diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000..6c573c9 Binary files /dev/null and b/.DS_Store differ diff --git a/.eslintrc.js b/.eslintrc.js new file mode 100644 index 0000000..f3f2a51 --- /dev/null +++ b/.eslintrc.js @@ -0,0 +1,4 @@ +require("eslint-config-teselagen/patch"); +module.exports = { + extends: "teselagen/node" +} \ No newline at end of file diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..bd07d4e --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +node_modules +/dist diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..b823bcc --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,39 @@ +CC0 1.0 Universal +================== + +Statement of Purpose +--------------------- + +The laws of most jurisdictions throughout the world automatically confer exclusive Copyright and Related Rights (defined below) upon the creator and subsequent owner(s) (each and all, an "owner") of an original work of authorship and/or a database (each, a "Work"). + +Certain owners wish to permanently relinquish those rights to a Work for the purpose of contributing to a commons of creative, cultural and scientific works ("Commons") that the public can reliably and without fear of later claims of infringement build upon, modify, incorporate in other works, reuse and redistribute as freely as possible in any form whatsoever and for any purposes, including without limitation commercial purposes. These owners may contribute to the Commons to promote the ideal of a free culture and the further production of creative, cultural and scientific works, or to gain reputation or greater distribution for their Work in part through the use and efforts of others. + +For these and/or other purposes and motivations, and without any expectation of additional consideration or compensation, the person associating CC0 with a Work (the "Affirmer"), to the extent that he or she is an owner of Copyright and Related Rights in the Work, voluntarily elects to apply CC0 to the Work and publicly distribute the Work under its terms, with knowledge of his or her Copyright and Related Rights in the Work and the meaning and intended legal effect of CC0 on those rights. + +1. Copyright and Related Rights. +-------------------------------- +A Work made available under CC0 may be protected by copyright and related or neighboring rights ("Copyright and Related Rights"). Copyright and Related Rights include, but are not limited to, the following: + +i. the right to reproduce, adapt, distribute, perform, display, communicate, and translate a Work; +ii. moral rights retained by the original author(s) and/or performer(s); +iii. publicity and privacy rights pertaining to a person's image or likeness depicted in a Work; +iv. rights protecting against unfair competition in regards to a Work, subject to the limitations in paragraph 4(a), below; +v. rights protecting the extraction, dissemination, use and reuse of data in a Work; +vi. database rights (such as those arising under Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases, and under any national implementation thereof, including any amended or successor version of such directive); and +vii. other similar, equivalent or corresponding rights throughout the world based on applicable law or treaty, and any national implementations thereof. + +2. Waiver. +----------- +To the greatest extent permitted by, but not in contravention of, applicable law, Affirmer hereby overtly, fully, permanently, irrevocably and unconditionally waives, abandons, and surrenders all of Affirmer's Copyright and Related Rights and associated claims and causes of action, whether now known or unknown (including existing as well as future claims and causes of action), in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the "Waiver"). 