X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=nast.cpp;h=647e0e4f1e17e205c183c78615a966b7a98545cc;hp=50d3b2440f3a2523257d20faabba51098b345cd4;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=2a07f8664a7fd1ef0d572b88e8b5bede24cc0b3c

diff --git a/nast.cpp b/nast.cpp
index 50d3b24..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");
@@ -38,8 +40,7 @@ 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 {
-
+	try {	
 		alignment->align(candidateSeq->getUnaligned(), templateSeq->getUnaligned());
 
 		string candAln = alignment->getSeqAAln();
@@ -77,6 +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");
@@ -90,12 +92,12 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 
 //	here we do steps C-F of Fig. 2 from DeSantis et al.
 	try {
-	
+		
 		int longAlignmentLength = newTemplateAlign.length();	
 	
 		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
 				
@@ -128,75 +130,84 @@ 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' << insertLength << endl;
 							string leftTemplateString = newTemplateAlign.substr(0,i);
-							string rightTemplateString = newTemplateAlign.substr(i+insertLength);
+							string rightTemplateString = newTemplateAlign.substr((i+insertLength));
 							newTemplateAlign = leftTemplateString + rightTemplateString;
 							longAlignmentLength = newTemplateAlign.length();
-							
-							string leftCandidateString = candAln.substr(0,leftIndex-insertLength+1);
-							string rightCandidateString = candAln.substr(leftIndex+1);
+			//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;
-		
-						}
-						else{									//	not enough room to the left, have to steal some space to
-							string leftTemplateString = newTemplateAlign.substr(0,i);	//	the right
-							string rightTemplateString = newTemplateAlign.substr(i+insertLength);
+							
+						}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);	
+							string rightTemplateString = newTemplateAlign.substr((i+insertLength));
 							newTemplateAlign = leftTemplateString + rightTemplateString;
 							longAlignmentLength = newTemplateAlign.length();
-							
-							string leftCandidateString = candAln.substr(0,leftIndex-leftRoom+1);
-							string insertString = candAln.substr(leftIndex+1,rightIndex-leftIndex-1);
-							string rightCandidateString = candAln.substr(rightIndex+(insertLength-leftRoom));
+			//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);
-							string rightTemplateString = newTemplateAlign.substr(i+insertLength);
+							string rightTemplateString = newTemplateAlign.substr((i+insertLength));
 							newTemplateAlign = leftTemplateString + rightTemplateString;
 							longAlignmentLength = newTemplateAlign.length();
-							
+			//cout << "rr candAln = " << candAln.length() << '\t' << i << '\t' << rightIndex << '\t' << rightIndex+insertLength << endl;				
 							string leftCandidateString = candAln.substr(0,rightIndex);
-							string rightCandidateString = candAln.substr(rightIndex+insertLength);
+							string rightCandidateString = candAln.substr((rightIndex+insertLength));
 							candAln = leftCandidateString + rightCandidateString;	
 									
 						}
 						else{									//	not enough room to the right, have to steal some 	
 							//	space to the left lets move left and then right...
+					//cout << "in else rr newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << i+insertLength << endl;
 							string leftTemplateString = newTemplateAlign.substr(0,i);
-							string rightTemplateString = newTemplateAlign.substr(i+insertLength);
+							string rightTemplateString = newTemplateAlign.substr((i+insertLength));
 							newTemplateAlign = leftTemplateString + rightTemplateString;
 							longAlignmentLength = newTemplateAlign.length();
-									
-							string leftCandidateString = candAln.substr(0,leftIndex-(insertLength-rightRoom)+1);
-							string insertString = candAln.substr(leftIndex+1,rightIndex-leftIndex-1);
-							string rightCandidateString = candAln.substr(rightIndex+rightRoom);
+					//cout << "in else rr candAln = " << candAln.length() << '\t' << '\t' << (leftIndex-(insertLength-rightRoom)+1) << '\t' <<  (leftIndex+1,rightIndex-leftIndex-1) << '\t' << (rightIndex+rightRoom) << endl;				
+							string leftCandidateString = candAln.substr(0,(leftIndex-(insertLength-rightRoom)+1));
+							string insertString = candAln.substr((leftIndex+1),(rightIndex-leftIndex-1));
+							string rightCandidateString = candAln.substr((rightIndex+rightRoom));
 							candAln = leftCandidateString + insertString + rightCandidateString;	
 									
 						}
 					}
-					i -= insertLength;
+					
+					if ((i - insertLength) < 0) {  i = 0; }
+					else { i -= insertLength; }
 
 				}
 				else{
 			//	there could be a case where there isn't enough room in either direction to move stuff
-
+//cout << "in else else newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << (i+leftRoom+rightRoom) << endl;
 					string leftTemplateString = newTemplateAlign.substr(0,i);	
-					string rightTemplateString = newTemplateAlign.substr(i+leftRoom+rightRoom);
+					string rightTemplateString = newTemplateAlign.substr((i+leftRoom+rightRoom));
 					newTemplateAlign = leftTemplateString + rightTemplateString;
 					longAlignmentLength = newTemplateAlign.length();
 							
-					string leftCandidateString = candAln.substr(0,leftIndex-leftRoom+1);
-					string insertString = candAln.substr(leftIndex+1,rightIndex-leftIndex-1);
-					string rightCandidateString = candAln.substr(rightIndex+rightRoom);
+		//cout << "in else else newTemplateAlign = " << candAln.length() << '\t' << (leftIndex-leftRoom+1) << '\t' << (leftIndex+1) << '\t' << (rightIndex-leftIndex-1) << '\t' << (rightIndex+rightRoom) << endl;	
+					string leftCandidateString = candAln.substr(0,(leftIndex-leftRoom+1));
+					string insertString = candAln.substr((leftIndex+1),(rightIndex-leftIndex-1));
+					string rightCandidateString = candAln.substr((rightIndex+rightRoom));
 					candAln = leftCandidateString + insertString + rightCandidateString;
 					
 					i -= (leftRoom + rightRoom);
 				}
 			
 //				i -= insertLength;
+				
+				//if i is negative, we want to remove the extra gaps to the right
+				if (i < 0) { m->mothurOut("i is negative"); m->mothurOutEndLine(); } 
 			} 
 		}
 	}
@@ -210,7 +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 = "";
 		
@@ -239,6 +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
@@ -345,6 +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");