more changes to error.seqs command and quality scores classses

[mothur.git] / heatmapsimcommand.h

diff --git a/heatmapsimcommand.h b/heatmapsimcommand.h
index 091da26af7db4cf4e9302c0e9a9d0e8a4587f5de..cd12c176f44994e4ea1da4128737dabe2931b6ac 100644 (file)
--- a/heatmapsimcommand.h
+++ b/heatmapsimcommand.h
@@ -22,7 +22,12 @@ class HeatMapSimCommand : public Command {
 
 public:
        HeatMapSimCommand(string);
+       HeatMapSimCommand();
        ~HeatMapSimCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -38,10 +43,13 @@ private:
        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 format, groups, line, label, calc;
-       vector<string> Estimators, Groups;
+       string format, groups, label, calc, phylipfile, columnfile, namefile, outputDir;
+       vector<string> Estimators, Groups, outputNames;
+       map<string, vector<string> > outputTypes;
+       
+       int runCommandShared();
+       int runCommandDist();
 
 
 };