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In addition, to the extent the Waiver is so judged Affirmer hereby grants to each affected person a royalty-free, non transferable, non sublicensable, non exclusive, irrevocable and unconditional license to exercise Affirmer's Copyright and Related Rights in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the "License"). The License shall be deemed effective as of the date CC0 was applied by Affirmer to the Work. Should any part of the License for any reason be judged legally invalid or ineffective under applicable law, such partial invalidity or ineffectiveness shall not invalidate the remainder of the License, and in such case Affirmer hereby affirms that he or she will not (i) exercise any of his or her remaining Copyright and Related Rights in the Work or (ii) assert any associated claims and causes of action with respect to the Work, in either case contrary to Affirmer's express Statement of Purpose. + +4. Limitations and Disclaimers. +-------------------------------- + +a. No trademark or patent rights held by Affirmer are waived, abandoned, surrendered, licensed or otherwise affected by this document. +b. Affirmer offers the Work as-is and makes no representations or warranties of any kind concerning the Work, express, implied, statutory or otherwise, including without limitation warranties of title, merchantability, fitness for a particular purpose, non infringement, or the absence of latent or other defects, accuracy, or the present or absence of errors, whether or not discoverable, all to the greatest extent permissible under applicable law. +c. Affirmer disclaims responsibility for clearing rights of other persons that may apply to the Work or any use thereof, including without limitation any person's Copyright and Related Rights in the Work. Further, Affirmer disclaims responsibility for obtaining any necessary consents, permissions or other rights required for any use of the Work. +d. Affirmer understands and acknowledges that Creative Commons is not a party to this document and has no duty or obligation with respect to this CC0 or use of the Work. diff --git a/README.md b/README.md new file mode 100644 index 0000000..df7ef6d --- /dev/null +++ b/README.md @@ -0,0 +1,45 @@ +# electron-quick-start + +**Clone and run for a quick way to see Electron in action.** + +This is a minimal Electron application based on the [Quick Start Guide](https://electronjs.org/docs/tutorial/quick-start) within the Electron documentation. + +**Use this app along with the [Electron API Demos](https://electronjs.org/#get-started) app for API code examples to help you get started.