# Append this to your ~/.nedit file in the Background Menu Section
# ie after this heading (uncommented of course)

# nedit.bgMenuCommands: \

tacg>LinMap  Opts rebase mag # frames2cotranslate
#1st grab the current selection
buf = get_selection()

# want a different pattern file?
patfile = string_dialog("Pattern File? [rebase.data]", "OK" )  
if (patfile == "") patfile = "rebase.data"

# what magnitude of recog site?
n = dialog("Magnitude?", "4", "5", "6", "8") 
if (n == "1") mag = "4"
else if (n == "2")  mag = "5"
else if (n == "3")  mag = "6"
else if (n == "4")  mag = "8"

# what frames to cotranslate?
cotr = dialog("Frames to Cotranslate?", "None", "1F", "3F", "6F")  
if (cotr == 1) frames = " "
else if (cotr == 2) frames = " -T1,1 "
else if (cotr == 3) frames = " -T3,1 "
else if (cotr == 4) frames = " -T6,1 "

# build the command
cmd = "/usr/local/bin/tacg3 -Ls -n" mag frames " --raw -R " patfile

# and execute it
answer = shell_command(cmd, buf)

if (length(answer) == 0) {
   dialog("Command Failed!\n\n" cmd "\n\n", "OK")
} else {
   # Put the result into a new NEdit window
   new()
   focus_window("last")
   insert_string(answer)
}

===========================================================================

tacg>LadMap mag width? sorting 
#1st grab the current selection
buf = get_selection()

# want a different pattern file?
patfile = string_dialog("Pattern File? [rebase.data]", "OK" )  
if (patfile == "") patfile = "rebase.data"

# what magnitude of recog site?
n = dialog("Magnitude? [4]", "4", "5", "6", "8") 
if (n == "1") mag = "4"
else if (n == "2")  mag = "5"
else if (n == "3")  mag = "6"
else if (n == "4")  mag = "8"

# how wide do you want it?
width = dialog("Width? [60]", "60", "90", "120", "150")  
if (width == 1) wid = " -w 60 "
else if (width == 2) wid = " -w 90 "
else if (width == 3) wid = " -w 120 "
else if (width == 4) wid = " -w 150 "

# sorting?
sort = dialog("StriderSort? [Y]", "Yes", "No")  
if (sort == 1) SS = " -c "
else SS = " "

# build the command
cmd = "/usr/local/bin/tacg3 -l -n" mag SS wid " --raw -R " patfile

# and execute it
answer = shell_command(cmd, buf)

if (length(answer) == 0) {
   dialog("Command Failed!\n\n" cmd "\n\n", "OK")
} else {
   # Put the result into a new NEdit window
   new()
   focus_window("last")
   insert_string(answer)
}

===========================================================================

tacg>Translate frames to translate  xtrainfo  minorflength
#1st grab the current selection
buf = get_selection()

# How many frames to translate and search for ORFs?
opt = string_dialog("Frames to Translate? (####)[1]", "OK" )  
if (opt == "") f2t = "1"
else f2t = opt

# Need the extra 3 lines of AA stats?
opt = dialog("3 Extra Info lines? [Y]", "Yes", "No") 
if (opt == "1") xtra = "x"
else xtra = ""

# Minimum ORF length?
opt = string_dialog("Minimum ORF length? [50 AAs]", "OK" )  
if (opt == "") mol = "50"
else mol = opt

# how wide do you want it?
width = dialog("Width? [60]", "60", "90", "120", "150")  
if (width == 1) wid = " -w 60 "
else if (width == 2) wid = " -w 90 "
else if (width == 3) wid = " -w 120 "
else if (width == 4) wid = " -w 150 "


# build the command
cmd = "/usr/local/bin/tacg3 --raw -O" f2t xtra "," mol wid

# and execute it
answer = shell_command(cmd, buf)

if (length(answer) == 0) {
   dialog("Command Failed!\n\n" cmd "\n\n", "OK")
} else {
   # Put the result into a new NEdit window
   new()
   focus_window("last")
   insert_string(answer)
}


===========================================================================

tacg>IUPACSrch set name to Tmp pattern, # errors(buttons)

#1st grab the current selection
buf = get_selection()

