@@ -12,7 +12,7 @@ run = function (dataDir)

                                  raw.metadata.filename="md-raw.tsv")

   matrices <- normalizeMatrices (matrices)

   matrices <- renameMatrices (matrices, tbl.md)

-

+  

   serializedFile <- file.path(dataDir, "demo.RData")

   printf("writing %s to %s", "demo.RData", dataDir)

@@ -35,7 +35,6 @@ readRawMatrices = function (dataDir)

   filename <- file.path(dataDir, "sample.pcm")

   printf("checking for readable matrix file:")

   printf("     %s", filename)

-  browser()

   stopifnot(file.exists(filename))

   all.lines = scan (filename, what=character(0), sep='\n', quiet=TRUE)

@@ -77,7 +76,7 @@ createMetadataTable = function (dataDir, matrices, raw.metadata.filename)

   tbl.raw <- read.table(filename, sep="\t", header=TRUE, as.is=TRUE)

   tbl.md = data.frame ()

-  matrix.ids = names (matrices)

+  matrix.ids = names(matrices)

   for (matrix.id in matrix.ids) {

     matrix <- matrices[[matrix.id]]

@@ -102,7 +101,7 @@ createMetadataTable = function (dataDir, matrices, raw.metadata.filename)

                     experimentType=md$type,

                     pubmedID="24194598")

     tbl.md = rbind (tbl.md, data.frame (new.row, stringsAsFactors=FALSE))

-    full.name = sprintf ('%s-%s-%s', organism, dataSource, matrix.id)

+    full.name = sprintf ('%s-%s-%s-%s', organism, dataSource, md$gene.symbol, short.matrix.name)

     rownames (tbl.md) [nrow (tbl.md)] = full.name

     } # for i

@@ -153,7 +152,6 @@ normalizeMatrices = function (matrices)

 parsePwm = function (text)

 {

    lines = strsplit (text, '\t')

-   #browser()

    stopifnot(length(lines)==5) # title line, one line for each base

    title = lines [[1]][1]

    line.count = length(lines)