** + +A basic Electron application needs just these files: + +- `package.json` - Points to the app's main file and lists its details and dependencies. +- `main.js` - Starts the app and creates a browser window to render HTML. This is the app's **main process**. +- `index.html` - A web page to render. This is the app's **renderer process**. + +You can learn more about each of these components within the [Quick Start Guide](https://electronjs.org/docs/tutorial/quick-start). + +## To Use + +To clone and run this repository you'll need [Git](https://git-scm.com) and [Node.js](https://nodejs.org/en/download/) (which comes with [npm](http://npmjs.com)) installed on your computer. From your command line: + +```bash +# Clone this repository +git clone https://github.com/electron/electron-quick-start +# Go into the repository +cd electron-quick-start +# Install dependencies +npm install +# Run the app +npm start +``` + +Note: If you're using Linux Bash for Windows, [see this guide](https://www.howtogeek.com/261575/how-to-run-graphical-linux-desktop-applications-from-windows-10s-bash-shell/) or use `node` from the command prompt. + +## Resources for Learning Electron + +- [electronjs.org/docs](https://electronjs.org/docs) - all of Electron's documentation +- [electronjs.org/community#boilerplates](https://electronjs.org/community#boilerplates) - sample starter apps created by the community +- [electron/electron-quick-start](https://github.com/electron/electron-quick-start) - a very basic starter Electron app +- [electron/simple-samples](https://github.com/electron/simple-samples) - small applications with ideas for taking them further +- [electron/electron-api-demos](https://github.com/electron/electron-api-demos) - an Electron app that teaches you how to use Electron +- [hokein/electron-sample-apps](https://github.com/hokein/electron-sample-apps) - small demo apps for the various Electron APIs + +## License + +[CC0 1.0 (Public Domain)](LICENSE.md) diff --git a/icon.png b/icon.png new file mode 100644 index 0000000..a8ebf81 Binary files /dev/null and b/icon.png differ diff --git a/index.html b/index.html new file mode 100644 index 0000000..f26ae67 --- /dev/null +++ b/index.html @@ -0,0 +1,22 @@ + + + + + Open Vector Editor + + + + + + + + + + diff --git a/main.js b/main.js new file mode 100644 index 0000000..659283a --- /dev/null +++ b/main.js @@ -0,0 +1,105 @@ +// Modules to control application life and create native browser window +const { app, BrowserWindow } = require("electron"); +const path = require("path"); +const bioParsers = require("bio-parsers"); +const fs = require("fs"); +const createMenu = require("./src/utils/menu"); + +// Keep a global reference of the window object, if you don't, the window will +// be closed automatically when the JavaScript object is garbage collected. +let windows = []; +let startupWindowVars = {}; +createMenu({ windows, createWindow, getSeqJsonFromPath }); + +function getSeqJsonFromPath(_filePath) { + let filePath = _filePath || process.argv[1]; + if (filePath === ".") return; + const data = fs.readFileSync(path.resolve(filePath), "utf-8"); + + //open, read, handle file + if (!data) return; + return bioParsers.anyToJson(data).then(res => { + return res[0].parsedSequence; + }); +} + +async function createWindow(windowVars) { + //if no windowVars are passed then we should + // Create the browser window. + let newWindow = new BrowserWindow({ + width: 800, + height: 600, + webPreferences: { + nodeIntegration: true + // preload: path.join(__dirname, 'preload.js') + } + }); + windows.push(newWindow); + + if (!windowVars && process.platform === "win32") { + //windows only + try { + startupWindowVars.initialSeqJson = await getSeqJsonFromPath( + startupWindowVars + ); + } catch (e) { + console.error(`e123421231:`, e); + } + } + Object.keys(windowVars || startupWindowVars).forEach(k => { + newWindow[k] = (windowVars || startupWindowVars)[k]; + }); + // if (process.argv.length >= 2) { + + // } else { + // // and load the index.html of the app. + // } + newWindow.loadFile("index.html"); + + // Open the DevTools. + // newWindow.webContents.openDevTools() + + // newWindow. + + // Emitted when the window is closed. + newWindow.on("closed", function() { + // Dereference the window object, usually you would store windows + // in an array if your app supports multi windows, this is the time + // when you should delete the corresponding element. + windows.splice(windows.indexOf(newWindow), 1); + newWindow = null; + }); +} + +app.on("will-finish-launching", () => { + app.on("open-file", async (event, path) => { + //mac only + event.preventDefault(); + try { + startupWindowVars.initialSeqJson = await getSeqJsonFromPath(path); + } catch (e) { + console.error(`e73562891230:`, e); + } + }); +}); + +// This method will be called when Electron has finished +// initialization and is ready to create browser windows. +// Some APIs can only be used after this event occurs. +app.on("ready", createWindow); + +// Quit when all windows are closed. +app.on("window-all-closed", function() { + // On macOS it is common for applications and their menu bar + // to stay active until the user quits explicitly with Cmd + Q + if (process.platform !== "darwin") app.quit(); +}); + +app.on("activate", function() { + // On macOS it's common to re-create a window in the app when the + // dock icon is clicked and there are no other windows open. + if (!windows.length) createWindow(); +}); + +// In this file you can include the rest of your app's specific main process +// code. You can also put them in separate files and require them here. diff --git a/pA11990.gb b/pA11990.gb new file mode 100644 index 0000000..e9ebc2a --- /dev/null +++ b/pA11990.gb @@ -0,0 +1,180 @@ +LOCUS pA11990 6705 bp DNA circular 06-FEB-2019 +FEATURES Location/Qualifiers + promoter 1..19 + /label="T7 prom" + misc_feature 19..46 + /label="lacO reg" + misc_feature 53..127 + /label="RiboJ10" + primer_bind 89..106 + /label="oIG00007" + primer complement(94..127) + /label="pARZ4_backbone_new_REV" + primer_bind complement(94..122) + /label="oIG00006" + RBS 128..169 + /label="RiboJ10-RBSmax-F13557" + CDS 170..1315 + /label="F13557" + misc_feature 170..1315 + /label="insert synthon" + primer_bind 424..469 + /label="oIG00005" + primer_bind complement(424..453) + /label="oIG00008" + primer 1316..1344 + /label="pARZ4_backbone_new_FOR" + terminator 1316..1516 + /label="DT10" + plasmid 1316..127 + /label="backbone plasmid" + misc_feature 1517..1556 + /label="INS230" + misc_structure 1557..1562 + /label="linker" + misc_feature 1563..1580 + /label="6X His tag" + terminator 1591..1719 + /label="T7 term" + rep_origin 1730..2174 + /label="M13 origin" + rep_origin 1747..2053 + /label="f1 origin" + CDS complement(2278..3093) + /label="kan2 marker" + rep_origin 3139..3821 + /label="colE1 origin" + terminator 3195..3237 + /label="terminator" + rep_origin 3199..3818 + /label="pBR322 origin" + terminator 3688..3728 + /label="putative terminator" + terminator 3796..3863 + /label="putative terminator(1)" + terminator 4419..4458 + /label="putative terminator(2)" + CDS 4456..4824 + /label="uncharacterized