# dbUtilities.R
#
# Purpose: Utility functions for a Protein datamodel
# Version: 0.7.2
# Date:    Nov 2015
# Author:  Boris and class
#
# ToDo:    Add more tables.
#          Accept either taxID OR organism name
#             and pull the other from NCBI.
#          Allow search by either feature name or psID in
#             getFeatureFasta()
#          Write function to type-check and str_trim arguments.
#          Write function to renumber pdb.
#          Split code into ABCdbUtil, ABC3DUtil, ABCphyloUtil.
# Notes:   Cf. schema sketch at 
# http://steipe.biochemistry.utoronto.ca/abc/index.php/File:ProteinDataModel.1.jpg
#          Currently implements "protein",
#              "taxonomy", "proteinFeature" and "feature"
#              tables.
#
# V 0.7.2  bugfix in addFeatureToDB() ... this time for real.
# V 0.7.1  bugfix in addFeatureToDB()
# V 0.7    added format and selection options to getFeatureFasta()
#              to support more flexible output.
#          fixed bug in getSeq() ... wrong variable name.
#          fixed bug in makeNames() ... wrong variable name.
#          manually added "KilA" to the E. coli gene.
#          added a safeIter function to skip iteration over
#              an empty object.
#          added option to scan Prosite with sequence instead
#              of ID, in fetchPrositeFeatures(),
#              update Feature Data version to 1.1
#          align addFeatureToDB() function with new Feature
#              Data Format.
#          sanitize all relevant input with str_trim()
# V 0.6.2  fixed bug in AddProteinToDB() that mixed up list
#              input with dataframe output.
# V 0.6.1  fixed wrong argument in printArgs
#          fixed logic of removing tmp file in updateVerifiedFile 
# V 0.6    added proteinFeature and feature tables, function
#              to fetch features from prositeScan and
#              function to get FASTA for feture ranges.
#          added function to mereg old an new DB versions.
#          extensive maintenance.
#          update refDB with scanProsite features. 
# V 0.5    added refDB database object with 48 reference 
#              APSES domain proteins from 10 fungi and
#              E. Coli as outgroup. Optionally load it
#              into memory upon sourcing this script.
#          generalize update function to handle all sources
#              and target, while making the update of
#              THIS file in its proper location the default.
# V 0.4.1: issue: fails on incomplete data from NCBI
#              fixed. NCBI sent empty values for missing
#              genome coordinates. Set all missing values
#              to NA before calling addProteinToDB
# V 0.4:   added fetchProteinData() for data retrieval from
#              NCBI and UniProt
#          changed addProteinToDB() to accept either output of
#              fetchProteinData() or named arguments
#          make symbol names internally consistent
#          added DB version check
#          Test whether an entry for addProteinToDB()
#              already exists, allow to add duplicate or
#              replace existing entry.
#          Style maintenance:
#              use CamelCase consistently
#              keep variables and messages in the same line
#                  of code when using paste()
# V 0.3.1: maintenace update
# V 0.3:   replaced MD5 verification with digest() sha-1 of
#              of R-object, since MD5 of files on Windows
#              gave varying results.
# V 0.2:   Changed get functions to return vectors of
#              multiple matches.
#          added makeNames()
#          added biCodes()
#          added updateDbUtilities())
#  
# ==========================================================


# ====  MESSAGE ============================================

cat("Loading db_utilities.R ...\n")

# ====  CONSTANTS  =========================================
cat("  Constants:\n")

DBVERSION <- "Protein Data 1.0"
cat(paste("    DBVERSION: \"",
          DBVERSION,
          "\"\n",
          sep=""))
          
UTILVERSION <- "dbUtilities 0.7.2"
cat(paste("    UTILVERSION: \"",
          UTILVERSION,
          "\"\n",
          sep=""))
          
LOADREFDB <- TRUE
cat(paste("    LOADREFDB: \"",
          as.character(LOADREFDB),
          "\"\n",
          sep=""))
          
          

# ====  PACKAGES  ==========================================
cat("  Packages:\n")

# Needed for in memory sha-1 hash for verification of
# file updates.
if (! require(digest, quietly=TRUE)) {
	install.packages("digest")
	library(digest)
}
cat("    \"digest\" (hash functions)\n")

# Needed for fetching UniProt data via POST 
if (!require(httr, quietly=TRUE)) { 
	install.packages("httr")
	library(httr)
}
cat("    \"httr\" (http GET and POST functions)\n")

# Needed to parse NCBI etuils XML responses
if (!require(XML, quietly=TRUE)) {
	install.packages("XML")
	library(XML)
}
cat("    \"XML\" (parsing XML trees)\n")

# Needed for str_trim()
if (!require(stringr, quietly=TRUE)) {
	install.packages("stringr")
	library(stringr)
}
cat("    \"stringr\" (convenient string manipulation)\n")


# ====  FUNCTIONS  =========================================
cat("  Functions:\n")

# Utility functions to list arguments of functions contained
# in this file when it is being sourced.
printArgs <- function(fName) {
	fArgs <- formals(fName)
	fName <- deparse(substitute(fName))
	if (length(fArgs) == 0) {
		cat(paste("    ", fName, "()\n", sep=""))
	}
	else if (length(fArgs) == 1) {
	
		cat(paste("    ", fName, "(",
		makeArgText(fArgs[1]),
		")\n", sep=""))
	}
	else {
		cat(paste("    ", fName, "(", sep=""))
		for (i in 1:length(fArgs)) {
    		cat(paste(makeArgText(fArgs[i]),
		    sep=""))
		    if (i < length(fArgs)) {
		    	cat(", ")
		    }
		    else {
		    	cat(")\n")
		    }
		}
	}
}

makeArgText <- function(pl) {
	arg <- names(pl)
	return(arg)
}

safeIter <- function(idx) {
	# returns a vector 1:idx if idx is greater than
	# zero. Returns NULL otherwise. This avoids iterating
	# a loop once over a zero length object.
	# use: for (i in safeIter(length(idx))) { ... }
    if (length(idx) != 1 | ! is.null(nrow(idx))) {
    	stop("Value to iterate over is not a scalar.")
    }
    if (idx > 0) {
    	return(1:idx)
    } else {
    	return(NULL)
    }
}

# ==== createDB ============================================
createProteinDB <- function() {
	# Returns an empty list with DBVERSION and database
	# tables initialized
    db <- list()

    db$version <- DBVERSION	

    db$taxonomy <- data.frame(id = numeric(),
                              organismName = character(),
                              stringsAsFactors = FALSE)

    db$protein <- data.frame(id = numeric(),
                             name = character(),
                             refSeqID = character(),
                             uniProtID = character(),
                             taxID = numeric(),
                             genomeXref = character(),
                             genomeFrom = numeric(),
                             genomeTo = numeric(),
                             seq = character(),
                             stringsAsFactors = FALSE)

    db$proteinFeature <- data.frame(
                             id = numeric(),
                             proteinID = character(),
                             featureID = character(),
                             start = numeric(),
                             end = numeric(),
                             stringsAsFactors = FALSE)

    db$feature <- data.frame(id = character(),
                             def = character(),
                             stringsAsFactors = FALSE)

	return(db)
}
printArgs(createProteinDB)


# ==== checkVersion ========================================
checkVersion <- function(db) {
	# stop if db does not have current version
    if (db$version != DBVERSION) {
        stop(paste("Database in argument has version \"",
    		       db$version,
    		       "\". Expecting \"",
    		       DBVERSION,
    		       "\" instead.",
    		       sep=""))
    }
}
printArgs(checkVersion)


# ==== in2seq ==============================================

in2seq <- function(s, uc = TRUE, lc = FALSE, noAmbig = TRUE) {
	# Sanitizes protein sequence input and converts it into a
	# sequence string. Case can be optionally changed, 
	# default is to convert to upper case.
	# Letters that are not one-letter aa code - such as
	# ambiguity codes - throw an error, if not explicitly
	# permitted.
	
	s <- paste(unlist(s), collapse="") # flatten whatever structure it has
	s <- gsub("[^a-zA-Z]", "", s) # remove all non-letters
	if (noAmbig) {
		ambCodes <- "([bjouxzBJOUXZ])"  # parentheses capture the match
		ambChar <- unlist(regmatches(s, regexec(ambCodes, s)))[1] 
         if (! is.na(ambChar)) {
         	    stop(paste("Input contains ambiguous letter: \"", ambChar, "\"", sep=""))
         }		
	}
	if (uc) { s <- toupper(s)}
	if (lc) { s <- tolower(s)}
	return(s)
}
printArgs(in2seq)


# ==== in2vec ==============================================

in2vec <- function(s, ...) {
	# Sanitizes protein sequence input and expands it into a
	# vector of single characters. Arguments for in2seq are
	# passed through via the three-dots parameter syntax.
	
	s <- in2seq(s, ...)
	return(unlist(strsplit(s, "")))
}
printArgs(in2vec)


# ==== node2string =========================================

node2string <- function(doc, tag) {
    # Extracts tagged contents from an XML response.
    # Contents between any <tag> and </tag> is returned in
    # a vector of strings.
	path <- paste("//", tag, "/text()", sep="")
	nodes <- getNodeSet(doc, path)
	return(unlist(lapply(nodes, toString.XMLNode)))
}
printArgs(node2string)


# ==== fetchProteinData ====================================

fetchProteinData <- function(refSeqID, verbose=TRUE) {
	# Retrieves data for a given protein refseq ID from
	# NCBI and UniProt. NCBI data is retrived via the 
	# eutils API. 
	# cf. http://www.ncbi.nlm.nih.gov/books/n/helpeutils/
	# UniProt IDs are retrieved from the
	# ID mapping service via a POST call. 
	# cf. http://www.uniprot.org/help/programmatic_access
	# Returns a list of data items.
	
	data <- list()
	data$type <- "Protein Data V 1.0"
	data$refSeqID <- str_trim(refSeqID)

    # get UniProt ID for refseq
	URL <- "http://www.uniprot.org/mapping/"
	response <- POST(URL, 
	                 body = list(from = "P_REFSEQ_AC",
	                             to = "ACC",
	                             format = "tab",
	                             query = data$refSeqID))
	if (response$status_code == 200) { # 200: oK
		data$uniProtID <- str_trim(unlist(strsplit(content(response), "\\s+"))[4])
		if (is.na(data$uniProtID)) {
	        warning(paste("UniProt ID mapping service returned NA.",
	                      "Check your RefSeqID."))
	}

	} else {
		data$uniProtID <- NA
		warning(paste("UniProt ID mapping not available:",
		              "server returned status",
		              response$status_code))
	}

    # Base URL for NCBI eutils API calls
	eUtilsBase <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/"

	# search for GI of this refSeqID
	URL <- paste(eUtilsBase,
	             "esearch.fcgi?",
	             "db=protein",
	             "&term=", data$refSeqID,
	             sep="")
	data$GID <- as.integer(node2string(htmlParse(URL), "id"))
	if (is.null(data$GID)) { stop("No GID found for this refSeqID. Check your input.")}

	# get NCBI summary data
	URL <- paste(eUtilsBase,
	             "esummary.fcgi?",
	             "db=protein",
	             "&id=", data$GID,
	             "&version=2.0",
	             sep="")
	response <- htmlParse(URL)
	data$taxID <- as.integer(node2string(response, "taxid"))
	data$organismName <- str_trim(node2string(response, "organism"))
	
	# Fetch the sequence
	URL <- paste(eUtilsBase,
	             "efetch.fcgi?",
	             "db=protein",
	             "&id=", data$GID,
	             "&retmode=text",
	             "&rettype=fasta",
	             sep="")
	# retrieve FASTA, split into lines
	tmp <- node2string(htmlParse(URL), "p")
	tmp <- str_trim(tmp)
	tmp <- unlist(strsplit(tmp, "\\n"))
	data$FASTAheader <- tmp[1]
	data$seq <- in2seq(tmp[-1])
	
	# Fetch the crossreference to the gene DB
	URL <- paste(eUtilsBase,
	             "elink.fcgi?",
	             "dbfrom=protein",
	             "&db=gene",
	             "&id=", data$GID,
	             sep="")
	data$geneID <- as.integer(node2string(htmlParse(URL), "linksetdb/id"))
	
	# Fetch the gene summary
	URL <- paste(eUtilsBase,
	             "esummary.fcgi?",
	             "&db=gene",
	             "&id=", data$geneID,
	             sep="")
	response <- htmlParse(URL)
	
	data$name <- str_trim(node2string(response, "name"))
	data$genomeXref <- str_trim(node2string(response, "chraccver"))
	data$genomeFrom <- as.integer(node2string(response, "chrstart")[1])
	data$genomeTo <- as.integer(node2string(response, "chrstop")[1])
	
	if (verbose) {
        cat(paste("Data retrieved:\n"))
        cat(paste("  $name:         ", data$name,         "\n"))
        cat(paste("  $refSeqID:     ", data$refSeqID,     "\n"))
        cat(paste("  $uniProtID:    ", data$uniProtID,    "\n"))
        cat(paste("  $GID:          ", data$GID,          "\n"))
        cat(paste("  $taxID:        ", data$taxID,        "\n"))
        cat(paste("  $organismName: ", data$organismName, "\n"))
        cat(paste("  $genomeXref:   ", data$genomeXref,   "\n"))
        cat(paste("  $geneID:       ", data$geneID,       "\n"))
        cat(paste("  $genomeFrom:   ", data$genomeFrom,   "\n"))
        cat(paste("  $genomeTo:     ", data$genomeTo,     "\n"))
        cat(paste("  $FASTAheader:  ", data$FASTAheader,  "\n"))
        len <- nchar(data$seq)
        cat(paste("  $seq:           ", 
                  substr(data$seq, 1, 10),
                  " ... ",
                  substr(data$seq, len-10, len),
                  " (", len, " AA)",
                  "\n\n", sep=""))	
	}

    return(data)
}
printArgs(fetchProteinData)


# ==== fetchPrositeFeatures ====================================

fetchPrositeFeatures <- function(database,
                                 extID,
                                 useSeq = TRUE,
                                 verbose=TRUE) {
	# Retrieves data from Scan Prosite using a query sequence.
	# UniProt or RefSeq ID or Name are passed as argument extID,
	# the correpsonding sequence is retrieved from the protein
	# table and processed.
	# 
	# This function screen-scrapes the tabular ScanProsite
	# output.
	# Returns a list:
	#     $pID:    protein table ID of query
	#     $start:  Feature start
	#     $end:    Feature end
	#     $id:     Prosite ID of feature
	#     $def:    Prosite name of feature
	
    # ToDo: is the first argument a database object or the string? 
    #     If it's a string, useSeq must be FALSE to continue...
    #     If it's a database, verify it, then continue below
	
	extID <- str_trim(extID)
	
	# Identify the type of ext ID and fetch its internal id
	pN <- getTableID(database, "protein", name = extID)
	pU <- getTableID(database, "protein", uniProtID = extID)
	pR <- getTableID(database, "protein", refSeqID = extID)

#ToDo.: If useSeq is FALSE, work with the prosite ID

	
	nMatch <- length(pN) + length(pU) + length(pR)
	if (nMatch == 0) {
		stop(paste("ID \"", extID, "\" not found in database.", sep=""))
	} else if (nMatch > 1) {
		stop(paste("ID \"", extID, "\" is not unique in database.", sep=""))
	}
	
	if (length(pN) == 1) {
		pID <- pN
	} else if (length(pU) == 1) {
		pID <- pU
	} else {
		pID <- pR
	}
	
	# Retrieve the sequence
	seq <- database$protein$seq[database$protein$id == pID]

	# prepare the output
	features <- list()
	features$type   <- "Feature Data V 1.1"
	features$pID    <- pID
	features$extID  <- character()   
	features$start  <- numeric()
	features$end    <- numeric()
	features$id     <- character()
	features$def    <- character()
	
	PREFIX <- "ps|"
	
	fasta <- paste(">", extID, "\n", seq, "\n", sep="")

