pca command

[mothur.git] / collectsharedcommand.h

diff --git a/collectsharedcommand.h b/collectsharedcommand.h
index 67e8e0c1073dae0a81f5d4d8e88ac7ee4981d708..327ce5d28832dbe7f25d69f6c0755f6e931c747d 100644 (file)
--- a/collectsharedcommand.h
+++ b/collectsharedcommand.h
@@ -21,26 +21,18 @@
 #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 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, 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. */
-
-
 class GlobalData;
 
 class CollectSharedCommand : public Command {
        
 public:
        CollectSharedCommand(string);   
+       CollectSharedCommand(); 
        ~CollectSharedCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help();
        
@@ -55,14 +47,14 @@ private:
        ValidCalculators* validCalculator;
        Collect* cCurve;
        vector<Display*> cDisplays;
-       int freq;
+       float freq;
        string format;
 
-       bool abort, allLines;
-       set<int> lines; //hold lines to be used
+       bool abort, allLines, all;
        set<string> labels; //holds labels to be used
-       string line, label, calc, groups;
-       vector<string>  Estimators, Groups;
+       string label, calc, groups, outputDir;
+       vector<string>  Estimators, Groups, outputNames;
+       map<string, vector<string> > outputTypes;
 
 
 };