X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=nast.cpp;h=647e0e4f1e17e205c183c78615a966b7a98545cc;hp=9cdf1b26619a170b7f7d67cc9edc60d89d66559a;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=515c3398ea27e2105f616fc5662b2a7ceb486aa0

diff --git a/nast.cpp b/nast.cpp
index 9cdf1b2..647e0e4 100644
--- a/nast.cpp
+++ b/nast.cpp
@@ -25,8 +25,10 @@ Nast::Nast(Alignment* method, Sequence* cand, Sequence* temp) : alignment(method
 	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) {
 		m->errorOut(e, "Nast", "Nast");
@@ -43,7 +45,7 @@ void Nast::pairwiseAlignSeqs(){	//	Here we call one of the pairwise alignment me
 
 		string candAln = alignment->getSeqAAln();
 		string tempAln = alignment->getSeqBAln();
-
+	
 		if(candAln == ""){
 
 			candidateSeq->setPairwise("");
@@ -76,6 +78,7 @@ 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) {
 		m->errorOut(e, "Nast", "pairwiseAlignSeqs");
@@ -89,11 +92,6 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 
 //	here we do steps C-F of Fig. 2 from DeSantis et al.
 	try {
-	
-		//cout << candAln << endl;
-		//cout << tempAln << endl;
-		//cout << newTemplateAlign << endl;
-		//cout << endl;
 		
 		int longAlignmentLength = newTemplateAlign.length();	
 	
@@ -141,24 +139,22 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 							string leftCandidateString = candAln.substr(0,(leftIndex-insertLength+1));
 							string rightCandidateString = candAln.substr((leftIndex+1));
 							candAln = leftCandidateString + rightCandidateString;
-		
-						}
-						else{									//	not enough room to the left, have to steal some space to
+							
+						}else{									//	not enough room to the left, have to steal some space to the right
 						
 			//cout << "in else lr newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << insertLength << endl;
-							string leftTemplateString = newTemplateAlign.substr(0,i);	//	the right
+							string leftTemplateString = newTemplateAlign.substr(0,i);	
 							string rightTemplateString = newTemplateAlign.substr((i+insertLength));
 							newTemplateAlign = leftTemplateString + rightTemplateString;
 							longAlignmentLength = newTemplateAlign.length();
-			//cout << " in else lr candAln = " << candAln.length() << '\t' << " leftIndex = " << leftIndex << " leftroom = " << leftRoom << " rightIndex = " << rightIndex << '\t' << endl;					
+			//cout << " in else lr candAln = " << candAln.length() << '\t' << " leftIndex = " << leftIndex << " leftroom = " << leftRoom << " rightIndex = " << rightIndex << '\t' << " rightroom = " << rightRoom << '\t' << endl;					
 							string leftCandidateString = candAln.substr(0,(leftIndex-leftRoom+1));
 							string insertString = candAln.substr((leftIndex+1),(rightIndex-leftIndex-1));
 							string rightCandidateString = candAln.substr((rightIndex+(insertLength-leftRoom)));
 							candAln = leftCandidateString + insertString + rightCandidateString;
 				
 						}
-					}
-					else{										//	the right gap is closer - > move stuff right there's
+					}else{										//	the right gap is closer - > move stuff right there's
 						if(rightRoom >= insertLength){			//	enough room to the right to move
 			//cout << "rr newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << i+insertLength << endl;
 							string leftTemplateString = newTemplateAlign.substr(0,i);
@@ -186,7 +182,9 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 									
 						}
 					}
-					i -= insertLength;
+					
+					if ((i - insertLength) < 0) {  i = 0; }
+					else { i -= insertLength; }
 
 				}
 				else{
@@ -209,7 +207,7 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 //				i -= insertLength;
 				
 				//if i is negative, we want to remove the extra gaps to the right
-				if (i < 0) { cout << "i is negative" << endl; }
+				if (i < 0) { m->mothurOut("i is negative"); m->mothurOutEndLine(); } 
 			} 
 		}
 	}
@@ -223,7 +221,7 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 
 void Nast::regapSequences(){	//This is essentially part B in Fig 2. of DeSantis et al.
 	try { 
-	
+	//cout << candidateSeq->getName() << endl;
 		string candPair = candidateSeq->getPairwise();
 		string candAln = "";
 		
@@ -252,6 +250,7 @@ void Nast::regapSequences(){	//This is essentially part B in Fig 2. of DeSantis
 		string lastLoop = "";
 		
 		while(pairwiseAlignIndex<pairwiseLength){
+	//cout << pairwiseAlignIndex << '\t' << fullAlignIndex << '\t' << pairwiseLength << endl;
 			if(isalpha(tempPair[pairwiseAlignIndex]) && isalpha(tempAln[fullAlignIndex])
 			   && isalpha(candPair[pairwiseAlignIndex])){
 				//  the template and candidate pairwise and template aligned have characters
@@ -358,6 +357,7 @@ void Nast::regapSequences(){	//This is essentially part B in Fig 2. of DeSantis
 		}												//	2 of Desantis et al.
 
 		candidateSeq->setAligned(candAln);
+	//cout << "here" << endl;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "Nast", "regapSequences");