changes while testing

[mothur.git] / distancecommand.h

diff --git a/distancecommand.h b/distancecommand.h
index 9d5477d7ee1dca3d715189db8d61fab432c87cf3..2f53232b5943d835e8c27adf7374a5e3a8ce168f 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;
@@ -33,7 +33,7 @@ typedef struct distanceData {
        vector<string> Estimators;
        MothurOut* m;
        string output;
-       int numNewFasta;
+       int numNewFasta, count;
        string countends;
        
        distanceData(){}
@@ -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;
@@ -86,7 +86,7 @@ static DWORD WINAPI MyDistThreadFunction(LPVOID lpParam){
                ofstream outFile(pDataArray->dFileName.c_str(), ios::trunc);
                outFile.setf(ios::fixed, ios::showpoint);
                outFile << setprecision(4);
-               
+               pDataArray->count = 0;
                
                if (pDataArray->output != "square") { 
                        if((pDataArray->output == "lt") && (pDataArray->startLine == 0)){       outFile << pDataArray->alignDB.getNumSeqs() << endl;    }
@@ -119,11 +119,10 @@ static DWORD WINAPI MyDistThreadFunction(LPVOID lpParam){
                                if (pDataArray->output == "lt") { outFile << endl; }
                                
                                if(i % 100 == 0){
-                                       pDataArray->m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
-                               }
-                               
+                                       pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");                               }
+                               pDataArray->count++;
                        }
-                       pDataArray->m->mothurOut(toString(pDataArray->endLine-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+                       pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)+"\n");
                }else{
                        if(pDataArray->startLine == 0){ outFile << pDataArray->alignDB.getNumSeqs() << endl;    }
                        
@@ -148,11 +147,11 @@ static DWORD WINAPI MyDistThreadFunction(LPVOID lpParam){
                                outFile << endl; 
                                
                                if(i % 100 == 0){
-                                       pDataArray->m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+                                       pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 
                                }
-                               
+                               pDataArray->count++;
                        }
-                       pDataArray->m->mothurOut(toString(pDataArray->endLine-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+                       pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)+"\n"); 
                }
                
                outFile.close();
@@ -178,7 +177,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "dist.seqs";                   }
        string getCommandCategory()             { return "Sequence Processing"; }
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        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);