added shannonrange calc.

[mothur.git] / summarycommand.h

diff --git a/summarycommand.h b/summarycommand.h
index c03a6c61b34cef50b064593e346518d4ad741083..891d1570e3e55fd24f4d58260c023924584d7756 100644 (file)
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -9,43 +9,49 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
 #include "command.hpp"
 #include "sabundvector.hpp"
 #include "inputdata.h"
 #include "calculator.h"
-#include "readmatrix.hpp"
-
-/* The summary() command:
-       The summary command can only be executed after a successful read.list, read.sabund or read.rabund command, with one exception. 
-       The summary command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster. 
-       The summary command outputs a file for each estimator you choose to use.  The summary command parameters are label, line, summary. 
-        No parameters are required, but you may not use both the line and label  parameters at the same time. 
-        The summary command should be in the following format: summary(label=yourLabel, line=yourLines, summary=yourEstimators). 
-        Example summary(label=unique-.01-.03, line=0,5,10, summary=collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson). 
-        The default value for summary is collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson.  
-        The valid summary estimators are: collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson.  
-        The label and line parameters are used to analyze specific lines in your input.  */
-
-
-class GlobalData;
+#include "validcalculator.h"
 
 class SummaryCommand : public Command {
 
 public:
+       SummaryCommand(string);
        SummaryCommand();
-       ~SummaryCommand();
-       int execute();
+       ~SummaryCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "summary.single";                      }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Summary.single"; }
+       string getDescription()         { return "generate summary file that has the calculator value for each line in the OTU data"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       GlobalData* globaldata;
-       ReadMatrix* read;
        vector<Calculator*> sumCalculators;     
        InputData* input;
        SAbundVector* sabund;
-       string outputFileName;
-       ofstream outputFileHandle;
+       int abund, size, iters, subsampleSize, alpha;
+
+       bool abort, allLines, groupMode, subsample;
+       set<string> labels; //holds labels to be used
+       string label, calc, outputDir, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
+       vector<string>  Estimators;
+       vector<string> inputFileNames, outputNames;
+       vector<string> groups;
+       
+       vector<string> parseSharedFile(string);
+       vector<string> createGroupSummaryFile(int, int, vector<string>&, map<string, string>);
+    int process(SAbundVector*&, ofstream&, ofstream&);
+
+
 };
 #endif