@opencloning/ui 1.0.0

package/src/components/assembler/assembler_data2.json

@@ -0,0 +1,50 @@
+[
+    {
+        "name": "A",
+        "overhang": "GGAG"
+    },
+    {
+        "name": "B",
+        "overhang": "TACT"
+    },
+    {
+        "name": "T1",
+        "overhang": "CCAT"
+    },
+    {
+        "name": "T2",
+        "overhang": "GTCA"
+    },
+    {
+        "name": "T3",
+        "overhang": "TCCA"
+    },
+    {
+        "name": "C",
+        "overhang": "AATG"
+    },
+    {
+        "name": "D",
+        "overhang": "AGGT"
+    },
+    {
+        "name": "T4",
+        "overhang": "TTCG"
+    },
+    {
+        "name": "T5",
+        "overhang": "CGGC"
+    },
+    {
+        "name": "E",
+        "overhang": "GCTT"
+    },
+    {
+        "name": "F",
+        "overhang": "CGCT"
+    },
+    {
+        "name": "backbone",
+        "overhang": "GGAG"
+    }
+]

package/src/components/assembler/assembly_component.module.css

@@ -0,0 +1,81 @@
+/* CSS variables - can be defined at the module level or use :root */
+:root {
+    --border-color: #EE220C;
+    --border-width: 2.5px;
+    --border-style: dashed;
+}
+
+.dna {
+    font-family: monospace;
+}
+
+.dna div {
+    white-space: pre;
+    min-height: 1em;
+}
+
+.overhang div {
+    padding-left: calc(2px + var(--border-width));
+    padding-right: 2px;
+}
+
+.container {
+    margin:auto;
+    display: flex;
+    flex-direction: row;
+    align-items: center;
+    height: auto;
+    text-align: left;
+}
+
+.boxContainer {
+    position: relative;
+    display: flex;
+    align-items: center;
+    justify-content: center;
+}
+
+.box {
+    align-self: stretch;
+    border: 3px solid black;
+    width: 5em;
+    margin-left: .2em;
+    margin-right: .2em;
+    overflow: hidden;
+    border-radius: 6px;
+    margin-bottom: var(--border-width);
+}
+
+.box .imageContainer {
+    text-align: center;
+}
+
+.imageContainer img {
+    height: 2.2em;
+}
+
+.overhang .watson {
+    border-left: var(--border-width) var(--border-style) var(--border-color);
+    border-bottom: var(--border-width) var(--border-style) var(--border-color);
+    padding-left: 2px;
+}
+
+.overhang .crick {
+    border-right: var(--border-width) var(--border-style) var(--border-color);
+}
+
+.insideLeft {
+    margin-left: .2em;
+}
+
+.insideRight {
+    margin-right: .2em;
+}
+
+.overhang.left .watson {
+    font-weight: bold;
+}
+
+.overhang.right .crick {
+    font-weight: bold;
+}

