added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / collectsharedcommand.h

diff --git a/collectsharedcommand.h b/collectsharedcommand.h
index 8c7aa009ca346670482679ac17b4c9f75d58fa82..10efcc80077c193694ee7297e40027a35f8bb10a 100644 (file)
--- a/collectsharedcommand.h
+++ b/collectsharedcommand.h
@@ -17,38 +17,26 @@
 #include "groupmap.h"
 #include "collect.h"
 #include "display.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "validcalculator.h"
 #include "sharedutilities.h"
 
-/* The collect.shared() command:
-       The collect command generates a collector's curve from the given file representing several groups.  
-       The collect.shared command can only be executed after a successful read.shared command. 
-       It outputs a file for each estimator you choose to use.  The collect.shared command parameters are label, line, freq, jumble and shared.  
-       No parameters are required, but you may not use both the line and label parameters at the same time. 
-       The collect.shared command should be in the following format: collect.shared(label=yourLabel, line=yourLines, 
-       freq=yourFreq,  jumble=yourJumble, shared=yourEstimators). Example collect.shared(label=unique-.01-.03, line=0,5,10, freq=10, jumble=1, 
-       shared=sharedChao-sharedAce-sharedJabund). The default values for jumble is 0 (meaning don’t jumble, if it’s set to 1 then it will jumble), 
-       freq is 100 and shared are sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN.  
-       The valid shared 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 CollectSharedCommand : public Command {
        
 public:
-       CollectSharedCommand(); 
+       CollectSharedCommand(string);   
        ~CollectSharedCommand();
        int execute();  
+       void help();
        
 private:
        GlobalData* globaldata;
        SharedUtil* util;
        GroupMap* groupmap;
        SharedListVector* SharedList;
-       ReadMatrix* read;
+       ReadOTUFile* read;
        SharedOrderVector* order;
        InputData* input;
        ValidCalculators* validCalculator;
@@ -57,6 +45,12 @@ private:
        int freq;
        string format;
 
+       bool abort, allLines, all;
+       set<string> labels; //holds labels to be used
+       string label, calc, groups, outputDir;
+       vector<string>  Estimators, Groups;
+
+
 };
 
 #endif