added diffs and percent parameters to cluster.fragments command

[mothur.git] / rarefactcommand.h

diff --git a/rarefactcommand.h b/rarefactcommand.h
index 5ac970ee8542b7d0793734d56d813afe506e1e09..7da0b2f9f5301d80302d97f7da23d1cd8fee12c1 100644 (file)
--- a/rarefactcommand.h
+++ b/rarefactcommand.h
@@ -18,28 +18,20 @@
 #include "validcalculator.h"
 
 
-/*The rarefaction() command:
-       The rarefaction command generates a rarefaction curve from a given file.  
-       The rarefaction command can only be executed after a successful read.list, read.sabund or read.rabund command, with one exception. 
-       The rarefaction command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster. 
-       The rarefaction command outputs a file for each estimator you choose to use.  It is recommended to only use rarefaction estimator.  
-       The rarefaction command parameters are label, line, iters, freq, rarefaction.  No parameters are required, 
-       but you may not use both the line and label  parameters at the same time. The rarefaction command should be in the following format: 
-       rarefaction(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, rarefaction=yourEstimators). 
-       Example rarefaction(label=unique-.01-.03, line=0,5,10, iters=10000, freq=10, rarefaction=rarefaction-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson). 
-       The default values for iters is 1000, freq is 100, and rarefaction is rarefaction which calculates the rarefaction curve for the observed richness. 
-       The valid rarefaction estimators are: rarefaction-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson.  
-       Rarefaction is the only recommended estimator.  The label and line parameters are used to analyze specific lines in your input. */
-       
-
 class GlobalData;
 
 class RareFactCommand : public Command {
        
 public:
+       RareFactCommand(string);
        RareFactCommand();      
        ~RareFactCommand();
-       int execute();  
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       int execute();
+       void help();    
        
 private:
        GlobalData* globaldata;
@@ -49,7 +41,21 @@ private:
        InputData* input;
        ValidCalculators* validCalculator;
        Rarefact* rCurve;
-       int freq, nIters, abund;
+       int nIters, abund, processors;
+       float freq;
+       
+       bool abort, allLines;
+       set<string> labels; //holds labels to be used
+       string label, calc;
+       vector<string>  Estimators;
+       vector<string> inputFileNames, outputNames;
+       vector<string> groups;
+       map<string, vector<string> > outputTypes;
+       string outputDir;
+       
+       vector<string> parseSharedFile(string);
+
+
 };
 
 #endif