	URL <- "http://prosite.expasy.org/cgi-bin/prosite/PSScan.cgi"
    if (verbose) { cat(paste("Scanning Prosite for ", extID, "... ")) }

	response <- POST(URL, 
                     body = list(meta = "opt1",
                                 meta1_protein = "opt1",
                                 seq = fasta,
                                 skip = "on",
                                 output = "tabular"))
    lines <- unlist(strsplit(content(response,"text"), "\\n"))
    pattern <- paste("^", extID, sep="")
    lines <- lines[grep(pattern, lines)]
    if (length(lines) > 0) {
        for (line in lines) {
            tokens <- unlist(strsplit(line, "\\t|\\|"))
            features$extID <- c(features$extID,            tokens[1])
	        features$start <- c(features$start, as.integer(tokens[2]))
	        features$end   <- c(features$end,   as.integer(tokens[3]))
	        features$id    <- c(features$id, paste(PREFIX, tokens[4], sep=""))
	        features$def   <- c(features$def,              tokens[5])
        }
        if (verbose) {cat(paste(" ", length(lines), "feature(s).\n")) }
    } else {
        if (verbose) { cat(paste(" WARNING: No feature found.\n")) }
    }

	return(features)
}
printArgs(fetchPrositeFeatures)


# ==== addProteinToDB =============================================

addProteinToDB <- function(database,
                  x,
                  override = FALSE,
                  replace = TRUE) {
	# Add a new protein entry to the database, with associated
	# taxonomy entry. x is a protein data list item produced by
	# fetchProteinData. If override is true, replace an existing
	# entry (replace: TRUE), or add a duplicate entry
	# (replace: FALSE)
	
    if (missing(database)) {
    	stop("\"database\" argument is missing with no default.")
    }
    
    checkVersion(database)
    
    if (missing(x)) {
    	stop("No protein data list was passed as argument.")    	
    } else {
    	# expect that x is list of data items
    	if (is.null(x$type)) {
    		stop("Protein data argument must be a list of data items.")
    	}
    	expectedType <- "Protein Data V 1.0"
    	if (x$type != expectedType) {
    		stop(paste("List of data items has type \"", x$type,
    		            "\". Expecting \"", expectedType, "\" instead.",
    		            sep=""))
    	}
    }

    if (length(x$taxID) == 0) {
    	stop("taxID argument is missing with no default.")
    }
    
    if (! is.numeric(x$taxID)) {
   		stop(paste("taxID \"", x$taxID, 
   		            "\" is not numeric. Please correct.", sep=""))
   	}
    
    # handle taxID
    if (! any(database$taxonomy$id == x$taxID, na.rm = TRUE)) {  # new taxID
        if (length(x$organismName) == 0) {
    		stop(paste("taxID", x$taxID, 
    		           "is not yet in database, but organismName", 
    		           "is missing with no default."))
    	}
    	else {
    		# add this organism to the taxonomy table
    		entry <- data.frame(id = x$taxID,
                                organismName = x$organismName,
                                stringsAsFactors = FALSE)
            database$taxonomy <- rbind(database$taxonomy, entry)
    	}
    }

    # handle protein.   
    # pID is 1 if the table is empty, max() + 1 otherwise.
    if (nrow(database$protein) == 0) {
        pID <- 1
    } else {
    	pID <- max(database$protein$id) + 1
    }
    

    
    # Ensure all of the values exist.
    if (length(x$name)         == 0) { x$name         <- NA }
    if (length(x$refSeqID)     == 0) { x$refSeqID     <- NA }
    if (length(x$uniProtID)    == 0) { x$uniProtID    <- NA }
    if (length(x$taxID)        == 0) { x$taxID        <- NA }
    if (length(x$genomeXref)   == 0) { x$genomeXref   <- NA }

    if (length(x$genomeFrom)   == 0) { x$genomeFrom       <- NA 
    } else if (x$genomeFrom == 999999999) { x$genomeFrom  <- NA
    } else if (x$genomeFrom == 0) { x$genomeFrom          <- NA}

    if (length(x$genomeTo)   == 0) { x$genomeTo       <- NA 
    } else if (x$genomeTo == 999999999) { x$genomeTo  <- NA
    } else if (x$genomeTo == 0) { x$genomeTo          <- NA}

    if (length(x$seq)          == 0) { x$seq          <- NA }
    if (length(x$organismName) == 0) { x$organismName <- NA }
    
    # fix any sequence problems
	x$seq <- in2seq(x$seq)
	
	
	# prepare a dataframe row
    entry <- data.frame(id = pID,
                        name = x$name,
                        refSeqID = x$refSeqID,
                        uniProtID = x$uniProtID,
                        taxID = x$taxID,
                        genomeXref = x$genomeXref,
                        genomeFrom = x$genomeFrom,
                        genomeTo = x$genomeTo,
                        seq = x$seq,
                        stringsAsFactors = FALSE)
	
	
	# put columns in correct table order
	entry <- entry[ , colnames(database$protein)]
	
    # check whether refSeqID or uniProtID already exist in the
    # database. Overwrite or duplicate as requested.
    if (any(database$protein$refSeqID  == entry$refSeqID, na.rm = TRUE) ||
        any(database$protein$uniProtID == entry$uniProtID, na.rm = TRUE)) {
    	    duplicate <- TRUE
    	} else {
    		duplicate <- FALSE
    	}

    	if (duplicate) {
    		if (! override) {
    			stop(paste("refSeqID and/or uniProtID already exist in database.\n",
    			           " You must set \"override = TRUE\" to add duplicate entries",
    			           "or replace existing entries."))
    		} else if (replace){
    			pid <-        database$protein$id[which(database$protein$refSeqID  == entry$refSeqID)]
    			pid <- c(pid, database$protein$id[which(database$protein$uniProtID == entry$uniProtID)])
    			pid <- unique(pid)
    			if (length(pid) == 1) {
    				# replace existing unique entry
    			entry$id <- pid
    			database$protein[which(database$protein$id  == entry$id), ] <- entry
    			} else {
    			stop(paste("More than one matching refSeqID and/or uniProtID found in database.\n",
    			           " This function can't replace more than one entry.",
    			           "First delete additional entries."))
    			}
    		} else { # do not replace existing but
    			     # add entry as new record to database
            database$protein <- rbind(database$protein, entry)
    		}
    	} else { # not duplicate
        database$protein <- rbind(database$protein, entry)
    	}
    	
    return(database)
}
printArgs(addProteinToDB)


# ==== addFeatureToDB =============================================

addFeatureToDB <- function(database, x) {  
                   
	# Add new proteinFeature table entries to the database, with associated
	# feature table entries. x is a feature data list item produced by
	# fetchPrositeFeatures. 
	
    if (missing(database)) {
    	stop("\"database\" argument is missing with no default.")
    }
    
    checkVersion(database)
    
    if (! missing(x)) {
    	# expect that x is list of feature items
    	if (is.null(x$type)) {
    		stop("Argument is not a feature list.")
    	}
    	expectedType <- "Feature Data V 1.1"
    	if (x$type != expectedType) {
    		stop(paste("List of feature data items has type \"", x$type,
    		            "\". Expecting \"", expectedType, "\" instead.",
    		            sep=""))
    	}
    } else {
    	stop("Argument missing. Function needs a feature list to work with.")
    }
    
    len <- length(x$extID)
    
    if (len == 0) {
    	    cat("WARNING: skipping this empty list.\n")
    } else {
    
	    testIntegrity(x$extID, len, is.character)
	    testIntegrity(x$start, len, is.numeric)
	    testIntegrity(x$end,   len, is.numeric)
	    testIntegrity(x$id,    len, is.character)
	    testIntegrity(x$def,   len, is.character)

	    	pID <- x$pID	    
	    
	    # Iterate over all features in table
	    for (i in safeIter(len)) {
	
	   	    # get existing feature ID or add new feature to table
	    	fID <- getTableID(database, "feature", featureID = x$id[i])
	    	if (length(fID) == 0) { # new ID: add to table
	    		entry <- data.frame(id = x$id[i],
	                                def = x$def[i],
	                                stringsAsFactors = FALSE)
	            database$feature <- rbind(database$feature, entry)
	    		fID <- x$id[i]
	    	}
	
	        # make or create pfID for proteinFeature table
	        if (length(database$proteinFeature$id) == 0) {
	        	pfID <- 1
	        } else {
	        	pfID <- max(database$proteinFeature$id) + 1
	        }
	
	   	    # we may add the same feature to the same protein several
	   	    # times, even with the same start and end coordinates. We
	   	    # don't enforce uniqueness here (but may at a later point).
	   	    
	   	    # Make entry for proteinFeature table
	   		entry <- data.frame(id = pfID,
	                            proteinID = pID,
	                            featureID = fID,
	                            start     = x$start[i],
	                            end       = x$end[i],
	                            stringsAsFactors = FALSE)
	        database$proteinFeature <- rbind(database$proteinFeature,
	                                         entry[colnames(database$proteinFeature)])
	    } # end for (i in safeIter(len))
	} # end if (len == 0)
    return(database)
}
printArgs(addFeatureToDB)


testIntegrity <- function(x, len, fConfirm) {
	# utility function to test whether feature values exist and
	# are of the expected type
    if (length(x) == 0 | 
        any(x == "") |
        any(is.na(x)) |
        !any(fConfirm(x))) {
    	stop(paste("Data integrity check failed:", paste(x, collapse=" ")))
    }
    if (length(x) != len) {
    	stop(paste("Vector does not have expected length", len, ":", paste(x, collapse=" ")))
    }
}



# ==== setTableValue =======================================

setTableValue <- function(database,
                  table,
                  id   =         NULL,
                  name =         NULL,
                  refSeqID =    NULL,
                  uniProtID =   NULL,
                  taxID =  NULL,
                  genomeXref =  NULL,
                  genomeFrom =  NULL,
                  genomeTo =    NULL,
                  seq =     NULL,
                  organismName = NULL) {
    # Set database values for existing entries
    
    if (missing(database) | missing(table)) {
    	stop("Database or table is missing with no default.")
    }

    checkVersion(database)

	table <- str_trim(table)
    if (table == "protein") {
	    if (is.null(id)) {
	    	stop("Protein id is missing with no default.")
	    }
    	row <- which(database$protein$id == id)
    	if (! is.null(name)) { database$protein[row, "name"] <- as.character(name) } 
    	if (! is.null(refSeqID)) { database$protein[row, "refSeqID"] <- as.character(refSeqID) } 
    	if (! is.null(uniProtID)) { database$protein[row, "uniProtID"] <- as.character(uniProtID) } 

    	if (! is.null(taxID)) {
    		# must be numeric ...
    		if (! is.numeric(taxID)) {
    		stop(paste("taxID", 
    		           taxID, 
    		           "is not numeric. Please correct."))
    		}
    		# must exist in taxonomy table ...
	        if (! any(database$taxonomy$id == taxID, na.rm = TRUE)) {  # new taxID
	    		stop(paste("taxID", taxID, "not found in taxonomy table.", 
	    		           "Please update taxonomy table and try again."))
	        }
	        # all good, update it...
    		database$protein[row, "taxID"] <- taxID
        } 
    	if (! is.null(genomeXref)) { database$protein[row, "genomeXref"] <- genomeXref} 
    	if (! is.null(genomeFrom)) { database$protein[row, "genomeFrom"] <- genomeFrom} 
    	if (! is.null(genomeTo)) { database$protein[row, "genomeTo"] <- genomeTo} 
    	if (! is.null(seq)) { database$protein[row, "seq"] <- in2seq(seq)} 
    }
    else if (table == "taxonomy") {
	    if (missing(taxID)) {
	    	stop("taxID is missing with no default.")
	    }
    if (! any(database$taxonomy$id == taxID, na.rm = TRUE)) { 
	       stop(paste(" Can't set values for this taxID.", 
	    		       taxID, "was not found in taxonomy table."))
	    }
    	row <- which(database$taxonomy$id == taxID)
    	if (organismName != "") { database$taxonomy[row, "organismName"] <- organismName } 
    }
    else {
    	stop(paste("This function has no code to update table \"", table, "\".",
	    	       "Please enter a valid table name."))
	}
    
    return(database)
}
printArgs(setTableValue)


# ==== getTableID =============================================

getTableID <- function(database,
                  table,
                  name         = NULL,
                  refSeqID     = NULL,
                  uniProtID    = NULL,
                  taxID        = NULL,
                  organismName = NULL,
                  proteinID    = NULL,
                  featureID    = NULL,
                  featureDef   = NULL) {
	# Get a vector of IDs from a database table from all rows
	# for which all of the requested attributes are true.
	# Note: if no restrictions are entered, ALL ids are returned.
	# Currently there is no code to select from genome coordinates,
	# or query for sequence substrings.
	
    if (missing(database) | missing(table)) {
    	stop("Database or table is missing with no default.")
    }

    checkVersion(database)

    if (table == "protein") {
    	sel <- rep(TRUE, nrow(database$protein))  # initialize
    	if (! is.null(name))      { sel <- sel & database$protein[, "name"]      %in% name } 
    	if (! is.null(refSeqID))  { sel <- sel & database$protein[, "refSeqID"]  %in% refSeqID } 
    	if (! is.null(uniProtID)) { sel <- sel & database$protein[, "uniProtID"] %in% uniProtID } 
    	if (! is.null(taxID))     { sel <- sel & database$protein[, "taxID"]     %in% taxID } 
        sel <- database$protein$id[sel]  # get ids by selecting from vector
    }
    else if (table == "taxonomy") {
    	sel <- rep(TRUE, nrow(database$taxonomy))  # initialize
    	if (! is.null(taxID))        { sel <- sel & database$taxonomy[, "id"]           %in% taxID } 
    	if (! is.null(organismName)) { sel <- sel & database$taxonomy[, "organismName"] %in% organismName } 
        sel <- database$taxonomy$id[sel]  # get ids by selecting from vector
    }
    else if (table == "proteinFeature") {
    	sel <- rep(TRUE, nrow(database$proteinFeature))  # initialize
    	if (! is.null(proteinID)) { sel <- sel & database$proteinFeature[, "proteinID"]  %in% proteinID } 
    	if (! is.null(featureID)) { sel <- sel & database$proteinFeature[, "featureID"]  %in% featureID } 
        sel <- database$proteinFeature$id[sel]  # get ids by selecting from vector
    }
    else if (table == "feature") {
    	sel <- rep(TRUE, nrow(database$feature))  # initialize
    	if (! is.null(featureID))  { sel <- sel & database$feature[, "id"]   %in% featureID } 
    	if (! is.null(featureDef)) { sel <- sel & database$feature[, "def"]  %in% featureDef } 
        sel <- database$feature$id[sel]  # get ids by selecting from vector
    }
    else {
    	stop(paste("This function has no code to select from table \"", table, "\".",
	    	       "Please enter a valid table name."))
	}
    
    return(sel)

}
printArgs(getTableID)


# ==== getSeq ==============================================

getSeq <- function(database, ...) {
	# Retrieves all sequences for given id matches from the
	# protein table. Uppercase, to make Biostrings happy.

    if (missing(database)) {
    	stop("Database argument is missing with no default.")
    }

    checkVersion(database)

    IDs <- getTableID(database, table= "protein", ...)
    seq <- database$protein[database$protein$id %in% IDs, "seq"]
    return(toupper(seq))
}
printArgs(getSeq)


# ==== getFeatureFasta =====================================

getFeatureFasta <- function(database,
                            fName,
                            ids,
                            exactlyOne = FALSE,
                            outFormat = "raw",
                            width=60) {
	# Retrieves sequences for given fName matches in
	# multi FASTA format.
	# ids is a vector of unique identifiers from the protein
	#     table. If ids is missing, we retrieve feature
	#     sequences for all ids.
	# If exactlyOne is TRUE, we guarantee one sequence for
	#     each id. If an id does not have a requested feature,
	#     a pseudo sequence of ten hyphens is returned. If an
	#     id has more than one of a requested feature, only
	#     the first one is returned, with a warning.
	# outFormat = raw returns a raw string that can be displayed
	#     with cat(). Each header and each line of sequence is
	#     "\n" terminated.
	# outFormat = df  returns a dataframe with head and seq
	#     columns. No "\n" is added to the strings.
	# width controls the number of characters in a line of
	# raw string output.
	

