Adds timestamp check to reference shortcut files

source/classifier/classify.cpp

@@ -45,6 +45,12 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
             ifstream kmerFileTest(kmerDBName.c_str());
             if(kmerFileTest){
                 bool GoodFile = m->checkReleaseVersion(kmerFileTest, m->getVersion());
+                int shortcutTimeStamp = m->getTimeStamp(kmerDBName);
+                int referenceTimeStamp = m->getTimeStamp(tempFile);
+                
+                //if the shortcut file is older then the reference file, remake shortcut file
+                if (shortcutTimeStamp < referenceTimeStamp) {  GoodFile = false;  }
+
                 if (GoodFile) {  needToGenerate = false;	}
             }
         }

source/commands/chimerauchimecommand.h

@@ -188,9 +188,9 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
             
 			int error;
             if (pDataArray->hasCount) { 
-                error = cparser->getSeqs(pDataArray->groups[i], pDataArray->filename, true); if ((error == 1) || pDataArray->m->control_pressed) {  delete cparser; return 0; }
+                error = cparser->getSeqs(pDataArray->groups[i], pDataArray->filename, "/ab=", "/", true); if ((error == 1) || pDataArray->m->control_pressed) {  delete cparser; return 0; }
             }else {
-               error = parser->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, "/ab=", "/", 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);

source/datastructures/alignmentdb.cpp

@@ -67,13 +67,19 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
 		string kmerDBName;
 		if(method == "kmer")			{	
 			search = new KmerDB(fastaFileName, kmerSize);			
-			
-			
+
             kmerDBName = fastaFileName.substr(0,fastaFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
+            
             ifstream kmerFileTest(kmerDBName.c_str());
 				
             if(kmerFileTest){
                 bool GoodFile = m->checkReleaseVersion(kmerFileTest, m->getVersion());
+                int shortcutTimeStamp = m->getTimeStamp(kmerDBName);
+                int referenceTimeStamp = m->getTimeStamp(fastaFileName);
+                
+                //if the shortcut file is older then the reference file, remake shortcut file
+                if (shortcutTimeStamp < referenceTimeStamp) {  GoodFile = false;  }
+                
                 if (GoodFile) {  needToGenerate = false;	}
             }
 			

source/mothurout.cpp

@@ -3927,27 +3927,6 @@ void MothurOut::splitAtDash(string& estim, vector<string>& container) {
 		string individual = "";
 		int estimLength = estim.size();
 		bool prevEscape = false;
-		/*for(int i=0;i<estimLength;i++){
-			if(prevEscape){
-				individual += estim[i];
-				prevEscape = false;
-			}
-			else{
-				if(estim[i] == '\\'){
-					prevEscape = true;
-				}
-				else if(estim[i] == '-'){
-					container.push_back(individual);
-					individual = "";
-					prevEscape = false;				
-				}
-				else{
-					individual += estim[i];
-					prevEscape = false;
-				}
-			}
-		}*/
-        
         
         for(int i=0;i<estimLength;i++){
             if(estim[i] == '-'){
@@ -3983,28 +3962,6 @@ void MothurOut::splitAtDash(string& estim, set<string>& container) {
 		string individual = "";
 		int estimLength = estim.size();
 		bool prevEscape = false;
-        /*
-		for(int i=0;i<estimLength;i++){
-			if(prevEscape){
-				individual += estim[i];
-				prevEscape = false;
-			}
-			else{
-				if(estim[i] == '\\'){
-					prevEscape = true;
-				}
-				else if(estim[i] == '-'){
-					container.insert(individual);
-					individual = "";
-					prevEscape = false;				
-				}
-				else{
-					individual += estim[i];
-					prevEscape = false;
-				}
-			}
-		}
-		*/
         
         for(int i=0;i<estimLength;i++){
             if(estim[i] == '-'){
@@ -4038,28 +3995,6 @@ void MothurOut::splitAtDash(string& estim, set<int>& container) {
 		int lineNum;
 		int estimLength = estim.size();
 		bool prevEscape = false;
-        /*
-		for(int i=0;i<estimLength;i++){
-			if(prevEscape){
-				individual += estim[i];
-				prevEscape = false;
-			}
-			else{
-				if(estim[i] == '\\'){
-					prevEscape = true;
-				}
-				else if(estim[i] == '-'){
-					convert(individual, lineNum); //convert the string to int
-					container.insert(lineNum);
-					individual = "";
-					prevEscape = false;				
-				}
-				else{
-					individual += estim[i];
-					prevEscape = false;
-				}
-			}
-		}*/
         
         for(int i=0;i<estimLength;i++){
             if(estim[i] == '-'){
@@ -4125,20 +4060,6 @@ void MothurOut::splitAtComma(string& estim, vector<string>& container) {
 		}
 		container.push_back(individual);
 		
