X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=clustersplitcommand.cpp;h=95693cc420a7e55d5c9a96a102e3d9e55ad0221c;hp=270ea6208d8ead0683d8cf46fb8d7a417469c243;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=a91c60b9d7fd350dd7a03afc205d05d558db8126

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 270ea62..95693cc 100644
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -61,7 +61,7 @@ string ClusterSplitCommand::getHelpString(){
         helpString += "The cluster parameter allows you to indicate whether you want to run the clustering or just split the distance matrix, default=t";
 		helpString += "The cutoff parameter allow you to set the distance you want to cluster to, default is 0.25. \n";
 		helpString += "The precision parameter allows you specify the precision of the precision of the distances outputted, default=100, meaning 2 decimal places. \n";
-		helpString += "The method allows you to specify what clustering algorythm you want to use, default=average, option furthest, nearest, or average. \n";
+		helpString += "The method allows you to specify what clustering algorithm you want to use, default=average, option furthest, nearest, or average. \n";
 		helpString += "The splitmethod parameter allows you to specify how you want to split your distance file before you cluster, default=distance, options distance, classify or fasta. \n";
 		helpString += "The taxonomy parameter allows you to enter the taxonomy file for your sequences, this is only valid if you are using splitmethod=classify. Be sure your taxonomy file does not include the probability scores. \n";
 		helpString += "The taxlevel parameter allows you to specify the taxonomy level you want to use to split the distance file, default=3, meaning use the first taxon in each list. \n";
@@ -1330,9 +1330,10 @@ string ClusterSplitCommand::clusterFile(string thisDistFile, string thisNamefile
         m->mothurOutEndLine(); m->mothurOut("Clustering " + thisDistFile); m->mothurOutEndLine();
 		
         //create cluster
-        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);	}
+        float adjust = -1.0;
+        if (method == "furthest")	{	cluster = new CompleteLinkage(rabund, list, matrix, cutoff, method, adjust); }
+        else if(method == "nearest"){	cluster = new SingleLinkage(rabund, list, matrix, cutoff, method, adjust); }
+        else if(method == "average"){	cluster = new AverageLinkage(rabund, list, matrix, cutoff, method, adjust);	}
         tag = cluster->getTag();
 		
         if (outputDir == "") { outputDir += m->hasPath(thisDistFile); }