added pipeline commands which involved change to command factory and command class...

[mothur.git] / eachgapignore.h

diff --git a/eachgapignore.h b/eachgapignore.h
index f6824cf8d3e407dce231f3fc18194cb5f7b8bc0e..824a8b87b936c75dbfe21fdaf6a1b9a54c1440b0 100644 (file)
--- a/eachgapignore.h
+++ b/eachgapignore.h
@@ -23,6 +23,7 @@ public:
                int length = 0;
                int start = 0;
                int end = 0;
+               bool overlap = false;
                
                string seqA = A.getAligned();
                string seqB = B.getAligned();
@@ -32,6 +33,7 @@ public:
                        if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
                                start = i;
 //                             cout << "start: " << start << endl;
+                               overlap = true;
                                break;
                        }
                }
@@ -39,6 +41,7 @@ public:
                        if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
                                end = i;
 //                             cout << "end: " << end << endl;
+                               overlap = true;
                                break;
                        }
                }
@@ -55,6 +58,9 @@ public:
                        }
                }
                
+               //non-overlapping sequences
+               if (!overlap) { length = 0; }
+               
                if(length == 0) {       dist = 1.0000;                                                          }
                else                    {       dist = ((double)diff  / (double)length);        }