X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=nast.cpp;h=50d3b2440f3a2523257d20faabba51098b345cd4;hb=2a07f8664a7fd1ef0d572b88e8b5bede24cc0b3c;hp=f247037cc915fd1d54d9d1e050abde8f73711fba;hpb=c4fb347858dd8cfea4d2933f429fff4130dca65b;p=mothur.git

diff --git a/nast.cpp b/nast.cpp
index f247037..50d3b24 100644
--- a/nast.cpp
+++ b/nast.cpp
@@ -23,16 +23,15 @@
 
 Nast::Nast(Alignment* method, Sequence* cand, Sequence* temp) : alignment(method), candidateSeq(cand), templateSeq(temp) {
 	try {
+		m = MothurOut::getInstance();
 		maxInsertLength = 0;
 		pairwiseAlignSeqs();	//	This is part A in Fig. 2 of DeSantis et al.
 		regapSequences();		//	This is parts B-F in Fig. 2 of DeSantis et al.
-
 	}
 	catch(exception& e) {
-		errorOut(e, "Nast", "Nast");
+		m->errorOut(e, "Nast", "Nast");
 		exit(1);
 	}
-
 }
 
 /**************************************************************************************************/
@@ -40,12 +39,12 @@ Nast::Nast(Alignment* method, Sequence* cand, Sequence* temp) : alignment(method
 void Nast::pairwiseAlignSeqs(){	//	Here we call one of the pairwise alignment methods to align our unaligned candidate
 								//	and template sequences
 	try {
-		
+
 		alignment->align(candidateSeq->getUnaligned(), templateSeq->getUnaligned());
-	
+
 		string candAln = alignment->getSeqAAln();
 		string tempAln = alignment->getSeqBAln();
-
+	
 		if(candAln == ""){
 
 			candidateSeq->setPairwise("");
@@ -78,10 +77,9 @@ void Nast::pairwiseAlignSeqs(){	//	Here we call one of the pairwise alignment me
 
 		candidateSeq->setPairwise(candAln);					//	set the pairwise sequences in the Sequence objects for
 		templateSeq->setPairwise(tempAln);					//	the candidate and template sequences
-
 	}
 	catch(exception& e) {
-		errorOut(e, "Nast", "pairwiseAlignSeqs");
+		m->errorOut(e, "Nast", "pairwiseAlignSeqs");
 		exit(1);
 	}	
 }
@@ -104,7 +102,7 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 				rightRoom = 0; leftRoom = 0;
 				
 				//	Part D of Fig. 2 from DeSantis et al.		//	template sequence and the official template sequence
-				for(leftIndex=i-1;leftIndex>0;leftIndex--){	//	then we've got problems...
+				for(leftIndex=i-1;leftIndex>0;leftIndex--){		//	then we've got problems...
 					if(!isalpha(candAln[leftIndex])){
 						leftRoom = 1;	//count how far it is to the nearest gap on the LEFT side of the anomaly
 						while(leftIndex-leftRoom>=0 && !isalpha(candAln[leftIndex-leftRoom]))	{	leftRoom++;		}
@@ -119,7 +117,7 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 						break;
 					}
 				}
-					
+								
 				int insertLength = 0;							//	figure out how long the anomaly is
 				while(!isalpha(newTemplateAlign[i + insertLength]))	{	insertLength++;	}
 				if(insertLength > maxInsertLength){	maxInsertLength = insertLength;	}
@@ -130,7 +128,6 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 					if((i-leftIndex) <= (rightIndex-i)){		//	the left gap is closer - > move stuff left there's
 	
 						if(leftRoom >= insertLength){			//	enough room to the left to move
-	
 							string leftTemplateString = newTemplateAlign.substr(0,i);
 							string rightTemplateString = newTemplateAlign.substr(i+insertLength);
 							newTemplateAlign = leftTemplateString + rightTemplateString;
@@ -156,7 +153,6 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 					}
 					else{										//	the right gap is closer - > move stuff right there's
 						if(rightRoom >= insertLength){			//	enough room to the right to move
-			
 							string leftTemplateString = newTemplateAlign.substr(0,i);
 							string rightTemplateString = newTemplateAlign.substr(i+insertLength);
 							newTemplateAlign = leftTemplateString + rightTemplateString;
@@ -167,8 +163,7 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 							candAln = leftCandidateString + rightCandidateString;	
 									
 						}
-						else{									//	not enough room to the right, have to steal some 
-			
+						else{									//	not enough room to the right, have to steal some 	
 							//	space to the left lets move left and then right...
 							string leftTemplateString = newTemplateAlign.substr(0,i);
 							string rightTemplateString = newTemplateAlign.substr(i+insertLength);
@@ -182,10 +177,13 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 									
 						}
 					}
+					i -= insertLength;
+
 				}
 				else{
-			//	there could be a case where there isn't enough room in
-					string leftTemplateString = newTemplateAlign.substr(0,i);			//	either direction to move stuff
+			//	there could be a case where there isn't enough room in either direction to move stuff
+
+					string leftTemplateString = newTemplateAlign.substr(0,i);	
 					string rightTemplateString = newTemplateAlign.substr(i+leftRoom+rightRoom);
 					newTemplateAlign = leftTemplateString + rightTemplateString;
 					longAlignmentLength = newTemplateAlign.length();
@@ -194,15 +192,16 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 					string insertString = candAln.substr(leftIndex+1,rightIndex-leftIndex-1);
 					string rightCandidateString = candAln.substr(rightIndex+rightRoom);
 					candAln = leftCandidateString + insertString + rightCandidateString;
-
+					
+					i -= (leftRoom + rightRoom);
 				}
 			
-				i -= insertLength;
+//				i -= insertLength;
 			} 
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "Nast", "removeExtraGaps");
+		m->errorOut(e, "Nast", "removeExtraGaps");
 		exit(1);
 	}	
 }
@@ -305,14 +304,14 @@ void Nast::regapSequences(){	//This is essentially part B in Fig 2. of DeSantis
 				//	would skip the gaps and not progress through full alignment sequence
 				//	not tested yet
 				
-				mothurOut("We're into D " + toString(fullAlignIndex) + " " +  toString(pairwiseAlignIndex)); mothurOutEndLine();
+				m->mothurOut("We're into D " + toString(fullAlignIndex) + " " +  toString(pairwiseAlignIndex)); m->mothurOutEndLine();
 				pairwiseAlignIndex++;
 			}
 			else{
 				//	everything has a gap - not possible
 				//	not tested yet
 				
-				mothurOut("We're into F " +  toString(fullAlignIndex) + " " +  toString(pairwiseAlignIndex)); mothurOutEndLine();
+				m->mothurOut("We're into F " +  toString(fullAlignIndex) + " " +  toString(pairwiseAlignIndex)); m->mothurOutEndLine();
 				pairwiseAlignIndex++;
 				fullAlignIndex++;			
 			}		
@@ -348,7 +347,7 @@ void Nast::regapSequences(){	//This is essentially part B in Fig 2. of DeSantis
 		candidateSeq->setAligned(candAln);
 	}
 	catch(exception& e) {
-		errorOut(e, "Nast", "regapSequences");
+		m->errorOut(e, "Nast", "regapSequences");
 		exit(1);
 	}	
 }
@@ -383,7 +382,7 @@ float Nast::getSimilarityScore(){
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "Nast", "getSimilarityScore");
+		m->errorOut(e, "Nast", "getSimilarityScore");
 		exit(1);
 	}	
 }