GSS Document Selectors - phac-nml/gview-wiki GitHub Wiki
Overview
| Selector | Property | Property Value Type |
|---|---|---|
| background | color | color |
| backbone | color | color |
| thickness | real >= 0 | |
| backbone-effect | feature-effect | |
| slot | spacing | real >= 0 |
| slot#slot_number | thickness | real >= 0 |
| tooltip-text | text-extractor | |
| hyperlink | text-extractor | |
| feature-shape | shape | |
| feature-effect | shape-effect | |
| property-mapper | continuous-map or discrete-map | |
| color | color | |
| tooltip | text-color | color |
| outline-color | color | |
| background-color | color | |
| font | font | |
| ruler | major-tick-color | color |
| minor-tick-color | color | |
| label-color | color | |
| label-background-color | color | |
| label-font | font | |
| major-tick-length | real >= 0 | |
| minor-tick-length | real >= 0 | |
| tick-density | real in [0,1] | |
| tick-thickness | real >= 0 | |
| tick-padding | real >= 0 | |
| tick-effect | shape-effect | |
| label-location | none, above, below or all | |
| FeatureSet#set_name | color | color |
| thickness-proportion | real in [0,1] | |
| feature-effect | shape-effect | |
| feature-shape | shape | |
| property-mapper | continuous-map or discrete-map | |
| tooltip-text | text-extractor | |
| hyperlink | text-extractor | |
| link | alpha-numeric string | |
| labels | text-color | color |
| background-color | color | |
| font | font | |
| label-extractor | text-extractor | |
| show-labels | boolean | |
| plot | color | color |
| colors | colors | |
| data | plot-file, plot-calculator | |
| type | bar, line, center | |
| grid-lines | integer >= 0 | |
| grid-color | color | |
| legend#legendId | background-color | color |
| border-color | color | |
| text-color | color | |
| text-font | font | |
| alignment | legend-alignment | |
| legenditem#legendItemId | show-swatch | boolean |
| swatch-color | color | |
| text-color | color | |
| text-font | font | |
| legend-text | string | |
| link | alpha-numeric string | |
| FeatureFilter | setName | feature-filter |
Background
Description
The background selector defines style information about the background on which the map is drawn.
Properties
| Property | Property Description | Property Value Type |
|---|---|---|
| color | The color of the background | color |
Example
background
{
color: color("white"); /* white color for background */
}
Backbone
Description
The backbone selector defines style information about the backbone item (the centre ribbon) of the genome map.
Properties
| Property | Property Description | Property value type |
|---|---|---|
| color | The color of the backbone ribbon | color |
| thickness | The thickness of the backbone ribbon | real >= 0 |
| backbone-effect | The effect used to draw the backbone ribbon | feature-effect |
Example
backbone
{
color : color("gray");
thickness : 5.0;
backbone-effect : shape-effect("basic");
}
Slot
Description
The slot selector defines information for the slots on a genome map. Each slot is a different track along the backbone. Tracks are stacked on top of each other, and can display information such as sequence features, or plots.
Defining the Slot
A slot is selected by specifying an id which describes the slot. For example slot#1 specifies that this selector applies only to slot number 1 which is the first slot above the backbone ribbon.Selecting slot#-1 specifies that this selector applies only to slot number -1 which is the first slot below the backbone ribbon.
If no id is specified, then the selector applies globally to all slots.
Global Properties
| Property | Property Description | Property Value Type |
|---|---|---|
| spacing | The spacing between slots | real >= 0 |
Properties for a Particular Slot
| Property | Property Description | Property value type |
|---|---|---|
| thickness | The thickness of the slot | real >= 0 |
| tooltip-text | Defines how to extract the text for displaying in a tooltip for the features in this slot. Can be overridden by child FeatureSet selectors. | text-extractor |
| hyperlink | Defines how to extract the text for defining a hyperlink for features in this slot. Can be overridden by child FeatureSet selectors. | text-extractor |
| feature-shape | The shape to use when drawing the features in this slot. Can be overridden by child FeatureSet selectors. | shape |
| feature-effect | The effect to use when drawing the features in this slot. Can be overridden by child FeatureSet selectors. | shape-effect |
| property-mapper | The property mapper to use when for any features within this slot. Can be overridden by child FeatureSet selectors. | continuous-map or discrete-map |
| color | The color used when drawing the features in this slot. Can be overridden by child FeatureSet selectors. | color |
Examples
slot /* defines styles for all slots */
{
spacing: 10.0; /* how spaced out the slots are from each other */
}
slot#-1 /* defines style information for the slot number -1 */
{
color : color("red");
thickness : 35.0;
feature-shape : shape("basic");
feature-effect : shape-effect("basic");
property-mapper : continuous-map(score(90,100), opacity);
hyperlink : text-extractor(stringbuilder("http:_www.ncbi.nlm.nih.gov/protein/%s",annotation("protein_id")));
}
Tooltip
Description The tooltip selector defines how the tooltip item should be displayed for the interactive view of the genome map.
