@@ -156,21 +156,13 @@ test.geneIdsAndTypes = function ()

   geneIdTypes = tbl$geneIdType

   typeCounts = as.list (table (geneIdTypes))

-  #browser()

-  #fout <- file("/tmp/pshannon.txt", "w")

-  #write("ENTREZ", file=fout)

-  #write(typeCounts$ENTREZ, file=fout)

-  checkTrue(typeCounts$ENTREZ == 2180)

+  checkTrue(typeCounts$ENTREZ == 2347)

   checkTrue(typeCounts$FLYBASE >= 47)

-  checkTrue(typeCounts$SGD >= 453)

-  checkEquals(nrow(subset(tbl, is.na(geneIdType))), 932)

+  checkTrue(typeCounts$SGD >= 629)

+  checkEquals(nrow(subset(tbl, is.na(geneIdType))), 1181)

-  #checkEquals(typeCounts, list(ENTREZ=2197, FLYBASE=30, SGD=453, comment=683))

-

-  #na.count = length (which (is.na (geneIds)))

-  #checkEquals (na.count, 304) 

   empty.count = length (which (geneIds == ''))

   checkEquals (empty.count, 0)

@@ -278,7 +270,7 @@ test.flyBindingDomains = function ()

   checkEquals (tmp$Homeobox, 212)

   checkEquals (tmp[['zf-C2H2']], 160)

-  checkEquals (tmp$HLH, 109)

+  checkEquals (tmp[["Helix-Turn-Helix"]], 182)

   checkEquals (length (which (is.na (subset (x, organism=='Dmelanogaster')$bindingDomain))), 24)

 } # test.flyBindingDomains

@@ -514,7 +506,7 @@ test.export_memeFormatStdOut = function ()

   print ('--- test.export_memeFormatStdOut')

   mdb = MotifDb # ()

   mdb.chicken = subset (mdb, organism=='Gallus')

-  checkEquals (length (mdb.chicken), 2)

+  checkEquals (length (mdb.chicken), 3)

     # text is cat-ed to stdout, so not avaialable here to check.

     # but just like print, export also returns the text invisibly.

     # so that CAN be checked.

@@ -532,7 +524,7 @@ test.export_memeFormatToFile = function ()

   print ('--- test.export_memeFormatToFile')

   mdb = MotifDb # ()

   mdb.chicken = subset (mdb, organism=='Gallus')

-  checkEquals (length (mdb.chicken), 2)

+  checkEquals (length (mdb.chicken), 3)

   output.file = tempfile ()

   meme.text = export (mdb.chicken, output.file, 'meme')

   retrieved = scan (output.file, what=character (0), sep='\n', quiet=TRUE)

@@ -545,7 +537,7 @@ test.export_memeFormatToFileDuplication = function ()

   print ('--- test.export_memeFormatToFileDuplication')

   mdb = MotifDb # ()

   mdb.mouse = subset (mdb, organism=='Mmusculus')

-  checkEquals (length (mdb.mouse), 462)

+  checkEquals (length (mdb.mouse), 528)

   output.file = 'mouse.txt' # tempfile ()

   max = 3

   meme.text = export (mdb.mouse [1:max], output.file, 'meme')