Pat's fix

[mothur.git] / trimflowscommand.h

diff --git a/trimflowscommand.h b/trimflowscommand.h
index ab8ca91a42b35a9a283a3f9c6f2ee4606a01f7a4..8656fd0b5b314084c6fd08cf614288aca2bbc763 100644 (file)
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -25,9 +25,9 @@ public:
        
        vector<string> setParameters();
        string getCommandName()                 { return "trim.flows";  }
-       string getCommandCategory()             { return "Hidden";              }
+       string getCommandCategory()             { return "Sequence Processing";         }
        string getHelpString(); 
-       string getCitation() { return "no citation"; }
+       string getCitation() { return "http://www.mothur.org/wiki/Trim.flows"; }
        string getDescription()         { return "trim.flows"; }
 
        
@@ -58,7 +58,9 @@ private:
        bool allFiles;
        int processors;
        int numFPrimers, numRPrimers;
-       int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
+    int numLinkers, numSpacers;
+
+    int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
        int numFlows;
        float signal, noise;
        bool fasta;
@@ -66,7 +68,6 @@ private:
        
        string flowFileName, oligoFileName, outputDir;
 
-
        map<string, int> barcodes;
        map<string, int> primers;
        vector<string> revPrimer;
@@ -83,7 +84,7 @@ private:
 //custom data structure for threads to use.
 // This is passed by void pointer so it can be any data type
 // that can be passed using a single void pointer (LPVOID).
-typedef struct trimFlowData {
+struct trimFlowData {
        string flowFileName; 
        string trimFlowFileName; 
        string scrapFlowFileName;