Properties
| Property | Property Description | Property Value Type |
|---|---|---|
| text-color | The color of the text in the tooltip text box | color |
| outline-color | The color of the outlining border of the tooltip text box | color |
| background-color | The color of the background of the tooltip text box | color |
| font | The font of the tooltip text | font |
Example
tooltip
{
text-color : color("black");
outline-color : color(0,0,0,128);
background-color : color(134,134,255,255);
font : font("SansSerif","plain",12);
}
Ruler
Description
The ruler selector defines how the ruler on the map is styled. This includes the tick marks and the ruler labels displaying the base pair position on the genome.
Properties
| Property | Property Description | Property value type |
|---|---|---|
| major-tick-color | The color of the major tick marks | color |
| minor-tick-color | The color of the minor tick marks | color |
| label-color | The color of the ruler labels | color |
| label-background-color | The color of the background of the label text box | color |
| label-font | The font of the ruler labels | font |
| major-tick-length | The length of the major tick marks | real >= 0 |
| minor-tick-length | The length of the minor tick marks | real >= 0 |
| tick-density | The density of the labels ranging from 0 (least dense) to 1 (most dense) | real in [0,1] |
| tick-thickness | The thickness of the ruler labels | real >= 0 |
| tick-padding | The padding or spacing to put in between the ruler tick marks and the feature slots | real >= 0 |
| tick-effect | The effect to apply to the tick mark shapes | shape-effect |
| label-location | The placement of ruler labels, relative to the ruler |
Example
ruler
{
major-tick-color : color("black");
minor-tick-color : color("black");
label-color : color("black");
label-background-color : color(“white”);
major-tick-length : 15.0;
minor-tick-length : 5.0;
tick-density : 1.0;
tick-thickness : 2.0;
tick-padding : 10.0;
label-font : font("SansSerif","bold",12);
label-location : "below";
}
FeatureSet
Description
The FeatureSet selector defines how a set of features is displayed. This selector must be a descendant of a slot selector or a FeatureSet selector. If it is a descendant from a slot selector, the FeatureSet defines how the set of features is styled within a particular slot. If the FeatureSet is a descendant of another FeatureSet selector, it will override any style information provided by the parent FeatureSet for this subset of the features.
Defining the Set
A FeatureSet is defined by specifying an “id” which will describe the set. FeatureSet#set1 specifies that the selector applies to all features defined in “set1”. The set set1 is defined in the FeatureFilter structure.
Properties
| Property | Property Description | Property Value Type |
|---|---|---|
| color | The color used to display features in this set | color |
| thickness-proportion | The thickness of the features in this set, provided as a ratio to the thickness of the parent slot | real in [0,1] |
| feature-effect | The effect to be applied when drawing the shape of the feature | shape-effect |
| feature-shape | The shape to draw to represent the feature | shape |
| property-mapper | The property mapper to use for the features. These style properties may override some other style properties (for example color). | continuous-map or discrete-map |
| tooltip-text | The text to display in the tooltip for the feature | text-extractor |
| hyperlink | A definition of how to construct a hyperlink to follow when a user clicks on a feature using Ctrl+Alt+Click or Middle Mouse Click. | text-extractor |
| link | The unique legend link group to associate the set with. | alpha-numeric string |
Example
slot#1 FeatureSet#set1
{
color : color("blue");
thickness-proportion : 1.0;
feature-effect : shape-effect("null");
feature-shape : shape("clockwise-arrow");
property-mapper : continuous-map(score(90,100), opacity);
tooltip-text : text-extractor(annotation("product"));
hyperlink : text-extractor(stringbuilder("http://www.ncbi.nlm.nih.gov/protein/%s",annotation("protein_id")));
link : "1";
}
FeatureFilter
Description
The FeatureFilter selector is used to define sets of features to display. These sets are defined by specifying a set name, and the method of filtering out features that belong in the set. The syntax for defining a set is as follows:
FeatureFilter
{
setname : feature-filter(filter definition);
}
Set Name
The set name can be any valid string.This same name is used later on in the GSS file under FeatureSet to refer to this particular set of features. For example: set1, myset, positive are all valid set names.
Filter Definition
The filter definition defines the method of filtering out valid features to include in this set.These can consist of a number of different filter functions.More information can be found in the filter definitions section.
Example
FeatureFilter
{
/* Defines a set of features, in this case all negative stranded features */
set0 : feature-filter(strand("negative"));
/* Defines a set of features, in this case all CDS features on the positive strand */
set1 : feature-filter(and(type("CDS"), strand("positive")));
}
Labels
Description
The labels selector defines how labels for features drawn on the map will be displayed. The labels selector must be a descendant of a FeatureSet selector, and defines how labels for the features in the parent set will be displayed.
