X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectcommand.h;h=773bdae5c1d0b71bdad01e4403d3af3702274e70;hb=5a86e9e5a5a9e061e17b3ae64fb8881f14e53b8a;hp=04dcc602628695c5381048dbb67f4bad8be682e3;hpb=cd37904452dc95b183ff313ff05720c562902487;p=mothur.git

diff --git a/collectcommand.h b/collectcommand.h
index 04dcc60..773bdae 100644
--- a/collectcommand.h
+++ b/collectcommand.h
@@ -22,13 +22,13 @@
 	The collect command generates a collector's curve from the given file.  
 	The collect command can only be executed after a successful read.list, read.sabund or read.rabund command, with one exception. 
 	The collect command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster.  
-	The collect command outputs a file for each estimator you choose to use.  The collect command parameters are label, line, freq, single, abund.  
-	No parameters are required, but you may not use both the line and label  parameters at the same time.  
-	The collect command should be in the following format: collect(label=yourLabel, line=yourLines, freq=yourFreq, single=yourEstimators, abund=yourAbund). 
-	example collect(label=unique-.01-.03, line=0,5,10, freq=10, single=collect-chao-ace-jack).  
+	The collect command outputs a file for each estimator you choose to use.  The collect command parameters are label, freq, single, abund.  
+	No parameters are required.  
+	The collect command should be in the following format: collect(label=yourLabel, freq=yourFreq, single=yourEstimators, abund=yourAbund). 
+	example collect(label=unique-.01-.03, freq=10, single=collect-chao-ace-jack).  
 	The default values for  freq is 100, for abund is 10, and single are collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson.  
 	The valid single estimators are: collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson. 
-	The label and line parameters are used to analyze specific lines in your input. */
+	The label parameter is used to analyze specific labels in your input. */
 
 
 
@@ -46,18 +46,21 @@ private:
 	GlobalData* globaldata;
 	ReadOTUFile* read;
 	OrderVector* order;
-	OrderVector* lastOrder;
 	InputData* input;
 	Collect* cCurve;
 	ValidCalculators* validCalculator;
 	vector<Display*> cDisplays;
-	int freq, abund, size;
+	int abund, size;
+	float freq;
 
 	bool abort, allLines;
-	set<int> lines; //hold lines to be used
 	set<string> labels; //holds labels to be used
-	string line, label, calc;
+	string label, calc, outputDir;
 	vector<string>  Estimators;
+	vector<string> inputFileNames;
+	vector<string> groups;
+	
+	vector<string> parseSharedFile(string);
 
 
 };