    if (missing(database)) {
    	stop("Database argument is missing with no default.")
    }

    if (missing(fName)) {
    	stop("Feature name argument is missing with no default.")
    }

    checkVersion(database)

    if (missing(ids)) {
    	# use all ids in the database
    	ids <- database$protein$id
    }
    
	fName <- str_trim(fName)          
    # get the Feature ID for the requested fName
    fID <- getTableID(database, table= "feature", featureDef = fName)
    if (length(fID) == 0) {
    	    stop(paste("No entry in feature table for feature Name \"", fName, "\"."))
    }
    if (length(fID) > 1) {
    	    stop(paste("Feature name \"", fName, "\" is not unique in the features table.\n",
    	               "I can't tell which one to use."))
    }


    # prepare empty "fasta" output object    
    if (outFormat == "raw") {
        fasta <- character()
    } else if (outFormat == "df") {
        fasta <- data.frame(head = character(),
                            seq = character(),
                            stringsAsFactors = FALSE)
    } else {
        stop("Unknown format \"", outFormat, "\" requested.")
    }


    # process all protein IDs
    for (i in safeIter(length(ids))) {  	
        pID   <- ids[i]
        if (! pID %in% database$protein$id) {
    	    stop(paste("ID \"", pID, "\" is not present in protein table."))        	
        }
        pRow <- which(database$protein$id == pID)
        
        # fetch the data that is the same for each proteinFeature
    	tmp    <- database$protein$taxID[pRow]
    	tmp    <- database$taxonomy[database$taxonomy$id == tmp, "organismName"]
    	pCode  <- biCode(tmp)
    	pName  <- database$protein$name[pRow]

        # get all proteinFeature ids that match pID AND  fID
        pfIDs <- getTableID(database,
                            table = "proteinFeature",
                            proteinID = pID,
                            featureID = fID)
                            
        if (length(pfIDs) > 1 & exactlyOne) { # there's more than one match
        	                                  # but we requested to get only
        	                                  # one ...
            # ... drop a warning and use only the first one.
            warning("     More than one ", fName, 
                    " annotation found for ", pName,
                    " (pfIDs: ", paste(pfIDs, collapse=", "), ").\n",
                    "       Using only the first one.")
            pfIDs <- pfIDs[1]
        }
                                        
        # prepare a dataframe to collect the information
        fOut <- data.frame(start = numeric(),
                          end   = numeric(),
                          seq   = character(),
                          stringsAsFactors = FALSE)

        if (length(pfIDs) == 0) { # No annotation of this
        	                          # feature for this pID ...

            if (exactlyOne) { # but we requested to get at least
        	                  # one ...
                # make a dummy feature sequence
                fTmp <- data.frame(start = 0,
                                  end   = 0,
                                  seq   = "----------",
                                  stringsAsFactors = FALSE)
                fOut <- rbind(fOut, fTmp)
            } else {
            	# do nothing
            }

        } else { # Annotation exists, process it
            for (j in safeIter(length(pfIDs))) {
                fStart <- database$proteinFeature$start[pfIDs[j]]
                fEnd <- database$proteinFeature$end[pfIDs[j]]
                fSeq <- substr(database$protein$seq[pRow], fStart, fEnd)
                fTmp <- data.frame(start = fStart,
                                   end   = fEnd,
                                   seq   = fSeq,
                                   stringsAsFactors = FALSE)
                fOut <- rbind(fOut, fTmp)
            }
        }

        
        # process fOut according to the requested output format
        for (j in safeIter(nrow(fOut))) {
            start <- fOut$start[j]
            end <- fOut$end[j]
            header <- paste(">", 
    	                     pName, "_", pCode, "    ",
    	                     fName, " ", start, ":", end,
    	                     sep = "")
            seq <- fOut$seq[j]
            
            if (outFormat == "raw") {
                fasta <- paste(c(fasta,
                                 header, "\n",
                                 chopString(seq, width)),
                                 sep = "", collapse ="")
            }
            if (outFormat == "df") {
            	  fasta <- rbind(fasta, data.frame(head = header,
            	                                   seq = seq,
            	                                   stringsAsFactors = FALSE))
            }
        }
    } # end for (i in 1:length(ids))
    
    return(fasta)
}
printArgs(getFeatureFasta)


chopString <- function(s, w) {
	# Chop strings into lines of width w.
	# All lines are terminated with a newline "\n"
	pattern <- paste(".{1,", w, "}", sep="")
	tmp <- paste(unlist(str_match_all(s, pattern)[[1]]),
	             collapse = "\n")
	return(paste(tmp, "\n", sep=""))
}

# ==== writeSeqSet =============================================

writeSeqSet <- function(seqSet,
                        file,
                        format = "mfa",
                        blockSize = 50) {
    # Output a seqSet of class "MsaAAMultipleAlignment" or 
    # "AAStringSet" to multi-FASTA format. FASTA headers are
    # taken from object names.
    # if format == "mfa", write a multi FASTA output
    # if format == "ali", write a Claustal W output
    #
    
    MAXNAMEWID <- 15 # Maximum name width for "ali" format
    
    format <- str_trim(format)
    
	if (missing(seqSet)) {
		stop("Input object missing from arguments with no default.")
	}
	if (missing(file)) {
		writeToFile <- FALSE
	}
	else {
		writeToFile <- TRUE
        file <- str_trim(file)
        sink(file) # divert output to file 
	}
	# Extract the raw data from the objects depending on
	# their respective class and put this
	# into a named vector of strings.
	if (class(seqSet)[1] == "MsaAAMultipleAlignment") {
		strings <- character(nrow(seqSet))
		for (i in 1:nrow(seqSet)) {
			strings[i] <- as.character(seqSet@unmasked[i])
			names(strings)[i] <- seqSet@unmasked@ranges@NAMES[i]
		}
	}
	else if (class(seqSet)[1] == "AAStringSet") {
		strings <- character(length(seqSet))
		for (i in 1:length(seqSet)) {
			strings[i] <- as.character(seqSet[i])
			names(strings)[i] <- seqSet@ranges@NAMES[i]
		}
	}
	else {
		stop(paste("Input object of class",
		            class(seqSet)[1],
		            "can't be handled by this function."))
	}
 
    if (format == "mfa") {
        for (i in 1:length(strings)) {
            # output FASTA header
            cat(paste(">", names(strings)[i], "\n", sep=""))
            # output sequence in blocks
            cat(chopString(strings[i], blockSize))
            cat("\n") # output an empty line
        }
    } else if (format == "ali") {
    	
    	SEP <- paste(rep(" ", MAXNAMEWID), collapse="")
    	cat("CLUSTAL W formatted alignment\n")
    	cat("\n")

    	pattern <- paste(".{1,", blockSize, "}", sep="")
    	allBlocks <- character()
    	for (i in 1:length(strings)) {
            # make labels for rownames
        	label <- substr(paste(names(strings)[i], SEP, sep = ""), 1, MAXNAMEWID)
    	    label <- paste(label, " ", sep="")
    	    # chop strings into blocks
    	    blocks <- unlist(str_match_all(strings[i], pattern)[[1]])
    	    dim(blocks) <-c(1, length(blocks))
    	    rownames(blocks) <- label
    	    allBlocks <- rbind(allBlocks, blocks)
        }
        for (i in 1:ncol(allBlocks)) {
        	for (j in 1:nrow(allBlocks)) {
                cat(rownames(allBlocks)[j])
                cat(allBlocks[j, i])
                cat("\n")
            }
            cat("\n\n")
        }
    }
	if (writeToFile) {
		sink()  # Done. Close the diversion.
	}
}
printArgs(writeSeqSet)


# ==== mergeDB =====================================

# This function is now retired. If it is reactivated: caution -
# can't simply merge protein table but need to construct unique IDs
# and update proteinID's  in proteinFeature table.
# mergeDB <- function(old, new) {
	# # Merge records in protein and taxonomy table
	# # from old to new

    # oTx <- old$taxonomy$id
    # nTx <- new$taxonomy$id
    # missing <- !(oTx %in% nTx)
    # new$taxonomy <- rbind(new$taxonomy, old$taxonomy[missing, ])
    
    # oRef <- old$protein$refSeqID
    # nRef <- new$protein$refSeqID
    # missing <- !(oRef %in% nRef)
    # new$protein <- rbind(new$protein, old$protein[missing, ])
    
    # return(new)
# }
# printArgs(mergeDB)


# ==== biCode ==============================================
biCode <- function(s) { 
	# Creates an uppercase five-letter code from a
	# binomial species name. Drops strain IDs etc.

	s <- str_trim(s)
	substr(s, 4, 5) <- substr(strsplit(s,"\\s+")[[1]][2], 1, 2)
	return (toupper(substr(s, 1, 5)))
}
printArgs(biCode)


# ==== makeNames ===========================================
makeNames <- function(database, width = 10, ...) {
    # Return a vector of meanigful names for database
    # proteins. Names are the last (width - six) characters
    # of the proteinName entry, plus a biCode, separeated
    # by an underscore.
    
    if (missing(database)) {
    	stop("Database argument is missing with no default.")
    }

    checkVersion(database)

    ids <- getTableID(database, table= "protein", ...)
    vNames <- character(length(ids))
    for (i in 1:length(ids)) {
    	# fetch the name
        n <- database$protein[database$protein$id == ids[i], "name"]
    	# replace blanks with underscores
    	n <- gsub("\\s+", "_", n)
    	# take only the last  (width - six) characters
    	n <- substr(n, nchar(n) - (width - 6) + 1, nchar(n))
    	# fetch the organismName
    	tax <- database$protein[database$protein$id == ids[i], "taxID"]
    	s <- database$taxonomy[database$taxonomy$id == tax, "organismName"]
    	# make a five-letter code from the species name
    	s <- biCode(s)
    	# paste it together
    	vNames[i] <- paste(n, s, sep="_")
    }
    return(vNames)
}
printArgs(makeNames)


# ==== updateVerifiedFile ==================================

updateVerifiedFile <- function(key,
                              fromPath = "http://steipe.biochemistry.utoronto.ca/abc/images/",
                              fromFile = "f/f9/DbUtilities.R",
                              toPath = PROJECTDIR,
                              toFile = "dbUtilities.R",
                              sourceDownloadedFile = TRUE) {
	# Fetch file from URL, verify it, save it, and source it.
	# Defaults are to download THIS file from the
	# course repository for update, and replace its
	# old copy locally.
	# Requires package digest.
	
    sourceFile <- paste(fromPath, fromFile, sep="")
	targetFile <- paste(toPath, toFile, sep="")

    # download file to temporary file
    tmpFile <- tempfile()
    download.file(sourceFile, tmpFile, method="auto")
    # verify hash
    sha1 <- digest(paste(readLines(tmpFile, warn=FALSE), collapse=" "),
                    file=FALSE,
                    algo="sha1")
    if (sha1 == key) {
	    	# move the file
	    	file.rename(from = tmpFile,
	    	            to = targetFile)
	    	if (sourceDownloadedFile) {
	    		# run the file... 
	    		source(targetFile)
	    	}
    }
    else {
        file.remove(tmpFile)
    	stop("SHA-1 hash of downloaded file does not match the key passed to this function.")
    }
}
printArgs(updateVerifiedFile)


# Undocumented function to verify the update key:
verifyKey <- function(key,
                      fromPath = "http://steipe.biochemistry.utoronto.ca/abc/images/",
                      fromFile = "f/f9/DbUtilities.R") {
    sourceFile <- paste(fromPath, fromFile, sep="")
    tmpFile <- tempfile()
    download.file(sourceFile, tmpFile, method="auto")
    sha1 <- digest(paste(readLines(tmpFile, warn=FALSE), collapse=" "),
                   file=FALSE,
                   algo="sha1")
    if (sha1 == key) {
    	cat("\nSuccess: key matches digest of downloaded file.\n\n")
    }
    else {
    	cat("\nPANIC: KEY DOESN'T MATCH DIGEST OF DOWNLOADED FILE.\n\n")
    }
    file.remove(tmpFile)
}



# ==== makeKey =============================================

makeKey <- function() {
	# Make a SHA-1 hash from the local version of this file
	# for verifying downloads.

    localFile <- dir(paste(PROJECTDIR),
                           pattern="dbUtilities.R",
                           full.names=TRUE)
    sha1 <- digest(paste(readLines(localFile, warn=FALSE), collapse=" "),
                    file=FALSE,
                    algo="sha1")
    return(sha1)
}
printArgs(makeKey)


# ==== LOAD refDB REFERENCE DATABASE =======================
#  48 reference APSES domain proteins from 10 fungi and
#  E. Coli as outgroup. ScanProsite annotations included.

