merged pat's trim seqs edits with sarah's major overhaul of global data; also added...

[mothur.git] / binsequencecommand.h

diff --git a/binsequencecommand.h b/binsequencecommand.h
index e2ff648283a9c00569a8d2a4170a040b4a494902..6f9f69d3a7b13dbabe73c09e21e787f55dadff81 100644 (file)
--- a/binsequencecommand.h
+++ b/binsequencecommand.h
@@ -24,9 +24,10 @@ class GlobalData;
 class BinSeqCommand : public Command {
        
 public:
-       BinSeqCommand();        
+       BinSeqCommand(string);  
        ~BinSeqCommand();
-       int execute();  
+       int execute();
+       void help();    
        
 private:
        GlobalData* globaldata;
@@ -35,11 +36,15 @@ private:
        InputData* input;
        FastaMap* fasta;
        GroupMap* groupMap;
-       string filename, fastafile, namesfile, groupfile;
+       bool abort, allLines;
+       set<int> lines; //hold lines to be used
+       set<string> labels; //holds labels to be used
+       string filename, fastafile, namesfile, groupfile, line, label;
        ofstream out;
        ifstream in, inNames;
        
        void readNamesFile();
+       int process(ListVector*, int);
 };
 
 #endif