-		
-		
-		
-//		string individual;
-//		
-//		while (estim.find_first_of(',') != -1) {
-//			individual = estim.substr(0,estim.find_first_of(','));
-//			if ((estim.find_first_of(',')+1) <= estim.length()) { //checks to make sure you don't have comma at end of string
-//				estim = estim.substr(estim.find_first_of(',')+1, estim.length());
-//				container.push_back(individual);
-//			}
-//		}
-//		//get last one
-//		container.push_back(estim);
 	}
 	catch(exception& e) {
 		errorOut(e, "MothurOut", "splitAtComma");
@@ -4163,18 +4084,6 @@ void MothurOut::splitAtChar(string& prefix, string& suffix, char c){
             }
         }
         
-        
-        /*
-        
-		prefix = suffix.substr(0,suffix.find_first_of(c));
-		if ((suffix.find_first_of(c)+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
-			suffix = suffix.substr(suffix.find_first_of(c)+1, suffix.length());
-			string space = " ";
-			while(suffix.at(0) == ' ')
-				suffix = suffix.substr(1, suffix.length());
-		}else {  suffix = "";  }
-         */
-        
     }
 	catch(exception& e) {
 		errorOut(e, "MothurOut", "splitAtChar");
@@ -4430,6 +4339,63 @@ bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
 	}
 }
 /**************************************************************************************************/
+int MothurOut::getTimeStamp(string filename) {
+    try {
+        int timeStamp = 0;
+        
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+        struct stat st;
+        int errorCode = stat (filename.c_str(), &st);
+        if (errorCode != 0) {
+            mothurOut("[ERROR]: Can't find timestamp for " + filename + "\n"); control_pressed = true;
+        }else {
+            timeStamp = st.st_mtime;
+        }
+#else
+        HANDLE hFile;
+        
+        hFile = CreateFile(filename.c_str(), GENERIC_READ, FILE_SHARE_READ, NULL,
+                           OPEN_EXISTING, 0, NULL);
+        
+        if(hFile == INVALID_HANDLE_VALUE) {
+            mothurOut("[ERROR]: Can't find timestamp for " + filename + "\n"); control_pressed = true;
+            return timestamp;
+        }
+            
+        FILETIME ftCreate, ftAccess, ftWrite;
+        SYSTEMTIME stUTC;
+        DWORD dwRet;
+        
+        // Retrieve the file times for the file.
+        bool success = GetFileTime(hFile, &ftCreate, &ftAccess, &ftWrite);
+        
+        if (success) {
+            FileTimeToSystemTime(&ftWrite, &stUTC);
+            
+            tm time;
+            time.tm_sec = stUTC.wSecond;
+            time.tm_min = stUTC.wMinute;
+            time.tm_hour = stUTC.wHour;
+            time.tm_mday = stUTC.wDay;
+            time.tm_mon = stUTC.wMonth - 1;
+            time.tm_year = stUTC.wYear - 1900;
+            time.tm_isdst = -1;
+            time_t t = mktime(&time);
+            
+            timeStamp = t;
+        }
+        else { mothurOut("[ERROR]: Can't find timestamp for " + filename + "\n"); control_pressed = true; }
+        
+#endif
+    
+        return timeStamp;
+    }
+    catch(exception& e) {
+        errorOut(e, "MothurOut", "getTimeStamp");
+        exit(1);
+    }
+}
+/**************************************************************************************************/
 vector<double> MothurOut::getAverages(vector< vector<double> >& dists) {
 	try{
         vector<double> averages; //averages.resize(numComp, 0.0);

source/mothurout.h

@@ -150,6 +150,7 @@ class MothurOut {
 		
 		//searchs and checks
 		bool checkReleaseVersion(ifstream&, string);
+        int getTimeStamp(string filename);
 		bool anyLabelsToProcess(string, set<string>&, string);
 		bool inUsersGroups(vector<string>, vector<string>); //returns true if any of the strings in first vector are in second vector
         bool inUsersGroups(vector<int>, vector< vector<int> >);

source/trimoligos.cpp

@@ -1615,7 +1615,7 @@ vector<int> TrimOligos::stripForward(Sequence& forwardSeq, Sequence& reverseSeq,
                 //check for reverse match
                 if (alignment != NULL) { delete alignment; }
                 
-                if (irbarcodes.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxRPrimerLength+pdiffs+1)); }
+                if (irprimers.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxRPrimerLength+pdiffs+1)); }
                 else{ alignment = NULL; }
                 
                 //can you find the barcode