package/src/components/assembler/moclo.json

@@ -0,0 +1,110 @@
+[
+    {
+        "header": "Assembly connector",
+        "body": "",
+        "glyph": "three-prime-sticky-restriction-site",
+        "left_overhang": "CCCT",
+        "right_overhang": "AACG",
+        "left_inside": "",
+        "right_inside": "",
+        "left_codon_start": null,
+        "right_codon_start": null,
+        "color": "#92C3DC"
+    },
+    {
+        "header": "Promoter",
+        "body": "",
+        "glyph": "promoter",
+        "left_overhang": "AACG",
+        "right_overhang": "TATG",
+        "left_inside": "",
+        "right_inside": "",
+        "left_codon_start": null,
+        "right_codon_start": null,
+        "color": "#B2D06E"
+    },
+    {
+        "header": "Coding sequence",
+        "body": "You can use the ATG from the fusion site as translation start. If possible omit STOP codon and make your protein in frame with the Ser.",
+        "glyph": "cds",
+        "left_overhang": "TATG",
+        "right_overhang": "ATCC",
+        "left_inside": "",
+        "right_inside": "",
+        "left_codon_start": 2,
+        "right_codon_start": 2,
+        "color": "#F1EC9B"
+    },
+    {
+        "header": "Terminator",
+        "body": "",
+        "glyph": "terminator",
+        "left_overhang": "ATCC",
+        "right_overhang": "GCTG",
+        "left_inside": "",
+        "right_inside": "",
+        "left_codon_start": null,
+        "right_codon_start": null,
+        "color": "#E2929E"
+    },
+    {
+        "header": "Assembly connector",
+        "body": "",
+        "glyph": "three-prime-sticky-restriction-site",
+        "left_overhang": "GCTG",
+        "right_overhang": "TACA",
+        "left_inside": "",
+        "right_inside": "",
+        "left_codon_start": null,
+        "right_codon_start": null,
+        "color": "#7C6AA9"
+    },
+    {
+        "header": "Yeast marker",
+        "body": "",
+        "glyph": "engineered-region",
+        "left_overhang": "TACA",
+        "right_overhang": "GAGT",
+        "left_inside": "",
+        "right_inside": "",
+        "left_codon_start": null,
+        "right_codon_start": null,
+        "color": "#EFD198"
+    },
+    {
+        "header": "Yeast plasmid origin of replication",
+        "body": "",
+        "glyph": "origin-of-replication",
+        "left_overhang": "GAGT",
+        "right_overhang": "CCGA",
+        "left_inside": "",
+        "right_inside": "",
+        "left_codon_start": null,
+        "right_codon_start": null,
+        "color": "#85643E"
+    },
+    {
+        "header": "Bacterial marker and origin",
+        "body": "",
+        "glyph": "engineered-region",
+        "left_overhang": "CCGA",
+        "right_overhang": "CCCT",
+        "left_inside": "",
+        "right_inside": "",
+        "left_codon_start": null,
+        "right_codon_start": null,
+        "color": "#7F7F7F"
+    },
+    {
+        "header": "Dummy",
+        "body": "promoter text",
+        "glyph": "cds-stop",
+        "left_overhang": "CATG",
+        "right_overhang": "TATG",
+        "left_inside": "AAAATA",
+        "right_inside": "AATG",
+        "left_codon_start": 2,
+        "right_codon_start": 1,
+        "color": "greenyellow"
+    }
+]

package/src/components/assembler/sbol_visual_glyphs/LICENSE.html

@@ -0,0 +1,21 @@
+<a rel="license" href="http://creativecommons.org/licenses/by/4.0/">
+  <img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a>
+<br />Except as noted below, this work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.
+
+<p xmlns:dct="http://purl.org/dc/terms/" xmlns:vcard="http://www.w3.org/2001/vcard-rdf/3.0#">
+  <a rel="license"
+     href="http://creativecommons.org/publicdomain/zero/1.0/">
+    <img src="http://i.creativecommons.org/p/zero/1.0/88x31.png" style="border-style: none;" alt="CC0" />
+  </a>
+  <br />
+  Exception: to the extent possible under law,
+  <a rel="dct:publisher"
+     href="http://www.sbolstandard.org/">
+    <span property="dct:title">the SBOL developers</span></a>
+  have waived all copyright and related or neighboring rights to
+  <span property="dct:title">SBOL Visual glyphs</span>.
+This work is published from:
+<span property="vcard:Country" datatype="dct:ISO3166"
+      content="US" about="http://www.sbolstandard.org/">
+  United States</span>.
+</p>

package/src/components/assembler/sbol_visual_glyphs/assembly-scar.svg

@@ -0,0 +1,63 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<svg
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+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   viewBox="0 0 44.999998 44.999998"
+   version="1.1"
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+   y="0px"
+   width="0.5in"
+   height="0.5in"
+   id="svg2"
+   inkscape:version="0.91 r13725"
+   sodipodi:docname="assembly-scar.svg"
+   inkscape:export-filename="/Users/jakebeal/projects/SBOL/SBOLv-realizations/Glyphs/assembly-scar/assembly-scar.png"
+   inkscape:export-xdpi="300"
+   inkscape:export-ydpi="300"><metadata
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+     bordercolor="#666666"
+     borderopacity="1"
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+     gridtolerance="10"
+     guidetolerance="10"
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+     inkscape:pageshadow="2"
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+     units="in"
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+     id="defs4"><style
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+       id="style6"><![CDATA[
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+        stroke-linecap: round;
+        stroke-linejoin: round;
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package/src/components/assembler/sbol_visual_glyphs/cds-stop.svg

