28030cc609b3965a9d55b763e0648c5e2e68bc0f
ceisenhart
  Wed Aug 27 12:48:18 2014 -0700
Fixing comments, normalizing output values
diff --git src/hg/expData/expData.c src/hg/expData/expData.c
index 91d54dd..fbc731a 100644
--- src/hg/expData/expData.c
+++ src/hg/expData/expData.c
@@ -427,30 +427,32 @@
    }
 
 /* Set first color to correspond to 0, since not set in above loop */
 struct bioExpVector *bio = leafList->val;
 bio->color = saturatedRainbowAtPos(0);
 }
 
 void expData(char *matrixFile, char *nameFile, char *outFile, bool forceLayout, int normConstant, int cgConstant)
 /* Read matrix and names into a list of bioExpVectors, run hacTree to
  * associate them, and write output. */
 {
 struct bioExpVector *list = bioExpVectorListFromFile(matrixFile);
 FILE *f = mustOpen(outFile,"w");
 struct lm *localMem = lmInit(0);
 fillInNames(list, nameFile);
+//struct hacTree *clusters = hacTreeForCostlyMerges((struct slList *)list, localMem,
+//					    slBioExpVectorDistance, slBioExpVectorMerge, NULL);
 struct hacTree *clusters = hacTreeFromItems((struct slList *)list, localMem,
 					    slBioExpVectorDistance, slBioExpVectorMerge, NULL, NULL);
 struct slRef *orderedList = getOrderedLeafList(clusters);
 colorLeaves(orderedList);
 if (forceLayout)
     printForceLayoutJson(normConstant,f,clusters);
 if (!clForceLayout)
     printHierarchicalJson(f, clusters, normConstant, cgConstant);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 clForceLayout = optionExists("forceLayout");