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annotate MsDbInputDataFrameStream.R @ 7:882f2f20028b draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 608d9e59a0d2dcf85a037968ddb2c61137fb9bce
author prog
date Sun, 09 Apr 2017 10:44:21 -0400
parents 1ba222315fd5
children
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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1 if ( ! exists('MsDbInputDataFrameStream')) { # Do not load again if already loaded
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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3 library(methods)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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4 source('MsDbInputStream.R')
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6 #####################
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7 # CLASS DECLARATION #
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8 #####################
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10 MsDbInputDataFrameStream <- setRefClass("MsDbInputDataFrameStream", contains = 'MsDbInputStream', fields = list( .df = "ANY", .i = "integer", .rtunit = 'character'))
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12 ###############
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13 # CONSTRUCTOR #
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14 ###############
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16 MsDbInputDataFrameStream$methods( initialize = function(df = data.frame(), input.fields = msdb.get.dft.input.fields(), rtunit = MSDB.RTUNIT.SEC, ...) {
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb
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18 callSuper(input.fields = input.fields, ...)
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20 .df <<- df
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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21 .i <<- 0L
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22 .rtunit <<- rtunit
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23 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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25 ##########
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26 # GET MZ #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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27 ##########
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29 MsDbInputDataFrameStream$methods( getMz = function() {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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31 if (.self$.i > 0 && .self$.i <= nrow(.self$.df) && ! is.null(.self$.input.fields[[MSDB.TAG.MZ]]))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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32 return(.self$.df[.self$.i, .self$.input.fields[[MSDB.TAG.MZ]]])
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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34 return(NULL)
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35 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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37 ##########
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38 # GET RT #
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39 ##########
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41 MsDbInputDataFrameStream$methods( getRt = function() {
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43 rt <- NULL
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45 if (.self$.i > 0 && .self$.i <= nrow(.self$.df) && ! is.null(.self$.input.fields[[MSDB.TAG.RT]])) {
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb
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46 rt <- .self$.df[.self$.i, .self$.input.fields[[MSDB.TAG.RT]]]
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47 if (.self$.rtunit == MSDB.RTUNIT.MIN)
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48 rt <- rt * 60
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb
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49 }
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51 return(rt)
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52 })
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54 ###########
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55 # GET ALL #
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56 ###########
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58 MsDbInputDataFrameStream$methods( getAll = function(but = NULL) {
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60 if (.self$.i > 0 && .self$.i <= nrow(.self$.df)) {
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62 vals <- .self$.df[.self$.i, , drop = FALSE]
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64 if ( ! is.null(but))
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65 vals <- vals[, ! colnames(vals) %in% .self$.input.fields[but], drop = FALSE]
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67 return(vals)
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68 }
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70 return(NULL)
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71 })
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73 ###############
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74 # NEXT VALUES #
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75 ###############
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77 MsDbInputDataFrameStream$methods( nextValues = function() {
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79 if (.self$.i <= nrow(.self$.df))
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80 .i <<- .self$.i + 1L
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81 })
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83 ###################
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84 # HAS NEXT VALUES #
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85 ###################
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87 MsDbInputDataFrameStream$methods( hasNextValues = function() {
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88 return(.self$.i < nrow(.self$.df))
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89 })
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90
1
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91 #########
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92 # RESET #
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93 #########
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95 MsDbInputDataFrameStream$methods( reset = function() {
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96 .i <<- 0L
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97 })
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98
0
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99 } # end of load safe guard