working on pam

[mothur.git] / onegapignore.h

diff --git a/onegapignore.h b/onegapignore.h
index 6421741c0d4c153794ab40efc9318af6d64349a4..fdbc196e9f2f7ff539a9b61bf35a8120483ac66b 100644 (file)
--- a/onegapignore.h
+++ b/onegapignore.h
@@ -9,6 +9,7 @@
  *
  */
 
+
 #include "dist.h"
 
 /**************************************************************************************************/
@@ -16,6 +17,9 @@
 class oneGapIgnoreTermGapDist : public Dist {
        
 public:
+       
+       oneGapIgnoreTermGapDist() {}
+       
        void calcDist(Sequence A, Sequence B){
                
                int difference = 0;
@@ -24,21 +28,26 @@ public:
                int minLength = 0;
                int start = 0;
                int end = 0;
+               bool overlap = false;
                
                string seqA = A.getAligned();
                string seqB = B.getAligned();
                int alignLength = seqA.length();
-               
+
                // this assumes that sequences start and end with '.'s instead of'-'s.
                for(int i=0;i<alignLength;i++){
-                       if(seqA[i] != '.' && seqB[i] != '.'){
+                       if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
                                start = i;
+//                             cout << "start: " << start << endl;
+                               overlap = true;
                                break;
                        }
                }
                for(int i=alignLength-1;i>=0;i--){
-                       if(seqA[i] != '.' && seqB[i] != '.'){
+                       if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
                                end = i;
+//                             cout << "end: " << end << endl;
+                               overlap = true;
                                break;
                        }
                }
@@ -70,7 +79,10 @@ public:
                                openGapB = 0;
                        }
                }
-
+               
+               //non-overlapping sequences
+               if (!overlap) { minLength = 0; }
+               
                if(minLength == 0)      {       dist = 1.0000;                                                  }
                else                            {       dist = (double)difference / minLength;  }
        }