removed line option

[mothur.git] / summarysharedcommand.h

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index 24ce04b8f278e0a4dd938831a8fe9a434dc047f5..119a75c47438a85460b4b798501edbf0807569c0 100644 (file)
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -9,57 +9,43 @@
  *
  */
 
-#include <Carbon/Carbon.h>
-#include <iostream>
-#include <fstream>
-#include <vector>
+
 #include "command.hpp"
 #include "sharedrabundvector.h"
 #include "inputdata.h"
 #include "calculator.h"
-#include "readmatrix.hpp"
-#include "sharedlistvector.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. */
-
+#include "readotu.h"
+#include "validcalculator.h"
 
 class GlobalData;
 
-
 class SummarySharedCommand : public Command {
 
 public:
-       SummarySharedCommand();
+       SummarySharedCommand(string);
        ~SummarySharedCommand();
        int execute();
+       void help();
        
 private:
-       void getGroupComb();
-       void getSharedVectors();
-       
        GlobalData* globaldata;
-       ReadMatrix* read;
+       ReadOTUFile* read;
        vector<Calculator*> sumCalculators;     
        InputData* input;
+       ValidCalculators* validCalculator;
        SharedListVector* SharedList;
-       SharedOrderVector* order;
+       OptionParser* parser;
+       map<string, string> parameters;
+       map<string, string>::iterator it;
+       bool abort, allLines, mult;
+       set<string> labels; //holds labels to be used
+       string label, calc, groups;
+       vector<string>  Estimators, Groups;
        vector<SharedRAbundVector*> lookup;
-       SharedRAbundVector* shared1, shared2;
-       string outputFileName;
-       ofstream outputFileHandle;
-       vector<string> groupComb;
+       string outputFileName, format, outAllFileName;
+       ofstream outputFileHandle, outAll;
+       void process(vector<SharedRAbundVector*>);
 
 };
 
-#endif
\ No newline at end of file
+#endif