added dups parameter to chimera.uchime. working on make.contigs command.

[mothur.git] / distancecommand.h

diff --git a/distancecommand.h b/distancecommand.h
index 9d5477d7ee1dca3d715189db8d61fab432c87cf3..9dea351250b7c7550a1071ca3189051345245d01 100644 (file)
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -24,7 +24,7 @@
 //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 distanceData {
+struct distanceData {
        int startLine;
        int endLine;
        string dFileName;
@@ -53,7 +53,7 @@ typedef struct distanceData {
 };
 
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyDistThreadFunction(LPVOID lpParam){ 
        distanceData* pDataArray;
@@ -178,6 +178,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "dist.seqs";                   }
        string getCommandCategory()             { return "Sequence Processing"; }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "Schloss PD (2010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844. \nhttp://www.mothur.org/wiki/Dist.seqs"; }
        string getDescription()         { return "calculate the pairwaise distances between aligned sequences"; }
@@ -213,8 +214,8 @@ private:
        
        #ifdef USE_MPI 
        int driverMPI(int, int, MPI_File&, float);
-       int driverMPI(int, int, string, unsigned long int&);
-       int driverMPI(int, int, string, unsigned long int&, string);
+       int driverMPI(int, int, string, unsigned long long&);
+       int driverMPI(int, int, string, unsigned long long&, string);
        #endif
        
        //int convertMatrix(string);