fixed phylo.diversity

[mothur.git] / summarycommand.h

diff --git a/summarycommand.h b/summarycommand.h
index 8f42f459bf2de9a6c12679a42ea8bbf35c7835a1..7c7ee2c8eea829a9c6dc95fa794df5fcccc7bda1 100644 (file)
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -16,26 +16,15 @@
 #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;
@@ -44,8 +33,18 @@ private:
        InputData* input;
        ValidCalculators* validCalculator;
        SAbundVector* sabund;
-       string outputFileName;
-       ofstream outputFileHandle;
-       int abund;
+       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