if (LOADREFDB) {
	refDB <- structure(list(version = "Protein Data 1.0", taxonomy = structure(list(
    id = c(240176L, 283643L, 930090L, 671144L, 418459L, 237631L, 
    227321L, 367110L, 284812L, 559292L, 562L), organismName = c("Coprinopsis cinerea okayama7#130", 
    "Cryptococcus neoformans var. neoformans B-3501A", "Bipolaris oryzae ATCC 44560", 
    "Wallemia mellicola CBS 633.66", "Puccinia graminis f. sp. tritici CRL 75-36-700-3", 
    "Ustilago maydis 521", "Aspergillus nidulans FGSC A4", "Neurospora crassa OR74A", 
    "Schizosaccharomyces pombe 972h-", "Saccharomyces cerevisiae S288c", 
    "Escherichia coli")), .Names = c("id", "organismName"), row.names = c(NA, 
11L), class = "data.frame"), protein = structure(list(id = c(1, 
2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 
20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 
36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48), name = c("CC1G_01306", 
"CNBB4890", "COCMIDRAFT_338", "WALSEDRAFT_68476", "PGTG_08863", 
"CC1G_00846", "WALSEDRAFT_59726", "UMAG_11222", "COCMIDRAFT_8533", 
"PGTG_02039", "AN3154.2", "AN6715.2", "NCU07587", "UMAG_05338", 
"NCU07246", "CNBD0840", "res1", "MBP1", "res2", "SWI4", "cdc10", 
"AN5836.2", "PHD1", "Asm-1", "SOK2", "CC1G_08099", "UMAG_15042", 
"COCMIDRAFT_103135", "PGTG_11943", "UMAG_04778", "WALSEDRAFT_68479", 
"PGTG_03082", "bqt4", "COCMIDRAFT_81480", "NCU06560", "AN5405.2", 
"AN0162.2", "PGTG_05590", "COCMIDRAFT_105954", "WALSEDRAFT_69819", 
"CNBB2840", "CC1G_13964", "COCMIDRAFT_96253", "CC1G_14426", "XBP1", 
"NCU06339", "UMAG_11055", "KilA"), refSeqID = c("XP_001837394", "XP_776961", 
"XP_007682304", "XP_006957790", "XP_003327086", "XP_001831299", 
"XP_006957051", "XP_011392621", "XP_007691662", "XP_003320997", 
"XP_660758", "XP_664319", "XP_962967", "XP_011392041", "XP_955821", 
"XP_776035", "NP_595496", "NP_010227", "NP_593032", "NP_011036", 
"NP_596132", "XP_663440", "NP_012881", "XP_960837", "NP_013729", 
"XP_001836714", "XP_011388143", "XP_007690905", "XP_003330006", 
"XP_011391646", "XP_006957792", "XP_003321545", "NP_596166", 
"XP_007682909", "XP_962267", "XP_663009", "XP_657766", "XP_003323688", 
"XP_007691967", "XP_006959479", "XP_777052", "XP_002911924", 
"XP_007688318", "XP_002911429", "NP_012165", "XP_962373", "XP_011390537", 
"WP_000200358"), uniProtID = c("A8NYC6", "F5HFJ0", "W6ZM86", 
"I4YDD8", "E3KED4", "A8N8X1", "I4YGC0", "A0A0D1DP35", "W6ZE71", 
"E3JX03", "Q5B8H6", "Q5AYB5", "Q7SBG9", "A0A0D1BWD8", "Q7RW59", 
"F5HBL5", "P33520", "P39678", "P41412", "P25302", "P01129", "P36011", 
"P36093", "Q1K6U0", "P53438", "A8NVH3", "A0A0D1CVS5", "W6ZGE9", 
"E3KMR2", "A0A0D1DQM4", "I4YDE0", "E3JYK1", "O60158", "W6ZKJ4", 
"Q7S9H5", "Q5B225", "Q5BH18", "E3K4V4", "W6Z1H5", "I4Y911", "F5HHR9", 
"D6RKH9", "W6ZCR2", "D6RMB0", "P40489", "Q7S9W7", "A0A0D1DZM8", 
"D7ZJS9"), taxID = c(240176L, 283643L, 930090L, 671144L, 418459L, 
240176L, 671144L, 237631L, 930090L, 418459L, 227321L, 227321L, 
367110L, 237631L, 367110L, 283643L, 284812L, 559292L, 284812L, 
559292L, 284812L, 227321L, 559292L, 367110L, 559292L, 240176L, 
237631L, 930090L, 418459L, 237631L, 671144L, 418459L, 284812L, 
930090L, 367110L, 227321L, 227321L, 418459L, 930090L, 671144L, 
283643L, 240176L, 930090L, 240176L, 559292L, 367110L, 237631L, 
562L), genomeXref = c(NA, "NC_009178.1", NA, NA, NA, NA, NA, 
"NC_026499.1", NA, NA, NA, NA, "NC_026504.1", "NC_026496.1", 
"NC_026505.1", "NC_009180.1", "NC_003423.3", "NC_001136.10", 
"NC_003424.3", "NC_001137.3", "NC_003423.3", NA, "NC_001143.9", 
"NC_026505.1", "NC_001145.3", NA, "NC_026480.1", NA, NA, "NC_026494.1", 
NA, NA, "NC_003423.3", NA, "NC_026504.1", NA, NA, NA, NA, NA, 
"NC_009178.1", NA, NA, NA, "NC_001141.2", "NC_026504.1", "NC_026488.1", 
NA), genomeFrom = c(NA, 2043901L, NA, NA, NA, NA, NA, 150554L, 
NA, NA, NA, NA, 160232L, 247386L, 6093554L, 292497L, 1232587L, 
352876L, 686542L, 385875L, 2763829L, NA, 356747L, 3980679L, 305592L, 
NA, 689244L, NA, NA, 235674L, NA, NA, 2840822L, NA, 1632913L, 
NA, NA, NA, NA, NA, 792098L, NA, NA, NA, 177249L, 2857075L, 486507L, 
NA), genomeTo = c(NA, 2046558L, NA, NA, NA, NA, NA, 152738L, 
NA, NA, NA, NA, 156399L, 250703L, 6097220L, 289386L, 1235586L, 
355377L, 689178L, 382594L, 2760740L, NA, 357847L, 3977114L, 303235L, 
NA, 691118L, NA, NA, 237248L, NA, NA, 2842833L, NA, 1630182L, 
NA, NA, NA, NA, NA, 790646L, NA, NA, NA, 175306L, 2854774L, 485047L, 
NA), seq = c("MPEAQIFKATYSGIPVYEMMCKGVAVMRRRSDSWLNATQILKVAGFDKPQRTRVLEREVQKGEHEKVQGGYGKYQGTWIPLERGMQLAKQYNCEHLLRPIIEFTPAAKSPPLAPKHLVATAGNRPVRKPLTTDLSAAVINTRSTRKQVADGVGEESDHDTHSLRGSEDGSMTPSPSEASSSSRTPSPIHSPGTYHSNGLDGPSSGGRNRYRQSNDRYDEDDDASRHNGMGDPRSYGDQILEYFISDTNQIPPILITPPPDFDPNMAIDDDGHTSLHWACAMGRIRIVKLLLSAGADIFKVNKAGQTALMRSVMFANNYDVRKFPELYELLHRSTLNIDNSNRTVFHHVVDVAMSKGKTHAARYYMETILTRLADYPKELADVINFQDEDGETALTMAARCRSKRLVKLLIDHGADPKINNHDGKNAEDYILEDERFRSSPAPSSRVAAMSYRNAQVAYPPPGAPSTYSFAPANHDRPPLHYSAAAQKASTRCVNDMASMLDSLAASFDQELRDKERDMAQAQALLTNIQAEILESQRTVLQLRQQAEGLSQAKQRLADLENALQDKMGRRYRLGFEKWIKDEETREKVIRDAANGDLVLTPATTSYTVDEDGDSDSGSNGDKNKGKRKAQVQQEEVSDLVELYSNIPTDPEELRKQCEALREEVSQSRKRRKAMFDELVTFQAEAGTSGRMSDYRRLIAAGCGGLEPLEIDSVLGMLLETLEAEDPSSTSATWSGSKGQQTG", 
"MGKKVIASGGDNGPNTIYKATYSGVPVYEMVCRDVAVMRRRSDAYLNATQILKVAGFDKPQRTRVLEREVQKGEHEKVQGGYGKYQGTWIPIERGLALAKQYGVEDILRPIIDYVPTSVSPPPAPKHSVAPPSKARRDKEKETGRTKATPSRTGPTSAAALQAQAQLNRAKMHDSTPDADASFRSFEERVSLTPEDDSSSDTPSPVASVMTDQDMEVDKMGMHMSMPNVTLSQNMEELGAGSRKRSAAMMMEDEDQFGQLRSIRGNSAVHTPHGTPRHLGIGMPPEPIGPEQYTDIILNYFVSETSQIPSILVSPPHDFDPNAPIDDDGHTALHWACAMGRVRVVKLLLTAGASIFAGNNAEQTPLMRSVMFSNNYDMRKFPELYELLHRSTLNIDKQNRTVFHHIANLALTKGKTHAAKYYMETILARLADYPQELADVINFQDEEGETALTIAARARSRRLVKALLDHGANPKIKNRDSRSAEDYILEDERFRSSPVPAPNGGIGKASTSAAAEKPLFAPQLYFSEAARLCGGQALTDITSHMQSLARSFDAELQGKERDILQAKALLTNIHTEVTENGRSITAITNQAAPLEEKRRELEALQASLKTRVKDALKKGYIGWLEGELVREQRWENGELEGNEEEKAAVQALRDVPTGGQEVVQAEEEKLRWEIEEKRKRRAMFVEKFVRAQTEAGTSEQIAKYRKLVSAGLGGVSTNEVDELMNQLLEGLEEENDNQVYNTTAGESGPSSWVQ", 
"MPPAPDGKIYSATYSNVPVYECNVNGHHVMRRRADDWINATHILKVADYDKPARTRILEREVQKGVHEKVQGGYGKYQGTWIPLEEGRGLAERNGVLDKMRAIFDYVPGDRSPPPAPKHATAASNRMKPPRQTAAAVAAAAVAAAAAAAAVANHNALMSNSRSQASEDPYENSQRSQIYREDTPDNETVISESMLGDADLMDMSQYSADGNRKRKRGMDQMSLLDQQHQIWADQLLDYFMLLDHEAAVSWPEPPPSINLDRPIDEKGHAAMHWAAAMGDVGVVKELIHRGARLDCLSNNLETPLMRAVMFTNNFDKETMPSMVKIFQQTVHRTDWFGSTVFHHIAATTSSSNKYVCARWYLDCIINKLSETWIPEEVTRLLNAADQNGDTAIMIAARNGARKCVRSLLGRNVAVDIPNKKGETADDLIRELNQRRRMHGRTRQASSSPFAPAPEHRLNGHVPHFDGGPLMSVPVPSMAVRESVQYRSQTASHLMTKVAPTLLEKCEELATAYEAELQEKEAEFFDAERVVKRRQAELEAVRKQVAELQSMSKGLHIDLNDEEAERQQEDELRLLVEEAESLLEIEQKAELRRLCSSMPQQNSDSSPVDITEKMRLALLLHRAQLERRELVREVVGNLSVAGMSEKQGTYKKLIAKALGEREEDVESMLPEILQELEEAETQERAEGLDGSPV", 
"MKEEKEKTPPNNITGPPTPAQNILHSTPAAFGTAGTVGQGAGGFGSQLYQSPYVDSQQSVIGSPVTPAPLPKKATLKTPQPRIYSAVYSGVGVYEAMIRGIAVMRRRADGYMNATQILKVAGVDKGRRTKILEREILAGLHEKIQGGYGKYQGTWIPFERGRELALQYGCDHLLAPIFDFNPSVMQPSAGRSAKSPSKKRQNSIVLSPTQERHQSSIIALNTARASGIYVGGADDPNDDGLSKKEKSPVKKSKYDEVPVNVSKRPYVPPPGTNAHILTRTQQSLTALFQQPTTNSDFIPEAVAILDTTSGALHPDLAIDELGHTALHWAASLGRISNVQQLIKKGADMKRGNIEGETPLERSVLVNDNYDKKTFAYLLQELGSSIRVVDRTGRSILHHIALIAAVNGRSMSAKYYMENVLEYIARYENGEFKSLVDLQDEHGDTALNISARVGNRNLVKMLVDAGANKTVVNKLGLKASDFGVEHETLNSVTGDEMLSNLQPPPPLNVDSSASVLENIHNLLNGITQQYTDETSGKNALLFEIQAELKQHSHELADVRKEIQYWQNKATQMAEVDQKIKNINEAIENEKVQTWSLLGEANADKMEGIETSSSSNTSEIKIPTGDNEESLKQLRKLSKWLEGTQKLTEERVASIDGLSASKEVKYKSIVSVCTGVPVNEVEGMLAQLLEAMESDANADLNKVQEFLAREC", 
"MAYGGSIQPLRPPSRESATLHLHQPDLTVTSPPLSLTHCPPCVYSHFTHTPTSLIVIQVSLHSLLDQETYHLLPSRSPPTVSVRMGTTTIYKATYSGVPVLEMPCEGIAVMRRRSDSWLNATQILKVAGFDKPQRTRVLEREIQKGTHEKIQGGYGKYQGTWVPLDRGIDLAKQYGVDHLLSALFNFQPSSNESPPLAPKHVTALSTRVKVSKVSAASAARAARAVVPSLPSTSGLGGRNTNNSWSNFDSDNEPGLPPAASSRESNGNWATQSKLARSSNLARARANINNSHPEDLPVPAPDQLQASPLPSMQTADPENDNSLTPSELSLPSRTPSPIEDLPLTVNTASSQSTRNKGKSRDLPDDEDLSRGQKRKYDTSLVEDTSYSDGADDQYINGNPSNAASAKYAKLILDYFVSESSQIPNFLNDPPSDFDPNVVIDDDGHTALHWACAMGRIKIIKLLLTCGADIFRANNAGQTALMRAVMFTNNHDLRTFPELFESFSGSVINIDRTDRTVFHYVIDIALTKGKVPAARYYLETILSQLSEYPKELIDILNFQDEDGETALTLAARCRSKKLVKILLDHGANPKTANRDGKSAEDYILEDDKFRALSPTPCSSGPIRQLDQNSPGGTSNRSDFVDLVDPVPIDSNLIPQRSPNASPPHYSETGQRVTKQLLPEVTSMIELLATTFDTELQDKERDLDHAVGLLSNIEKEYLEGQRKILNYERMLSDFGEKKLALGDLEKELNDKLGKRYRFGWEKYVRDEEERARRITEQRSKYLQELSIEDRKLLDSSNLRFADPSKQEVLMKLQADERENSDLLNLIRTNSTDVESECDLLRESVQKLSEERERLFKEFINLSSENTGGENEEDDGANHTSANTSRLNNYRKLISLGCGGIGLDEVDEVIESLNEGIDVNELNDNGFLTEQDEELGNHQNYHNIHTQGR", 
