Merge pull request #269 from grunwaldlab/znk/format

run air format

Author: zkamvar

R/Index_calculations.r

@@ -4,37 +4,37 @@
 #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!#
 #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!#
 #
-# This software was authored by Zhian N. Kamvar and Javier F. Tabima, graduate 
+# This software was authored by Zhian N. Kamvar and Javier F. Tabima, graduate
 # students at Oregon State University; Jonah C. Brooks, undergraduate student at
 # Oregon State University; and Dr. Nik Grünwald, an employee of USDA-ARS.
 #
 # Permission to use, copy, modify, and distribute this software and its
-# documentation for educational, research and non-profit purposes, without fee, 
+# documentation for educational, research and non-profit purposes, without fee,
 # and without a written agreement is hereby granted, provided that the statement
 # above is incorporated into the material, giving appropriate attribution to the
 # authors.
 #
 # Permission to incorporate this software into commercial products may be
-# obtained by contacting USDA ARS and OREGON STATE UNIVERSITY Office for 
+# obtained by contacting USDA ARS and OREGON STATE UNIVERSITY Office for
 # Commercialization and Corporate Development.
 #
 # The software program and documentation are supplied "as is", without any
-# accompanying services from the USDA or the University. USDA ARS or the 
-# University do not warrant that the operation of the program will be 
-# uninterrupted or error-free. The end-user understands that the program was 
-# developed for research purposes and is advised not to rely exclusively on the 
+# accompanying services from the USDA or the University. USDA ARS or the
+# University do not warrant that the operation of the program will be
+# uninterrupted or error-free. The end-user understands that the program was
+# developed for research purposes and is advised not to rely exclusively on the
 # program for any reason.
 #
-# IN NO EVENT SHALL USDA ARS OR OREGON STATE UNIVERSITY BE LIABLE TO ANY PARTY 
+# IN NO EVENT SHALL USDA ARS OR OREGON STATE UNIVERSITY BE LIABLE TO ANY PARTY
 # FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING
-# LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, 
-# EVEN IF THE OREGON STATE UNIVERSITY HAS BEEN ADVISED OF THE POSSIBILITY OF 
-# SUCH DAMAGE. USDA ARS OR OREGON STATE UNIVERSITY SPECIFICALLY DISCLAIMS ANY 
-# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF 
-# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE AND ANY STATUTORY 
+# LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION,
+# EVEN IF THE OREGON STATE UNIVERSITY HAS BEEN ADVISED OF THE POSSIBILITY OF
+# SUCH DAMAGE. USDA ARS OR OREGON STATE UNIVERSITY SPECIFICALLY DISCLAIMS ANY
+# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE AND ANY STATUTORY
 # WARRANTY OF NON-INFRINGEMENT. THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS"
 # BASIS, AND USDA ARS AND OREGON STATE UNIVERSITY HAVE NO OBLIGATIONS TO PROVIDE
-# MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS. 
+# MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
 #
 #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!#
 #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!#
@@ -44,74 +44,79 @@
 setClassUnion("charORLang", c("character", "language"))
 #==============================================================================#
 #' MLG class
-#' 
+#'
 #' A class to store multilocus genotypes in genclone objects. This is intended
 #' for internal use only.
-#' 
+#'
 #' @name MLG-class
 #' @rdname MLG-class
 #' @aliases MLG
 #' @export
-#' @slot mlg a list containing four vectors, one for each type of MLG 
+#' @slot mlg a list containing four vectors, one for each type of MLG
 #'   manipulation.
-#' @slot visible a character specifying which MLG type is to be displayed and 
+#' @slot visible a character specifying which MLG type is to be displayed and
 #'   accessed.
-#' @slot distname the name of the distance function or matrix used to collapse 
+#' @slot distname the name of the distance function or matrix used to collapse
 #'   mlgs.
 #' @slot distenv the environment that contains the distance function or matrix
 #' @slot distargs the arguments provided to compute the distance function.
 #' @slot distalgo the algorithm used to contract multilocus genotypes.
-#' @slot cutoff Two numbers specifying the cutoff value for expanding and 
+#' @slot cutoff Two numbers specifying the cutoff value for expanding and
 #'   collapsing MLGs.
 #' @author Zhian N. Kamvar
 #' @seealso \code{\linkS4class{genclone}} \code{\linkS4class{snpclone}}
 #'   \code{\link{mll}} For developers: \code{\link{visible}}
 #' @keywords internal
 #' @examples
-#' 
+#'
 #' # These examples will simply show you what you can do with these
 #' set.seed(5000)
 #' (x <- sample(10, 20, replace = TRUE))
 #' (m <- new("MLG", x))
-#' 
+#'
 #'  visible(m) # original is always default
-#'  
-#'  m[]       # adding braces after the object will always return a vector of 
+#'
+#'  m[]       # adding braces after the object will always return a vector of
 #'            # the same type as defined in "visible"
-#'            
+#'
 #'  m + 1     # You can do math on the numeric ones
-#'  
+#'
 #'  visible(m) <- "custom"
 #'  m + 2     # This should throw a warning
 #'  # The types are stored in a data frame. You can retrieve them easily:
 #'  visible(m) <- "original"
 #'  m
 #'  m[, "custom"]
-#'  
-#'  # Important for subsetting, if you subset the object, normally, it will 
+#'
+#'  # Important for subsetting, if you subset the object, normally, it will
 #'  # return a vector unless you specify all = TRUE
 #'  m[1:10]             # original vector
 #'  m[1:10, all = TRUE] # still class MLG
-#' 
+#'
 #==============================================================================#
-setClass("MLG", 
-         representation(visible = "character",
-                        cutoff = "numeric",
-                        distname = "charORLang",
-                        distenv  = "environment",
-                        distargs = "list",
-                        distalgo = "character",
-                        mlg = "data.frame"),
-         prototype(visible = character(0), 
-                   cutoff = numeric(0), 
-                   distname = character(0), 
-                   distenv = as.environment(.GlobalEnv),
-                   distargs = list(),
-                   distalgo = "farthest_neighbor", 
-                   mlg = data.frame(expanded = numeric(0), 
-                                    original = numeric(0), 
-                                    contracted = numeric(0), 
-                                    custom = factor(character(0))
-                                    )
-                   )
-         )
+setClass(
+  "MLG",
+  representation(
+    visible = "character",
+    cutoff = "numeric",
+    distname = "charORLang",
+    distenv = "environment",
+    distargs = "list",
+    distalgo = "character",
+    mlg = "data.frame"
+  ),
+  prototype(
+    visible = character(0),
+    cutoff = numeric(0),
+    distname = character(0),
+    distenv = as.environment(.GlobalEnv),
+    distargs = list(),
+    distalgo = "farthest_neighbor",
+    mlg = data.frame(
+      expanded = numeric(0),
+      original = numeric(0),
+      contracted = numeric(0),
+      custom = factor(character(0))
+    )
+  )
+)