protein" + CDS complement(4821..5177) + /label="tet" + CDS complement(5233..6315) + /label="lacI" + 5'UTR complement(6316..6343) + /label="lacI 5' UTR" + misc_feature complement(6407..6670) + /label="tet(1)" +ORIGIN + 1 TAATACGACT CACTATAGGG GAATTGTGAG CGGATAACAA TTCCCCTCTA GAAGCGCTCA + 61 ACGGGTGTGC TTCCCGTTCT GATGAGTCCG TGAGGACGAA AGCGCCTCTA CAAATAATTT + 121 TGTTTAAAGT AGAGCTCGCG TTTTTTAGCG ATAAGGAGGT TTTTTTTTTA TGCGTGTAGG + 181 AATCCCGACT GAAACCAAAA ACAATGAGTT CCGTGTTGCG ATTACCCCAG CGGGCGTGGC + 241 GGAACTGACC CGTCGTGGTC ACGAAGTGCT GATTCAGGCG GGTGCGGGCG AAGGTTCTGC + 301 GATTACCGAT GCAGATTTCA AAGCGGCAGG TGCCCAGTTG GTGGGCACCG CTGACCAGGT + 361 GTGGGCGGAT GCCGACCTGC TGTTGAAAGT CAAAGAACCG ATTGCCGCAG AGTATGGTCG + 421 TCTGCGTCAC GGTCAGATTC TGTTTACCTT TCTCCACCTG GCGGCAAGCC GTGCCTGTAC + 481 CGATGCCCTG CTGGATAGCG GCACGACCAG CATTGCCTAT GAAACCGTTC AGACCGCAGA + 541 TGGTGCCCTG CCGTTACTGG CACCGATGAG TGAAGTGGCG GGTCGACTTG CGGCACAAGT + 601 TGGTGCGTAT CACCTGATGC GTACCCAGGG CGGTCGTGGC GTGCTGATGG GCGGTGTTCC + 661 AGGAGTGGAA CCAGCGGATG TGGTTGTGAT TGGTGCTGGC ACCGCAGGCT ATAATGCGGC + 721 ACGCATTGCC AATGGTATGG GTGCGACGGT GACCGTTCTG GACATCAACA TTGATAAACT + 781 GCGTCAACTG GATGCCGAGT TTTGCGGTCG TATTCACACC CGTTATTCCA GTGCGTATGA + 841 ACTGGAAGGT GCGGTGAAGC GTGCGGATTT AGTTATTGGT GCCGTGCTGG TGCCAGGTGC + 901 GAAAGCCCCG AAACTGGTGA GCAACAGCCT GGTTGCCCAC ATGAAACCAG GTGCCGTTCT + 961 GGTGGACATT GCCATTGACC AGGGCGGTTG CTTTGAAGGC AGCCGCCCGA CCACCTATGA + 1021 CCATCCGACC TTCGCCGTTC ACGATACCCT GTTTTATTGC GTGGCGAATA TGCCAGCGTC + 1081 GGTGCCGAAA ACCAGCACCT ATGCCCTGAC CAACGCCACG ATGCCGTATG TTCTGGAACT + 1141 GGCGGACCAC GGCTGGCGTG CGGCGTGTCG AAGCAATCCA GCACTGGCGA AAGGTCTGAG + 1201 CACCCACGAA GGTGCTCTGC TGAGCGAACG GGTTGCAACC GATTTAGGCG TGCCGTTTAC + 1261 CGAACCAGCG TCTGTTCTGG CGGGCAGCGG CAGTCACCAT CATCATCACC ATTAATTCAG + 1321 CCAAAAAACT TAAGACCGCC GGTCTTGTCC ACTACCTTGC AGTAATGCGG TGGACAGGAT + 1381 CGGCGGTTTT CTTTTCTCTT CTCAATACAA ATGAAAGTAC ATAGAAATTA CTCGGTACCA + 1441 AATTCCAGAA AAGAGGCCTC CCGAAAGGGG GGCCTTTTTT CGTTTTGGTC CTCATAGGCA + 1501 ATACGATCGC ATGTCCGTTC TACCCTGGAC TTACAGTTGT CGGCTGAAAG CGAAACCTCG + 1561 AGCACCACCA CCACCACCAC TGAGATCCGG CTGCTAACAA AGCCCGAAAG GAAGCTGAGT + 1621 TGGCTGCTGC CACCGCTGAG CAATAACTAG CATAACCCCT TGGGGCCTCT AAACGGGTCT + 1681 TGAGGGGTTT TTTGCTGAAA GGAGGAACTA TATCCGGATG GCGAATGGGA CGCGCCCTGT + 1741 AGCGGCGCAT TAAGCGCGGC GGGTGTGGTG GTTACGCGCA GCGTGACCGC TACACTTGCC + 1801 AGCGCCCTAG CGCCCGCTCC TTTCGCTTTC TTCCCTTCCT TTCTCGCCAC GTTCGCCGGC + 1861 TTTCCCCGTC AAGCTCTAAA TCGGGGGCTC CCTTTAGGGT TCCGATTTAG TGCTTTACGG + 1921 CACCTCGACC CCAAAAAACT TGATTAGGGT GATGGTTCAC GTAGTGGGCC ATCGCCCTGA + 1981 TAGACGGTTT TTCGCCCTTT GACGTTGGAG TCCACGTTCT TTAATAGTGG ACTCTTGTTC + 2041 CAAACTGGAA CAACACTCAA CCCTATCTCG GTCTATTCTT TTGATTTATA AGGGATTTTG + 2101 CCGATTTCGG CCTATTGGTT AAAAAATGAG CTGATTTAAC AAAAATTTAA CGCGAATTTT + 2161 AACAAAATAT TAACGTTTAC AATTTCAGGT GGCACTTTTC GGGGAAATGT GCGCGGAACC + 2221 CCTATTTGTT TATTTTTCTA AATACATTCA AATATGTATC CGCTCATGAA TTAATTCTTA + 2281 GAAAAACTCA TCGAGCATCA AATGAAACTG CAATTTATTC ATATCAGGAT TATCAATACC + 2341 ATATTTTTGA AAAAGCCGTT TCTGTAATGA AGGAGAAAAC TCACCGAGGC AGTTCCATAG + 2401 GATGGCAAGA TCCTGGTATC GGTCTGCGAT TCCGACTCGT CCAACATCAA TACAACCTAT + 2461 TAATTTCCCC TCGTCAAAAA TAAGGTTATC AAGTGAGAAA TCACCATGAG TGACGACTGA + 2521 ATCCGGTGAG AATGGCAAAA GTTTATGCAT TTCTTTCCAG ACTTGTTCAA CAGGCCAGCC + 2581 ATTACGCTCG TCATCAAAAT CACTCGCATC AACCAAACCG TTATTCATTC GTGATTGCGC + 