X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=matrixoutputcommand.h;h=ff7519ee00751dcad80ebdb9bc04e384f54cd45b;hb=2397df97b12cd5d21ea10dc4248c18a5803ddd41;hp=d6099326a69ac5ef1daf95ce192bc3cad1fd712f;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index d609932..ff7519e 100644
--- a/matrixoutputcommand.h
+++ b/matrixoutputcommand.h
@@ -18,7 +18,7 @@
 // aka. dist.shared()
 
 /* This command create a tree file for each similarity calculator at distance level, using various calculators to find the similiarity between groups. 
-	The user can select the lines or labels they wish to use as well as the groups they would like included.
+	The user can select the labels they wish to use as well as the groups they would like included.
 	They can also use as many or as few calculators as they wish. */
 	
 class GlobalData;
@@ -42,16 +42,13 @@ private:
 	InputData* input;
 	ValidCalculators* validCalculator;
 	vector<SharedRAbundVector*> lookup;
-	string exportFileName;
+	string exportFileName, output;
 	int numGroups;
 	ofstream out;
-	OptionParser* parser;
-	map<string, string> parameters;
-	map<string, string>::iterator it;
+
 	bool abort, allLines;
-	set<int> lines; //hold lines to be used
 	set<string> labels; //holds labels to be used
-	string outputFile, calc, groups, line, label;
+	string outputFile, calc, groups, label, outputDir;
 	vector<string>  Estimators, Groups; //holds estimators to be used