"MQASTRPPGSNQPPVKIYNAVYSSVQVYECMVRGIAVMRRRNDSYVNATQILKVAGVDKGRRTKILEKEILPGKHEIVQGGYGKYQGTWIPLERGRDIAAQYGVAPLLSPLFDFQPSTNSLGALPVSTPGGTASPRPLSASSSYSSMGVAGQYIPSSIPSNLPPAPIMPGSALRLLNQGRAQGLFTPSTTSATLRPAGYHSPGPYGTSYAPSPQPQSSQTPPPGSGLKRNRSEAEVEGYHSQPHDVQMADAPPPNTASQPNEDNPSPAKRLRTDGSITTEPASSQGQWQQQQPLPYASQQRSGPGLSQLSGHNGHGSSRPPSSLSAPNGNRPAHTNPEDQTRKTRFSSKPSMPRGMDPHMPFKDARRSALIALICHRDDPTSVIDLLREISADHLNPPSFDVDTVLDDQGHTALHLAASMARTQTVDMLIQTGADMHRGNHLGETPLIRACLATPNSDQQSFATLVNYLHDSIWTLDTSKKSVVHHIVSLAGVKGRAVVARYYLDQIFYWIAQHEGGDFRSLVDLQDEHGDTAINIAARVGNRSLVRTLLDVGANRVLANKLGLRPGDFGVETEELSSGLRAEDLISSLRTGPPAPVQKSQDVIADMTSMIQSLSTEFQAEIKSKQDSLDVTQAHLRAATRELSEQRKQIQTWQARCGDLDQINQRVRNVEKAIAEEDMFDWTGRTELDGKDGKEKGGPAFAYRGSKSTMVGVGGSVDVSFSVESEPPLPTTDTAASLVKLRRLKMWHQRMEELVKGRLKGLQGASAEKEYQCKKIVALCTGIPLDKVEEMLDNLVIAVESEAQVVDIGRVSGFMQKVRDGII", 
"MSAPPIYKACYSGVPVYEFNCKNVAVMKRRSDSWMNATQILKVANFDKPQRTRILEREVQKGTHEKVQGGYGKYQGTWIPMERSVELARQYRIELLLDPIINYLPGPQSPPLAPKHATNVGSRARKSTAPAAQTLPSTSKVFHPLSSTKHPAKLAAATNAKAEISDGEDASIPSSPSFKSNSSRTPSPIRINARKRKLEDEATIPSSAIDGSISYEDIILDYFISESTQIPALLIHPPSDFNPNMSIDDEGHTAMHWACAMGKVRVVKLLLSAGADIFRVNHSEQTALMRSVMFSNNYDIRKFPQLYELLHRSTLNLDKHDRTVLHHIVDLALTKSKTHAARYYMECVLSKLANYPDELADVINFQDDEGESALTLAARARSKRLVKLLLEHGADSKLPNKDGKTAEDYILEDERFRQSPLLNSNHLRLHPPDTSIYAPPAHLFNSETSQNIANTSMSSVANLLESLAQSYDKEITQKERDYQQAQVILRNIKTDIVEAKSNIEKMTIDSSEFEHLKHKLRELEMKLEEHSNDVYNKGWEEYSRNVDDPAIDAPSDNVQEECASLRNKIKDLQEKRISSMQELIKRQKEVGTGKKMSEYRKLISVGCGIPTTEIDAVLEMLLESLESENANKKAALASGISGALSSTSSAPSQATTSAPTGVATPGAPVPASSEKAGLLPPAPVMQ", 
"MSGDKTIFKATYSGVPVYECIINNVAVMRRRSDDWLNATQILKVVGLDKPQRTRVLEREIQKGIHEKVQGGYGKYQGTWIPLDVAIELAERYNIQGLLQPITSYVPSAADSPPPAPKHTISTSNRSKKIIPADPGALGRSRRATSIETESEVIGAAPNNVSEGSMSPSPSDISSSSRTPSPLPADRAHPLHANHALAGYNGRDANNHARYADIILDYFVTENTTVPSLLINPPPDFNPDMSIDDDEHTALHWACAMGRIRVVKLLLSAGADIFRVNSNQQTALMRATMFSNNYDLRKFPELFELLHRSILNIDRNDRTVFHHVVDLALSRGKPHAARYYMETMINRLADYGDQLADILNFQDDEGETPLTMAARARSKRLVRLLLEHGADPKIRNKEGKNAEDYIIEDERFRSSPSRTGPAGIELGADGLPVLPTSSLHTSEAGQRTAGRAVTLMSNLLHSLADSYDSEINTAEKKLTQAHGLLKQIQTEIEDSAKVAEALHHEAQGVDEERKRVDSLQLALKHAINKRARDDLERRWSEGKQAIKRARLQAGLEPGALSTSNATNAPATGDQKSKDDAKSLIEALPAGTNVKTAIAELRKQLSQVQANKTELVDKFVARAREQGTGRTMAAYRRLIAAGCGGIAPDEVDAVVGVLCELLQESHTGARAGAGGERDDRARDVAMMLKGAGAAALAANAGAP", 
"MSTSHSFPAASPSHQQSALYANSPHGHALMAAPAALNRSFSDMSAFHHHAMDKPQIYTAVYSGVSVYEMEVNRVAVMRRRSDGWLNATQILKVAGVDKGKRTKVLEKEILTGEHEKVQGGYGKYQGTWINYRRGREFCRQYGVEDVLRPLLDYDITLDGSHAPGHAIETPTKEQAMAANRKRFYTQSIDGRTTTQNLTGTFFSNISSTATSALAAMNKVARLNSPAPRPSSSSQRRTSATRPSQSQPPLASQDSFRTSSQQSITSEPSFAGHNGQTDSAYATAVDESQEPPRKRIRASHDDSYSQPTAADMSIHPLSSPTEPSESFDQHHPAQPITLADGDVPTALPPLPYPDTKQDEEKQAMLTDLFADQTRSDFTNHPAILHLSGPDLDMPIDNSSNTALHWAATLARVSLIRLLVSKGANMFRGNASGQTALMSAVSVNNSLDHSCFPETLEILAPLIELRDSQGRTILHHIAVTCAIKGRAASSKYYLEALLEYLVRSNIGGGQPPPFHDTSNHSKPIGLMRFMQEMVNARDKAGNTALNLAARIGNRNIISQLMEVQADPTIPNHKGTRPMDFGVGTDLGDGQGIITATSPTKAKAPLSKAEETSREIQPLMSGILQSASLQFTQEARLKQDAIDQTNELITQLSSQQKQEQQKLQTLRARLRQRQDRAKRISNLKRWLEPQRHMLSVNDGAIDLHDKKRIGYADTQGAGLLIKEDDLPYELRQAGDHLDRRASDGPIYLSTSVPLDPSTLSQVSHQPQCQNFLLQQLPAASVLRQRIETYTATNTALLKRSRMLKEKDGQLEMMYRKVVSLCTKVEENRIEECLEGLVAALDSEEGEGVEVGRVREFLRKVEGVD", 
"MAAHKTTNDIPVSSSHHINPESGTGTSSTQAFPIPNIKNNPHVYMAVYSSVPVYEMMVRGIGVMRRRSDSYMNATQILKVAGLDKSKRTRILEREIIQGEHEKIQGGYGRYQGTWVPFTRAQELATQLNVAQLLAPLFDYRPEPNSEVNIRSTNTKPSSSASRANSHKTTLARQTSRQSLNEKRERSGDTTPLPHDPPEAGPSKRSRLNTPSRQSNGSANTPSSLIDHSHSAMDPDFIIPHSQSQPTAASQCTTSTFAPIHGATVEYPAGPSHLRKSNSSSRSHLEVALKAERNIHTLMALFSNPPDGDELESETHHENPNSVAEVNEVLEDPELEIDTPIDEHCHTALHWASSLARLGLVRAFLRSGADVNRGNDVGETPLMRSTLVTNNFERESFNQLLELLHPSLWTLDNQDRTVLHHICLTASIKGRGESSRYYLECICEWIVNKHGAQFDSQLFDAVDLNGDTALNIAARVGNKHLVRMLLDVGADMTIGNNLGLKPIDFGVGAGETSASYTDDMISAPLRRNPTASAPARSSRDIITSITSSVNSLSEDFENEIRSKTDRLESVRAQLMVATRQLTTQRRQLESLKHDLDERALLELRLKKLRMAIAEEDGFDWTGRSDLDGRPAQAGKLFEQNGIASTLAGLSASQIQLELEPDPFIPPENNQDSLVYLRRLEKWYVRVLSLLRERIGRMKGSNLEQEAKYLKVIGSFIGNTCTNDLSSSGSSMTGRPANQTTSTTQEVPSRATQNVNPADIHDLESMDGHRRKVSTTDAVNKSHEFGRTRSELLKASMIDNKLLKQLMAAIESDGPELDLNRVAGFMQRVQSGSL", 
"MAAVDFSNVYSATYSSVPVYEFKIGTDSVMRRRSDDWINATHILKVAGFDKPARTRILEREVQKGVHEKVQGGYGKYQGTWIPLQEGRQLAERNNILDKLLPIFDYVAGDRSPPPAPKHTSAASKPRAPKINKRVVKEDVFSAVNHHRSMGPPSFHHEHYDVNTGLDEDESIEQATLESSSMIADEDMISMSQNGPYSSRKRKRGINEVAAMSLSEQEHILYGDQLLDYFMTVGDAPEATRIPPPQPPANFQVDRPIDDSGNTALHWACAMGDLEIVKDLLRRGADMKALSIHEETPLVRAVLFTNNYEKRTFPALLDLLLDTISFRDWFGATLFHHIAQTTKSKGKWKSSRYYCEVALEKLRTTFSPEEVDLLLSCQDSVGDTAVLVAARNGVFRLVDLLLSRCPRAGDLVNKRGETASSIMQRAHLAERDIPPPPSSITMGNDHIDGEVGAPTSLEPQSVTLHHESSPATAQLLSQIGAIMAEASRKLTSSYGAAKPSQKDSDDVANPEALYEQLEQDRQKIRRQYDALAAKEAAEESSDAQLGRYEQMRDNYESLLEQIQRARLKERLASTPVPTQTAVIGSSSPEQDRLLTTFQLSRALCSEQKIRRAAVKELAQQRADAGVSTKFDVHRKLVALATGLKEEELDPMAAELAETLEFDRMNGKGVGPESPEADHKDSASLPFPGPVVSVDA", 
"MTTSNHHQQRPSLSMSYSQGSIGSANGMSFSQSQMSSLNASQSVASTPRATPPPKSSQQSAMSFNYSNGLPNGARASFSGFEDMNGYGTMIYHEEFKPQIYRAVYSNVSVYEMEVNGVAVMKRRSDGWLNATQILKVAGVVKARRTKTLEKEIAAGEHEKVQGGYGKYQGTWVNYQRGVELCREYHVEELLRPLLEYDMNPNGTAASGQDSLDTPTKEQAMAAQRKRLYSGMENRSMSQPQQGTFFQNISRTAATAVNAMSKARFESPAARGGDSRRLSVIRKPSQQMGSQDAQPPFGSQQSFYSAASDSGFASNIPTNGRYAPQDAMSFEQEEPMEPPRKRIRSSQAFSLPIDGTSMSMSEPTPTEPNDSFYQDMEPLHHIDEGRHGLDPLPPATTPERFQKMKLIMTLFLDKTTKDFSTHPALIQLSGEDLEVPLDEYRNNALHWAAMLARMPLVYALVKKGVNIARLNGAGETALQKAVGTRNNLDYRSFPRLLQVLAPTIDMVDRSGRTILHHIAVMAATGHGGHVSAKHYLEALLEFIVRHGGTSLNQQSNGTASQPGMPLSNEVITLGRFISEIVNLRDDQGDTALNLAGRARSVLVPQLLEVGADPHIPNHTGLRPADYGVGVDMVDGSSQPAGSRSDTFLAQLAKTRKEILEATTAQVTAIVQETLGTFDKELAASLTSKQEKFDHWHAKIRESAKARQIEQKQLDELKRRSIDRTETSRRLKNLEKSSTDLLEAHKEILTNLGDTSKPVSLGDADQESGFEIAEFEALFPETFDPASGFSEAQIAYLRKLPSAEILEQRVSCYRAFNKETLDEIDALRSKNVVLGQNYRRMVMACTGWSAEQVDEAAEGLTQCVKELNDNPVPEDEAIEILMRDRGQDW", 
"MQPPQLGGASQQSQPSSQQSFSMSQSSQSVYRQYTDPPNRLHNDHAVPTIYSATYSGVGVYEMEVNNVAVMRRQKDGWVNATQILKVANIDKGRRTKILEKEIQIGEHEKVQGGYGKYQGTWIPFERGLEVCRQYGVEELLSKLLTHNRGQEGETGNVDTPTKEQAMAAQRKRMYNASSQENRGIGSTGTFFKNISSTASTAVAAISKARFDSPAPRNRSGPSRAPSFNRQSSMQDVADFPNSQQSLVSTEYATQTQNADSGFGSQTTQPLAGDGLEQPPRKRQRVLTPARSFGGQTPGHQPLDPFNAGNIANGDSGSPTEPSNSFNYDQVTANDGDASYALGPLRPLPYENNADAEAKRGMLMGLFMDANGPEEAIQAALCNVSPQELDSPIDTQSHTALHWAATLSRMPLLRALIHAGANPWRVNACGETALMRACTVTNSMENNTFPELLDLLGCTLDVTDDKGRTVLHHIAVTSAVKGRHYASRYYLESLLEWVVRQGSAPSSQENGIGDRKGRRMGIARFMSEIVNAQDNSGDTALNVAARVGNRSIISQLLEVGADPTIPNRANLKPLDFGIGIADAETNDDPAQEKTGATTGSGHKSRETSDEVVRSITHLIGESASIFQNELKKKQESIDTLHSQLRVTSSQVGDARRTLESLQEKLKAQQLAKQKIVNFNRACEEEEQILIELEQRHGRLDVASANAWEMELESALEIVKTQSPKGLDPDSRPSLPSAAVLRARIKALRARSSKTRQAVAALQAQSKEKELKYRRLVSLCTRRPEIEVEALLDTLTRAVESEKPELEIARVRRFLGGVEGVVH", 
"MPLNYFANQDQTASDTYAHEASSFPAPSSILTDTSKPLQPVQEVAASSLVDGVSFTSPHASIIHASKQSPRAASSLSFTTSALQRAGLLPANPNMSTTATSGTSAASESLQRVITQGTASAAAINGASTPAHSGPLTPAHLKNLTPAQANAALQNPVGNIPTVYLATYSNVPVYEITVRGIAVMRRRGDGWLNATQILKIAGIEKTRRTKILEKSILTGEHEKIQGGYGKFQGTWIPLQRAQQVAAEYNVSHLLQPILEFDPATADQIPKLYQRKKPAASARNSSASAINDARGSTPSKIYSPAPASLGGPSQQPRFLSLRPPKETHEQEISSAIFMPPGTAGLLSNGTFVDDRAASALAYPGPPAIPPGSTPAEQAALRSYNVYGYTPQGVPLPSSAAADGNGTEAAATAASTGAGKREASETDQDGASAAKRSRLTSPQQQRRDDGLLLGPSPVKDLNALGPAGGSLRAASAPRGHRITVGPPDAAGRDGAVPRYADRALPPKPYDEGEKRMRDRLVSLFSDDGVLPGVSEATGAGASQSAADEDDDAYVAKLDSLLADLREKASLGGLGASGTDGPKATVDLITDDHGHTALHWASALCRVKLVRTLVARPPWQGGANIHAGNHAGETALHRSVLVTNSYDASSFPTLLNLLSSSLNTRDFKKRTVLHHISLVAALKGRAASARYYLACVLEHISAEKNSKYKGLIDAQDEDGETALGIVARLGNASMVRMLLDVGARKDLANALGIRPSDWGIESSADGASLTPSQNDGTNTVASLPPLTAADLASQNPSDIISALTRPAQVPVMKSSDVRDQLSSTLDDLQSSFERELKEKQDAVSTVQSHLQAATRDLAARRKTVSAAQAKLAEKDEARQRVQNLRRAIVAQLGLEEADADLSLEQLVEEAANAASAAPADKSADKMDIDGAEDVKPVRASNLETLIDDILSFDTIQSDLKAVGTSAVTQEVVEQDELVRLRWLVSFYQSSCDELSSTISELEDSSAKKESQCQQVVAICANIPQDKVESMLDELLTAMESDGPDVDLARVANFMQKVGKTRENGDQPGVGAQLSSSTSLSTAVSSGGTAASSVVPAVERDGEDAKPDA", 
