continued work on chimeras and fixed bug in trim.seqs and reverse.seqs that was due...

[mothur.git] / nast.cpp

diff --git a/nast.cpp b/nast.cpp
index 804e3c174d4408c2ae55963ba391098002978c18..294940cd6aabd49f67aca028311d21529f0912ee 100644 (file)
--- a/nast.cpp
+++ b/nast.cpp
@@ -94,7 +94,7 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
        try {
        
                int longAlignmentLength = newTemplateAlign.length();    
-               
+       
                for(int i=0; i<longAlignmentLength; i++){                               //      use the long alignment as the standard
                        int rightIndex, rightRoom, leftIndex, leftRoom;
                        
@@ -123,7 +123,7 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
                                int insertLength = 0;                                                   //      figure out how long the anomaly is
                                while(!isalpha(newTemplateAlign[i + insertLength]))     {       insertLength++; }
                                if(insertLength > maxInsertLength){     maxInsertLength = insertLength; }
-                                       
+               
                                if((leftRoom + rightRoom) >= insertLength){
        
                                        //      Parts D & E from Fig. 2 of DeSantis et al.
@@ -168,6 +168,7 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
                                                                        
                                                }
                                                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);
@@ -183,7 +184,7 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
                                        }
                                }
                                else{
-                                                                                                       //      there could be a case where there isn't enough room in
+                       //      there could be a case where there isn't enough room in
                                        string leftTemplateString = newTemplateAlign.substr(0,i);                       //      either direction to move stuff
                                        string rightTemplateString = newTemplateAlign.substr(i+leftRoom+rightRoom);
                                        newTemplateAlign = leftTemplateString + rightTemplateString;
@@ -193,9 +194,9 @@ 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 -= insertLength;
                        } 
                }
@@ -337,12 +338,11 @@ void Nast::regapSequences(){      //This is essentially part B in Fig 2. of DeSantis
                        candAln[i] = toupper(candAln[i]);                       //      everything is upper case
                }
                
-               
+       
                if(candAln.length() != tempAln.length()){               //      if the regapped candidate sequence is longer than the official
                        removeExtraGaps(candAln, tempAln, newTemplateAlign);//  template alignment then we need to do steps C-F in Fig.
                }                                                                                               //      2 of Desantis et al.
-               
-               
+                       
                candidateSeq->setAligned(candAln);
        }
        catch(exception& e) {