9e202e04f8cf765f39561741d1c5f780ff24be13
kent
  Wed Jan 30 17:51:40 2013 -0800
Removing some debugging code.
diff --git src/kehayden/alphaAsm/alphaAsm.c src/kehayden/alphaAsm/alphaAsm.c
index f761e1d..0c47c2d 100644
--- src/kehayden/alphaAsm/alphaAsm.c
+++ src/kehayden/alphaAsm/alphaAsm.c
@@ -845,37 +845,34 @@
  * Substitute in center at one of these places chosen at random and return TRUE if possible. */
 {
 struct slRef *centerRefList = refsToPossibleCenters(center, neighborhood, ll);
 verbose(3, "sub %s in neighborhood: ", center->word);
 if (verboseLevel() >= 3)
     printMonomerRefList(neighborhood, stderr);
 verbose(3, "Got %d possible centers\n", slCount(centerRefList));
 
 if (centerRefList == NULL)
     return FALSE;
 int commonCount = 0;
 char *commonWord = NULL;
 mostCommonMonomerWord(centerRefList, &commonWord, &commonCount);
 struct monomer *commonMonomer = hashFindVal(store->monomerHash, commonWord);
 verbose(3, "Commonest word to displace with %s is %s which occurs %d times in context and %d overall\n", center->word, commonWord, commonCount, commonMonomer->subbedOutCount);
-uglyf("Commonest word to displace with %s is %s which occurs %d times in context and %d overall\n", center->word, commonWord, commonCount, commonMonomer->subbedOutCount);
 if (commonMonomer->subbedOutCount < 2)
     {
     verbose(2, "Want to substitute %s for %s, but %s only occurs %d time.\n", 
 	center->word, commonWord, commonWord, commonMonomer->subbedOutCount);
-    uglyf("Want to substitute %s for %s, but %s only occurs %d time.\n", 
-	center->word, commonWord, commonWord, commonMonomer->subbedOutCount);
     return FALSE;
     }
 
 /* Select a random one of the most commonly occuring possible centers. */
 int targetIx = rand() % commonCount;
 struct slRef *ref;
 int currentIx = 0;
 for (ref = centerRefList; ref != NULL; ref = ref->next)
     {
     struct dlNode *node = ref->val;
     struct monomer *monomer = node->val;
     if (sameString(monomer->word, commonWord))
          {
 	 if (currentIx == targetIx)
 	     {
@@ -931,42 +928,41 @@
         {
 	commonCount = monomer->subbedOutCount;
 	common = monomer;
 	}
     }
 return common;
 }
 
 boolean subIntoFirstMostCommonOfType(struct alphaStore *store, struct monomer *unused, 
     struct dlList *ll)
 /* Substitute unused for first occurence of most common monomer of same type. */
 {
 struct monomer *common = mostCommonInType(unused->type);
 if (common->subbedOutCount < 2)
     {
-    uglyf("Trying to sub in %s, but there's no monomers of type %s that are used more than once.\n", unused->word, unused->type->name);
+    verbose(2, "Trying to sub in %s, but there's no monomers of type %s that are used more than once.\n", 
+	unused->word, unused->type->name);
     return FALSE;
     }
 struct dlNode *node;
 for (node = ll->head; !dlEnd(node); node = node->next)
     {
     struct monomer *monomer = node->val;
     if (monomer == common)
         {
-	verbose(2, "Subbing %s for %s of type %s\n", unused->word, monomer->word, 
-	    unused->type->name);
-	uglyf("Subbing %s for %s (used %d times) of type %s\n", unused->word, monomer->word, monomer->subbedOutCount, unused->type->name);
+	verbose(2, "Subbing %s for %s of type %s\n", unused->word, monomer->word, unused->type->name);
 	node->val = unused;
 	unused->subbedOutCount += 1;
 	monomer->subbedOutCount -= 1;
 	break;
 	}
     }
 return TRUE;
 }
 
 void setInitialSubbedOutCount(struct alphaStore *store, struct dlList *ll)
 /* Set subbedOutCount based on how many times monomers occur in list. */
 {
 struct dlNode *node;
 for (node = ll->head; !dlEnd(node); node = node->next)
     {
@@ -981,39 +977,37 @@
     {
     uglyf("%s %d %d\n", monomer->word, monomer->outCount, monomer->subbedOutCount);
     if (monomer->outCount != monomer->subbedOutCount)
         ++mismatchCount;
     }
 uglyf("mismatch count = %d\n", mismatchCount);
 #endif /* PARANOID */
 }
 
 void subInMissing(struct alphaStore *store, struct dlList *ll)
 /* Go figure out missing monomers in ll, and attempt to substitute them in somewhere they would fit. */
 {
 setInitialSubbedOutCount(store, ll);
 struct slRef *unusedList = listUnusedMonomers(store, ll);
 verbose(2, "%d monomers, %d unused\n", slCount(store->monomerList), slCount(unusedList));
-uglyf("%d monomers, %d unused\n", slCount(store->monomerList), slCount(unusedList));
 struct slRef *unusedRef;
 for (unusedRef = unusedList; unusedRef != NULL; unusedRef = unusedRef->next)
     {
     struct monomer *unused = unusedRef->val;
     struct monomerRef *neighborhood = findNeighborhoodFromReads(unused);
     if (!subCenterInNeighborhood(store, unused, neighborhood, ll))
 	{
-	uglyf("Couldn't substitute in %s with context, falling back to type logic\n", unused->word);
 	verbose(2, "Couldn't substitute in %s with context, falling back to type logic\n", 
 	    unused->word);
         subIntoFirstMostCommonOfType(store, unused, ll);
 	}
     slFreeList(&neighborhood);
     }
 }
 
 static void writeMonomerList(char *fileName, struct dlList *ll)
 /* Write out monomer list to file. */
 {
 FILE *f = mustOpen(fileName, "w");
 struct dlNode *node;
 for (node = ll->head; !dlEnd(node); node = node->next)
     {