broke up globaldata and moved error checking and help into commands

[mothur.git] / collectsharedcommand.h

diff --git a/collectsharedcommand.h b/collectsharedcommand.h
index aac31c1e32a0b270d03d7b64d69ae1825b5a6af0..7024d0b5fc1ceecc1700d8592a91b9fe873d52c7 100644 (file)
--- a/collectsharedcommand.h
+++ b/collectsharedcommand.h
@@ -24,11 +24,11 @@
 /* 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. */
@@ -39,9 +39,10 @@ class GlobalData;
 class CollectSharedCommand : public Command {
        
 public:
-       CollectSharedCommand(); 
+       CollectSharedCommand(string);   
        ~CollectSharedCommand();
        int execute();  
+       void help();
        
 private:
        GlobalData* globaldata;
@@ -56,6 +57,15 @@ private:
        vector<Display*> cDisplays;
        int freq;
        string format;
+       OptionParser* parser;
+       map<string, string> parameters;
+       map<string, string>::iterator it;
+       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;
+
 
 };