added code to format fast files for uchime. started work on sff.multiple command

[mothur.git] / chimerauchimecommand.h

diff --git a/chimerauchimecommand.h b/chimerauchimecommand.h
index 659d1ea39963f05a245cda03acf56f3b6e3d10e9..67c77f24f4597838f959224ceaf6bab4467ce5df 100644 (file)
--- a/chimerauchimecommand.h
+++ b/chimerauchimecommand.h
@@ -64,6 +64,7 @@ private:
        int deconvoluteResults(map<string, string>&, string, string, string);
        int driverGroups(string, string, string, string, int, int, vector<string>);
        int createProcessesGroups(string, string, string, string, vector<string>, string, string, string);
+    int prepFile(string filename, string);
 
 
 };
@@ -524,16 +525,31 @@ static DWORD WINAPI MyUchimeSeqsThreadFunction(LPVOID lpParam){
         strncat(tempUchime, uchimeCommand.c_str(), uchimeCommand.length());
         cPara.push_back(tempUchime);
                
-               char* tempIn = new char[8]; 
-               *tempIn = '\0'; strncat(tempIn, "--input", 7);
-               //strcpy(tempIn, "--input"); 
-               cPara.push_back(tempIn);
-               char* temp = new char[filename.length()+1];
-               *temp = '\0'; strncat(temp, filename.c_str(), filename.length());
-               //strcpy(temp, filename.c_str());
-               cPara.push_back(temp);
-       
-               //add reference file
+        string outputFileName = filename.substr(1, filename.length()-2) + ".uchime_formatted";
+        //prepFile(filename.substr(1, filename.length()-2), outputFileName);
+        //prepFile(filename, outputFileName);
+        /******************************************/
+        ifstream in23;
+        m->openInputFile((filename.substr(1, filename.length()-2)), in23);
+        
+        ofstream out23;
+        m->openOutputFile(outputFileName, out23);
+        
+        while (!in23.eof()) {
+            if (m->control_pressed) { break;  }
+            
+            Sequence seq(in23); m->gobble(in23);
+            
+            if (seq.getName() != "") { seq.printSequence(out23); }
+        }
+        in23.close();
+        out23.close();
+        /******************************************/
+        
+        filename = outputFileName;
+        filename = "\"" + filename + "\"";
+        
+        //add reference file
                char* tempRef = new char[5]; 
                //strcpy(tempRef, "--db"); 
                *tempRef = '\0'; strncat(tempRef, "--db", 4);
@@ -542,6 +558,15 @@ static DWORD WINAPI MyUchimeSeqsThreadFunction(LPVOID lpParam){
                //strcpy(tempR, templatefile.c_str());
                *tempR = '\0'; strncat(tempR, templatefile.c_str(), templatefile.length());
                cPara.push_back(tempR);
+        
+               char* tempIn = new char[8]; 
+               *tempIn = '\0'; strncat(tempIn, "--input", 7);
+               //strcpy(tempIn, "--input"); 
+               cPara.push_back(tempIn);
+               char* temp = new char[filename.length()+1];
+               *temp = '\0'; strncat(temp, filename.c_str(), filename.length());
+               //strcpy(temp, filename.c_str());
+               cPara.push_back(temp);
                
                char* tempO = new char[12]; 
                *tempO = '\0'; strncat(tempO, "--uchimeout", 11);