appl: prettyplot [
  documentation: "Displays aligned sequences, with colouring and boxing"
  groups: "Alignment:Multiple, Display"
]

section: input [ info: "input Section" type: page ]
seqset: msf  [
  parameter: "Y"
  type: "gapany"
  information: "Sequences file to be read in"
  help: "File containing a sequence alignment"
]

endsection: input

section: advanced [ info: "advanced Section" type: page ]
integer: residuesperline  [
  optional: "Y"
  default: "50"
  information: "Number of residues to be displayed on each line"
  help: "The number of residues to be displayed on each line"
]

integer: resbreak  [
  optional: "Y"
  minimum: "1"
  maximum: "$(residuesperline)"
  information: "Residues before a space"
  default: "$(residuesperline)"
  expected: "Same as -residuesperline to give no breaks"
]

bool: ccolours  [
  optional: "Y"
  default: "Y"
  information: "Colour residues by their consensus value."
]

string: cidentity  [
  optional: "Y"
  information: "Colour to display identical residues (RED)"
  default: "RED"
]

string: csimilarity  [
  optional: "Y"
  information: "Colour to display similar residues (GREEN)"
  default: "GREEN"
]

string: cother  [
  optional: "Y"
  information: "Colour to display other residues (BLACK)"
  default: "BLACK"
]

bool: docolour  [
  optional: "Y"
  information: "Colour residues by table oily, amide etc."
  default: "N"
]

bool: title  [
  optional: "Y"
  information: "Do not display the title"
  default: "Y"
]

string: shade  [
  optional: "Y"
  information: "shading"
  help: "Set to BPLW for normal shading \ so for pair = 1.5,1.0,0.5 and shade = BPLW \ Residues score Colour \ 1.5 or over....... BLACK (B) \ 1.0 to 1.5 ....... BROWN (P) \ 0.5 to 1.0 ....... WHEAT (L) \ under 0.5 ....... WHITE (W) \ The only four letters allowed are BPLW, in any order."
  default: ""
]

string: pair  [
  optional: "Y"
  information: "Values to represent identical similar related"
  default: "1.5,1.0,0.5"
]

integer: identity  [
  optional: "Y"
  information: "Only match those which are identical in all sequences."
  default: "0"
  minimum: "0"
]

bool: box  [
  optional: "Y"
  information: "Display prettyboxes"
  default: "Y"
]

bool: boxcol  [
  optional: "Y"
  information: "Colour the background in the boxes"
  default: "N"
]

string: boxcolval  [
  optional: "Y"
  information: "Colour to be used for background. (GREY)"
  default: "GREY"
]

bool: name  [
  optional: "Y"
  information: "Display the sequence names"
  default: "Y"
]

integer: maxnamelen  [
  optional: "Y"
  information: "Margin size for the sequence name."
  default: "10"
]

bool: number  [
  optional: "Y"
  information: "Display the residue number"
  default: "Y"
]

bool: listoptions  [
  optional: "Y"
  information: "Display the date and options used"
  default: "Y"
]

float: plurality  [
  optional: "Y"
  information: "Plurality check value (totweight/2)"
  default: "@( $(msf.totweight) / 2)"
  expected: "Half the total sequence weighting"
]

section: consensussection [ info: "consensus Section" type: frame ]
bool: consensus  [
  optional: "Y"
  information: "Display the consensus"
  default: "N"
]

bool: collision  [
  optional: "Y"
  information: "Allow collisions in calculating consensus"
  default: "Y"
]

integer: alternative  [
  optional: "Y"
  information: "Use alternative collisions routine"
  help: "Use alternative collisions routine \ 0) Normal collision check. (default) \ 1) checks identical scores with the max score found. So if any other residue matches the identical score then a collision has occurred. \ 2) If another residue has a greater than or equal to matching score and these do not match then a collision has occurred. \ 3) Checks all those not in the current consensus.If any of these give a top score for matching or identical scores then a collision has occured."
  default: "0"
  minimum: "0"
  maximum: "3"
]

matrix: matrixfile  [
  optional: "Y"
  information: "Matrix file"
  protein: "$(msf.protein)"
]

endsection: consensussection

integer: showscore  [
  optional: "Y"
  information: "Print residue scores"
  default: "-1"
]

bool: portrait  [
  optional: "Y"
  information: "Set page to Portrait"
  default: "N"
]

endsection: advanced

section: output [ info: "output Section" type: page ]
bool: data  [
  optional: "N"
  default: "N"
]

graph: graph  [
  required: "@(!$(data))"
]
endsection: output