"MVKENVGGNPEPGIYSATYSGIPVWEYQFGVDLKEHVMRRRHDDWVNATHILKAAGFDKPARTRILEREVQKDTHEKIQGGYGRYQGTWIPLEQAEALARRNNIYERLKPIFEFQPGNESPPPAPRHASKPKAPKVKPAVPTWGSKSAKNANPPQPGTFLPPGRKGLPAQAPDYNDADTHMHDDDTPDNLTVASASYMAEDDRYDHSHFSTGHRKRKRDELIEDMTEQQHAVYGDELLDYFLLSRNEQPAVRPDPPPNFKPDWPIDNERHTCLHWASAMGDVDVMRQLKKFGASLDAQNVRGETPFMRAVNFTNCFEKQTFPQVMKELFSTIDCRDLSGCTVIHHAAVMKIGRVNSQSCSRYYLDIILNRLQETHHPEFVQQLLDAQDNDGNTAVHLAAMRDARKCIRALLGRGASTDIPNKQGIRAEELIKELNASISKSRSNLPQRSSSPFAPDTQRHDAFHEAISESMVTSRKNSQPNYSSDAANTVQNRITPLVLQKLKDLTATYDSEFKEKDDAEKEARRILNKTQSELKALTASIDDYNSRLDTDDVAAKTAAEMATARHKVLAFVTHQNRISVQEAVKQELAALDRANAVTNGTSTKSKSSSPSKKPKLSPIPDQKDKPPKDENETESEAEHPDPPAAQAHQQQPGPSSQDTEVEDQDREEEEDDYTHRLSLAAELRSILQEQRSAENDYVEARGMLGTGERIDKYKHLLMSCLPPDEQENLEENLEEMIKLMEQEDESVTDLPAGAVGGGGGGNAADGSGGGGQPSNGRRESVLPALRGGNGDGEMSRRGSRTAAAAAAQVDGEREINGRAGAERTERIQEIAAV", 
"MEPPSNPIQPPVTPSHHSLLSAISPALSEQTPAPIHTLPPHLRPSIPQPHIAPPRPSSVQPTMEEQQRMHHIQQHQQQQHFQQQQNDENVFGSVMGAPGHVPGHEAPMSTQPKVYASVYSGVPVFEAMIRGISVMRRASDSWVNATQILKVAGVHKSARTKILEKEVLNGIHEKIQGGYGKYQGTWVPLDRGRDLAEQYGVGSYLSSVFDFVPSASVIAALPVIRTGTPDRSGQQTPSGLPGHPNQRVISPFANHGQTTPHMPPPQFIHQGNEQMMNLPPHPSSLAYPTQPKPYFSMPLQHTVGPQYDERHEGMTMTPTMSMDGLAPPADIARMGFPYNPSDIYIDQYGQPHATYQASPYGKESGHPSKRQRSDAEGSYIESGAAVQQHVEQDEEADDGLDNDSTASDDARDPPPLPSSMLLPHKPIRPKATPANGRIKSRLVQIFNVEGQVNLRSVFGLAPDQLPNFDIDMVIDDQGHSALHWACALARLSIVQQLIELGADIHRGNYAGETPLIRAVLTSNHAEAGSFTDLLHLLSPSIRTLDHAYRTVLHHIALVAGVKGRVPAARTYMASVLEWVAREQQANNTHSITNPPNPADRNELAPINLRTLVDVQDVHGDTALNVAARVGNKGLVGLLLDAGADKTRANKLGLRPENFGLEIEALKISNGEAVMANLKSEVSKPERKSRDVQKNIATIFESISSTFSSEMLAKQTKLNATEASVRHATRALADKRQHLHRAQEKLATMQLFEQRSENVRRIMDAIAAGTLLTPAEFTGRTQTMHEKSTGQLPPLAFRHVPGLALDASSQSQLNGAPPSTPLSVEDQEDIALPERDDPECLVKLRRMALWEDRIAEVLEDKIRAMEGEGVDRAVKYRKLVSVCAKVPVDKVDSMLDGLVAAVESEGQGLDFSRASNFVNRIKATKS", 
"MYNDQIHKITYSGVEVFEYTINGFPLMKRCHDNWLNATQILKIAELDKPRRTRILEKFAQKGLHEKIQGGCGKYQGTWVPSERAVELAHEYNVFDLIQPLIEYSGSAFMPMSTFTPQSNRKPTEAYRRNSPVKKSFSRPSHSLLYPYTSSNNMTSTSRMSGIHDALSLQSDFTRSPDMPSDSFTGSLHDIKASPFSSNNYAQSLLDYFLLPNTTQPPDFVYDRPSDWDVNAGIDEDGHTALHWAAAMGNLEMMHALLQAGANVVAVNYLQQTSLMRCVMFTMNYDLQTFEVVSELLQSAICMNDSFGQTVFHHIALLASSKSKMEAARYYMDILLQNLTATQSVDVAAQIINLQDDHGDTALLICARNGAKKCARLLLSFYASSSIPNNQGQYPTDFLSSKDMSFPENDDSPLNSKIEDNLIDNLKYPQSLDDHLSSKKPISYFSNKLTHQTLPNVFTQLSELSKCHEASLAEKQLTYNLAMEALEQTVRETETCQRLWNERTNNDENYLVNQREDLIHQCKKFLHTLKTARYYLETVQLHQLKKYVTYFSQIWSTDELADISETKNLVGHDTKTNRSSLSSKHEVDLFTAENEAAREKLVEQLCSLQAQRKQKINEILNLLSMGMYNTINTDQSGS", 
"MSNQIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDFTQTDGSASPPPAPKHHHASKVDRKKAIRSASTSAIMETKRNNKKAEENQFQSSKILGNPTAAPRKRGRPVGSTRGSRRKLGVNLQRSQSDMGFPRPAIPNSSISTTQLPSIRSTMGPQSPTLGILEEERHDSRQQQPQQNNSAQFKEIDLEDGLSSDVEPSQQLQQVFNQNTGFVPQQQSSLIQTQQTESMATSVSSSPSLPTSPGDFADSNPFEERFPGGGTSPIISMIPRYPVTSRPQTSDINDKVNKYLSKLVDYFISNEMKSNKSLPQVLLHPPPHSAPYIDAPIDPELHTAFHWACSMGNLPIAEALYEAGTSIRSTNSQGQTPLMRSSLFHNSYTRRTFPRIFQLLHETVFDIDSQSQTVIHHIVKRKSTTPSAVYYLDVVLSKIKDFSPQYRIELLLNTQDKNGDTALHIASKNGDVVFFNTLVKMGALTTISNKEGLTANEIMNQQYEQMMIQNGTNQHVNSSNTDLNIHVNTNNIETKNDVNSMVIMSPVSPSDYITYPSQIATNISRNIPNVVNSMKQMASIYNDLHEQHDNEIKSLQKTLKSISKTKIQVSLKTLEVLKESSKDENGEAQTNDDFEILSRLQEQNTKKLRKRLIRYKRLIKQKLEYRQTVLLNKLIEDETQATTNNTVEKDNNTLERLELAQELTMLQLQRKNKLSSLVKKFEDNAKIHKYRRIIREGTEMNIEEVDSSLDVILQTLIANNNKNKGAEQIITISNANSHA", 
"MAPRSSAVHVAVYSGVEVYECFIKGVSVMRRRRDSWLNATQILKVADFDKPQRTRVLERQVQIGAHEKVQGGYGKYQGTWVPFQRGVDLATKYKVDGIMSPILSLDIDEGKAIAPKKKQTKQKKPSVRGRRGRKPSSLSSSTLHSVNEKQPNSSISPTIESSMNKVNLPGAEEQVSATPLPASPNALLSPNDNTIKPVEELGMLEAPLDKYEESLLDFFLHPEEGRIPSFLYSPPPDFQVNSVIDDDGHTSLHWACSMGHIEMIKLLLRANADIGVCNRLSQTPLMRSVIFTNNYDCQTFGQVLELLQSTIYAVDTNGQSIFHHIVQSTSTPSKVAAAKYYLDCILEKLISIQPFENVVRLVNLQDSNGDTSLLIAARNGAMDCVNSLLSYNANPSIPNRQRRTASEYLLEADKKPHSLLQSNSNASHSAFSFSGISPAIISPSCSSHAFVKAIPSISSKFSQLAEEYESQLREKEEDLIRANRLKQDTLNEISRTYQELTFLQKNNPTYSQSMENLIREAQETYQQLSKRLLIWLEARQIFDLERSLKPHTSLSISFPSDFLKKEDGLSLNNDFKKPACNNVTNSDEYEQLINKLTSLQASRKKDTLYIRKLYEELGIDDTVNSYRRLIAMSCGINPEDLSLEILDAVEEALTREK", 
"MPFDVLISNQKDNTNHQNITPISKSVLLAPHSNHPVIEIATYSETDVYECYIRGFETKIVMRRTKDDWINITQVFKIAQFSKTKRTKILEKESNDMQHEKVQGGYGRFQGTWIPLDSAKFLVNKYEIIDPVVNSILTFQFDPNNPPPKRSKNSILRKTSPGTKITSPSSYNKTPRKKNSSSSTSATTTAANKKGKKNASINQPNPSPLQNLVFQTPQQFQVNSSMNIMNNNDNHTTMNFNNDTRHNLINNISNNSNQSTIIQQQKSIHENSFNNNYSATQKPLQFFPIPTNLQNKNVALNNPNNNDSNSYSHNIDNVINSSNNNNNGNNNNLIIVPDGPMQSQQQQQHHHEYLTNNFNHSMMDSITNGNSKKRRKKLNQSNEQQFYNQQEKIQRHFKLMKQPLLWQSFQNPNDHHNEYCDSNGSNNNNNTVASNGSSIEVFSSNENDNSMNMSSRSMTPFSAGNTSSQNKLENKMTDQEYKQTILTILSSERSSDVDQALLATLYPAPKNFNINFEIDDQGHTPLHWATAMANIPLIKMLITLNANALQCNKLGFNCITKSIFYNNCYKENAFDEIISILKICLITPDVNGRLPFHYLIELSVNKSKNPMIIKSYMDSIILSLGQQDYNLLKICLNYQDNIGNTPLHLSALNLNFEVYNRLVYLGASTDILNLDNESPASIMNKFNTPAGGSNSRNNNTKADRKLARNLPQKNYYQQQQQQQQPQNNVKIPKIIKTQHPDKEDSTADVNIAKTDSEVNESQYLHSNQPNSTNMNTIMEDLSNINSFVTSSVIKDIKSTPSKILENSPILYRRRSQSISDEKEKAKDNENQVEKKKDPLNSVKTAMPSLESPSSLLPIQMSPLGKYSKPLSQQINKLNTKVSSLQRIMGEEIKNLDNEVVETESSISNNKKRLITIAHQIEDAFDSVSNKTPINSISDLQSRIKETSSKLNSEKQNFIQSLEKSQALKLATIVQDEESKVDMNTNSSSHPEKQEDEEPIPKSTSETSSPKNTKADAKFSNTVQESYDVNETLRLATELTILQFKRRMTTLKISEAKSKINSSVKLDKYRNLIGITIENIDSKLDDIEKDLRANA", 
"MASANFIRQFELGNDSFSYQKRPEDEPSQPLSNRNINKLNDSSTLKDSSSRIFINSQVLRDGRPVELYAVECSGMKYMELSCGDNVALRRCPDSYFNISQILRLAGTSSSENAKELDDIIESGDYENVDSKHPQIDGVWVPYDRAISIAKRYGVYEILQPLISFNLDLFPKFSKQQQIESSSISKNLNTSSFNTRSPLRNHNFSNPSKSSKNGVHTINNMQSSPSPSSSFLLPLTQIDSQNVKRSNNYLSTSPPILEQRLKRHRIDVSDEDLHPSSQLNDNEASSLFPDTPRLNHSLSFVSLVSSLPPLDQNIMQDYHTSKDILTSIFLDVNFADSSALEAKLSDSLDLDVPIDELGHAALHWAAAVAKMPLLQALIHKGANPLRGNLTGETALMRSVLVTNHLNQNSFGDLLDLLYASLPCTDRAGRTVVHHICLTAGIKGRGSASRYYLETLLNWAKKHASGNNGYMLKDFINYLNHQDKNGDTALNIAARIGNKNIVEVLMQAGASAYIPNRAGLSVANFGIFVENALKQPEDSKQTKVSLMSENLSSKEKTAVPPRQKSRDIIASVTDVISSLDKDFQDEMAAKQSMIDSAYTQLRESTKKLSDLREQLHVSETQRTLFLELRQRCKNLMTSIEEQKSELSNLYESFDPNGIHDSLSLDADAPFTVNENNNKNLSIAELKFQVAAYERNEARLNELANKLWQRNSNIKSKCRRVVSLCTGVDESRVDSLLESLLQAVESDGQQGEVDMGRVAGFLRVVKEHQA", 
"MASMNQPQPYMDVHSHLSSGQTYASHPATAGALTHYQYPQQPPVLQPTSTYGPASSYSQYPYPNSVASSQSVPPPTTSISSQVPAQLLPLPVTNHPVPTHGYGNNSGTPMQGYVYDPTGQMAPPGAKPRVTATLWEDEGSLCYQVEAKGVCVARREDNGMINGTKLLNVAGMTRGRRDGILKSEKVRNVVKIGPMHLKGVWIPFDRALEFANKEKITDLLYPLFVQHISNLLYHPANQNQRNMTVPDSRRLEGPQPVVRTPQAQQPPSLHHHSLQTPVPSHMSQPGGRPSLDRAHTFPTPPARMNSSVPNTQPLSIDTSLSNARSMPTTPATTPPGNNLQGMQSYQPQSGYDSKPYYSAAPSTHPQYAPQQPLPQQSMAQYGHSMPTSSYRDMAPPSSQRGSVTEIESDVKTERYGQGTVAKTEPEQEQEYAQPDSGYNTGRGSYYTTNPSVGGLAHDHSQLTPDMTGSPQQNGSGRMTPRTSNTAPQWAPGYTTPPRPAAASSLYNIVSDTRGTSGANGSTSDNYSVASNSGYSTGMNGSMGSNKRMRDDDDDRIVPPDSRGEFDTKRRKTLTETPVGGPVGGVPLGLQPMKAGGSLISARR", 
"MYHVPEMRLHYPLVNTQSNAAITPTRSYDNTLPSFNELSHQSTINLPFVQRETPNAYANVAQLATSPTQAKSGYYCRYYAVPFPTYPQQPQSPYQQAVLPYATIPNSNFQPSSFPVMAVMPPEVQFDGSFLNTLHPHTELPPIIQNTNDTSVARPNNLKSIAAASPTVTATTRTPGVSSTSVLKPRVITTMWEDENTICYQVEANGISVVRRADNNMINGTKLLNVTKMTRGRRDGILRSEKVREVVKIGSMHLKGVWIPFERAYILAQREQILDHLYPLFVKDIESIVDARKPSNKASLTPKSSPAPIKQEPSDNKHEIATEIKPKSIDALSNGASTQGAGELPHLKINHIDTEAQTSRAKNELS", 
"MNPNTPADVYYGQMSQGSSMPVTTVPSHSHYASQQPPPLLQPGSTYAHQYGTPQYGYANALSSPASIPPSLPPSMNSMAGQSVLPLPGSGSMNPAVYASGGFDTTGQVAPPGMKPRVTATLWEDEGSLCFQVEARGICVARREDNAMINGTKLLNVAGMTRGRRDGILKSEKVRHVVKIGPMHLKGVWIPFERALDFANKEKITELLYPLFVHNIGALLYHPTNQSRTSQVMAAAEQRRKDSHGQLRGPPGLPSLQQHHHHHSMLPGPPSLPSHPSMGRPALDRAHTFPTPPTSASSVMGPMGNSDGYQWSQQSMSGTQGNSSLSLDTSLGSNARSMPSTPATTPPGSTIQSMQNYPPVSQSYESSRQMYQGQSAQQAQYQSQQHYSSQPQHQERPVYSQSSYIKNDMGPPSGRPTGQSNDASDSKPPTGMIHQGQGQSDPGTHAGSEEDDDANNEAEYTHDSGGYDANRGSYNYNTQAVNSLPHDHGLAPEIGGSPHQAGSGRATPRTAAAPSSYYSAQGYHTPPRGQPSSSLYNVMSNERTGSNGTQGNEMYAGQADMPSSLPNGYSAQPSVMNGSSGGLKRGRDDDDDGGRPTTSAPNLGPGMDMKRRKTMMDGGSLPSPTYTATIAQAAPSAIAAHRRR", 
"MPIGNPINTNDIKSNRMRQESNMSAVSNSESTIGQSTQQQQQQQQYLGQSVQPLMPVSYQYVVPEQWPYPQYYQQPQSQSQQQLQSQPQMYQVQESFQSSGSDSNASNPPSTSVGVPSNATATALPNGSAITTKKSNNSTNISNNVPYYYYFPQMQAQQSMAYSYPQAYYYYPANGDGTTNGATPSVTSNQVQNPNLEKTYSTFEQQQQHQQQQQLQAQTYPAQPPKIGNAFSKFSKSGPPSDSSSGSMSPNSNRTSRNSNSISSLAQQPPMSNYPQPSTYQYPGFHKTSSIPNSHSPIPPRSLTTPTQGPTSQNGPLSYNLPQVGLLPPQQQQQVSPLYDGNSITPPVKPSTDQETYLTANRHGVSDQQYDSMAKTMNSFQTTTIRHPMPLIATTNATGSNTSGTSASIIRPRVTTTMWEDEKTLCYQVEANGISVVRRADNDMVNGTKLLNVTKMTRGRRDGILKAEKIRHVVKIGSMHLKGVWIPFERALAIAQREKIADYLYPLFIRDIQSVLKQNNPSNDSSSSSSSTGIKSISPRTYYQPINNYQNPNGPSNISAAQLTYSSMNLNNKIIPNNSIPAVSTIAAGEKPLKKCTMPNSNQLEGHTITNLQTLSATMPMKQQLMGNIASPLSYPRNATMNSASTLGITPADSKPLTPSPTTTNTNQSSESNVGSIHTGITLPRVESESASHSKWSKEADSGNTVPDNQTLKEPRSSQLPISALTSTDTDKIKTSTSDEATQPNEPSEAEPVKESESSKSQVDGAGDVSNEEIAADDTKKQEK", 
