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

[mothur.git] / collectsharedcommand.h

diff --git a/collectsharedcommand.h b/collectsharedcommand.h
index 8c7aa009ca346670482679ac17b4c9f75d58fa82..67e8e0c1073dae0a81f5d4d8e88ac7ee4981d708 100644 (file)
--- a/collectsharedcommand.h
+++ b/collectsharedcommand.h
@@ -17,18 +17,18 @@
 #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.  
+       It outputs a file for each estimator you choose to use.  The collect.shared command parameters are label, line, freq 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=yourFreq, shared=yourEstimators). Example collect.shared(label=unique-.01-.03, line=0,5,10, freq=10, 
+       shared=sharedChao-sharedAce-sharedJabund). The default value for
        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. */
@@ -39,16 +39,17 @@ 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 +58,13 @@ private:
        int freq;
        string format;
 
+       bool abort, allLines;
+       set<int> lines; //hold lines to be used
+       set<string> labels; //holds labels to be used
+       string line, label, calc, groups;
+       vector<string>  Estimators, Groups;
+
+
 };
 
 #endif