added homova command

[mothur.git] / subsamplecommand.h

diff --git a/subsamplecommand.h b/subsamplecommand.h
index f068ac32eb975f6fa246fe654d84f56db0e33c3a..b00defdd9d63e797675d8a7809e32fe1d92d6a63 100644 (file)
--- a/subsamplecommand.h
+++ b/subsamplecommand.h
@@ -34,17 +34,28 @@ public:
 private:
        GlobalData* globaldata;
        
-       bool abort, pickedGroups, allLines;
+       bool abort, pickedGroups, allLines, persample;
        string listfile, groupfile, sharedfile, rabundfile, sabundfile, fastafile, namefile;
        set<string> labels; //holds labels to be used
        string groups, label, outputDir;
        vector<string> Groups, outputNames;
        map<string, vector<string> > outputTypes;
        int size;
+       vector<string> names;
+       map<string, vector<string> > nameMap;
        
        int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
        int getSubSampleShared();
+       int getSubSampleList();
+       int getSubSampleRabund();
+       int getSubSampleSabund();
+       int getSubSampleFasta();
        int processShared(vector<SharedRAbundVector*>&, ofstream&);
+       int processRabund(RAbundVector*&, ofstream&);
+       int processSabund(SAbundVector*&, ofstream&);
+       int processList(ListVector*&, ofstream&, set<string>&);
+       int getNames();
+       int readNames();
        
 };