changes for 1.12.2

[mothur.git] / nast.cpp

diff --git a/nast.cpp b/nast.cpp
index 9e26b11a7708590389f59b1c82e76ebca72f1bc1..8ed69fa6820cca9003dd8af1a0cb148c85899753 100644 (file)
--- a/nast.cpp
+++ b/nast.cpp
@@ -132,51 +132,56 @@ 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;
                                                        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-insertLength+1 << '\t' << leftIndex+1 << 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
+                                               
+                       //cout << "in else lr newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << i+insertLength << endl;
                                                        string leftTemplateString = newTemplateAlign.substr(0,i);       //      the right
-                                                       string rightTemplateString = newTemplateAlign.substr(i+insertLength);
+                                                       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-leftRoom+1 << '\t' << rightIndex-leftIndex-1 << '\t' << rightIndex+(insertLength-leftRoom) << 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
                                                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;    
                                                                        
                                                }
@@ -186,15 +191,16 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
                                }
                                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);