fixed io

[mothur.git] / trimflowscommand.h

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 0dc1cd977c9b106b4986e2cb839939cae7541db2..b7fbf4342b821d1f6eb6dbb7094d94c3e85d19a3 100644 (file)
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -26,6 +26,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "trim.flows";  }
        string getCommandCategory()             { return "Sequence Processing";         }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Trim.flows"; }
        string getDescription()         { return "trim.flows"; }
@@ -49,7 +50,8 @@ private:
        vector<unsigned long long> getFlowFileBreaks();
        int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >); 
        int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
-
+    string reverseOligo(string);
+    
        vector<string> outputNames;
        set<string> filesToRemove;
        
@@ -58,7 +60,7 @@ private:
        bool allFiles;
        int processors;
        int numFPrimers, numRPrimers;
-       int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
+       int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
        int numFlows;
        float signal, noise;
        bool fasta;
@@ -66,10 +68,11 @@ private:
        
        string flowFileName, oligoFileName, outputDir;
 
-
        map<string, int> barcodes;
        map<string, int> primers;
        vector<string> revPrimer;
+    vector<string> linker;
+    vector<string> spacer;
 
        vector<string> primerNameVector;        //needed here?
        vector<string> barcodeNameVector;       //needed here?
@@ -130,7 +133,7 @@ struct trimFlowData {
 };
 
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyTrimFlowThreadFunction(LPVOID lpParam){ 
        trimFlowData* pDataArray;