fixed bug in nast:removeextragaps

diff --git a/chimerarealigner.cpp b/chimerarealigner.cpp
index 0f2556aff6983107067635fba4015f88c9e9d33a..9a25162bd60fcd35b25c18073947f1a8f6502673 100644 (file)
--- 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 4a0b74aa412873b6bf98ee1b9e30e28a9cc8c21f..50d3b2440f3a2523257d20faabba51098b345cd4 100644 (file)
--- 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;
                        } 
                }
        }