added checks for ^C to quit command instead of program

[mothur.git] / summarysharedcommand.h

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index 0f2f75386b23382699fbb2b524268fee373dfc25..bcd8ab671f2727331179dbe3511d4acd72f72417 100644 (file)
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -17,30 +17,15 @@
 #include "readotu.h"
 #include "validcalculator.h"
 
-
-/*The summary.shared() command
-       The summary.shared command can only be executed after a successful read.shared command. 
-       It outputs a file for each estimator you choose to use.  The summary.shared command parameters are label, 
-       line, jumble and sharedsummary.  No parameters are required, but you may not use both the line and label parameters at the same time.  
-       The summary.shared command should be in the following format: summary.shared(label=yourLabel, 
-       line=yourLines, jumble=yourJumble, sharedsummary=yourEstimators).  
-       Example summary.shared(label=unique-.01-.03, line=0,5,10, jumble=1, sharedsummary=sharedChao-sharedAce-sharedJabund
-       -sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN).  
-       The default value for jumble is 0 (meaning don’t jumble, if it’s set to 1 then it will jumble) and 
-       sharedsummary is sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN. 
-       The valid sharedsummary estimators are: sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass
-       -sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN.  The label and line parameters are used to analyze specific lines in your input. */
-
-
 class GlobalData;
 
-
 class SummarySharedCommand : public Command {
 
 public:
-       SummarySharedCommand();
+       SummarySharedCommand(string);
        ~SummarySharedCommand();
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
@@ -48,12 +33,15 @@ private:
        vector<Calculator*> sumCalculators;     
        InputData* input;
        ValidCalculators* validCalculator;
-       SharedListVector* SharedList;
+       
+       bool abort, allLines, mult, all;
+       set<string> labels; //holds labels to be used
+       string label, calc, groups;
+       vector<string>  Estimators, Groups, outputNames;
        vector<SharedRAbundVector*> lookup;
-       string outputFileName, format, outAllFileName;
+       string outputFileName, format, outAllFileName, outputDir;
        ofstream outputFileHandle, outAll;
-       bool mult;
-       void process(vector<SharedRAbundVector*>);
+       int process(vector<SharedRAbundVector*>);
 
 };