working on pam

[mothur.git] / onegapignore.h

diff --git a/onegapignore.h b/onegapignore.h
index e280ce0ea45e3c828205a5d8872a47cacf8fcc02..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;
@@ -24,28 +28,33 @@ public:
                int minLength = 0;
                int start = 0;
                int end = 0;
+               bool overlap = false;
                
-               for(int i=0;i<A.getLength();i++){
-                       if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.' || A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-'){
-                       }
-                       else{
+               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] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
                                start = i;
+//                             cout << "start: " << start << endl;
+                               overlap = true;
                                break;
                        }
                }
-               for(int i=A.getLength()-1;i>=0;i--){
-                       if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.' || A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-'){
-                       }
-                       else{
+               for(int i=alignLength-1;i>=0;i--){
+                       if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
                                end = i;
+//                             cout << "end: " << end << endl;
+                               overlap = true;
                                break;
                        }
                }
                
-               
                for(int i=start;i<=end;i++){
-                       if(A.getUnaligned()[i] == '-' && B.getUnaligned()[i] == '-'){}
-                       else if(A.getUnaligned()[i] == '-' && B.getUnaligned()[i] != '-'){
+                       if(seqA[i] == '-' && seqB[i] == '-'){   ;       }
+                       else if(seqB[i] != '-' && seqA[i] == '-'){
                                if(openGapA == 0){
                                        difference++;
                                        minLength++;
@@ -53,7 +62,7 @@ public:
                                        openGapB = 0;
                                }
                        }
-                       else if(A.getUnaligned()[i] != '-' && B.getUnaligned()[i] == '-'){
+                       else if(seqA[i] != '-' && seqB[i] == '-'){
                                if(openGapB == 0){
                                        difference++;
                                        minLength++;
@@ -61,20 +70,19 @@ public:
                                        openGapB = 1;
                                }
                        }
-                       else if(A.getUnaligned()[i] != '-' && B.getUnaligned()[i] != '-'){
-                               if(A.getUnaligned()[i] != B.getUnaligned()[i]){
+                       else if(seqA[i] != '-' && seqB[i] != '-'){
+                               if(seqA[i] != seqB[i]){
                                        difference++;
-                                       minLength++;
-                                       openGapA = 0;
-                                       openGapB = 0;
-                               }
-                               else{
-                                       minLength++;
-                                       openGapA = 0;
-                                       openGapB = 0;
                                }
+                               minLength++;
+                               openGapA = 0;
+                               openGapB = 0;
                        }
                }
+               
+               //non-overlapping sequences
+               if (!overlap) { minLength = 0; }
+               
                if(minLength == 0)      {       dist = 1.0000;                                                  }
                else                            {       dist = (double)difference / minLength;  }
        }