Mercurial > repos > prog > lcmsmatching

annotate BiodbConn.R @ 3:abfba8eb1c8d draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 494194bb501d1d7033613131865f7bd68976041c
author prog
date Tue, 14 Mar 2017 12:35:23 -0400
parents 45e985cd8e9e
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1 #####################
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2 # CLASS DECLARATION #
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3 #####################
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5 BiodbConn <- methods::setRefClass("BiodbConn", contains = "BiodbObject", fields = list( .debug = "logical" ))
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7 ###############
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8 # CONSTRUCTOR #
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9 ###############
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11 BiodbConn$methods( initialize = function(debug = FALSE, ...) {
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12 .debug <<- debug
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13 })
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15 #######################
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16 # PRINT DEBUG MESSAGE #
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17 #######################
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19 BiodbConn$methods( .print.debug.msg = function(msg) {
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20 if (.self$.debug)
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21 .print.msg(msg = msg, class = class(.self))
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22 })
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24 ##########################
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25 # GET ENTRY CONTENT TYPE #
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26 ##########################
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28 BiodbConn$methods( getEntryContentType = function() {
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29 .self$.abstract.method()
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30 })
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32 #############
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33 # GET ENTRY #
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34 #############
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36 BiodbConn$methods( getEntry = function(id, drop = TRUE) {
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37 content <- .self$getEntryContent(id)
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38 return(.self$createEntry(content, drop = drop))
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39 })
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41 #####################
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42 # GET ENTRY CONTENT #
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43 #####################
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45 # Download entry content from the public database.
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46 # type The entry type.
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47 # id The ID of the entry to get.
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48 # RETURN An entry content downloaded from database.
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49 BiodbConn$methods( getEntryContent = function(id) {
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50 .self$.abstract.method()
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51 })
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53 #############################
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54 # CREATE ENTRY FROM CONTENT #
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55 #############################
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57 # Creates a Compound instance from file content.
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58 # content A file content, downloaded from the public database.
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59 # RETURN A compound instance.
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60 BiodbConn$methods( createEntry = function(content, drop = TRUE) {
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61 .self$.abstract.method()
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62 })
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64 #################
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65 # GET ENTRY IDS #
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66 #################
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68 # Get a list of IDs of all entries contained in this database.
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69 BiodbConn$methods( getEntryIds = function(max.results = NA_integer_) {
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70 .self$.abstract.method()
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71 })
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73 ##################
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74 # GET NB ENTRIES #
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75 ##################
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77 # Get the number of entries contained in this database.
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78 BiodbConn$methods( getNbEntries = function() {
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79 .self$.abstract.method()
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80 })