added count.groups command and paralellized align.seqs for windows

[mothur.git] / onegapignore.h

diff --git a/onegapignore.h b/onegapignore.h
index 785272e08c69a3e1491d5d1d2792bbc9ba3eda5d..dba3f38292ced957330631ece5572901ee3438ae 100644 (file)
--- a/onegapignore.h
+++ b/onegapignore.h
@@ -17,6 +17,10 @@
 class oneGapIgnoreTermGapDist : public Dist {
        
 public:
+       
+       oneGapIgnoreTermGapDist() {}
+       oneGapIgnoreTermGapDist(const oneGapIgnoreTermGapDist& ddb) {}
+       
        void calcDist(Sequence A, Sequence B){
                
                int difference = 0;
@@ -25,6 +29,7 @@ public:
                int minLength = 0;
                int start = 0;
                int end = 0;
+               bool overlap = false;
                
                string seqA = A.getAligned();
                string seqB = B.getAligned();
@@ -35,6 +40,7 @@ public:
                        if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
                                start = i;
 //                             cout << "start: " << start << endl;
+                               overlap = true;
                                break;
                        }
                }
@@ -42,6 +48,7 @@ public:
                        if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
                                end = i;
 //                             cout << "end: " << end << endl;
+                               overlap = true;
                                break;
                        }
                }
@@ -73,7 +80,10 @@ public:
                                openGapB = 0;
                        }
                }
-
+               
+               //non-overlapping sequences
+               if (!overlap) { minLength = 0; }
+               
                if(minLength == 0)      {       dist = 1.0000;                                                  }
                else                            {       dist = (double)difference / minLength;  }
        }