# What's the pattern to search for?
pat = string_dialog("IUPAC Pattern? (<30bp)", "OK" )  

# How many errors to allow?
opt = dialog("How many Errors to allow? [0]", "0", "1", "2", "3")  
if (opt == 1) err = "0"
else if (opt == 2) err = "1"
else if (opt == 3) err = "2"
else if (opt == 4) err = "3"

# Sites?
opt = dialog("Sites? [Y]", "Yes", "No") 
if (opt == 1) sites = " -S "
else sites = ""

# Ladder Map
opt = dialog("Ladder Map? [Y]", "Yes", "No") 
if (opt == 1) lad = " -l "
else lad = ""

# how wide do you want it?
width = dialog("Width? [60]", "60", "90", "120", "150")  
if (width == 1) wid = " -w 60 "
else if (width == 2) wid = " -w 90 "
else if (width == 3) wid = " -w 120 "
else if (width == 4) wid = " -w 150 "


# build the command
cmd = "/usr/local/bin/tacg3 --raw -pPat," pat "," err  wid lad sites

# and execute it
answer = shell_command(cmd, buf)

if (length(answer) == 0) {
   dialog("Command Failed!\n\n" cmd "\n\n", "OK")
} else {
   # Put the result into a new NEdit window
   new()
   focus_window("last")
   insert_string(answer)
}
===========================================================================

tacg>RegexSrch set name to Tmp pattern, # errors(buttons)

#1st grab the current selection
buf = get_selection()

# What's the pattern to search for?
pat = string_dialog("Regex Pattern?", "OK" )  

# Sites?
opt = dialog("Sites? [Y]", "Yes", "No") 
if (opt == 1) sites = " -S "
else sites = ""

# Ladder Map
opt = dialog("Ladder Map? [Y]", "Yes", "No") 
if (opt == 1) lad = " -l "
else lad = ""

# how wide do you want it?
width = dialog("Width? [60]", "60", "90", "120", "150")  
if (width == 1) wid = " -w 60 "
else if (width == 2) wid = " -w 90 "
else if (width == 3) wid = " -w 120 "
else if (width == 4) wid = " -w 150 "


# build the command
cmd = "/usr/local/bin/tacg3 --raw -r'Regex:" pat "'"  wid lad sites

# and execute it
answer = shell_command(cmd, buf)

if (length(answer) == 0) {
   dialog("Command Failed!\n\n" cmd "\n\n", "OK")
} else {
   # Put the result into a new NEdit window
   new()
   focus_window("last")
   insert_string(answer)
}

===========================================================================

tacg>Combined IUPAC/Regex Srch set name to Tmp pattern, # errors(buttons)

#1st grab the current selection
buf = get_selection()

# What's the pattern to search for?
## All that the Regex search wants
pat = string_dialog("Regex Pattern?", "IUPAC", "Regex" )  
# now eval is it's a IUPAC or Regex search
if ($string_dialog_button == 1) stype = "I"
else stype = "R"

if (stype == "R") {
	# if it's a regex search, that's all we need
	search = " -r 'Regex:" pat "' "
} else {
   # How many errors to allow?
   opt = dialog("How many Errors to allow? [0]", "0", "1", "2", "3")  
   if (opt == 1) err = "0"
   else if (opt == 2) err = "1"
   else if (opt == 3) err = "2"
   else if (opt == 4) err = "3"
	
   #and now build the entire search term
   search = " -pIUPAC," pat ",err " 
}

# Sites?
opt = dialog("Sites? [Y]", "Yes", "No") 
if (opt == 1) sites = " -S "
else sites = ""

# Ladder Map
opt = dialog("Ladder Map? [Y]", "Yes", "No") 
if (opt == 1) lad = " -l "
else lad = ""

#Linear Map
opt = dialog("Linear Map? [N]", "No", "Yes") 
if (opt == 1) lin = ""
else lin = " -L "

# how wide do you want it?
width = dialog("Width? [60]", "60", "90", "120", "150")  
if (width == 1) wid = " -w 60 "
else if (width == 2) wid = " -w 90 "
else if (width == 3) wid = " -w 120 "
else if (width == 4) wid = " -w 150 "


# build the command
cmd = "/usr/local/bin/tacg3 --raw " search  wid lad lin sites

# and execute it
answer = shell_command(cmd, buf)

if (length(answer) == 0) {
   dialog("Command Failed!\n\n" cmd "\n\n", "OK")
} else {
   # Put the result into a new NEdit window
   new()
   focus_window("last")
   insert_string(answer)
}