--- src/multipleAlign/MyersMillerProfileAlign.h.org	Fri Aug  8 11:50:43 2008
+++ src/multipleAlign/MyersMillerProfileAlign.h	Wed Aug  6 17:36:57 2008
@@ -50,7 +50,7 @@
         vector<int> HH;
         vector<int> DD;
         vector<int> RR;
-        vector<int> SS;
+        vector<int> SSDUMMY;
         vector<int> alnPath1;
         vector<int> alnPath2;
         int printPtr;
--- src/multipleAlign/MyersMillerProfileAlign.cpp.org	Fri Aug  8 11:51:37 2008
+++ src/multipleAlign/MyersMillerProfileAlign.cpp	Wed Aug  6 17:35:37 2008
@@ -424,7 +424,7 @@
     HH.resize(_maxAlnLength + 1);
     DD.resize(_maxAlnLength + 1);
     RR.resize(_maxAlnLength + 1);
-    SS.resize(_maxAlnLength + 1);
+    SSDUMMY.resize(_maxAlnLength + 1);
     gS.resize(_maxAlnLength + 1);
     displ.resize(_maxAlnLength + 1);
 
@@ -435,7 +435,7 @@
     HH.clear();
     DD.clear();
     RR.clear();
-    SS.clear();
+    SSDUMMY.clear();
     gS.clear();
 
     alignmentLength = progTracepath();
@@ -674,7 +674,7 @@
 
         DD[0] = HH[0];
 
-        /* In a reverse phase, calculate all RR[j] and SS[j] */
+        /* In a reverse phase, calculate all RR[j] and SSDUMMY[j] */
 
         RR[N] = 0;
         tl = 0;
@@ -683,7 +683,7 @@
             g =  - openPenalty1(A + M, B + j + 1);
             tl -= extPenalty1(A + M, B + j + 1);
             RR[j] = g + tl;
-            SS[j] = RR[j] - openPenalty2(A + M, B + j);
+            SSDUMMY[j] = RR[j] - openPenalty2(A + M, B + j);
             gS[j] = openPenalty2(A + M, B + j);
         }
 
@@ -718,11 +718,11 @@
                 hh = RR[j] - g - h;
                 if (i == (M - 1))
                 {
-                    e = SS[j] - h;
+                    e = SSDUMMY[j] - h;
                 }
                 else
                 {
-                    e = SS[j] - h - g + openPenalty2(A + i + 2, B + j);
+                    e = SSDUMMY[j] - h - g + openPenalty2(A + i + 2, B + j);
                     gS[j] = g;
                 }
                 if (hh > e)
@@ -741,14 +741,14 @@
 
                 s = RR[j];
                 RR[j] = hh;
-                SS[j] = e;
+                SSDUMMY[j] = e;
 
             }
         }
-        SS[N] = RR[N];
+        SSDUMMY[N] = RR[N];
         gS[N] = openPenalty2(A + midi + 1, B + N);
 
-        /* find midj, such that HH[j]+RR[j] or DD[j]+SS[j]+gap is the maximum */
+        /* find midj, such that HH[j]+RR[j] or DD[j]+SSDUMMY[j]+gap is the maximum */
 
         midh = HH[0] + RR[0];
         midj = 0;
@@ -757,7 +757,7 @@
         {
             hh = HH[j] + RR[j];
             if (hh >= midh)
-            if (hh > midh || (HH[j] != DD[j] && RR[j] == SS[j]))
+            if (hh > midh || (HH[j] != DD[j] && RR[j] == SSDUMMY[j]))
             {
                 midh = hh;
                 midj = j;
@@ -766,7 +766,7 @@
 
         for (j = N; j >= 0; j--)
         {
-            hh = DD[j] + SS[j] + gS[j];
+            hh = DD[j] + SSDUMMY[j] + gS[j];
             if (hh > midh)
             {
                 midh = hh;
--- src/pairwise/FullPairwiseAlign.h.org	Fri Aug  8 11:52:41 2008
+++ src/pairwise/FullPairwiseAlign.h	Wed Aug  6 17:35:45 2008
@@ -45,8 +45,8 @@
         vector<int> HH;
         vector<int> DD;
         vector<int> RR;
-        vector<int> SS;
-
+        vector<int> SSDUMMY;
+	int unused;
         int _gapOpen; // scaled to be an integer, this is not a mistake
         int _gapExtend; // scaled to be an integer, not a mistake
         int seq1;
--- src/pairwise/FullPairwiseAlign.cpp.org	Fri Aug  8 11:52:31 2008
+++ src/pairwise/FullPairwiseAlign.cpp	Wed Aug  6 17:35:13 2008
@@ -75,7 +75,7 @@
         HH.resize(_maxAlnLength);
         DD.resize(_maxAlnLength);
         RR.resize(_maxAlnLength);
-        SS.resize(_maxAlnLength);
+        SSDUMMY.resize(_maxAlnLength);
         // Note these 2 lines replace the stuff above because it is all done in the SubMatrix
         PairScaleValues scaleValues;
         maxRes = subMatrix->getPairwiseMatrix(matrix, scaleValues, _matAvgScore);
@@ -194,7 +194,7 @@
         HH.clear();
         DD.clear();
         RR.clear();
-        SS.clear();
+        SSDUMMY.clear();
     }
     catch(const exception& e)
     {
@@ -521,7 +521,7 @@
     for (j = N - 1; j >= 0; j--)
     {
         RR[j] = t = t - _gapExtend;
-        SS[j] = t - _gapOpen;
+        SSDUMMY[j] = t - _gapOpen;
     }
 
     t =  - te;
@@ -538,7 +538,7 @@
             {
                 f = hh;
             }
-            if ((hh = RR[j] - _gapOpen - _gapExtend) > (e = SS[j] - _gapExtend))
+            if ((hh = RR[j] - _gapOpen - _gapExtend) > (e = SSDUMMY[j] - _gapExtend))
             {
                 e = hh;
             }
@@ -554,12 +554,12 @@
 
             s = RR[j];
             RR[j] = hh;
-            SS[j] = e;
+            SSDUMMY[j] = e;
 
         }
     }
 
-    SS[N] = RR[N];
+    SSDUMMY[N] = RR[N];
 
     midh = HH[0] + RR[0];
     midj = 0;
@@ -568,7 +568,7 @@
     {
         hh = HH[j] + RR[j];
         if (hh >= midh)
-        if (hh > midh || (HH[j] != DD[j] && RR[j] == SS[j]))
+        if (hh > midh || (HH[j] != DD[j] && RR[j] == SSDUMMY[j]))
         {
             midh = hh;
             midj = j;
@@ -577,7 +577,7 @@
 
     for (j = N; j >= 0; j--)
     {
-        hh = DD[j] + SS[j] + _gapOpen;
+        hh = DD[j] + SSDUMMY[j] + _gapOpen;
         if (hh > midh)
         {
             midh = hh;