From 06c228ee9c6c29c052765fe7a842d40d48f4caee Mon Sep 17 00:00:00 2001
From: Nick Rosenau <nickrosenau@Nicks-MBP.lan>
Date: Mon, 27 Nov 2023 14:33:53 -0500
Subject: [PATCH] Upgrade annotation feature.

---
 README.md                                     |  29 ++++++++
 src/Linear/Annotations.tsx                    |  64 ++++++++++++++++--
 src/assets/aptamer.png                        | Bin 0 -> 691 bytes
 src/assets/assembly-scar.png                  | Bin 0 -> 224 bytes
 src/assets/association.png                    | Bin 0 -> 427 bytes
 src/assets/blunt-restriction-site.png         | Bin 0 -> 255 bytes
 src/assets/cds-arrow.png                      | Bin 0 -> 528 bytes
 src/assets/cds.png                            | Bin 0 -> 401 bytes
 src/assets/chromosomal-locus.png              | Bin 0 -> 611 bytes
 src/assets/circular-plasmid.png               | Bin 0 -> 470 bytes
 src/assets/complex-sbgn.png                   | Bin 0 -> 268 bytes
 src/assets/composite.png                      | Bin 0 -> 296 bytes
 src/assets/control.png                        | Bin 0 -> 273 bytes
 src/assets/degradation.png                    | Bin 0 -> 478 bytes
 src/assets/dissociation.png                   | Bin 0 -> 781 bytes
 src/assets/dna-stability-element.png          | Bin 0 -> 415 bytes
 src/assets/dsNA.png                           | Bin 0 -> 388 bytes
 src/assets/engineered-region.png              | Bin 0 -> 266 bytes
 src/assets/five-prime-overhang.png            | Bin 0 -> 213 bytes
 .../five-prime-sticky-restriction-site.png    | Bin 0 -> 267 bytes
 src/assets/generic-sbgn.png                   | Bin 0 -> 567 bytes
 src/assets/halfround-rectangle.png            | Bin 0 -> 378 bytes
 src/assets/inert-dna-spacer.png               | Bin 0 -> 720 bytes
 src/assets/inhibition.png                     | Bin 0 -> 204 bytes
 src/assets/insulator.png                      | Bin 0 -> 399 bytes
 src/assets/intron.png                         | Bin 0 -> 788 bytes
 src/assets/location-dna-no-top.png            | Bin 0 -> 201 bytes
 src/assets/location-dna.png                   | Bin 0 -> 565 bytes
 src/assets/location-protein-no-top.png        | Bin 0 -> 605 bytes
 src/assets/location-protein.png               | Bin 0 -> 817 bytes
 src/assets/location-rna-no-top.png            | Bin 0 -> 467 bytes
 src/assets/location-rna.png                   | Bin 0 -> 705 bytes
 src/assets/macromolecule.png                  | Bin 0 -> 568 bytes
 src/assets/na-sbgn.png                        | Bin 0 -> 378 bytes
 src/assets/ncrna.png                          | Bin 0 -> 507 bytes
 src/assets/no-glyph-assigned.png              | Bin 0 -> 228 bytes
 src/assets/nuclease-site.png                  | Bin 0 -> 441 bytes
 src/assets/omitted-detail.png                 | Bin 0 -> 149 bytes
 src/assets/operator.png                       | Bin 0 -> 258 bytes
 src/assets/origin-of-replication.png          | Bin 0 -> 654 bytes
 src/assets/origin-of-transfer.png             | Bin 0 -> 821 bytes
 src/assets/polyA.png                          | Bin 0 -> 309 bytes
 src/assets/polypeptide-region.png             | Bin 0 -> 662 bytes
 src/assets/primer-binding-site.png            | Bin 0 -> 293 bytes
 src/assets/process.png                        | Bin 0 -> 259 bytes
 src/assets/promoter.png                       | Bin 0 -> 470 bytes
 src/assets/protease-site.png                  | Bin 0 -> 723 bytes
 src/assets/protein-stability-element.png      | Bin 0 -> 638 bytes
 src/assets/protein.png                        | Bin 0 -> 438 bytes
 src/assets/replacement-glyph.png              | Bin 0 -> 511 bytes
 src/assets/ribonuclease-site.png              | Bin 0 -> 591 bytes
 src/assets/ribosome-entry-site.png            | Bin 0 -> 571 bytes
 src/assets/rna-stability-element.png          | Bin 0 -> 534 bytes
 src/assets/signature.png                      | Bin 0 -> 596 bytes
 src/assets/simple-chemical-circle.png         | Bin 0 -> 287 bytes
 src/assets/simple-chemical-hexagon.png        | Bin 0 -> 225 bytes
 src/assets/simple-chemical-pentagon.png       | Bin 0 -> 239 bytes
 src/assets/simple-chemical-triangle.png       | Bin 0 -> 255 bytes
 src/assets/specific-recombination-site.png    | Bin 0 -> 283 bytes
