added get.sharedotu command

[mothur.git] / decalc.cpp

diff --git a/decalc.cpp b/decalc.cpp
index 05897517d061540e6548b9bf2c51c9c97443248d..bfaae000386c872584952b27b5dcc64f52a785ea 100644 (file)
--- a/decalc.cpp
+++ b/decalc.cpp
@@ -13,16 +13,25 @@
 void DeCalculator::setMask(string m) { 
        try {
                seqMask = m; 
+               int count = 0;
+               maskMap.clear();
                
                if (seqMask.length() != 0) {
                        //whereever there is a base in the mask, save that value is query and subject
                        for (int i = 0; i < seqMask.length(); i++) {
                                if (isalpha(seqMask[i])) {
                                        h.insert(i);
+                                       maskMap[count] = i;
+                                       count++;
+                                       
                                }
                        }
                }else {
-                       for (int i = 0; i < alignLength; i++) {   h.insert(i);  }
+                       for (int i = 0; i < alignLength; i++) {   
+                               h.insert(i); 
+                               maskMap[count] = i;
+                               count++;
+                       }
                }
        }
        catch(exception& e) {
@@ -417,8 +426,7 @@ vector< vector<quanMember> > DeCalculator::getQuantiles(vector<Sequence*> seqs,
                                
                                quanMember newScore(de, i, j);
                                
-                               //dist-1 because vector indexes start at 0.
-                               quan[dist-1].push_back(newScore);
+                               quan[dist].push_back(newScore);
                                
                                delete subject;
                        }