working on pam

[mothur.git] / nast.cpp

diff --git a/nast.cpp b/nast.cpp
index bf65fa2b46ea319bf54ab74a9696bb9e7b22fafe..647e0e4f1e17e205c183c78615a966b7a98545cc 100644 (file)
--- a/nast.cpp
+++ b/nast.cpp
@@ -139,24 +139,22 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
                                                        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
+                                                       
+                                               }else{                                                                  //      not enough room to the left, have to steal some space to the right
                                                
                        //cout << "in else lr newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << insertLength << endl;
-                                                       string leftTemplateString = newTemplateAlign.substr(0,i);       //      the right
+                                                       string leftTemplateString = newTemplateAlign.substr(0,i);       
                                                        string rightTemplateString = newTemplateAlign.substr((i+insertLength));
                                                        newTemplateAlign = leftTemplateString + rightTemplateString;
                                                        longAlignmentLength = newTemplateAlign.length();
-                       //cout << " in else lr candAln = " << candAln.length() << '\t' << " leftIndex = " << leftIndex << " leftroom = " << leftRoom << " rightIndex = " << rightIndex << '\t' << endl;                                 
+                       //cout << " in else lr candAln = " << candAln.length() << '\t' << " leftIndex = " << leftIndex << " leftroom = " << leftRoom << " rightIndex = " << rightIndex << '\t' << " rightroom = " << rightRoom << '\t' << 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
+                                       }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);
@@ -184,7 +182,9 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
                                                                        
                                                }
                                        }
-                                       i -= insertLength;
+                                       
+                                       if ((i - insertLength) < 0) {  i = 0; }
+                                       else { i -= insertLength; }
 
                                }
                                else{
@@ -207,7 +207,7 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 //                             i -= insertLength;
                                
                                //if i is negative, we want to remove the extra gaps to the right
-                               if (i < 0) { cout << "i is negative" << endl; }
+                               if (i < 0) { m->mothurOut("i is negative"); m->mothurOutEndLine(); } 
                        } 
                }
        }