 src/assets/ssNA.png                           | Bin 0 -> 684 bytes
 src/assets/stimulation.png                    | Bin 0 -> 267 bytes
 src/assets/terminator.png                     | Bin 0 -> 249 bytes
 src/assets/three-prime-overhang.png           | Bin 0 -> 207 bytes
 .../three-prime-sticky-restriction-site.png   | Bin 0 -> 267 bytes
 src/assets/transcription-end.png              | Bin 0 -> 640 bytes
 src/assets/translation-end.png                | Bin 0 -> 784 bytes
 src/assets/unspecified-glyph.png              | Bin 0 -> 511 bytes
 src/elements.ts                               |  20 ++++++
 src/style.ts                                  |   9 ++-
 69 files changed, 115 insertions(+), 7 deletions(-)
 create mode 100644 src/assets/aptamer.png
 create mode 100644 src/assets/assembly-scar.png
 create mode 100644 src/assets/association.png
 create mode 100644 src/assets/blunt-restriction-site.png
 create mode 100644 src/assets/cds-arrow.png
 create mode 100644 src/assets/cds.png
 create mode 100644 src/assets/chromosomal-locus.png
 create mode 100644 src/assets/circular-plasmid.png
 create mode 100644 src/assets/complex-sbgn.png
 create mode 100644 src/assets/composite.png
 create mode 100644 src/assets/control.png
 create mode 100644 src/assets/degradation.png
 create mode 100644 src/assets/dissociation.png
 create mode 100644 src/assets/dna-stability-element.png
 create mode 100644 src/assets/dsNA.png
 create mode 100644 src/assets/engineered-region.png
 create mode 100644 src/assets/five-prime-overhang.png
 create mode 100644 src/assets/five-prime-sticky-restriction-site.png
 create mode 100644 src/assets/generic-sbgn.png
 create mode 100644 src/assets/halfround-rectangle.png
 create mode 100644 src/assets/inert-dna-spacer.png
 create mode 100644 src/assets/inhibition.png
 create mode 100644 src/assets/insulator.png
 create mode 100644 src/assets/intron.png
 create mode 100644 src/assets/location-dna-no-top.png
 create mode 100644 src/assets/location-dna.png
 create mode 100644 src/assets/location-protein-no-top.png
 create mode 100644 src/assets/location-protein.png
 create mode 100644 src/assets/location-rna-no-top.png
 create mode 100644 src/assets/location-rna.png
 create mode 100644 src/assets/macromolecule.png
 create mode 100644 src/assets/na-sbgn.png
 create mode 100644 src/assets/ncrna.png
 create mode 100644 src/assets/no-glyph-assigned.png
 create mode 100644 src/assets/nuclease-site.png
 create mode 100644 src/assets/omitted-detail.png
 create mode 100644 src/assets/operator.png
 create mode 100644 src/assets/origin-of-replication.png
 create mode 100644 src/assets/origin-of-transfer.png
 create mode 100644 src/assets/polyA.png
 create mode 100644 src/assets/polypeptide-region.png
 create mode 100644 src/assets/primer-binding-site.png
 create mode 100644 src/assets/process.png
 create mode 100644 src/assets/promoter.png
 create mode 100644 src/assets/protease-site.png
 create mode 100644 src/assets/protein-stability-element.png
 create mode 100644 src/assets/protein.png
 create mode 100644 src/assets/replacement-glyph.png
 create mode 100644 src/assets/ribonuclease-site.png
 create mode 100644 src/assets/ribosome-entry-site.png
 create mode 100644 src/assets/rna-stability-element.png
 create mode 100644 src/assets/signature.png
 create mode 100644 src/assets/simple-chemical-circle.png
 create mode 100644 src/assets/simple-chemical-hexagon.png
 create mode 100644 src/assets/simple-chemical-pentagon.png
 create mode 100644 src/assets/simple-chemical-triangle.png
 create mode 100644 src/assets/specific-recombination-site.png
 create mode 100644 src/assets/ssNA.png
 create mode 100644 src/assets/stimulation.png
 create mode 100644 src/assets/terminator.png
 create mode 100644 src/assets/three-prime-overhang.png
 create mode 100644 src/assets/three-prime-sticky-restriction-site.png
 create mode 100644 src/assets/transcription-end.png
 create mode 100644 src/assets/translation-end.png
 create mode 100644 src/assets/unspecified-glyph.png

diff --git a/README.md b/README.md
index 7377fc72a..1df4a05fe 100644
--- a/README.md
+++ b/README.md
@@ -143,6 +143,35 @@ The name of the sequence/plasmid. Shown at the center of the circular viewer.
