X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustercommand.cpp;h=d14af108d69c36f98617fc2e133c3dcfb537c553;hb=2397df97b12cd5d21ea10dc4248c18a5803ddd41;hp=93ba1f9b65b8146b666d32debb3df601c046b19a;hpb=832d53a9dfac6b1795735eec643d8cf627b0d8e3;p=mothur.git

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 93ba1f9..d14af10 100644
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -21,7 +21,7 @@ ClusterCommand::ClusterCommand(string option){
 		
 		else {
 			//valid paramters for this command
-			string Array[] =  {"cutoff","precision","method","showabund","timing"};
+			string Array[] =  {"cutoff","precision","method","showabund","timing","outputdir","inputdir"};
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 			
 			OptionParser parser(option);
@@ -36,6 +36,9 @@ ClusterCommand::ClusterCommand(string option){
 				}
 			}
 			
+			//if the user changes the output directory command factory will send this info to us in the output parameter 
+			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = "";		}
+			
 			//error checking to make sure they read a distance file
 			if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) {
 				mothurOut("Before you use the cluster command, you first need to read in a distance matrix."); mothurOutEndLine();
@@ -81,12 +84,13 @@ ClusterCommand::ClusterCommand(string option){
 				}
 				
 				//create cluster
-				if (method == "furthest")	{	cluster = new CompleteLinkage(rabund, list, matrix, cutoff); }
-				else if(method == "nearest"){	cluster = new SingleLinkage(rabund, list, matrix, cutoff); }
-				else if(method == "average"){	cluster = new AverageLinkage(rabund, list, matrix, cutoff);	}
+				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);	}
 				tag = cluster->getTag();
-
-				fileroot = getRootName(globaldata->inputFileName);
+				
+				if (outputDir == "") { outputDir += hasPath(globaldata->inputFileName); }
+				fileroot = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
 			
 				openOutputFile(fileroot+ tag + ".sabund",	sabundFile);
 				openOutputFile(fileroot+ tag + ".rabund",	rabundFile);
@@ -154,7 +158,7 @@ int ClusterCommand::execute(){
 
 			loops++;
 
-			cluster->update();
+			cluster->update(cutoff);
 			float dist = matrix->getSmallDist();
 			float rndDist = roundDist(dist, precision);