ccode working - still need to paralellize

[mothur.git] / decalc.cpp

diff --git a/decalc.cpp b/decalc.cpp
index 05897517d061540e6548b9bf2c51c9c97443248d..2d60899e7c9f9526d531336fc1159f65ebed05bc 100644 (file)
--- a/decalc.cpp
+++ b/decalc.cpp
@@ -13,13 +13,17 @@
 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[i] = count;
                                }
+                               count++;
                        }
                }else {
                        for (int i = 0; i < alignLength; i++) {   h.insert(i);  }