 
 An array of `Annotation`s to render. Each `Annotation` requires 0-based start (inclusive) and end (exclusive) indexes. `name`s are rendered on top of the annotations. Set the annotation's direction to `1` for forward arrows and `-1` for reverse arrows.
 
+Optional Parameters:
+ - Annotation border styling: `"dashed" | "dotted" | "bold"`
+ ```js
+annotations = [
+  { start: 0, end: 22, name: "Strong promoter", direction: 1, border: "dashed"},
+];
+```
+ - 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": "red"}},
+];
+```
+ - Adding an svg icon to annotation; the available icons are part of the SBOL library and can be viewed in the `assets` folder under `src/assets/`, the name of the desired icon must exactly match the filename of the icon in the `assets` folder:
+ ```js
+annotations = [
+  { start: 0, end: 22, name: "Strong promoter", direction: 1, border: "dashed", font: {"fontFamily": "Times New Roman", "fontWeight": 800, "fontSize": 17, "fontColor": "red"}},
+  svg: 'promoter'
+];
+```
+  here `promoter` matches the name of the promoter icon file `promoter.png`
+ - 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": "red"}},
+  svg: 'promoter', gradient: {start: 'lightblue', stop: 'green'}
+];
+```
+
 ```js
 annotations = [
   { start: 0, end: 22, name: "Strong promoter", direction: 1 }, // [0, 22)
diff --git a/src/Linear/Annotations.tsx b/src/Linear/Annotations.tsx
index 6e3607eb6..39700ea5a 100644
--- a/src/Linear/Annotations.tsx
+++ b/src/Linear/Annotations.tsx
@@ -182,7 +182,10 @@ 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) {
+    fontSize = element.font.fontSize;
+  }
   const annotationCharacterWidth = 0.591 * fontSize;
   const availableCharacters = Math.floor((width - 40) / annotationCharacterWidth);
 
@@ -198,10 +201,54 @@ const SingleNamedElement = (props: {
     }
   }
 
+  let strokeVal: string | null = null;
+  let strokeWidth: string | null = null;
+
+  if (element.border) {
+    switch (element.border) {
+      case "dashed":
+        strokeVal = "5, 5";
+        break;
+      case "dotted":
+        strokeVal = "1, 5";
+        break;
+      case "bold":
+        strokeWidth = "2";
+        break;
+    }
+  }
+
+  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;
+  }
+
+  let svg: any = null;
+  if (element.svg) {
+    svg = require(`../assets/${element.svg}.png`);
+  }
+
   return (
     <g id={element.id} transform={`translate(${x}, ${0.1 * height})`}>
       {/* <title> provides a hover tooltip on most browsers */}
       <title>{name}</title>
+      {element.gradient && (
+        <defs>
+          <linearGradient id="myGradient" x1="0%" y1="0%" x2="100%" y2="100%">
+            <stop offset="0%" stop-color={element.gradient.start} />
+            <stop offset="100%" stop-color={element.gradient.stop} />
+          </linearGradient>
+        </defs>
+      )}
       <path
         ref={inputRef(element.id, {
           end: end,
@@ -214,10 +261,12 @@ const SingleNamedElement = (props: {
         className={`${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}
+        style={{ annotation }}
+        stroke-dasharray={strokeVal}
+        stroke-width={strokeWidth}
         onBlur={() => {
           // do nothing
         }}
@@ -227,13 +276,20 @@ const SingleNamedElement = (props: {
         onMouseOut={() => hoverOtherAnnotationRows(element.id, 0.7)}
         onMouseOver={() => hoverOtherAnnotationRows(element.id, 1.0)}
       />
+      <image
+        href={svg ? String(svg.default.src) : undefined}
+        x={width / 2 - (width / 2) * 0.6}
+        y={height / 2 - 8}
+        width="15px"
+        height="15px"
+      />
       <text
         className="la-vz-annotation-label"
         cursor="pointer"
         dominantBaseline="middle"
         fontSize={fontSize}
         id={element.id}
-        style={annotationLabel}
+        style={{ ...annotationLabel, fontFamily, fontWeight, fill: fontColor }}
         textAnchor="middle"
         x={width / 2}
         y={height / 2 + 1}
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diff --git a/src/assets/dna-stability-element.png b/src/assets/dna-stability-element.png
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diff --git a/src/assets/inert-dna-spacer.png b/src/assets/inert-dna-spacer.png
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diff --git a/src/assets/inhibition.png b/src/assets/inhibition.png
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GIT binary patch
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HcmV?d00001