@@ -0,0 +1,85 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<svg
+   viewBox="0 0 72.57625 48.789663"
+   version="1.1"
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+   height="0.5421074in"
+   id="svg2"
+   inkscape:version="1.3.2 (091e20e, 2023-11-25)"
+   sodipodi:docname="cds-stop.svg"
+   inkscape:export-filename="/Users/jakebeal/projects/SBOL/SBOLv-realizations/Glyphs/cds/cds-specification.png"
+   inkscape:export-xdpi="300"
+   inkscape:export-ydpi="300"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:cc="http://creativecommons.org/ns#"
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+     inkscape:pagecheckerboard="0"
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+       type="text/css"
+       id="style6"><![CDATA[
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+        stroke:#000000;
+        stroke-width: 3;
+        stroke-linecap: round;
+        stroke-linejoin: round;
+        fill: none
+      }]]></style><mask
+       id="stop-mask"><!-- Octagon area (visible part) --><polygon
+         fill="#ffffff"
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+         y="12.3"
+         fill="#000000"
+         font-family="Arial, Helvetica, sans-serif"
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+         font-size="7.2px"
+         text-anchor="middle"
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+     height="24"
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package/src/components/assembler/sbol_visual_glyphs/cds.svg

@@ -0,0 +1,60 @@
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+<svg
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+   inkscape:version="0.91 r13725"
+   sodipodi:docname="cds.svg"
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package/src/components/assembler/sbol_visual_glyphs/chromosomal-locus.svg

@@ -0,0 +1,78 @@
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+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
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+   xmlns:svg="http://www.w3.org/2000/svg"
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package/src/components/assembler/sbol_visual_glyphs/engineered-region.svg

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+     inkscape:window-width="640"
+     inkscape:window-height="480"
+     id="namedview10"
+     showgrid="false"
+     units="in"
+     inkscape:zoom="2.36"
+     inkscape:cx="25"
+     inkscape:cy="50"
+     inkscape:window-x="0"
+     inkscape:window-y="0"
+     inkscape:window-maximized="0"
+     inkscape:current-layer="svg2" /><defs
+     id="defs4"><style
+       type="text/css"
+       id="style6"><![CDATA[
+      path,circle,polygon {
+        stroke:#000000;
+        stroke-width: 3;
+        stroke-linecap: round;
+        stroke-linejoin: round;
+        fill: none
+      }]]></style></defs><path
+     d="m 2.4999973,12.499997 0,20 39.9999997,0 0,-20 z"
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+     inkscape:connector-curvature="0"
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package/src/components/assembler/sbol_visual_glyphs/five-prime-sticky-restriction-site.svg

@@ -0,0 +1,56 @@
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+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   viewBox="0 0 44.999999 44.999998"
+   version="1.1"
+   xml:space="preserve"
+   x="0px"
+   y="0px"
+   width="0.5in"
+   height="0.5in"
+   id="svg2"
+   inkscape:version="0.91 r13725"
+   sodipodi:docname="five-prime-sticky-restriction-site.svg"><metadata
+     id="metadata12"><rdf:RDF><cc:Work
+         rdf:about=""><dc:format>image/svg+xml</dc:format><dc:type
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" /><dc:title></dc:title></cc:Work></rdf:RDF></metadata><sodipodi:namedview
+     pagecolor="#ffffff"
+     bordercolor="#666666"
+     borderopacity="1"
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+     guidetolerance="10"
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+     inkscape:pageshadow="2"
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+     inkscape:window-y="0"
+     inkscape:window-maximized="0"
+     inkscape:current-layer="svg2" /><defs
+     id="defs4"><style
+       type="text/css"
+       id="style6"><![CDATA[
+      path,circle {
+        stroke:#000000;
+        stroke-width: 3;
+        stroke-linecap: round;
+        stroke-linejoin: round;
+        fill: none
+      }]]></style></defs><path
+     d="m 7.5,9.499998 0,13 30,0 0,13"
+     id="path8"
+     inkscape:connector-curvature="0"
+     style="fill:none;stroke:#000000;stroke-width:3;stroke-linecap:round;stroke-linejoin:round" /></svg>