Properties
| Property | Property Description | Property Value Type |
|---|---|---|
| text-color | The color of the label text | color |
| background-color | The background color of label text boxes | color |
| font | The label font | font |
| label-extractor | Defines the text to display in the label | text-extractor |
| show-labels | Defines visibility of labels in the parent feature set | boolean |
Example
slot#-1 labels
{
text-color : color("red");
background-color : color(255,255,255,200);
font : font("SansSerif","plain",14);
label-extractor : text-extractor(annotation("product"));
show-labels : "true";
}
Plot
Description
The plot selector defines how data plots are to be drawn around the sequence. This selector must be a descendant of a slot selector, and defines the plot that will be drawn in a slot (see the example). If the plot type selected is a GC Skew plot, the data for the plot will be generated by GView. For any other type of plot, the data for the plot points will be taken from a Comma Separated Values (CSV) file that must be supplied. See the plot-file property for more details.
Properties
| Property | Property Description | Property value type |
|---|---|---|
| color | The color of the plot data | color |
| colors | An array of colors (for defining multiple colors for certain plots). | colors |
| data | The file and file type of the data file | plot-file, plot-calculator Deprecated: Use plot-calculator("gcContent") or plot-calculator("gcSkew") instead. gcContent,gcSkew |
| type | The type of plot to draw | bar, line, center |
| grid-lines | The number of horizontal grid lines to draw in the plot | integer >= 0 |
| grid-color | The color of the grid lines | color |
Examples
Sample GSS file:
slot#-1 plot
{
color : color("black");
grid-color : color("gray");
grid-lines : 5;
type : line;
data : plot-file("point", "plot-point.csv");
}
Sample CSV file:
50000,0.45
100000,0.45
150000,0.88
200000,0.72
250000,0.79
Sample GSS File 2:
slot#1
{
thickness : 25;
}
slot#1 plot
{
/* Colors for the plot of type "center". The first color is the color above the average gc content */
/* The second color is the color below the average gc convent. */
colors : colors(color("red"), color("blue"));
grid-color : color("gray");
grid-lines : 5;
type : center;
data : plot-calculator("gcContent"); /* Calculates data internally from the average gc content of the input data file */
}
Sample GSS File 3:
slot#1
{
thickness : 25;
}
slot#1 plot
{
/* Colors for the plot of type "center". The first color is the color above the average gc skew */
/* The second color is the color below the average gc skew. */
colors : colors(color("red"), color("blue"));
grid-color : color("gray");
grid-lines : 5;
type : center;
data : plot-calculator("gcSkew"); /* Calculates data internally from the average gc skew of the input data file */
}
Legend
Description
The legend selector defines how a particular legend is to be displayed. A legend consists of a group of text to display on the screen. An individual text box can be defined/styled by giving a particular "id" to the legend selector. Multiple legend text boxes can be styled by using a different "id" for each box. The text to go within the legend is styled using a legenditem selector, which is a descendant of the legend selector.
Properties
| Property | Property Description | Property Value Type |
|---|---|---|
| background-color | The color used as a background for the legend text box. | color |
| border-color | The color used for a border around the legend text box. | color |
| text-color | The default text color in this legend text box. | color |
| text-font | The default font in this legend text box. | font |
| alignment | The alignment of the legend text box. | One of (upper-left, upper-center, upper-right, middle-left, middle-center, middle-right, lower-left, lower-center, lower-right) |
Example
legend#0 /** Defines style information for a legend text box with id=0 **/
{
background-color : color(255,255,255,200);
border-color : color("black");
text-color : color("black");
text-font : font("SansSerif", "bold", 14);
alignment : upper-right;
}
Legend Items
Description
The legenditem selector defines how a particular piece of text is to be displayed on the legend. This selector must be a descendant of the legend selector defining the style of the text box. Multiple legend items can be styled by changing the "id" of the legend item.
Properties
| Property | Property Description | Property Value Type |
|---|---|---|
| text-color | The color used for the text, overrides the color in the parent legend selector. | color |
| swatch-color | The color used for the swatch to display, used for matching this legend item to any features of the same color. | color |
| show-swatch | Whether we should show the swatch for this legend text or not. | boolean |
| legend-text | The text to display for this legend | string |
| link | The unique legend link group to associate the legend item with. | alpha-numeric string |
Example
legend#0 legenditem#0 /** Defines style information for text item with id=0 under legend with id=0 **/
{
show-swatch : "false";
text-color : color("black");
text-font : font("SansSerif", "bold", 24);
legend-text : "Text for legend item 0";
link : "1";
}
legend#0 legenditem#1 /** Defines style information for text item with id=1 under legend with id=0 **/
{
show-swatch : "true";
swatch-color : color("red");
text-color : color("black");
text-font : font("SansSerif", "plain", 18);
legend-text : "Text for legend item 1";
link : "2";
}