diff --git a/src/assets/insulator.png b/src/assets/insulator.png
new file mode 100644
index 0000000000000000000000000000000000000000..be7c50803e13f321a389662b30091d05e50e473a
GIT binary patch
literal 399
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literal 0
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diff --git a/src/assets/intron.png b/src/assets/intron.png
new file mode 100644
index 0000000000000000000000000000000000000000..67b0784709e6fdb463dcce55f10be14c6cb06462
GIT binary patch
literal 788
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diff --git a/src/assets/location-dna-no-top.png b/src/assets/location-dna-no-top.png
new file mode 100644
index 0000000000000000000000000000000000000000..57ba93e001894813c7d95b485eb48601bd0a35ff
GIT binary patch
literal 201
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literal 0
HcmV?d00001

diff --git a/src/assets/location-dna.png b/src/assets/location-dna.png
new file mode 100644
index 0000000000000000000000000000000000000000..390c140bfb0d192cbf6f1f9bbb0217f992bdc6a5
GIT binary patch
literal 565
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literal 0
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diff --git a/src/assets/location-protein-no-top.png b/src/assets/location-protein-no-top.png
new file mode 100644
index 0000000000000000000000000000000000000000..eb9e804fff5a0cfeb91b86f45775405db1129270
GIT binary patch
literal 605
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literal 0
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diff --git a/src/assets/location-protein.png b/src/assets/location-protein.png
new file mode 100644
index 0000000000000000000000000000000000000000..ae32b406c824a2c1680d730580adfbe188648516
GIT binary patch
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literal 0
HcmV?d00001

diff --git a/src/assets/location-rna-no-top.png b/src/assets/location-rna-no-top.png
new file mode 100644
index 0000000000000000000000000000000000000000..ab9ab66209037598900337110d69053859a44446
GIT binary patch
literal 467
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literal 0
HcmV?d00001

diff --git a/src/assets/location-rna.png b/src/assets/location-rna.png
new file mode 100644
index 0000000000000000000000000000000000000000..6e7f49c35940e5ea26ebd0e53b45f356e4cbd0c9
GIT binary patch
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literal 0
HcmV?d00001

diff --git a/src/assets/macromolecule.png b/src/assets/macromolecule.png
new file mode 100644
index 0000000000000000000000000000000000000000..0c1a492f23fd8365061507e08a44b562bb6fb3da
GIT binary patch
literal 568
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literal 0
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diff --git a/src/assets/na-sbgn.png b/src/assets/na-sbgn.png
new file mode 100644
index 0000000000000000000000000000000000000000..079b86709eedb138621d867480e0a460027c170c
GIT binary patch
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diff --git a/src/assets/ncrna.png b/src/assets/ncrna.png
new file mode 100644
index 0000000000000000000000000000000000000000..a7bd969b6c19c9b3e72bb850614dc7a1a539eb28
GIT binary patch
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literal 0
HcmV?d00001

diff --git a/src/assets/no-glyph-assigned.png b/src/assets/no-glyph-assigned.png
new file mode 100644
index 0000000000000000000000000000000000000000..853d305b397f794313c438ca3737324a93467538
GIT binary patch
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literal 0
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diff --git a/src/assets/nuclease-site.png b/src/assets/nuclease-site.png
new file mode 100644
index 0000000000000000000000000000000000000000..915977dc07cb6cc1f046df262354d481119ffe8a
GIT binary patch
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literal 0
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diff --git a/src/assets/omitted-detail.png b/src/assets/omitted-detail.png
new file mode 100644
index 0000000000000000000000000000000000000000..621a828d54b9ed0b24092b215baf71fd47337bc9
GIT binary patch
literal 149
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diff --git a/src/assets/operator.png b/src/assets/operator.png
new file mode 100644
index 0000000000000000000000000000000000000000..7823ce94bdde38a5be83594dfdaa636a4a5c8678
GIT binary patch
literal 258
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literal 0
HcmV?d00001

diff --git a/src/assets/origin-of-replication.png b/src/assets/origin-of-replication.png
