************************