R/Classes.R

In jonkatz2/monitoR: Acoustic Template Detection in R

# Class definitions
# Modified: 2014 MAR 28
# Note: should switch back to slots argument at some point
# representation() is used for compatability with old version of R

setClass('binTemplate', 
#   slots = c(clip.path = 'character', samp.rate = 'integer', pt.on = 'matrix', pt.off = 'matrix', t.step = 'numeric', 
#                  frq.step = 'numeric', n.t.bins = 'integer', first.t.bin = 'numeric', n.frq.bins = 'integer', 
#                  duration = 'numeric', frq.lim = 'numeric', wl = 'integer', ovlp = 'integer', wn = 'character', 
#                  score.cutoff = 'numeric', comment = "character"
#   )
   representation = representation(clip.path = 'character', samp.rate = 'integer', pt.on = 'matrix', pt.off = 'matrix', t.step = 'numeric', 
                  frq.step = 'numeric', n.t.bins = 'integer', first.t.bin = 'numeric', n.frq.bins = 'integer', 
                  duration = 'numeric', frq.lim = 'numeric', wl = 'integer', ovlp = 'integer', wn = 'character', 
                  score.cutoff = 'numeric', comment = "character"
   )
)

setClass('binTemplateList', 
#   slots = c(templates = 'list'), 
   representation = representation(templates = 'list'), 
   validity = function(object) {
      if (any(sapply(object@templates, function(x) !is(x, 'binTemplate'))))
         return('templates slot is not a list of binTemplate objects')
      if (is.null(names(object@templates)))
         return('templates slot is missing names')
      return(TRUE) 
   }
)

setClass('corTemplate', 
#   slots = c(clip.path = 'character', samp.rate = 'integer', pts = 'matrix', t.step = 'numeric', 
#                  frq.step = 'numeric', n.t.bins = 'integer', first.t.bin = 'numeric', n.frq.bins = 'integer', 
#                  duration = 'numeric', frq.lim = 'numeric', wl = 'integer', ovlp = 'integer', wn = 'character', 
#                  score.cutoff = 'numeric', comment = "character"
#   )
   representation = representation(clip.path = 'character', samp.rate = 'integer', pts = 'matrix', t.step = 'numeric', 
                  frq.step = 'numeric', n.t.bins = 'integer', first.t.bin = 'numeric', n.frq.bins = 'integer', 
                  duration = 'numeric', frq.lim = 'numeric', wl = 'integer', ovlp = 'integer', wn = 'character', 
                  score.cutoff = 'numeric', comment = "character"
   )

)

setClass('corTemplateList', 
#   slots = c(templates = 'list'), 
   representation = representation(templates = 'list'), 
   validity = function(object) {
      if (any(sapply(object@templates, function(x) !is(x, 'corTemplate'))))
         return('templates slot is not a list of corTemplate objects')
      if (is.null(names(object@templates)))
         return('templates slot is missing names')
      return(TRUE) 
   }
)

# Create a class "union" for use in classes that may contain either type of template
setClassUnion('TemplateList', 
   c('binTemplateList', 'corTemplateList')
)
setClassUnion('Template', 
   c('binTemplate', 'corTemplate')
)

setClass('templateScores', 
#   slots = c(survey.name = 'character', survey = 'Wave', survey.data = 'list', templates = 'list', scores = 'list', time = 'character'), 
   representation = representation(survey.name = 'character', survey = 'Wave', survey.data = 'list', templates = 'list', scores = 'list', time = 'character'), 
   validity = function(object) {
      if (any(sapply(object@templates, function(x) !is(x, 'Template'))))
         return('templates slot is not a list of Template objects')
      if (is.null(names(object@templates)))
         return('templates slot is missing names')
      return(TRUE) 
   }
)

# MAY WANT TO ADD A validity CHECK FOR scores HERE
setClass('detectionList', 
#   slots = c(survey.name = 'character', survey = 'Wave', survey.data = 'list', templates = 'list', scores = 'list', peaks = 'list', detections = 'list'), 
   representation = representation(survey.name = 'character', survey = 'Wave', survey.data = 'list', templates = 'list', scores = 'list', peaks = 'list', detections = 'list'), 
   validity = function(object) {
      if (any(sapply(object@templates, function(x) !is(x, 'Template'))))
         return('templates slot is not a list of Template objects')
      if (is.null(names(object@templates)))
         return('templates slot is missing names')
      return(TRUE) 
   }
)