Mercurial > repos > prog > lcmsmatching

annotate MsBioDb.R @ 1:45e985cd8e9e draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
author prog
date Tue, 31 Jan 2017 05:27:24 -0500
parents
children b8f70d8216b3
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45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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1 if ( ! exists('MsBioDb')) { # Do not load again if already loaded
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45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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3 library(methods)
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4 source('MsDb.R')
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5 source(file.path('BiodbObject.R'), chdir = TRUE)
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6 source(file.path('BiodbFactory.R'), chdir = TRUE)
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8 #####################
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9 # CLASS DECLARATION #
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10 #####################
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12 MsBioDb <- setRefClass("MsBioDb", contains = "MsDb", fields = list(.massdb = "ANY"))
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13
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14 ###############
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15 # CONSTRUCTOR #
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16 ###############
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18 MsBioDb$methods( initialize = function(massdb = NULL, ...) {
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19
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20 # Check bio database
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21 ! is.null(massdb) || stop("You must set a bio database.")
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22 inherits(massdb, "MassdbConn") || stop("The bio database must inherit from MassdbConn class.")
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23 .massdb <<- massdb
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25 callSuper(...)
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26 })
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28 ####################
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29 # HANDLE COMPOUNDS #
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30 ####################
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31
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32 MsBioDb$methods( handleCompounds = function() {
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33 return(.self$.massdb$handlesEntryType(BIODB.COMPOUND))
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34 })
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36 ####################
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37 # GET MOLECULE IDS #
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38 ####################
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39
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40 MsBioDb$methods( getMoleculeIds = function(max.results = NA_integer_) {
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41 return(.self$.massdb$getEntryIds(type = BIODB.COMPOUND, max.results = max.results))
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42 })
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44 ####################
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45 # GET NB MOLECULES #
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46 ####################
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48 MsBioDb$methods( getNbMolecules = function() {
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49 return(.self$.massdb$getNbEntries(type = BIODB.COMPOUND))
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50 })
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51
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52 #################
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53 # GET MZ VALUES #
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54 #################
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55
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56 MsBioDb$methods( getMzValues = function(mode = NULL, max.results = NA_integer_) {
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57 return(.self$.massdb$getMzValues(mode = mode, max.results = max.results))
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58 })
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59
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60 #####################
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61 # GET MOLECULE NAME #
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62 #####################
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64 MsBioDb$methods( getMoleculeName = function(molid) {
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65 return(.self$.massdb$getMoleculeName(molid))
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66 })
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68 ###############################
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69 # GET CHROMATOGRAPHIC COLUMNS #
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70 ###############################
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72 MsBioDb$methods( getChromCol = function(molid = NULL) {
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73 return(.self$.massdb$getChromCol(molid))
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74 })
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76 ################
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77 # FIND BY NAME #
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78 ################
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80 MsBioDb$methods( findByName = function(name) {
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81 return(.self$.massdb$findCompoundByName(name))
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82 })
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83
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84 #######################
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85 # GET RETENTION TIMES #
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86 #######################
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87
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88 MsBioDb$methods( getRetentionTimes = function(molid, col = NA_character_) {
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89 return(.self$.massdb$getRetentionTimes(molid, chrom.cols = col))
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90 })
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91
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92 ################
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93 # GET NB PEAKS #
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94 ################
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95
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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96 MsBioDb$methods( getNbPeaks = function(molid = NA_integer_, mode = NA_character_) {
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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97 return(.self$.massdb$getNbPeaks(compound.ids = molid, mode = mode))
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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98 })
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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99
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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100 }