X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.cpp;h=8215de301b646f4d4571944de85dddb40478e7e5;hb=36a6b02cf7f09d2bc34376b588944a9ca73429c5;hp=389235a034918aa556d95e40bd05d98e95cc49ed;hpb=e8c014de33edac1fb91d7593e143bf1f5107ffce;p=mothur.git

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 389235a..8215de3 100644
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -16,7 +16,7 @@
 
 #include "aligncommand.h"
 #include "referencedb.h"
-//test comm
+
 //**********************************************************************************************************************
 vector<string> AlignCommand::setParameters(){	
 	try {
@@ -422,7 +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
@@ -430,7 +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++) {
@@ -617,7 +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
@@ -826,7 +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