R/allClasses.R

In spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data

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##  File   : allClasses.r                                                    ##
##  Date   : 05.Nov.2012                                                     ##
##  Content: Class definitions for package spliceSites                       ##
##  Version: 0.7.0                                                           ##
##  Author : W. Kaisers                                                      ##
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##  Changelog
##  03.Jul.13  Added unloading of spliceSites.so
##  09.Jul.13  Added maxEnt class
##  10.Jul.13  Removed gapRanges, gapProbes, and derived (aaX,dnaX) classes.
##  24.Jul.13  Changed alingGaps to gapSites
## 
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.onUnload<-function(libpath) { library.dynam.unload("spliceSites", libpath) }

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##                                                                           ##
##  Declarations for cRanges                                                 ##
##                                                                           ##
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# Centered Range: contains id and position
setClass("cRanges", representation(dt="data.frame"))
# Centered Range with DNAStringSet
setClass("cdRanges", representation(seq="DNAStringSet"), contains="cRanges")
# Centered Range with AAStringSet
setClass("caRanges", representation(seq="AAStringSet"), contains="cRanges")

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##                                                                           ##
##  Declarations for x-Ranges                                                ##
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## Model:                                                                    ##
##                                                                           ##
##                                                                           ##
##        1000 > > >  ascending reference positions > > > 2000               ##
##                                                                           ##
##                 left                        right                         ##
##                                                                           ##
##             lstart     lend            rstart     rend                    ##
##             ###############<- gaplen ->###############                    ##
##             |    lfeat    |    gap     |    rfeat    |                    ##
##                                                                           ##
##                                                                           ##
## alt_left :             alt             group                              ##
## alt_right:           group             alt                                ##
##                                                                           ##
##                                                                           ##
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setClassUnion("dataFrameOrNULL",c("data.frame","NULL"))

# Additionally contains information about Align-numbers
# plus eventually annotation data.
setClass("gapSites",
            representation(
                dt="data.frame",
                nAligns="numeric", 
                nAlignGaps="numeric",
                annotation="dataFrameOrNULL",
                profile="dataFrameOrNULL"
            ),
            prototype(
                dt=data.frame(),
                nAligns=0,
                nAlignGaps=0,
                annotation=NULL,
                profile=NULL
            )
)

# Additionally stores probe and Annotation overlap information in dt
setClass("annGapSites", contains="gapSites")

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##                                                                           ##
##  Declarations for dnaGapSites                                             ##
##  Additionally contain DNAStringSet                                        ##
##                                                                           ##
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setClass("dnaGapSites", 
            representation(seq="DNAStringSet"), 
            contains="gapSites")

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##                                                                           ##
##  Declarations for aaGapSites                                              ##
##  Additionally contain AAStringSet                                         ##
##                                                                           ##
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setClass("aaGapSites", 
            representation(seq="AAStringSet"),
            contains="gapSites")


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##  keyProfiler:                                                             ##
##  counts occurrence of profile (prof) items defined by factor levels       ## 
##  in profile table in successively added tables                            ##
##  by keys defined in object@ev$dt                                          ##
##                                                                           ##
##  unique: allows adding keys only once for each profile line               ##
##  values: when given, conditions are not simply counted but the given      ##
##          values are summed up for each condition.                         ##
##          values must either be absent or present for all accumulated data ##
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setClass("keyProfiler", 
            representation(
                ev="environment",
                unique="logical",
                counted="logical",
                useValues="logical"
            )
)


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##  SpliceCountSet                                                           ##
##                                                                           ##
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setClass("SpliceCountSet", contains="ExpressionSet")



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##  maxEnt                                                                   ##
##  Calculates splice site scores                                            ##
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setClass("maxEnt",
    representation(
        ev="environment",
        basedir="character"
    ),
    prototype=prototype(
        ev=new.env(),
        basedir="."
    )
)

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##  hbond                                                                    ##
##  Calculates H-bond scores                                                 ##
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setClass("hbond",
    representation(
        ev="environment",
        basedir="character"
    ),
    prototype(
        ev=new.env(),
        basedir="."
    )
)

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## END OF FILE
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