@@ -226,7 +226,7 @@ chargeCalculationGlobal <- function(

 #'   or vector of single characters.

 #'   It also supports a single character string that specifies

 #'   the location of a .fasta or .fa file.

-#' @param window a positive, odd integer. 7 by default.

+#' @param window a positive, odd integer. 9 by default.

 #'   Sets the size of sliding window, must be an odd number.

 #'   The window determines the number of residues to be analyzed and averaged

 #'   for each position along the sequence.

@@ -297,7 +297,7 @@ chargeCalculationGlobal <- function(

 #'  plot(gg)

-chargeCalculationLocal <- function(sequence, window = 7,  proteinName = NA,

+chargeCalculationLocal <- function(sequence, window = 9,  proteinName = NA,

                         pH = 7.0, pKaSet = "IPC_protein",

                         printCitation = FALSE, plotResults = FALSE, ...) {

     seqVector <- sequenceCheck(sequence = sequence, method = "stop",

@@ -25,7 +25,7 @@

 #' @param uniprotAccession character string specifying the UniProt Accession of

 #'   the protein of interest. Used to fetch predictions from IUPreds REST API.

 #'   Default is NA. Keep as NA if you do not have a UniProt Accession.

-#' @param window a positive, odd integer. 51 by default.

+#' @param window a positive, odd integer. 9 by default.

 #'   Sets the size of sliding window, must be an odd number.

 #'   The window determines the number of residues to be analyzed and averaged

 #'   for each position along the sequence. 51 is default for 

@@ -174,7 +174,7 @@ idprofile <- function(

     uniprotAccession = NA,

     proteinName = NA,

     iupredType = "long",

-    window = 51,

+    window = 9,

     pH = 7.2,

     pKaSet = "IPC_protein",

     structuralTendencyType = "bar",

@@ -199,12 +199,6 @@ idprofile <- function(

         plotResults = TRUE,

         pKaSet = pKaSet,

         proteinName = proteinName)

-    hydropPlot <- scaledHydropathyLocal(

-        sequence = sequence,

-        window = window,

-        plotResults = TRUE,

-        pKaSet = pKaSet,

-        proteinName = proteinName)

     tendencyPlot <- structuralTendencyPlot(

         sequence = sequence,

         graphType = structuralTendencyType,

@@ -5,7 +5,7 @@

 #'   showing the calculated scores for each window along the sequence.

 #' @inheritParams sequenceCheck

 #'

-#' @param window a positive, odd integer. 7 by default.

+#' @param window a positive, odd integer. 9 by default.

 #'   Sets the size of sliding window, must be an odd number.

 #'   The window determines the number of residues to be analyzed and averaged

 #'   for each position along the sequence.

@@ -6,7 +6,7 @@

 \usage{

 chargeCalculationLocal(

   sequence,

-  window = 7,

+  window = 9,

   proteinName = NA,

   pH = 7,

   pKaSet = "IPC_protein",

@@ -21,7 +21,7 @@ or vector of single characters.

 It also supports a single character string that specifies

 the location of a .fasta or .fa file.}

-\item{window}{a positive, odd integer. 7 by default.

+\item{window}{a positive, odd integer. 9 by default.

 Sets the size of sliding window, must be an odd number.

 The window determines the number of residues to be analyzed and averaged

 for each position along the sequence.}

@@ -43,7 +43,7 @@ disorder based on environmental conditions. Regions of predicted

 environmental sensitivity are highlighted. See the respective functions

 for more details. This is skipped if uniprotAccession = NA.}

-\item{window}{a positive, odd integer. 51 by default.

+\item{window}{a positive, odd integer. 9 by default.

 Sets the size of sliding window, must be an odd number.

 The window determines the number of residues to be analyzed and averaged

 for each position along the sequence. 51 is default for 

@@ -18,7 +18,7 @@ a vector of single characters, or an AAString object.

 It also supports a single character string that specifies

 the path to a .fasta or .fa file.}

-\item{window}{a positive, odd integer. 7 by default.

+\item{window}{a positive, odd integer. 9 by default.

 Sets the size of sliding window, must be an odd number.

 The window determines the number of residues to be analyzed and averaged

 for each position along the sequence.}