new file mode 100644
index 0000000000000000000000000000000000000000..ae30432827ed32eaf86a9bd696ae6f90a1240130
GIT binary patch
literal 654
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literal 0
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diff --git a/src/assets/origin-of-transfer.png b/src/assets/origin-of-transfer.png
new file mode 100644
index 0000000000000000000000000000000000000000..61421a2f854415676ba9799a22c5b9b739971a24
GIT binary patch
literal 821
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literal 0
HcmV?d00001

diff --git a/src/assets/polyA.png b/src/assets/polyA.png
new file mode 100644
index 0000000000000000000000000000000000000000..0f9044930cad5cfc7dd271cb9e4a9eaf7c47b0ff
GIT binary patch
literal 309
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literal 0
HcmV?d00001

diff --git a/src/assets/polypeptide-region.png b/src/assets/polypeptide-region.png
new file mode 100644
index 0000000000000000000000000000000000000000..10bcc004206fd69e6f259b6313c820b9e8238784
GIT binary patch
literal 662
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literal 0
HcmV?d00001

diff --git a/src/assets/primer-binding-site.png b/src/assets/primer-binding-site.png
new file mode 100644
index 0000000000000000000000000000000000000000..534556b22df4160251f5c35337d04d28cc6701c7
GIT binary patch
literal 293
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literal 0
HcmV?d00001

diff --git a/src/assets/process.png b/src/assets/process.png
new file mode 100644
index 0000000000000000000000000000000000000000..886b96dcc98f23f127c95616d54bcc0a26cc44dc
GIT binary patch
literal 259
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literal 0
HcmV?d00001

diff --git a/src/assets/promoter.png b/src/assets/promoter.png
new file mode 100644
index 0000000000000000000000000000000000000000..7ea4efc0fe006101413ca2e25b2b7fb93d8c8840
GIT binary patch
literal 470
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literal 0
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diff --git a/src/assets/protease-site.png b/src/assets/protease-site.png
new file mode 100644
index 0000000000000000000000000000000000000000..906b81ba0d99e255e24ccf6b4bf0ab4523f87fb8
GIT binary patch
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literal 0
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diff --git a/src/assets/protein-stability-element.png b/src/assets/protein-stability-element.png
new file mode 100644
index 0000000000000000000000000000000000000000..065a5ec9c98ced1333ab25df68f107e0afd0210a
GIT binary patch
literal 638
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diff --git a/src/assets/protein.png b/src/assets/protein.png
new file mode 100644
index 0000000000000000000000000000000000000000..1c841d46b90e6796a5059c1217f070aafddf3b81
GIT binary patch
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literal 0
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diff --git a/src/assets/replacement-glyph.png b/src/assets/replacement-glyph.png
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index 0000000000000000000000000000000000000000..3d8ca5941a4341e08874f5119ba23cf0bc2dece5
GIT binary patch
literal 511
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diff --git a/src/elements.ts b/src/elements.ts
index c81b327e9..be06715da 100644
--- a/src/elements.ts
+++ b/src/elements.ts
@@ -10,11 +10,31 @@ export interface NameRange extends Range {
   color?: string;
   id: string;
   name: string;
+  border?: "dashed" | "dotted" | "bold";
+  font?: Font;
+  svg?: string;
+  gradient?: Gradient;
+}
+
+interface Font {
+  fontFamily?: string;
+  fontSize: number;
+  fontWeight: number;
+  fontColor: string;
+}
+
+interface Gradient {
+  start: string;
+  stop: string;
 }
 
 /** AnnotationProp is an annotation provided to SeqViz via the annotations prop. */
 export interface AnnotationProp {
   color?: string;
+  border?: "dashed" | "dotted" | "bold";
+  font?: Font;
+  svg?: string;
+  gradient?: Gradient;
   direction?: number | string;
   end: number;
   name: string;
diff --git a/src/style.ts b/src/style.ts
index 797dd2fe1..90d0e80c5 100644
--- a/src/style.ts
+++ b/src/style.ts
@@ -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",
@@ -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",
@@ -151,3 +148,9 @@ export const seqBlock: CSS.Properties = {
   padding: 0,
   width: "100%",
 };
+
+export const iconStyle: CSS.Properties = {
+  width: "25px",
+  height: "25px",
+  zIndex: 100,
+};