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23 changes: 23 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -153,6 +153,29 @@ annotations = [

In the example above, the "Strong promoter" would span the first to twenty-second base pair.

Optional Annotation Parameters:
- Annotation border styling; user can customize border style and border color:
```js
annotations = [
{ start: 0, end: 22, name: "Strong promoter", direction: 1, border: {style: "dashed", borderColor: 'purple'},
];
```
- Annotation font styling; user can change font family, font weight, or font color:
```js
annotations = [
{ start: 0, end: 22, name: "Strong promoter", direction: 1, border: "dashed", font: {fontFamily: "Times New Roman", fontWeight: 800, fontSize: 17, fontColor: 'blue'}},
];
```
- Adding an svg icon to annotation: WIP

- Annotation background color gradient. User can enter a starting color and stopping color:
```js
annotations = [
{ start: 0, end: 22, name: "Strong promoter", direction: 1, border: "dashed", font: {fontFamily: "Times New Roman", fontWeight: 800, fontSize: 17, fontColor: 'blue'}},
svg: 'promoter', gradient: {start: 'lightblue', stop: 'green'}
];
```

#### `primers (=[])`

An array of `Primer`s to render. Each `Primer` requires 0-based start (inclusive) and end (exclusive) indexes. `name`s are rendered on top of the primers. Set the primer's direction to `1` for forward primer and `-1` for reverse primer.
Expand Down
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63 changes: 58 additions & 5 deletions src/Linear/Annotations.tsx
Original file line number Diff line number Diff line change
Expand Up @@ -182,7 +182,15 @@ const SingleNamedElement = (props: {
}

// 0.591 is our best approximation of Roboto Mono's aspect ratio (width / height).
const fontSize = 12;
let fontSize = 12;
if (element.font?.fontSize) {
// 19 is a subjective limit to fontSize that will fit inside bounds of annotation. If larger than 19, cap it.
if (element.font.fontSize > 19) {
fontSize = 19;
} else {
fontSize = element.font.fontSize;
}
}
const annotationCharacterWidth = 0.591 * fontSize;
const availableCharacters = Math.floor((width - 40) / annotationCharacterWidth);

Expand All @@ -198,10 +206,53 @@ const SingleNamedElement = (props: {
}
}

let strokeVal: string | null = null;
let strokeWidth: string | null = null;

if (element.border?.style) {
switch (element.border.style) {
case "dashed":
strokeVal = "5, 5";
break;
case "dotted":
strokeVal = "1, 5";
break;
case "bold":
strokeWidth = "2";
break;
}
}
let borderColor: string | null = null;
if (element.border?.borderColor) {
borderColor = element.border.borderColor;
}

let fontFamily: string | undefined = undefined;
let fontWeight: number = 400;
let fontColor: string = "rgb(42, 42, 42)";

if (element.font?.fontFamily) {
fontFamily = element.font.fontFamily;
}
if (element.font?.fontWeight) {
fontWeight = element.font.fontWeight;
}
if (element.font?.fontColor) {
fontColor = element.font.fontColor;
}

return (
<g id={element.id} transform={`translate(${x}, ${0.1 * height})`}>
{/* <title> provides a hover tooltip on most browsers */}
<title>{name}</title>
{element.gradient && (
<defs>
<linearGradient id="myGradient" x1="0%" y1="0%" x2="100%" y2="100%">
<stop offset="0%" stop-color={element.gradient.start} />
<stop offset="100%" stop-color={element.gradient.stop} />
</linearGradient>
</defs>
)}
<path
ref={inputRef(element.id, {
end: end,
Expand All @@ -214,10 +265,12 @@ const SingleNamedElement = (props: {
className={`${element.id} la-vz-annotation`}
cursor="pointer"
d={linePath}
fill={color}
fill={element.gradient ? "url(#myGradient)" : color}
id={element.id}
stroke={color ? COLOR_BORDER_MAP[color] || darkerColor(color) : "gray"}
style={annotation}
stroke={borderColor ? borderColor : color ? COLOR_BORDER_MAP[color] || darkerColor(color) : "gray"}
style={{ annotation }}
stroke-dasharray={strokeVal}
stroke-width={strokeWidth}
onBlur={() => {
// do nothing
}}
Expand All @@ -233,7 +286,7 @@ const SingleNamedElement = (props: {
dominantBaseline="middle"
fontSize={fontSize}
id={element.id}
style={annotationLabel}
style={{ ...annotationLabel, fontFamily, fontWeight, fill: fontColor }}
textAnchor="middle"
x={width / 2}
y={height / 2 + 1}
Expand Down
23 changes: 23 additions & 0 deletions src/elements.ts
Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,34 @@ export interface NameRange extends Range {
color?: string;
id: string;
name: string;
border?: Border;
font?: Font;
gradient?: Gradient;
}

interface Font {
fontFamily?: string;
fontSize?: number;
fontWeight?: number;
fontColor?: string;
}

interface Border {
style?: "dashed" | "dotted" | "bold";
borderColor?: string;
}

interface Gradient {
start: string;
stop: string;
}

/** AnnotationProp is an annotation provided to SeqViz via the annotations prop. */
export interface AnnotationProp {
color?: string;
border?: Border;
font?: Font;
gradient?: Gradient;
direction?: number | string;
end: number;
name: string;
Expand Down
9 changes: 6 additions & 3 deletions src/style.ts
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,6 @@ export const svgText: CSS.Properties = {
MozUserSelect: "none",
WebkitUserSelect: "none",
background: "none",
fill: "rgb(42, 42, 42)",
fontFamily: "Roboto Mono, Monaco, monospace",
msUserSelect: "none",
userSelect: "none",
Expand Down Expand Up @@ -98,8 +97,6 @@ export const annotation: CSS.Properties = {

export const annotationLabel: CSS.Properties = {
...svgText,
color: "rgb(42, 42, 42)",
fontWeight: 400,
shapeRendering: "geometricPrecision",
strokeLinejoin: "round",
textRendering: "optimizeLegibility",
Expand Down Expand Up @@ -151,3 +148,9 @@ export const seqBlock: CSS.Properties = {
padding: 0,
width: "100%",
};

export const iconStyle: CSS.Properties = {
width: "25px",
height: "25px",
zIndex: 100,
};
2 changes: 1 addition & 1 deletion webpack.config.js
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ const cdnBuild = {
module: {
rules: [
{ test: /\.(t|j)sx?$/, loader: "ts-loader", exclude: /node_modules/ },
{ test: /\.js$/, enforce: "pre", loader: "source-map-loader", exclude: /node_modules/ },
{ test: /\.js$/, enforce: "pre", loader: "source-map-loader", exclude: /node_modules/ }
],
},
optimization: {
Expand Down