From: pschloss <pschloss>
Date: Wed, 9 Jun 2010 17:00:29 +0000 (+0000)
Subject: fixed bug in nast:removeextragaps
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=2a07f8664a7fd1ef0d572b88e8b5bede24cc0b3c

fixed bug in nast:removeextragaps
---

diff --git a/chimerarealigner.cpp b/chimerarealigner.cpp
index 0f2556a..9a25162 100644
--- a/chimerarealigner.cpp
+++ b/chimerarealigner.cpp
@@ -24,7 +24,7 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
 			
 			string qAligned = query->getAligned();
 			string newQuery = "";
-	//cout << qAligned.length() << endl;		
+		
 			//sort parents by region start
 			sort(parents.begin(), parents.end(), compareRegionStart);
 
@@ -56,6 +56,7 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
 			//align each peice to correct parent from results
 			for (int i = 0; i < queryParts.size(); i++) {
 				alignment = new NeedlemanOverlap(-2.0, match, misMatch, longest+1); //default gapopen, match, mismatch, longestbase
+				
 				Nast nast(alignment, queryParts[i], parentParts[i]);
 				delete alignment;
 			}
@@ -80,7 +81,7 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
 		
 			//set query to new aligned string
 			query->setAligned(newQuery);
-	//cout << newQuery.length() << endl;		
+
 			//free memory
 			for (int i = 0; i < queryParts.size(); i++) { delete queryParts[i];  }
 			for (int i = 0; i < parentParts.size(); i++) { delete parentParts[i];  }
diff --git a/nast.cpp b/nast.cpp
index 4a0b74a..50d3b24 100644
--- a/nast.cpp
+++ b/nast.cpp
@@ -102,7 +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++;		}
@@ -117,7 +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;	}
@@ -128,7 +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;
@@ -154,7 +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;
@@ -165,8 +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);
@@ -180,10 +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();
@@ -192,10 +192,11 @@ 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;
 			} 
 		}
 	}