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bugfix: wrong iterator

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This commit is contained in:
hyginn 2020-10-13 21:45:14 +10:00
parent a50688e0d0
commit 5524832a75
1 changed files with 6 additions and 6 deletions
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12
scripts/ABC-dbUtilities.R
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@ -31,7 +31,7 @@
#TOC> ========================================================================== #TOC> ==========================================================================
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> ------------------------------------------------------- #TOC> -------------------------------------------------------
#TOC> 1 INITIALISATIONS AND PARAMETERS 61 #TOC> 1 INITIALISATIONS AND PARAMETERS 61
@ -54,7 +54,7 @@
#TOC> 3.15 dbSeq2JSON() 608 #TOC> 3.15 dbSeq2JSON() 608
#TOC> 3.16 dbRow2JSON() 637 #TOC> 3.16 dbRow2JSON() 637
#TOC> 4 TESTS 657 #TOC> 4 TESTS 657
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -197,7 +197,7 @@ dbAddProtein <- function(db, jsonDF) {
# jsonDF data frame protein data imported into a data frame with # jsonDF data frame protein data imported into a data frame with
# fromJSON() # fromJSON()
for (i in seq_len(nrow(jsonDF))) { for (i in seq_along(jsonDF$name)) {
isValid <- TRUE isValid <- TRUE
if (jsonDF$name[i] %in% db$protein$name) { if (jsonDF$name[i] %in% db$protein$name) {
cat(sprintf("Note: Protein No. %d in the input is \"%s\", but %s.\n", cat(sprintf("Note: Protein No. %d in the input is \"%s\", but %s.\n",
@ -229,7 +229,7 @@ dbAddFeature <- function(db, jsonDF) {
# db list a database created with dbInit() # db list a database created with dbInit()
# jsonDF data frame feature data imported into a data frame with # jsonDF data frame feature data imported into a data frame with
# fromJSON() # fromJSON()
for (i in seq_len(nrow(jsonDF))) { for (i in seq_along(jsonDF$name)) {
isValid <- TRUE isValid <- TRUE
if (jsonDF$name[i] %in% db$feature$name) { if (jsonDF$name[i] %in% db$feature$name) {
cat(sprintf("Note: Feature No. %d in the input is \"%s\", but %s.\n", cat(sprintf("Note: Feature No. %d in the input is \"%s\", but %s.\n",
@ -260,7 +260,7 @@ dbAddTaxonomy <- function(db, jsonDF) {
# db list A database created with dbInit() # db list A database created with dbInit()
# jsonDF data frame Taxonomy data imported into a data frame with # jsonDF data frame Taxonomy data imported into a data frame with
# fromJSON() # fromJSON()
for (i in seq_len(nrow(jsonDF))) { for (i in seq_along(jsonDF$species)) {
isValid <- TRUE isValid <- TRUE
if (jsonDF$species[i] %in% db$taxonomy$species) { if (jsonDF$species[i] %in% db$taxonomy$species) {
@ -295,7 +295,7 @@ dbAddAnnotation <- function(db, jsonDF) {
# db list a database created with dbInit() # db list a database created with dbInit()
# jsonDF data frame annotation data imported into a data frame with # jsonDF data frame annotation data imported into a data frame with
# fromJSON() # fromJSON()
for (i in seq_len(nrow(jsonDF))) { for (i in seq_along(jsonDF$pName)) {
isValid <- TRUE isValid <- TRUE
sel <- jsonDF$pName[i] == db$protein$name sel <- jsonDF$pName[i] == db$protein$name