X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=summarycommand.h;h=3c8420795550e1f39ef5529ad235d13e11e5e7a5;hp=8f42f459bf2de9a6c12679a42ea8bbf35c7835a1;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=154e089bcd37c2c2f773e53ffb88a20170b27037

diff --git a/summarycommand.h b/summarycommand.h
index 8f42f45..3c84207 100644
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -13,39 +13,45 @@
 #include "sabundvector.hpp"
 #include "inputdata.h"
 #include "calculator.h"
-#include "readotu.h"
 #include "validcalculator.h"
 
-/* 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;
-
 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;
-	ReadOTUFile* read;
 	vector<Calculator*> sumCalculators;	
 	InputData* input;
-	ValidCalculators* validCalculator;
 	SAbundVector* sabund;
-	string outputFileName;
-	ofstream outputFileHandle;
-	int abund;
+	int abund, size, iters, subsampleSize;
+
+	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