X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pairwiseseqscommand.cpp;h=a4ccbf8f33b34b5dd8eccebf91242249cc465f28;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=ed11dfbdd56e0ff480bfd281b944dcaa1fab34eb;hpb=a78fa674631a7d8a8d4e5043384ee244ed65cc09;p=mothur.git

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index ed11dfb..a4ccbf8 100644
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -203,12 +203,15 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
 			
 			temp = validParameter.validFile(parameters, "mismatch", false);		if (temp == "not found"){	temp = "-1.0";			}
 			m->mothurConvert(temp, misMatch);  
+            if (misMatch > 0) { m->mothurOut("[ERROR]: mismatch must be negative.\n"); abort=true; }
 			
 			temp = validParameter.validFile(parameters, "gapopen", false);		if (temp == "not found"){	temp = "-2.0";			}
 			m->mothurConvert(temp, gapOpen);  
+            if (gapOpen > 0) { m->mothurOut("[ERROR]: gapopen must be negative.\n"); abort=true; }
 			
 			temp = validParameter.validFile(parameters, "gapextend", false);	if (temp == "not found"){	temp = "-1.0";			}
 			m->mothurConvert(temp, gapExtend); 
+            if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
@@ -393,7 +396,7 @@ int PairwiseSeqsCommand::execute(){
 					if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
 					else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
 					
-					if (m->control_pressed) { delete distCalculator;  return 0; }
+					if (m->control_pressed) {  return 0; }
 				
 					//tell parent you are done.
 					MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
@@ -402,7 +405,7 @@ int PairwiseSeqsCommand::execute(){
 			MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 	#else		
 					
-		//#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		//#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			//if you don't need to fork anything
 			if(processors == 1){
 				if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
@@ -494,7 +497,7 @@ void PairwiseSeqsCommand::createProcesses(string filename) {
         int process = 1;
 		processIDS.clear();
         
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		
 		
 		//loop through and create all the processes you want
@@ -991,6 +994,22 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi
 			alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
 		}
 		
+        ValidCalculators validCalculator;
+        Dist* distCalculator;
+        if (countends) {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")			{	distCalculator = new ignoreGaps();	}
+                else if (Estimators[0] == "eachgap")	{	distCalculator = new eachGapDist();	}
+                else if (Estimators[0] == "onegap")		{	distCalculator = new oneGapDist();	}
+            }
+        }else {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")		{	distCalculator = new ignoreGaps();					}
+                else if (Estimators[0] == "eachgap"){	distCalculator = new eachGapIgnoreTermGapDist();	}
+                else if (Estimators[0] == "onegap")	{	distCalculator = new oneGapIgnoreTermGapDist();		}
+            }
+        }
+        
 		string outputString = "";
 		size = 0;