X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerauchimecommand.h;h=a5b42751dfd74ea3eb1fc3dc4ccf9bfa5bb9822b;hb=cc19310422f125d6628980bd1148e1e816792382;hp=659d1ea39963f05a245cda03acf56f3b6e3d10e9;hpb=01f8d2c7d982a6209211f5abbcf2a086fdf60d0a;p=mothur.git

diff --git a/chimerauchimecommand.h b/chimerauchimecommand.h
index 659d1ea..a5b4275 100644
--- a/chimerauchimecommand.h
+++ b/chimerauchimecommand.h
@@ -47,7 +47,7 @@ private:
 	int driver(string, string, string, string, int&);
 	int createProcesses(string, string, string, string, int&);
 		
-	bool abort, useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract, hasCount, hasName;
+	bool abort, useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract, hasCount, hasName, dups;
 	string fastafile, groupfile, templatefile, outputDir, namefile, countfile, abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract, uchimeLocation;
 	int processors;
 	
@@ -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);
 
 
 };
@@ -189,7 +190,7 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
             if (pDataArray->hasCount) { 
                 error = cparser->getSeqs(pDataArray->groups[i], pDataArray->filename, true); if ((error == 1) || pDataArray->m->control_pressed) {  delete cparser; return 0; }
             }else {
-               error = cparser->getSeqs(pDataArray->groups[i], pDataArray->filename, true); if ((error == 1) || pDataArray->m->control_pressed) {  delete parser; return 0; } 
+               error = parser->getSeqs(pDataArray->groups[i], pDataArray->filename, true); if ((error == 1) || pDataArray->m->control_pressed) {  delete parser; return 0; } 
             }
 			
 			//int numSeqs = driver((outputFName + groups[i]), filename, (accnos+ groups[i]), (alns+ groups[i]), numChimeras);
@@ -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;
+        pDataArray->m->openInputFile((filename.substr(1, filename.length()-2)), in23);
+        
+        ofstream out23;
+        pDataArray->m->openOutputFile(outputFileName, out23);
+        
+        while (!in23.eof()) {
+            if (pDataArray->m->control_pressed) { break;  }
+            
+            Sequence seq(in23); pDataArray->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);
@@ -733,6 +758,8 @@ static DWORD WINAPI MyUchimeSeqsThreadFunction(LPVOID lpParam){
 		for (int j = 0; j < cPara.size(); j++) {  uchimeParameters[j] = cPara[j];  commandString += toString(cPara[j]) + " "; } 
 		//int numArgs = cPara.size();
 		
+        commandString = "\"" + commandString + "\"";
+        
 		//uchime_main(numArgs, uchimeParameters); 
 		//cout << "commandString = " << commandString << endl;
         if (pDataArray->m->debug) { pDataArray->m->mothurOut("[DEBUG]: uchime command = " + commandString + ".\n"); }