pat's edits prior to v.1.5

[mothur.git] / nast.cpp

diff --git a/nast.cpp b/nast.cpp
index 4aed5903aec4985f92d5668d39301cabe3d779e6..804e3c174d4408c2ae55963ba391098002978c18 100644 (file)
--- a/nast.cpp
+++ b/nast.cpp
@@ -53,7 +53,6 @@ void Nast::pairwiseAlignSeqs(){       //      Here we call one of the pairwise alignment me
 
                }
                else{
-
                        if(tempAln[0] == '-'){
                                int pairwiseAlignmentLength = tempAln.length(); //      we need to make sure that the candidate sequence alignment
                                for(int i=0;i<pairwiseAlignmentLength;i++){             //      starts where the template sequence alignment starts, if it
@@ -64,7 +63,6 @@ void Nast::pairwiseAlignSeqs(){       //      Here we call one of the pairwise alignment me
                                        }
                                }
                        }
-                       
                        int pairwiseAlignmentLength = tempAln.length();
                        if(tempAln[pairwiseAlignmentLength-1] == '-'){          //      we need to make sure that the candidate sequence alignment
                                for(int i=pairwiseAlignmentLength-1; i>=0; i--){//      ends where the template sequence alignment ends, if it runs
@@ -113,8 +111,7 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
                                                break;
                                        }
                                }
-                               
-                               
+
                                for(rightIndex=i+1;rightIndex<longAlignmentLength-1;rightIndex++){
                                        if(!isalpha(candAln[rightIndex])){
                                                rightRoom = 1;  //count how far it is to the nearest gap on the RIGHT side of the anomaly
@@ -207,7 +204,6 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
                errorOut(e, "Nast", "removeExtraGaps");
                exit(1);
        }       
-       
 }
 
 /**************************************************************************************************/
@@ -239,7 +235,7 @@ void Nast::regapSequences(){        //This is essentially part B in Fig 2. of DeSantis
                        newTemplateAlign += tempAln[fullAlignIndex];//  pairwise sequences
                        fullAlignIndex++;
                }
-               
+
                string lastLoop = "";
                
                while(pairwiseAlignIndex<pairwiseLength){