X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=nast.cpp;h=804e3c174d4408c2ae55963ba391098002978c18;hb=9a339a6b007b23c39b7eb20cc777af66dd2cebef;hp=4aed5903aec4985f92d5668d39301cabe3d779e6;hpb=db2df3a6a0e6354a666472ede1de74642cfeb06b;p=mothur.git

diff --git a/nast.cpp b/nast.cpp
index 4aed590..804e3c1 100644
--- a/nast.cpp
+++ b/nast.cpp
@@ -53,7 +53,6 @@ void Nast::pairwiseAlignSeqs(){	//	Here we call one of the pairwise alignment me
 
 		}
 		else{
-
 			if(tempAln[0] == '-'){
 				int pairwiseAlignmentLength = tempAln.length();	//	we need to make sure that the candidate sequence alignment
 				for(int i=0;i<pairwiseAlignmentLength;i++){		//	starts where the template sequence alignment starts, if it
@@ -64,7 +63,6 @@ void Nast::pairwiseAlignSeqs(){	//	Here we call one of the pairwise alignment me
 					}
 				}
 			}
-			
 			int pairwiseAlignmentLength = tempAln.length();
 			if(tempAln[pairwiseAlignmentLength-1] == '-'){		//	we need to make sure that the candidate sequence alignment
 				for(int i=pairwiseAlignmentLength-1; i>=0; i--){//	ends where the template sequence alignment ends, if it runs
@@ -113,8 +111,7 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 						break;
 					}
 				}
-				
-				
+
 				for(rightIndex=i+1;rightIndex<longAlignmentLength-1;rightIndex++){
 					if(!isalpha(candAln[rightIndex])){
 						rightRoom = 1;	//count how far it is to the nearest gap on the RIGHT side of the anomaly
@@ -207,7 +204,6 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 		errorOut(e, "Nast", "removeExtraGaps");
 		exit(1);
 	}	
-	
 }
 
 /**************************************************************************************************/
@@ -239,7 +235,7 @@ void Nast::regapSequences(){	//This is essentially part B in Fig 2. of DeSantis
 			newTemplateAlign += tempAln[fullAlignIndex];//	pairwise sequences
 			fullAlignIndex++;
 		}
-		
+
 		string lastLoop = "";
 		
 		while(pairwiseAlignIndex<pairwiseLength){