X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=heatmapcommand.cpp;h=04f12456a49b623a82bf3e009929d7a31870da35;hb=315e38cf393c82be238da5b32574f225a020d25c;hp=1992ce593a7e65c2638f7d5ac0c5f39e4f50b5f9;hpb=c99f3846e7a7b6f06ab46508baa5409204ad6290;p=mothur.git

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index 1992ce5..04f1245 100644
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -24,7 +24,7 @@ HeatMapCommand::HeatMapCommand(string option){
 		
 		else {
 			//valid paramters for this command
-			string AlignArray[] =  {"groups","label","sorted","scale"};
+			string AlignArray[] =  {"groups","label","sorted","scale","outputdir","inputdir"};
 			vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
 			
 			OptionParser parser(option);
@@ -37,6 +37,12 @@ HeatMapCommand::HeatMapCommand(string option){
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
+			//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 = "";	
+				outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it	
+			}
+			
 			//make sure the user has already run the read.otu command
 			if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "") && (globaldata->getSharedFile() == "")) {
 				 mothurOut("You must read a list, rabund, sabund, or a list and a group, or a shared before you can use the heatmap.bin command."); mothurOutEndLine(); abort = true; 
@@ -69,7 +75,7 @@ HeatMapCommand::HeatMapCommand(string option){
 			scale = validParameter.validFile(parameters, "scale", false);				if (scale == "not found") { scale = "log10"; }
 			
 			if (abort == false) {
-				heatmap = new HeatMap(sorted, scale);
+				heatmap = new HeatMap(sorted, scale, outputDir);
 				format = globaldata->getFormat();
 			}
 		}