X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=nast.cpp;h=b2887523532c6b6bcaef1ca61b2c748a9ad77d14;hb=c6e5f84783b39a558119835963dec3c4facb0154;hp=8ed69fa6820cca9003dd8af1a0cb148c85899753;hpb=202846c98b9eff0eca7b20a570bfffa8ee4a5f4e;p=mothur.git

diff --git a/nast.cpp b/nast.cpp
index 8ed69fa..b288752 100644
--- a/nast.cpp
+++ b/nast.cpp
@@ -99,7 +99,7 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 	
 		for(int i=0; i<longAlignmentLength; i++){				//	use the long alignment as the standard
 			int rightIndex, rightRoom, leftIndex, leftRoom;
-			
+	
 			//	Part C of Fig. 2 from DeSantis et al.
 			if((isalpha(newTemplateAlign[i]) != isalpha(tempAln[i]))){	//if there is a discrepancy between the regapped
 				
@@ -132,12 +132,12 @@ 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
-			//cout << "lr newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << i+insertLength << endl;
+			//cout << "lr newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << insertLength << endl;
 							string leftTemplateString = newTemplateAlign.substr(0,i);
 							string rightTemplateString = newTemplateAlign.substr((i+insertLength));
 							newTemplateAlign = leftTemplateString + rightTemplateString;
 							longAlignmentLength = newTemplateAlign.length();
-			//cout << "lr candAln = " << candAln.length() << '\t' << leftIndex-insertLength+1 << '\t' << leftIndex+1 << endl;				
+			//cout << "lr candAln = " << candAln.length() << '\t' << leftIndex << '\t'  << endl;				
 							string leftCandidateString = candAln.substr(0,(leftIndex-insertLength+1));
 							string rightCandidateString = candAln.substr((leftIndex+1));
 							candAln = leftCandidateString + rightCandidateString;
@@ -145,12 +145,12 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 						}
 						else{									//	not enough room to the left, have to steal some space to
 						
-			//cout << "in else lr newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << i+insertLength << endl;
+			//cout << "in else lr newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << insertLength << endl;
 							string leftTemplateString = newTemplateAlign.substr(0,i);	//	the right
 							string rightTemplateString = newTemplateAlign.substr((i+insertLength));
 							newTemplateAlign = leftTemplateString + rightTemplateString;
 							longAlignmentLength = newTemplateAlign.length();
-			//cout << " in else lr candAln = " << candAln.length() << '\t' << leftIndex-leftRoom+1 << '\t' << rightIndex-leftIndex-1 << '\t' << rightIndex+(insertLength-leftRoom) << endl;					
+			//cout << " in else lr candAln = " << candAln.length() << '\t' << " leftIndex = " << leftIndex << " leftroom = " << leftRoom << " rightIndex = " << rightIndex << '\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)));
@@ -207,6 +207,9 @@ 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; }
 			} 
 		}
 	}
@@ -220,7 +223,7 @@ 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 = "";
 		
@@ -249,6 +252,7 @@ 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
@@ -355,6 +359,7 @@ 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");