X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustercommand.cpp;h=e9df82f6e430b9d11965248882cdc34a650b3a3f;hb=291eaab661778e1fd02c5c22bc388daa97bb1d54;hp=6f6e309331df3caf27dc5d2d0c6d4e19ab246590;hpb=e189982e0a9b7352ad57cc38ccee675f128be22e;p=mothur.git

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 6f6e309..e9df82f 100644
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -22,7 +22,7 @@ ClusterCommand::ClusterCommand(string option)  {
 		
 		else {
 			//valid paramters for this command
-			string Array[] =  {"cutoff","precision","method","showabund","timing","outputdir","inputdir"};
+			string Array[] =  {"cutoff","precision","method","showabund","timing","hard","outputdir","inputdir"};
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 			
 			OptionParser parser(option);
@@ -56,16 +56,19 @@ ClusterCommand::ClusterCommand(string option)  {
 			length = temp.length();
 			convert(temp, precision); 
 			
+			temp = validParameter.validFile(parameters, "hard", false);			if (temp == "not found") { temp = "F"; }
+			hard = isTrue(temp);
+			
 			temp = validParameter.validFile(parameters, "cutoff", false);
 			if (temp == "not found") { temp = "10"; }
 			convert(temp, cutoff); 
-			cutoff += (5 / (precision * 10.0));
+			cutoff += (5 / (precision * 10.0));  
 			
 			method = validParameter.validFile(parameters, "method", false);
 			if (method == "not found") { method = "furthest"; }
 			
-			if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
-			else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }
+			if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted")) { }
+			else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest, average, and weighted."); m->mothurOutEndLine(); abort = true; }
 
 			showabund = validParameter.validFile(parameters, "showabund", false);
 			if (showabund == "not found") { showabund = "T"; }
@@ -88,6 +91,7 @@ ClusterCommand::ClusterCommand(string option)  {
 				if (method == "furthest")	{	cluster = new CompleteLinkage(rabund, list, matrix, cutoff, method); }
 				else if(method == "nearest"){	cluster = new SingleLinkage(rabund, list, matrix, cutoff, method); }
 				else if(method == "average"){	cluster = new AverageLinkage(rabund, list, matrix, cutoff, method);	}
+				else if(method == "weighted"){	cluster = new WeightedLinkage(rabund, list, matrix, cutoff, method);	}
 				tag = cluster->getTag();
 				
 				if (outputDir == "") { outputDir += hasPath(globaldata->inputFileName); }
@@ -114,7 +118,7 @@ ClusterCommand::ClusterCommand(string option)  {
 void ClusterCommand::help(){
 	try {
 		m->mothurOut("The cluster command can only be executed after a successful read.dist command.\n");
-		m->mothurOut("The cluster command parameter options are method, cuttoff, precision, showabund and timing. No parameters are required.\n");
+		m->mothurOut("The cluster command parameter options are method, cuttoff, hard, precision, showabund and timing. No parameters are required.\n");
 		m->mothurOut("The cluster command should be in the following format: \n");
 		m->mothurOut("cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
 		m->mothurOut("The acceptable cluster methods are furthest, nearest and average.  If no method is provided then furthest is assumed.\n\n");	
@@ -178,7 +182,12 @@ int ClusterCommand::execute(){
 			cluster->update(cutoff);
 	
 			float dist = matrix->getSmallDist();
-			float rndDist = roundDist(dist, precision);
+			float rndDist;
+			if (hard) {
+				rndDist = ceilDist(dist, precision); 
+			}else{
+				rndDist = roundDist(dist, precision); 
+			}
 
 			if(previousDist <= 0.0000 && dist != previousDist){
 				printData("unique");