X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.cpp;h=8215de301b646f4d4571944de85dddb40478e7e5;hb=36a6b02cf7f09d2bc34376b588944a9ca73429c5;hp=960d70229a084923fd1cc8dc368ff4b71d815cbd;hpb=ae57e166b2ed7b475ec3f466106bd76fabadd063;p=mothur.git

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 960d702..8215de3 100644
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -224,34 +224,29 @@ AlignCommand::AlignCommand(string option)  {
 			// ...at some point should added some additional type checking...
 			string temp;
 			temp = validParameter.validFile(parameters, "ksize", false);		if (temp == "not found"){	temp = "8";				}
-			convert(temp, kmerSize); 
+			m->mothurConvert(temp, kmerSize); 
 			
 			temp = validParameter.validFile(parameters, "match", false);		if (temp == "not found"){	temp = "1.0";			}
-			convert(temp, match);  
+			m->mothurConvert(temp, match);  
 			
 			temp = validParameter.validFile(parameters, "mismatch", false);		if (temp == "not found"){	temp = "-1.0";			}
-			convert(temp, misMatch);  
+			m->mothurConvert(temp, misMatch);  
 			
 			temp = validParameter.validFile(parameters, "gapopen", false);		if (temp == "not found"){	temp = "-2.0";			}
-			convert(temp, gapOpen);  
+			m->mothurConvert(temp, gapOpen);  
 			
 			temp = validParameter.validFile(parameters, "gapextend", false);	if (temp == "not found"){	temp = "-1.0";			}
-			convert(temp, gapExtend); 
+			m->mothurConvert(temp, gapExtend); 
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors); 
+			m->mothurConvert(temp, processors); 
 			
 			temp = validParameter.validFile(parameters, "flip", false);			if (temp == "not found"){	temp = "f";				}
 			flip = m->isTrue(temp); 
 			
 			temp = validParameter.validFile(parameters, "save", false);			if (temp == "not found"){	temp = "f";				}
 			save = m->isTrue(temp); 
-			//this is so the threads can quickly load the reference data
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-			#else
-				if (processors != 1) { save = true; }
-			#endif
 			rdb->save = save; 
 			if (save) { //clear out old references
 				rdb->clearMemory();
@@ -272,7 +267,7 @@ AlignCommand::AlignCommand(string option)  {
 			else {	if (save) {	rdb->setSavedReference(templateFileName);	}	}
 			
 			temp = validParameter.validFile(parameters, "threshold", false);	if (temp == "not found"){	temp = "0.50";			}
-			convert(temp, threshold); 
+			m->mothurConvert(temp, threshold); 
 			
 			search = validParameter.validFile(parameters, "search", false);		if (search == "not found"){	search = "kmer";		}
 			if ((search != "suffix") && (search != "kmer") && (search != "blast")) { m->mothurOut("invalid search option: choices are kmer, suffix or blast."); m->mothurOutEndLine(); abort=true; }
@@ -427,7 +422,7 @@ int AlignCommand::execute(){
 #else
 
 			vector<unsigned long long> positions; 
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			positions = m->divideFile(candidateFileNames[s], processors);
 			for (int i = 0; i < (positions.size()-1); i++) {	lines.push_back(new linePair(positions[i], positions[(i+1)]));	}
 		#else
@@ -435,7 +430,8 @@ int AlignCommand::execute(){
 				lines.push_back(new linePair(0, 1000));
 			}else {
 				positions = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); 
-				
+				if (positions.size() < processors) { processors = positions.size(); }
+                
 				//figure out how many sequences you have to process
 				int numSeqsPerProcessor = numFastaSeqs / processors;
 				for (int i = 0; i < processors; i++) {
@@ -622,7 +618,7 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
 			}
 			delete candidateSeq;
 			
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				unsigned long long pos = inFASTA.tellg();
 				if ((pos == -1) || (pos >= filePos->end)) { break; }
 			#else
@@ -831,7 +827,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
 	try {
 		int num = 0;
 		processIDS.resize(0);
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		int process = 1;
 		
 		//loop through and create all the processes you want
@@ -923,7 +919,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
 			string extension = "";
 			if (i != 0) { extension = toString(i) + ".temp"; }
 			
-			alignData* tempalign = new alignData((alignFileName + extension), (reportFileName + extension), (accnosFName + extension), filename, align, search, kmerSize, m, lines[i]->start, lines[i]->end, flip, match, misMatch, gapOpen, gapExtend, threshold, i);
+			alignData* tempalign = new alignData(templateFileName, (alignFileName + extension), (reportFileName + extension), (accnosFName + extension), filename, align, search, kmerSize, m, lines[i]->start, lines[i]->end, flip, match, misMatch, gapOpen, gapExtend, threshold, i);
 			pDataArray.push_back(tempalign);
 			processIDS.push_back(i);