X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarycommand.h;h=6b3fa69c67e46cd92d44f0064404d2743dd29b7a;hb=2df35fdeea85f574630d75b11fb5b08c39aec31a;hp=8e2d74b0b52252250cd5cede8a1bf9b10a689449;hpb=09a01fb51eea9e81409d367410c831394193fd86;p=mothur.git

diff --git a/summarycommand.h b/summarycommand.h
index 8e2d74b..6b3fa69 100644
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -9,45 +9,42 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
 #include "command.hpp"
 #include "sabundvector.hpp"
 #include "inputdata.h"
 #include "calculator.h"
-#include "readmatrix.hpp"
+#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();
+	SummaryCommand(string);
 	~SummaryCommand();
 	int execute();
+	void help();
 	
 private:
 	GlobalData* globaldata;
-	ReadMatrix* read;
+	ReadOTUFile* read;
 	vector<Calculator*> sumCalculators;	
 	InputData* input;
 	ValidCalculators* validCalculator;
 	SAbundVector* sabund;
-	string outputFileName;
-	ofstream outputFileHandle;
+	int abund, size;
+
+	bool abort, allLines, groupMode;
+	set<string> labels; //holds labels to be used
+	string label, calc, outputDir;
+	vector<string>  Estimators;
+	vector<string> inputFileNames;
+	vector<string> groups;
+	
+	vector<string> parseSharedFile(string);
+	string createGroupSummaryFile(int, int, vector<string>);
+
+
 };
 #endif