"MSTGMLQETLQTTSASTSGTRFRPYASPNHQVTKGRYITSNDPRGYIPVYEYPLNGQWIMMDIDDGYILWTGIWKALGNSKADIVKMIDSQPDLAPLIRRVRGGYLKIQGTWMPYEVALKLSRRVAWPIRHDLVPLFGPTFPSTCLSPDQPGYGQVVASSNVRRRARRNTQATAQPPREAHSNWTVMTPGPMVGLSFPHSQFSRPPLPPLAPTPARSPSDYAPSSHYGNQLDPQDARRYSHSPYSPLASPPERKSSISSKALSLEIPPVRPSSSKAREDISLPPLKQPDGADPEMSPYALPPISALEDLRGVDTQDSAAVLRRLRLDDDYPSSSRSSTSQDSIWGRRHSLSAHSPHPRSSDNSRFQPYLSSRSYQDSTLKRSRSPAESYADRRRASDFSQEDSTSAYSPISPATPNSSILSHSSFSDLKKLASSTDTRYNFPRISGRDWAPLKGDTDHIRSSYRSGPSPLELDSDSESSAPHRPW", 
"MSTASPLHHGHGNGSYANSPAPTGVTGRDAGVAAAAVADSAVRSGSVPASASGSAPGSASGSMYGEAHTQHHTGHHHYSAHHTHSHGALTSPVNGGHSSSWSPYGYPAAPVYGGSPSPYGHNAYSQYASGYGYANGTAHHVATAPTTPSATSTAYHTGVNGMMMHHGQHAGYGYSSHHLGSHTPTHTHTHSSAYFMNGDGAHSHLNSSAHLTSPSYTTAPQYSTQLPLAGRHRVTTTLWEDEGTLCFQVDARGVCVARRHDNNMINGTKLLNVCGMSRGKRDGILKNEKERIVVKVGAMHLKGVWISFARAKQLAEQNGIADALYPLFEPNIQSFLYHPDNYPRTAAVIAAAQERQAQRQRAPGGQPSPGANGTSQAPPLMRANTTPSNGDTSTFSSGLSSLGSWTGSHDQGHASAPTTAQPSPSSMHNGATQMHMSLSNHGTASPTYAQSQQQQQQQQQQQQQQQQQQQQQQQQAYPMTAAQQLARPSVGDRRQSAPISLNNSVGHAENPYGATNLGGAANGGLVNGARKVSGLKRSWNDADDLNGSAAASPTERDMQRSGSGGSNGLKLDGDDLHSPDSSDDRLAKKTRGMPQRGGGATTAMPSMSTNMLMGVGNGSGIHHE", 
"PRHSKQTTNLRCRLFASSILSPCQASRRIPPHARLSGQLTRESLRQTSQPWTPTKPLSREHVNTVKLELPSISSVHARGPADTWYPSHYATKPAVSGERLPALPQIQSHPSTSSNYSSPRGDSISSGSVSGGSASSNTSYAASVNGQTTGFKTPSPKHTPQSLRRDSQSLNTQSVQSSPFGTTQEGYSFAPSGYNSMNQMQSYADVHQSHMATAAHAPASAPPSGLSHYSYPPQPSMMQSQHQYSQGPPGYPPYGYPGGVPSQIPASSSMNQAMVPSTLQLPAMSSGAPASSLPGSQSYQTQTFDHTGQVAPPGMKPRVTATLWEDEGSLCFQVEAKGVCVARREDNHMINGTKLLNVAGMTRGRRDGILKSEKTRHVVKIGPMHLKGVWIPFERALEFANKEKITEQLYPLFVHDIGALLYHPSNQTRSSVGSAAMAAVDRNRRPDPMQTHQRYLSGPAASQPPSLHHHHSMSNPIATAISQPPHAIQPHPSSGRPGIDRAHTFPTPPTSASSIMGMGNQGSSYEWNGNNVQNPQGGQPLSIDTGLSNARSVPTTPASTPPGAVQQGMSYASGQSFDGSRPMYSGPPSQPGQYTQGQPMMGYRQDGSYPKTEMAPPSRINDVPDEGEVKQPDGMMPQGHEQVAPPPQGTEGEHDHGNEYTHSNASYNGNRGPYGYPPNGPPGAMHPDHPHLSPEMTGSPHQNGSGRATPRSAATGQPQWSSGYPTPQRQAPPSSNLYNVMSDPRGASNGNATHDAYQGPGAVPQYATQGYPPTNGVNSGKRGRDDEEEDPYRPDSVQGDDMSGLKRRKTLEGGAVGGPYADPTPGLQRAHTMTAQRGRR", 
"MAAAPTSSFLTSMSAQPPRTVQALVNEEVRAPPPVRLYPSQHRVSMTRYATSTDPRGYIPVFEYPLNGQYIMIDCETGMVHFTGIWKALGHTKADVVKLVESDPTIAPYLRKVRGGYLKIQGTWLPFDTAQTLARRVAWQVRYDLVPLFGPDFPDTCLGPGEPGFGQLLLSAPKPRGRRGAKKAAAAPTVAHERTASPQDNRSQSRPGPYPSQESFGNRCSGRVEAVGAMNGYSPMLSQARYSPYTRAPVHRITQLEPLPSLIQPNQSCPHPTADSMYSSHYHQSPRQSMMTSHGAGPYGQQHLTGSTASGMQSTAPLPSMRPHQAHQSENNFFETYRGPDSFEALSNKWLAPEVANPSLNDSGLLHGEGGCLPPLQYSNNPVLRNGPSGSPTNQYNFPNQIDSAHSSHHIDSNQTQHVHRHAGFPYESQHQSNFRHDLSTEEAAHHPASPSQQPPPSVTYDKAHNSEPQAGSQAANVTAGCYAASGSNSTGNPAGSPGSHSSHVPKSPTPSSASTSTHMQNSHNPNSHRSPSNTLTNMSNNGGFNSNTQGEEAIQFSVLTSPAHLETSGPSENSIPPAQSSDSDWNPAQNTTGLSPSQAPRQ", 
"MNQAPLSATGVNFYISGPRPARLFPTPIHEFRKGKYATAGGESGFMTVFEYDVRGHTMMIDVDTSFVRFTSITQALGKNKVNFGRLVKTCPALDPHITKLKGGYLSIQGTWLPFDLAKELSRRIAWEIRDHLVPLFGYDFPSTCLRPDSEGFGQLAIGMSQKRARKRHNNGGPHQTSCYGPSLPISIELWQHSTDPLRDLGESSVVGGQAIEHVSAKNSAVQPCYGSSQPATFHYSKGYGLESRPWYGQDYLESNSLESMWNSAQAGGGSVGLQVPISTCGATASPCLAAIGANGGSPILSSPPSSNASSSSNQSYTAAGYGLMVPPTVPSHSVNSEAGANQAEGPTPIDGSRSYASLTAHGYATGYGDANASLSTWNDATHASTFTLHVHAHVHFQPPDPESAQLFTIHDFGSDPFYAEQVERG", 
"MTNKVQELWWEENKTRVWQVEVDNGNYVARRQDNDQINGTKLLNITKITRGKRDGILKNEKSRQVVKTGTITLKGVWIPFERAIILARQFNIEQQLYPLFETNLGDYVENSIGSHQIKRKSLNNLMDSLTTNRELVSKRRSTVSTYNPATSAYVSPYGFSPQHCYQTEFEDMNQHSGEIQSGRPRNTSSASDWMTNWSTSSSSPVIPATPNTFSPVMNTFQSLALHSPPIPIPNYYYDSSSSYFPSYHQKQQQQQVQMQMQMHTTASIGGDRQSNEYIQR", 
"MILISPTRTLPSPRPIDTDPILNYRHIQPAAAAAAVGPWLGQNQHHHHHHDTLAKSPNITTAPATHSPSELSASPAPSAVSTGSSLLDPQSVPHIKIPHSSSPPAIMLPQPSSDDDSSTAEEEQPSAQSSNATLNTPTPHTNAPHQLDSHASSVGLYDLPPTSSSAPTTSSSSSPFPSNVPSHQQPSPYSSSPHPNQEHHPHHPHHGNQFYQQSPPALHSPLQSAHHPQQSFDARPHSSLFAHQHYHSRPQSAPHSTSQFSLDPHVLAAAAANVEVKKWDEENTYYYQVAHKGVTVGRLKGSGLVNGTKLLNLAGISRGKRDGILKNEKIRKVVKHGTMHLKGVWIAFDRAVFLAEQHSIADKIFPLLVVNLEHYVPIEPPLMAGGTKLGPGSLFHHHHPRHPRLLPQPIKFPPSTISLAPASANSFSSTGGWPSGPSSALPSIGYNEPFSAPPIPRSAATADTSPSIYEQAQFQYLNSAQANNPDLLERRHTLPNNSFHGYNSVPSFGSSQPPPPVSYSFHYNSTHVPGYPPRSSTAESATPNQFEYQSKNHNGNGNGDAAGSYPATLYHSQPAARPVSSTTAQPSPALNSAPLLLGDLSPGSSTQIVDHGAGDFRLSTGTSNGQVKQEGDDESCNEKRLIMEWNPSC", 
"MTENEKSRSLPAERNPLYKDDTLDHTPLIPKCRAQVIEFPDGPATFVRLKCTNPESKVPHFLMRMAKDSSISATSMFRSAFPKATQEEEDLEMRWIRDNLNPIEDKRVAGLWVPPADALALAKDYSMTPFINALLEASSTPSTYATPSRPTAQKSETSEGEPESSTSATTTSVARRTRQRLAEHLENSKKTILQHDNKEEDKEIHSEENETKDEIKSEKKEPEIKKQEGGSSTEKVGQPSSSDDKAKGSTSKDQPSEEEEKTSDIQDRKIKTPIKPSLLGKIRSSVNKGMTDVASQVNRGMTDVASQVNKGVNGVASQVNKGMNGVANQVNKGVTGVASQVRKPVGKLEKKFENLEKSIGDTLKSSIRSSPKSKKRSREDFEENEDYNAMVPVKRSRITKLESEVYYEKRKVRALGGIAIGLGVGAILPFLF", 
"MVVDRVLPERKNPLLEPTDSTSIEILIERRRLGQTNLGVKAGVSGIANATKPENMGTFDYAHLRVPLPKDLTGSGIFSRNRMSAFPESYFLMRRSSDGYISATGMFKAAFPWASLQEEDLERKYQKTFPSAGDEEVAGSVWIAPEEALALSEEYSMRHWIEALLDPAPIEKGGKDKSNAAIQMPPRFDVANAQPATLPTFGFRQTRARSARSVSPSKAMTPGRKYATPRKGRSTRSAMKPDATHADDMFRPIEAVTPSTALQNSIARRIAPAETIASSIEGEVKEVEQEVKAALDAEKKPEPELEVQEGTVHIEVKQTVETNGDTEKTSTSVTVDVPHDHAALPEPEDPTAMIEEAKRMVAEAQKLEGGSPSVTRSSKRGIEEVLDEEDLADERLNKLAKKAYTTEQKMTKEKVTRRALVGLGVMAAIGTAFQYFV", 
"MAQVARHLPARRNPLMLEDVPSHTDLASRRRLGQTQLTPRMVTAVPGAEVDPSSLLAFDYAHLRAPLPKGIVSGIFKSSPPSYFLMRRSQDGYISATGMFKATFPYASQEEEEAERKYIKSIPTTSSEETAGNVWIPPEQALILAEEYQITPWIRALLDPSDIAVTATDSSAPKQIAPPPKFFGAQPPLVAPTPPTTRSTRSRPSSRRSSSPAKSTTTSKRGTTPRNTKRTVTTEASATTVTTTATATAVPSAETPATSFADSQAPTLINGEIPTSTPINTVPVTKIQTTEAELKVESIEKEPVVVLEPIEEEPKIKVRVDEDVKLDKDGEEVKHTKVELEVPLMAGEPPSKEEARKMIEEAKAMVEAAVKADAEAAAALVEASKAGAEDEKAEDEAKAETEATKEEEADSKGKRKAEKISVDEDEKAADEAEQPRQAKRVKTEAELRKDRIRKRAYLGLTATFAVGALGALLPIITPYVANVL", 
"MASIQFLLNPLPSLPSSDRCPLPTPSPTISSSTAMLRSPRQKKQKMAKDAPIFQRGKPRGEVRYPPYEDRDGKFSCQHQDFRIHPLGNIADYPRHIPYNSDKKSFQERTGRESFEVFQYTFQLPGEEKQWTVMWDYNIGLVRTTHLFKCNDYSKTTPAKMLNQNPGLRDICHSITGGALAAQGYWMPYEAAKAIAATFCWKIRFALTPLFGDNFPDLCIHPDDRARFGRMVIDPGIVRIATEKANLYRMLELRCSTTNSLRADYVLRPSSAPDIDRTDPNLERDRVALGRHILPKSHRHHHHRSKTSPSTNTSLVGYGSSPEVEYYSCGTEPYCVSPESPIRSSFTPVNTPRSTDIYPSSSSTNFLRSPHELLASLSSSASIARARIERASKISGARVIPSSVPSNVTSITTKGRDNTGHSALMEESDIDADAETDSGHEHDLDFELSSSDESSTSSTVSSSTSSASLGFAANSRNRPYRDDDEPHRDTDEEMVDYRAPKRIATAGARDRRWGRGRRVIHQEHSDIETSRRARKHAQRSSNARLVCEMTAAHALISLLHDATGSDVDVDTHNRLECGRSPDGGVKNNLKGSYFGIRLNHNPSTESGQKRRRASA", 
"MVRSLPKKNNPFVTPDAAPPYEELLMRRRLGKTNLAVKPTQVGTSNATKPENLGPFEYAHLRAPLPKDLKGSEIFPSHSPQQHPETYFLMRRSKDGYVSATGMFKIAFPWAKLEEERSEREYLKTRPETSEDEIAGNVWISPVLALELAAEYKMYDWVRALLDPTEIIQSPSSAKKQITPPPKFELPPIQAPEALVPSSRTRSRRSASPSKKAGTPRKPRQTKAQKEAAVAATNEANATLQSALDDTVSNADGEINGDVLPSVEDKREPETSPVKGKKAAAKAKKQAVSEEDQEDKVKIEIKSDAAEGSDVQAAQTTISVEMPISLPEAPSAEDTQEMIAKAKEMVKEAVKLQQEPAESSATAKKRGAEEAELGEEEEDEETKTLRTKRAKVLEEKLKRERVRNRALMGVTAAFALAKPALVLLEA", 
"MPKSSSCCEPEQKQSIPTNANPISAGGAGLDIRLAGMRSAHATLRGCSFSPYMVTQHPPLRDSVNRNKQQPTNNSTNPYTKKASRMSQTNLYKSNNPPNLPQDEFNQTLVNYQGKLRSIRIQDININGHTITIARIKIPSPEKLSSHLIKRFDTNAISASSFFRSAFPHSTEEEEAIQMRYLHQIYDTHTAGAVEFGSARKLTGVWVPIENAAELAEVYGLTRFAEPLLAFPNPKENPRSPTGTKIGGEDESSTTQTPKASQQSKLTGQISVTRSSKRSRAGPLSFGNTSPSSFSLNSFNKPPTETNKSGTHDDSKSTNDENDEKPASPTDRVAGRGARNSPSKKPTTVDENHEHTEHEDHQLIGTDELAQRAKQEALKLVSELKNSQPCTQSSLESPTNTLETELTRTTSPAKSNKVTRKRSSDEVSFEGEEQGEDEDEERTADETATHRSFLPKLLWRKSAAQAHPNSKKHKRTQLGGGGSSSSSSKSFVPLLTNSATPSVDDSSSTHNPNKRNLAIAGIVIAGAAA", 
"MNIQDLLNPSCGDRHDHRRSESATPPSRPVAILPALRRQKIPKDAPIFSEGNRTVGIVNFAPHEAGNDEELLAQHCRFQIYPLGEISRKGVRHIPYNSDKKDFLEKTGRDAFEMFQYTYKLPGEDKPYVVVWDYNVGLVRMTPFFKSCKYSKTIPAKTLRENPGLKDISYSITGGALVCQGYWIPYQAARAIAATFCYDIRWALTPVFGNDFPSICLTPDDPSFAKFVIDPAIVRYCTEETTKFRELGSAYEVHRPVAPTQVEAPTSRSDQPLSTSIVRQRRARPIDIESGYGTDTERNDRCLFSPEVSPRTRFTPINRPRSPYSPRTAESSFVSSPVSIRAPPGLHTPTSTPYEHSGEVFRAKRSHSKVAFCEHPADEAVIRPPTAATVDSAHGCEMCVGDDNHSHLDMDAAEMLLSLRTADSAMPPSKRTRRGS", 
"MTSPGLPKDFNELLDKSEIPSPKWQQITRDDRPITIARLKLPHPREKHTFILRRYDCNGISFGSLFKAAYPYATDEEEKIESGFVKKNYDVTLVPTEEYQERKLAKLAGFWIPIAIAEELGQRYAMAEYVDALAKADTPDLTDFKKRSSNRQTSEDIKSSPAKAQASLESPAKSASKIPTPTKNPAPRRSARHQSRSPSPSPLTHNLTPGKKKAKKAPKEAVIEESVEETIVVDKKESPLKKALNDDQVLADIERAKDLVDDIKQSKNLSQSSPVKVVKEEVLETIQPSVSTESLEGEGKRKRELEDETGNEIKVVSFGQNPPANPEEIQQRPVVQRRGVAAAVGAFALGVGFAASNILPRFLF", 
"MSHPAADAPPPYPGTTDDAQYDLTPLPHTANRPRLPEDKRNPHLNNLPEDTKIVKFQTIVRENKEIVVGRIKVPTENANGTHHAFILRRYDTNAISLTTMYKVAFPSATEEEEKREMDWVKSSFDTRGTNGGRDSEVVRLAGQWVSRNLAIHIAPAYNLVQLVAALSRAVPDPNVAYRKSQRSQAAADELARTKAKQSQAPSSVPAISNVPVRKPQAAIPSMATEISSPASKRQRKDSVTEASGSATQTITEAQPSADTSETDDTRHITIEATTTITSPSGANVDMDAEIEQAKQLVKDLRQEIQLRNEAGDSLEDQGVAVADDVRGVKRGKHEDEAVVISGGAGGKDRVVRTNKRIPQTAGGDVGQRFGWGAFVFSIGLGASLTLFSQYASSLL", 
