## ----LoadPackageToDetermineVersion,echo=FALSE,message=FALSE,results='hide'----
options(width=65)
set.seed(0)
library(msa)
msaVersion <- packageDescription("msa")$Version
msaDateRaw <- packageDescription("msa")$Date
msaDateYear <- as.numeric(substr(msaDateRaw, 1, 4))
msaDateMonth <- as.numeric(substr(msaDateRaw, 6, 7))
msaDateDay <- as.numeric(substr(msaDateRaw, 9, 10))
msaDate <- paste(month.name[msaDateMonth], " ",
                 msaDateDay, ", ",
                 msaDateYear, sep="")


## ----InstallMSA,eval=FALSE-----------------------------------------------
## source("http://www.bioconductor.org/biocLite.R")
## biocLite("msa")


## ----LoadMSA,eval=FALSE--------------------------------------------------
## library(msa)


## ----locateTeXshadeSty,eval=FALSE----------------------------------------
## system.file("tex", "texshade.sty", package="msa")


## ----SimpleExFileNames---------------------------------------------------
mySequenceFile <- system.file("examples", "exampleAA.fasta", package="msa")
mySequences <- readAAStringSet(mySequenceFile)
mySequences


## ----doAlignment---------------------------------------------------------
myFirstAlignment <- msa(mySequences)
myFirstAlignment


## ----IntegratePDF2-------------------------------------------------------
msaPrettyPrint(myFirstAlignment, output="pdf", showNames="none",
               showLogo="none", askForOverwrite=FALSE, verbose=FALSE)


## ----VisualizePDF,results='asis'-----------------------------------------
msaPrettyPrint(myFirstAlignment, y=c(164, 213), output="asis",
               showNames="none", showLogo="none", askForOverwrite=FALSE)


## ----OtherAlgorithms,----------------------------------------------------
myClustalWAlignment <- msa(mySequences, "ClustalW")
myClustalWAlignment
myClustalOmegaAlignment <- msa(mySequences, "ClustalOmega")
myClustalOmegaAlignment
myMuscleAlignment <- msa(mySequences, "Muscle")
myMuscleAlignment


## ----ShowConsensusBottom,results="asis"----------------------------------
msaPrettyPrint(myFirstAlignment, output="asis", y=c(164, 213),
               subset=c(1:6), showNames="none", showLogo="none",
               consensusColor="ColdHot", showLegend=FALSE,
               askForOverwrite=FALSE)


## ----ShowLogoDefault,results="asis"--------------------------------------
msaPrettyPrint(myFirstAlignment, output="asis", y=c(164, 213),
               subset=c(1:6), showNames="none", showLogo="top",
               logoColors="rasmol", shadingMode="similar",
               showLegend=FALSE, askForOverwrite=FALSE)


## ----Shading1,results='asis'---------------------------------------------
msaPrettyPrint(myFirstAlignment, output="asis", y=c(164, 213),
               showNames="none", shadingMode="similar",
               shadingColors="blues", showLogo="none",
               showLegend=FALSE, askForOverwrite=FALSE)


## ----Shading2,results='asis'---------------------------------------------
msaPrettyPrint(myFirstAlignment, output="asis", y=c(164, 213),
               showNames="none", shadingMode="functional",
               shadingModeArg="structure",
               askForOverwrite=FALSE)


## ----ShowConsensusBottom2,results="asis"---------------------------------
msaPrettyPrint(myFirstAlignment, output="asis", y=c(164, 213),
               subset=c(1:6), showNames="none", showLogo="none",
               consensusColor="ColdHot", showLegend=FALSE,
               shadingMode="similar", askForOverwrite=FALSE,
               furtherCode=c("\\defconsensus{.}{lower}{upper}",
                             "\\showruler{1}{top}"))


## ----GetBibTeX,eval=FALSE------------------------------------------------
## toBibtex(citation("msa"))