Mercurial > repos > prog > lcmsmatching

comparison MsXlsDb.R @ 6:b8f70d8216b3 draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
author prog
date Mon, 27 Mar 2017 06:27:29 -0400
parents 45e985cd8e9e
children
comparison
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5:18254e8d1b72 6:b8f70d8216b3
54 54
55 #################### 55 ####################
56 # GET MOLECULE IDS # 56 # GET MOLECULE IDS #
57 #################### 57 ####################
58 58
59 MsXlsDb$methods( getMoleculeIds = function() { 59 MsXlsDb$methods( getMoleculeIds = function(max.results = NA_integer_) {
60 60
61 # Init file list 61 # Init file list
62 .self$.init.file.list() 62 .self$.init.file.list()
63 63
64 # Get IDs 64 # Get IDs
65 mol.ids <- as.integer(which( ! is.na(.self$.files))) 65 mol.ids <- as.integer(which( ! is.na(.self$.files)))
66
67 # Cut
68 if ( ! is.na(max.results) && length(mol.ids) > max.results)
69 mol.ids <- mol.ids[max.results, ]
66 70
67 return(mol.ids) 71 return(mol.ids)
68 }) 72 })
69 73
70 #################### 74 ####################
799 # Use all molecules if no list is provided 803 # Use all molecules if no list is provided
800 if (is.null(mols)) 804 if (is.null(mols))
801 mols <- .self$getMoleculeIds() 805 mols <- .self$getMoleculeIds()
802 806
803 results <- data.frame(id = integer(), col = character(), colrt = double(), stringsAsFactors = FALSE) 807 results <- data.frame(id = integer(), col = character(), colrt = double(), stringsAsFactors = FALSE)
808 colnames(results) <- c(MSDB.TAG.MOLID, MSDB.TAG.COL, MSDB.TAG.COLRT)
804 809
805 # Loop on all molecules 810 # Loop on all molecules
806 for (molid in mols) { 811 for (molid in mols) {
807 no.col <- TRUE 812 no.col <- TRUE
808 for (c in col) { 813 for (c in col) {