"MDAAIPTPRLQRNNTITIPKPSLVLRTPNQPKSKSKHIADDDSNNQPLVPSQTRQSHSIVPKPQDQIPEFPPPHVILHKDDAGSKVFHALARSLLSVDNRATTVKDLADLAVNNGLGCQNSSAATQAITTYLRMHNERCEADHDQPLLLSHNMSGTDADDDLIPALYSLQGGNPKKLCPNRKTNFRKNTTVWYLSRATGAACPFARAGIRLCDYDVLTEEDPEKEHKRRRSKHFDSISAGQKRKRPLRSCVASGLASDSESEKGEDKRPQKRLTLRIKLNGAFTPRPQPERSQVSSDDDSSDEEEPMEVDNSDRESEAPESKKEEEEEWRLPPYPRRSISIPCYTPSYEGAYPQFPLHNHYHDPFRRSPSLAFSSGSPPPDSEDEVDDFHITMTRTDDFPEDFSSESESEGETQFESPGPRSPSAPPLPSTSITVKEEPRDLQSMLDAWDDLDAGLTEPNVVRVEAGPLALKSEPLDLWDWDSEPTARIKQEDLSFDSLFPSDSAFSTPSLSSPSTSSRLTPEFTGSQSISHDDVQDSPSRSNTVRLRSKTVPVFSTPSSNDTPASLSVPPPPSLNARSNTISGESAESPLLPSSSSLPPSIASLIQSMNTLSAAVSPSSLVLSPVTPPSGSDAVVVHTCQPCSPPITATQIEDISVYQMVLGSFHFLRRIDTDFVNLSPIAAYNKSPFPVITTIPNATPIKGSPTVSGIWVPLSAAQAYLRDHPAEGSEFDIFLSDQLYERFPSALQDFVKSNVPTRSLNQFGRHFGSTLQQFTQHPPVPLTPNEVLARNPPQLQLQQITTPSPTSNAYTLSASLSISEKHHAAMIEPPLNAAEQEIFELCVVPDWDRDVDSGSSAPGSATPGPNAEPRGSRGESDMQVDEQECTTLEAGDSDSSSLTSLSSSPEVSGEDDLMKEGAGPSSPTLPAPPQSLKPSPSSSDEMETALPPASSDLDVGSIVKEGTKETSTGVSANEDSSTTVVPQRKRKGSSSRPNRPAPLRRSKRVAEIAAHHNPSSPSTSTPASVNTRSRRRGSRNSLS", 
"MTFDHTGQIAPPGAEPRVTADLWEEEGTRYFQVEARGVCVARREDNHMINGTKLLSAAGITRSRRDGILKSEKTRHVVKTGPMYL", 
"MTARPPLPLRHANPSLRDGNATIPPVKYQILSCQGKDILVGRLKIDTTDGGHAFILRRFDTQAISLTTMFRAAFPTASEAEEKDEINYVKANFDLFGNNGSSKEPHITRLAGTWVNRDTAGQLAHDYNMVDLINTMVEAEPDPNGQYRRSNKSAQNNNPPTNAPEPTPATNVHATRSPAKQSPKPPSKTLPTPSPGSGDAQPPAPKRRREGSPATFTSGIPVASSPAVPKTPGPRRSTRTKSPAPSRVPQPLTATKPRSRASVAPPSPKKRPVDLPKSSPIKAEEDTAVEDNVAGNELYAQDISEQKKLIADLKAAASSKKPADTVKEDDDQQMEEEGQGPSKLKRIRQDEEKPLQFEFKEPEREERQIATNRRVGRFDMQPERKSLAWGIAAFAFGMTAITYLPNFL", 
"MKYPAFSINSDTVHLTDNPLDDYQRLYLVSVLDRDSPPASFSAGLNIRKVNYKSSIAAQFTHPNFIISARDAGNGEEAAAQNVLNCFEYQFPNLQTIQSLVHEQTLLSQLASSATPHSALHLHDKNILMGKIILPSRSNKTPVSASPTKQEKKALSTASRENATSSLTKNQQFKLTKMDHNLINDKLINPNNCVIWSHDSGYVFMTGIWRLYQDVMKGLINLPRGDSVSTSQQQFFCKAEFEKILSFCFYNHSSFTSEESSSVLLSSSTSSPPKRRTSTGSTFLDANASSSSTSSTQANNYIDFHWNNIKPELRDLICQSYKDFLINELGPDQIDLPNLNPANFTKRIRGGYIKIQGTWLPMEISRLLCLRFCFPIRYFLVPIFGPDFPKDCESWYLAHQNVTFASSTTGAGAATAATAAANTSTNFTSTAVARPRQKPRPRPRQRSTSMSHSKAQKLVIEDALPSFDSFVENLGLSSNDKNFIKKNSKRQKSSTYTSQTSSPIGPRDPTVQILSNLASFYNTHGHRYSYPGNIYIPQQRYSLPPPNQLSSPQRQLNYTYDHIHPVPSQYQSPRHYNVPSSPIAPAPPTFPQPYGDDHYHFLKYASEVYKQQNQRPAHNTNTNMDTSFSPRANNSLNNFKFKTNSKQ", 
"MLNQNPGLKDIAYSITGGAIKAQGYWMPYACAKAVCATFCYQIAGALIPLFGPDFPSECISPGEPRYGIMIIKPELISDTMRKAQELYRRYGNWGGGCTSSSPARRPLRTASSGSQERHHHHPYPNQEHLDHQQQQQRTVCSRRCPAEENSCVDARPQLRGISAPMPPAGEWTPPLLRSSAGRPRPVMPTSTHSSISYPERAPHRSAWTAVNHQPPNNSLDRYSLKRPLPSNEPDESVSHSNWPSRSQAPNPWLTAIPRSPRKTSSSPWASQPGSASRSRAGSIDSMASQHPQGLPSPSLILSSPSSSMVSLSSSNSPSPRPQLPPISQLCSLPVPSGRRRLPNGRPSRVGGDATSSHSRQDHSTCGAYQFSAGYQRALTPPSSTSAPMHWRSQRRPSLQDQHEHEHIEDTQPRRIAVEANMECGDDNESHLHLPLPLPRTSSSASIVADKNANDTTSDNSSSRNFNSASIGSGRDDGQTSLAARKTAALTLLHLRQQEEEKEAAAAAAAAAAAAYSSTKRPESPSSSLSSPVSPPPTSGQPSPTLSAVVTATNLRRGTTTATATAVIDTTEPLAPPPSPSSNYLGSPISTSIASSSSSFSPSTSCNGTRENSVVANEMTRYAGQEADAGGPRHCNGDADDEGDYEHEQQYRRKRRRLLLVGRAKSF", 
"MPAAASARKSTPTRKSTPRRARSSSVTSNASTGVPASPSASPRKTKKQKEAAAAAAAAVAAAAATAEQVNDDESDLLRPKLPTKRNPRLKEVDEAVVKLQIIKREGHNIIIGRVKLPTVNGQDHAFLLKRFDTNAMAASSMFRLAFPFADGTAEAAEMRFLDTKYDTNRANGGYIVEEVKVPETPKKRGRTRKTAENSKKESTPDTESVSADKQIRVLPEGSTGVRLQGTWIPAEDAIEVAEDYGIAKYALALIHATAEHAEDGGAPILTSEPVAEVKTPRKRQRVSAAAATASDTPDSPQLVQRVTRLENADGSISKVRVESTLEAPSSNGVPVALSQAEIEEQIAQAKALAAGIQQSITAGSGSASTRGQKRRAVNDRPTAEIDPLADDEDYSESGRVVRAFRRGTRVARRRPIATTAGAVAAAGAVGAGALAWVSGGNPEVAIQTLQASMQSIGLQNLQNLGLQNLQQIGTQLGAHLASILPW", 
"MTSFQLSLISREIDGEIIHLRAKDGYINATSMCRTAGKLLSDYTRLKTTQEFFDELSRDMGIPISELIQSFKGGRPENQGTWVHPDIAINLAQWLSPKFAVQVSRWVREWMSGERTTAEMPVHLKRYMVNRSRIPHTHFSILNELTFNLVAPLEQAGYTLPEKMVPDISQGRVFSQWLRDNRNVEPKTFPTYDHEYPDGRVYPARLYPNEYLADFKEHFNNIWLPQYAPKYFADRDKKALALIEKIMLPNLDGNEQF"
)), .Names = c("id", "name", "refSeqID", "uniProtID", "taxID", 
"genomeXref", "genomeFrom", "genomeTo", "seq"), row.names = c(NA, 
48L), class = "data.frame"), proteinFeature = structure(list(
    id = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 
    16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 
    31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 
    46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 
    61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 
    76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 
    91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 
    105, 106, 107), proteinID = c(1, 1, 1, 1, 2, 2, 2, 2, 3, 
    3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 6, 6, 6, 6, 7, 7, 7, 7, 
    8, 8, 8, 8, 9, 9, 9, 9, 10, 10, 10, 10, 11, 11, 11, 12, 12, 
    13, 13, 13, 13, 14, 14, 14, 15, 15, 15, 15, 16, 16, 16, 16, 
    17, 17, 17, 17, 18, 18, 18, 18, 19, 19, 19, 19, 20, 20, 20, 
    20, 20, 21, 21, 21, 21, 22, 23, 24, 25, 26, 27, 28, 28, 29, 
    30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 
    47, 48), featureID = c("ps|PS51299", "ps|PS50088", "ps|PS50297", 
    "ps|PS50088", "ps|PS51299", "ps|PS50088", "ps|PS50297", "ps|PS50088", 
    "ps|PS51299", "ps|PS50088", "ps|PS50297", "ps|PS50088", "ps|PS51299", 
    "ps|PS50088", "ps|PS50297", "ps|PS50088", "ps|PS51299", "ps|PS50088", 
    "ps|PS50297", "ps|PS50088", "ps|PS51299", "ps|PS50088", "ps|PS50297", 
    "ps|PS50088", "ps|PS51299", "ps|PS50088", "ps|PS50297", "ps|PS50088", 
    "ps|PS51299", "ps|PS50088", "ps|PS50297", "ps|PS50088", "ps|PS51299", 
    "ps|PS50088", "ps|PS50297", "ps|PS50088", "ps|PS51299", "ps|PS50088", 
    "ps|PS50297", "ps|PS50088", "ps|PS51299", "ps|PS50088", "ps|PS50297", 
    "ps|PS51299", "ps|PS50297", "ps|PS51299", "ps|PS50088", "ps|PS50297", 
    "ps|PS50088", "ps|PS51299", "ps|PS50297", "ps|PS50088", "ps|PS51299", 
    "ps|PS50088", "ps|PS50297", "ps|PS50088", "ps|PS51299", "ps|PS50088", 
    "ps|PS50297", "ps|PS50088", "ps|PS51299", "ps|PS50297", "ps|PS50088", 
    "ps|PS50297", "ps|PS51299", "ps|PS50088", "ps|PS50297", "ps|PS50088", 
    "ps|PS51299", "ps|PS50088", "ps|PS50297", "ps|PS50088", "ps|PS51299", 
    "ps|PS50297", "ps|PS50088", "ps|PS50297", "ps|PS50088", "ps|PS51299", 
    "ps|PS50088", "ps|PS50297", "ps|PS50088", "ps|PS51299", "ps|PS51299", 
    "ps|PS51299", "ps|PS51299", "ps|PS51299", "ps|PS51299", "ps|PS51299", 
    "ps|PS00152", "ps|PS51299", "ps|PS51299", "ps|PS51299", "ps|PS51299", 
    "ps|PS51299", "ps|PS51299", "ps|PS51299", "ps|PS51299", "ps|PS51299", 
    "ps|PS51299", "ps|PS51299", "ps|PS51299", "ps|PS51299", "ps|PS51299", 
    "ps|PS51299", "ps|PS51299", "ps|PS51299", "ps|PS51301"), 
    start = c(6, 270, 270, 389, 17, 328, 328, 447, 9, 266, 266, 
    387, 83, 321, 321, 441, 90, 442, 442, 561, 17, 409, 409, 
    529, 6, 250, 250, 369, 7, 245, 245, 364, 56, 397, 397, 538, 
    43, 344, 344, 465, 9, 260, 260, 100, 440, 50, 396, 396, 536, 
    163, 590, 715, 14, 268, 268, 390, 114, 477, 477, 618, 6, 
    236, 236, 351, 5, 394, 394, 512, 8, 247, 247, 368, 37, 520, 
    520, 635, 641, 66, 356, 356, 483, 129, 186, 116, 414, 36, 
    233, 318, 465, 48, 35, 4, 273, 38, 66, 62, 103, 64, 125, 
    101, 26, 62, 34, 282, 1, 105, 7), end = c(112, 302, 426, 
    421, 123, 360, 479, 479, 115, 298, 424, 419, 192, 353, 473, 
    473, 196, 474, 598, 593, 125, 441, 561, 561, 112, 282, 406, 
    401, 113, 277, 401, 396, 163, 429, 580, 570, 149, 376, 511, 
    497, 115, 292, 302, 207, 516, 161, 428, 568, 568, 269, 747, 
    747, 123, 300, 422, 422, 222, 509, 650, 650, 112, 268, 268, 
    394, 111, 426, 549, 544, 115, 279, 400, 400, 147, 552, 552, 
    678, 673, 173, 382, 515, 515, 235, 292, 222, 520, 148, 339, 
    424, 474, 160, 147, 111, 380, 147, 176, 169, 221, 176, 241, 
    219, 145, 178, 148, 395, 62, 267, 110)), .Names = c("id", 
"proteinID", "featureID", "start", "end"), row.names = c(NA, 
107L), class = "data.frame"), feature = structure(list(id = c("ps|PS51299", 
"ps|PS50088", "ps|PS50297", "ps|PS00152", "ps|PS51301"), def = c("HTH_APSES", 
"ANK_REPEAT", "ANK_REP_REGION", "ATPASE_ALPHA_BETA", "KILA_N"
)), .Names = c("id", "def"), row.names = c(NA, 5L), class = "data.frame")), .Names = c("version", 
"taxonomy", "protein", "proteinFeature", "feature"))
	
	cat("\nLoaded \"refDB\" reference database object\n")
}


# ====  MESSAGE ============================================

cat("\n")


# ====  TESTS  =============================================

# TBD



# [END]