added get.sharedotu command

[mothur.git] / decalc.cpp

diff --git a/decalc.cpp b/decalc.cpp
index 2d60899e7c9f9526d531336fc1159f65ebed05bc..bfaae000386c872584952b27b5dcc64f52a785ea 100644 (file)
--- a/decalc.cpp
+++ b/decalc.cpp
@@ -21,12 +21,17 @@ void DeCalculator::setMask(string m) {
                        for (int i = 0; i < seqMask.length(); i++) {
                                if (isalpha(seqMask[i])) {
                                        h.insert(i);
-                                       maskMap[i] = count;
+                                       maskMap[count] = i;
+                                       count++;
+                                       
                                }
-                               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) {
@@ -421,8 +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;
                        }