added warning about merging with something above cutoff to cluster. working on chimeras

[mothur.git] / matrixoutputcommand.h

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index d6099326a69ac5ef1daf95ce192bc3cad1fd712f..ff7519ee00751dcad80ebdb9bc04e384f54cd45b 100644 (file)
--- 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