@@ -1,6 +1,6 @@

 library (MotifDb)

 library (RUnit)

-#library (MotIV)

+library (MotIV)

 library (seqLogo)

 #------------------------------------------------------------------------------------------------------------------------

 run.tests = function ()

@@ -33,8 +33,8 @@ run.tests = function ()

   test.export_memeFormatToFile ()

   test.export_memeFormatToFileDuplication ()

   test.export_memeFormatToFile_run_tomtom ()

-  #test.run_MotIV ()

-  #test.MotIV.toTable ()

+  test.MotIV.toTable ()

+  test.run_MotIV.motifMatch()

   test.flyFactorGeneSymbols()

 } # run.tests

@@ -574,10 +574,11 @@ test.export_memeFormatToFile_run_tomtom = function (max=50)

 } # test.export_memeFormatToFile_run_tomtom

 #------------------------------------------------------------------------------------------------------------------------

-test.run_MotIV = function ()

+# MotIV::motifMatch fails with MotIV_1.25.0.  will look into this in September, 2015, pshannon

+test.run_MotIV.motifMatch = function ()

 {

   library (MotIV)

-  print ('--- test.run_MotIV')

+  print ('--- test.run_MotIV.motifMatch')

   mdb = MotifDb # ()

   db.tmp = mdb@listData

@@ -587,15 +588,16 @@ test.run_MotIV = function ()

      # the long way to extract the matrix name.  see MotIV.toTable below for more convenient way

   checkEquals (motif.hits@bestMatch[[1]]@aligns[[1]]@TF@name, names (db.tmp)[1])

-     # jaspar, uniprobe and ScerTF contribute a total of 1035 matrices

-  checkTrue (length (mdb) >= 1035)

-

-  motif.hits =  motifMatch (db.tmp [1035], database=db.tmp)

+     # match the last motif against all

+  last <- length(db.tmp)

+  motif.hits =  motifMatch (db.tmp [last], database=db.tmp)

   tbl.hits = MotIV.toTable (motif.hits)

-  checkEquals (names (db.tmp)[1035], tbl.hits [1, 'name'])   # first hit should be the target itself

+    # the 5 hits return should include the one we tried to match, but the MotIV search strategy

+    # may not place it first

+  checkTrue(names(db.tmp[last]) %in% tbl.hits$name)

   invisible (tbl.hits)

-} # test.run_MotIV

+} # test.run_MotIV.motifMatch

 #------------------------------------------------------------------------------------------------------------------------

 MotIV.toTable = function (match)

 {