DATASET_DOMAINS
#Protein domain datasets are visualized as schematic representations of proteins, with a protein backbone and various shapes depicting the locations of individual domains

#lines starting with a hash are comments and ignored during parsing

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#                    MANDATORY SETTINGS                           #
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#select the separator which is used to delimit the data below (TAB,SPACE or COMMA).This separator must be used throughout this file.
#SEPARATOR TAB
#SEPARATOR SPACE
SEPARATOR COMMA

#label is used in the legend table (can be changed later)
DATASET_LABEL,label1

#dataset color (can be changed later)
COLOR,#ff0000

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#                    OPTIONAL SETTINGS                            #
#=================================================================#

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#     all other optional settings can be set or changed later     #
#           in the web interface (under 'Datasets' tab)           #
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#dataset scale: you can simply set the values where the scale will be drawn
#DATASET_SCALE,100,200,1000
#or you can specify value, label, color, width, style and label size factor for each scale line (dash separated, format: VALUE-LABEL-COLOR-WIDTH-DASHED-LABEL_SCALE_FACTOR))
#DATASET_SCALE,100-amino acid 100-#0000ff-5-1-1,200-line at aa200-#ff0000-1-0-2,1000-3rd aa line-#00ff00-5-1-1

#Each dataset can have a legend, which is defined using LEGEND_XXX fields below
#For each row in the legend, there should be one shape, color and label.
#Optionally, you can define an exact legend position using LEGEND_POSITION_X and LEGEND_POSITION_Y. To use automatic legend positioning, do NOT define these values
#Optionally, shape scaling can be present (LEGEND_SHAPE_SCALES). For each shape, you can define a scaling factor between 0 and 1.
#To order legend entries horizontally instead of vertically, set LEGEND_HORIZONTAL to 1
#Shape should be a number between 1 and 6, or any protein domain shape definition (RE, HH, HV...).
#1: square
#2: circle
#3: star
#4: right pointing triangle
#5: left pointing triangle
#6: checkmark

#LEGEND_TITLE,Dataset legend
#LEGEND_SCALE,1
#LEGEND_POSITION_X,100
#LEGEND_POSITION_Y,100
#LEGEND_HORIZONTAL,0
#LEGEND_SHAPES,1,2,3
#LEGEND_COLORS,#ff0000,#00ff00,#0000ff
#LEGEND_LABELS,value1,value2,value3
#LEGEND_SHAPE_SCALES,1,1,0.5

#maximum width
#WIDTH,1000

#always show internal values; if set, values associated to internal nodes will be displayed even if these nodes are not collapsed. It could cause overlapping in the dataset display.
#SHOW_INTERNAL,0

#show dashed lines between leaf labels and the dataset
#DASHED_LINES,1

#left margin, used to increase/decrease the spacing to the next dataset. Can be negative, causing datasets to overlap.
#MARGIN,0

#protein height factor; Default height of each domain will be slightly less than the available space between leaves, but you can set a multiplication factor here to increase/decrease it (values from 0 to 1 will decrease it, values above 1 will increase it)
#HEIGHT_FACTOR,1

#proteins are aligned to the node lines by default. Using BAR_SHIFT, you can move them all up/down by a fixed amount
#BAR_SHIFT,0

#display or hide the text labels for each domain
#SHOW_DOMAIN_LABELS,1

#set the size factor for the text labels
#LABEL_SIZE_FACTOR,1

#with LABELS_ON_TOP set to 0, label text which does not fit into the shape will be hidden
#LABELS_ON_TOP,0

#color of the background rectangle representing the protein amino acid backbone
#BACKBONE_COLOR,#aaaaaa

#height of the background rectangle representing the protein amino acid backbone (in pixels)
#BACKBONE_HEIGHT,10

#border width; if set above 0, a border of specified width (in pixels) will be drawn around the domain shapes
#BORDER_WIDTH,0

#border color; used when BORDER_WIDTH is above 0
#BORDER_COLOR,#0000ff


#domains can be filled with solid color, or a gradient
#GRADIENT_FILL,1

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#       Actual data follows after the "DATA" keyword              #
#=================================================================#
#Internal tree nodes can be specified using IDs directly, or using the 'last common ancestor' method described in iTOL help pages
DATA
#Each node can have one protein definition assigned, with total protein length defined in field 2, followed by an unlimited number of domain definitions
#Each domain definition consists of 5 parts, separated with vertical lines:
#SHAPE|START|END|COLOR|LABEL

#there are 13 different possible shapes:
#RE  rectangle
#HH  horizontal hexagon
#HV  vertical hexagon
#EL  ellipse
#DI  rhombus (diamond)
#TR  right pointing triangle
#TL  left pointing triangle
#PL  left pointing pentagram
#PR  right pointing pentagram
#PU  up pointing pentagram
#PD  down pointing pentagram
#OC  octagon
#GP  rectangle (gap; black filled rectangle with 1/3 normal height)

#for example, a 1200 amino acid protein with 3 domains, displayed on node 9606:
#red colored rectangle representing a SH2 domain at positions 100 - 150
#blue colored ellipse representing a SH3 domain at positions 400 - 500
#green colored octagon representing a PH domain at positions 700 - 900
#9606,1200,RE|100|150|#ff0000|SH2,EL|400|500|#0000ff|SH3,OC|700|900|#00ff00|PH