Merge pull request #298 from mothur/Windows_vsearch

Windows vsearch

source/commands/chimeraperseuscommand.h

@@ -122,14 +122,15 @@ static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){
 		//parse fasta and name file by group
 		SequenceParser* parser;
         SequenceCountParser* cparser;
+        vector<string> temp;
 		if (pDataArray->hasCount) {
             CountTable* ct = new CountTable();
             ct->readTable(pDataArray->namefile, true, false);
-            cparser = new SequenceCountParser(pDataArray->fastafile, *ct);
+            cparser = new SequenceCountParser(pDataArray->fastafile, *ct, temp);
             delete ct;
         }else {
-            if (pDataArray->namefile != "") { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile);	}
-            else							{ parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile);						}
+            if (pDataArray->namefile != "") { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile, temp);	}
+            else							{ parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, temp);						}
         }
     
 		int totalSeqs = 0;

source/commands/chimerauchimecommand.cpp

@@ -557,9 +557,6 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
 			
 			//look for uchime exe
 			path = m->mothurProgramPath;
-			//string tempPath = path;
-			//for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
-			//path = path.substr(0, (tempPath.find_last_of('m')));
 			
 			string uchimeCommand;
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
@@ -575,7 +572,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
                 delete newCommand;
             }
 #else
-			uchimeCommand = path + "uchime.exe";
+			uchimeCommand = path + "\\uchime.exe";
 #endif
         
 			//test to make sure uchime exists
@@ -586,14 +583,15 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
                 m->mothurOut(uchimeCommand + " file does not exist. Checking path... \n");
                 //check to see if uchime is in the path??
                 
-                string uLocation = m->findProgramPath("uchime");
-                
+                string uLocation = ""; 
                 
                 ifstream in2;
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+                uLocation = m->findProgramPath("uchime");
                 ableToOpen = m->openInputFile(uLocation, in2, "no error"); in2.close();
 #else
-                ableToOpen = m->openInputFile((uLocation + ".exe"), in2, "no error"); in2.close();
+                uLocation = m->findProgramPath("uchime.exe");
+                ableToOpen = m->openInputFile(uLocation, in2, "no error"); in2.close();
 #endif
 
                 if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + uLocation + " file does not exist. mothur requires the uchime executable."); m->mothurOutEndLine(); abort = true; } 
@@ -1158,11 +1156,12 @@ int ChimeraUchimeCommand::driverGroups(string outputFName, string filename, stri
 			int start = time(NULL);	 if (m->control_pressed) {  outCountList.close(); m->mothurRemove(countlist); return 0; }
             
 			int error;
-            if (hasCount) { error = cparser->getSeqs(groups[i], filename, "/ab=", "/", true); if ((error == 1) || m->control_pressed) {  return 0; } }
-            else { error = sparser->getSeqs(groups[i], filename, "/ab=", "/", true); if ((error == 1) || m->control_pressed) {  return 0; } }
-			
-			int numSeqs = driver((outputFName + groups[i]), filename, (accnos+groups[i]), (alns+ groups[i]), numChimeras);
+            long long numSeqs = 0;
+            if (hasCount) { error = cparser->getSeqs(groups[i], filename, "/ab=", "/", numSeqs, true); if ((error == 1) || m->control_pressed) {  return 0; } }
+            else { error = sparser->getSeqs(groups[i], filename, "/ab=", "/", numSeqs, true); if ((error == 1) || m->control_pressed) {  return 0; } }
 			totalSeqs += numSeqs;
+            
+			driver((outputFName + groups[i]), filename, (accnos+groups[i]), (alns+ groups[i]), numChimeras);
 			
 			if (m->control_pressed) { return 0; }
 			
@@ -1660,7 +1659,8 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
 		//divide file
 		int count = 0;
 		int spot = 0;
-		
+        files.resize(processors, "");
+        
 		for (int i = 0; i < processors; i++) {
             ofstream temp;
 			files[i] = filename+toString(i)+".temp";
@@ -1802,7 +1802,6 @@ int ChimeraUchimeCommand::createProcessesGroups(string outputFName, string filen
             }
 
 		}
-		m->mothurOut(toString( getpid() ) + " here\n");
             
 		//do my part
 		num = driverGroups(outputFName, filename, accnos, alns, accnos + ".byCount", lines[0].start, lines[0].end, groups);

source/commands/chimerauchimecommand.h

@@ -165,14 +165,15 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
 		//parse fasta and name file by group
 		SequenceParser* parser;
         SequenceCountParser* cparser;
+        vector<string> temp;
 		if (pDataArray->hasCount) {
             CountTable* ct = new CountTable();
             ct->readTable(pDataArray->namefile, true, false);
-            cparser = new SequenceCountParser(pDataArray->fastafile, *ct);
+            cparser = new SequenceCountParser(pDataArray->fastafile, *ct, temp);
             delete ct;
         }else {
-            if (pDataArray->namefile != "") { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile);	}
-            else							{ parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile);						}
+            if (pDataArray->namefile != "") { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile, temp);	}
+            else							{ parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, temp);						}
         }
 		
 		int totalSeqs = 0;
@@ -187,13 +188,14 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
 			
             
 			int error;
+            long long numSeqs = 0;
             if (pDataArray->hasCount) { 
-                error = cparser->getSeqs(pDataArray->groups[i], pDataArray->filename, "/ab=", "/", true); if ((error == 1) || pDataArray->m->control_pressed) {  delete cparser; return 0; }
+                error = cparser->getSeqs(pDataArray->groups[i], pDataArray->filename, "/ab=", "/", numSeqs, true); if ((error == 1) || pDataArray->m->control_pressed) {  delete cparser; return 0; }
             }else {
-               error = parser->getSeqs(pDataArray->groups[i], pDataArray->filename, "/ab=", "/", true); if ((error == 1) || pDataArray->m->control_pressed) {  delete parser; return 0; }
+               error = parser->getSeqs(pDataArray->groups[i], pDataArray->filename, "/ab=", "/", numSeqs, 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);
+			//driver((outputFName + groups[i]), filename, (accnos+ groups[i]), (alns+ groups[i]), numChimeras);
 			////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 			
 			//to allow for spaces in the path