2641 CTGAGCGAGA CGAAATACGC GATCGCTGTT AAAAGGACAA TTACAAACAG GAATCGAATG + 2701 CAACCGGCGC AGGAACACTG CCAGCGCATC AACAATATTT TCACCTGAAT CAGGATATTC + 2761 TTCTAATACC TGGAATGCTG TTTTCCCGGG GATCGCAGTG GTGAGTAACC ATGCATCATC + 2821 AGGAGTACGG ATAAAATGCT TGATGGTCGG AAGAGGCATA AATTCCGTCA GCCAGTTTAG + 2881 TCTGACCATC TCATCTGTAA CATCATTGGC AACGCTACCT TTGCCATGTT TCAGAAACAA + 2941 CTCTGGCGCA TCGGGCTTCC CATACAATCG ATAGATTGTC GCACCTGATT GCCCGACATT + 3001 ATCGCGAGCC CATTTATACC CATATAAATC AGCATCCATG TTGGAATTTA ATCGCGGCCT + 3061 AGAGCAAGAC GTTTCCCGTT GAATATGGCT CATAACACCC CTTGTATTAC TGTTTATGTA + 3121 AGCAGACAGT TTTATTGTTC ATGACCAAAA TCCCTTAACG TGAGTTTTCG TTCCACTGAG + 3181 CGTCAGACCC CGTAGAAAAG ATCAAAGGAT CTTCTTGAGA TCCTTTTTTT CTGCGCGTAA + 3241 TCTGCTGCTT GCAAACAAAA AAACCACCGC TACCAGCGGT GGTTTGTTTG CCGGATCAAG + 3301 AGCTACCAAC TCTTTTTCCG AAGGTAACTG GCTTCAGCAG AGCGCAGATA CCAAATACTG + 3361 TCCTTCTAGT GTAGCCGTAG TTAGGCCACC ACTTCAAGAA CTCTGTAGCA CCGCCTACAT + 3421 ACCTCGCTCT GCTAATCCTG TTACCAGTGG CTGCTGCCAG TGGCGATAAG TCGTGTCTTA + 3481 CCGGGTTGGA CTCAAGACGA TAGTTACCGG ATAAGGCGCA GCGGTCGGGC TGAACGGGGG + 3541 GTTCGTGCAC ACAGCCCAGC TTGGAGCGAA CGACCTACAC CGAACTGAGA TACCTACAGC + 3601 GTGAGCTATG AGAAAGCGCC ACGCTTCCCG AAGGGAGAAA GGCGGACAGG TATCCGGTAA + 3661 GCGGCAGGGT CGGAACAGGA GAGCGCACGA GGGAGCTTCC AGGGGGAAAC GCCTGGTATC + 3721 TTTATAGTCC TGTCGGGTTT CGCCACCTCT GACTTGAGCG TCGATTTTTG TGATGCTCGT + 3781 CAGGGGGGCG GAGCCTATGG AAAAACGCCA GCAACGCGGC CTTTTTACGG TTCCTGGCCT + 3841 TTTGCTGGCC TTTTGCTCAC ATGTTCTTTC CTGCGTTATC CCCTGATTCT GTGGATAACC + 3901 GTATTACCGC CTTTGAGTGA GCTGATACCG CTCGCCGCAG CCGAACGACC GAGCGCAGCG + 3961 AGTCAGTGAG CGAGGAAGCG GAAGAGCGCC TGATGCGGTA TTTTCTCCTT ACGCATCTGT + 4021 GCGGTATTTC ACACCGCATA TATGGTGCAC TCTCAGTACA ATCTGCTCTG ATGCCGCATA + 4081 GTTAAGCCAG TATACACTCC GCTATCGCTA CGTGACTGGG TCATGGCTGC GCCCCGACAC + 4141 CCGCCAACAC CCGCTGACGC GCCCTGACGG GCTTGTCTGC TCCCGGCATC CGCTTACAGA + 4201 CAAGCTGTGA CCGTCTCCGG GAGCTGCATG TGTCAGAGGT TTTCACCGTC ATCACCGAAA + 4261 CGCGCGAGGC AGCTGCGGTA AAGCTCATCA GCGTGGTCGT GAAGCGATTC ACAGATGTCT + 4321 GCCTGTTCAT CCGCGTCCAG CTCGTTGAGT TTCTCCAGAA GCGTTAATGT CTGGCTTCTG + 4381 ATAAAGCGGG CCATGTTAAG GGCGGTTTTT TCCTGTTTGG TCACTGATGC CTCCGTGTAA + 4441 GGGGGATTTC TGTTCATGGG GGTAATGATA CCGATGAAAC GAGAGAGGAT GCTCACGATA + 4501 CGGGTTACTG ATGATGAACA TGCCCGGTTA CTGGAACGTT GTGAGGGTAA ACAACTGGCG + 4561 GTATGGATGC GGCGGGACCA GAGAAAAATC ACTCAGGGTC AATGCCAGCG CTTCGTTAAT + 4621 ACAGATGTAG GTGTTCCACA GGGTAGCCAG CAGCATCCTG CGATGCAGAT CCGGAACATA + 4681 ATGGTGCAGG GCGCTGACTT CCGCGTTTCC AGACTTTACG AAACACGGAA ACCGAAGACC + 4741 ATTCATGTTG TTGCTCAGGT CGCAGACGTT TTGCAGCAGC AGTCGCTTCA CGTTCGCTCG + 4801 CGTATCGGTG ATTCATTCTG CTAACCAGTA AGGCAACCCC GCCAGCCTAG CCGGGTCCTC + 4861 AACGACAGGA GCACGATCAT GCGCACCCGT GGGGCCGCCA TGCCGGCGAT AATGGCCTGC + 4921 TTCTCGCCGA AACGTTTGGT GGCGGGACCA GTGACGAAGG CTTGAGCGAG GGCGTGCAAG + 4981 ATTCCGAATA CCGCAAGCGA CAGGCCGATC ATCGTCGCGC TCCAGCGAAA GCGGTCCTCG + 5041 CCGAAAATGA CCCAGAGCGC TGCCGGCACC TGTCCTACGA GTTGCATGAT AAAGAAGACA + 5101 GTCATAAGTG CGGCGACGAT AGTCATGCCC CGCGCCCACC GGAAGGAGCT GACTGGGTTG + 5161 AAGGCTCTCA AGGGCATCGG TCGAGATCCC GGTGCCTAAT GAGTGAGCTA ACTTACATTA + 5221 ATTGCGTTGC GCTCACTGCC CGCTTTCCAG TCGGGAAACC TGTCGTGCCA GCTGCATTAA + 5281 TGAATCGGCC AACGCGCGGG GAGAGGCGGT TTGCGTATTG GGCGCCAGGG TGGTTTTTCT + 5341 TTTCACCAGT GAGACGGGCA ACAGCTGATT GCCCTTCACC GCCTGGCCCT GAGAGAGTTG + 5401 CAGCAAGCGG TCCACGCTGG TTTGCCCCAG CAGGCGAAAA TCCTGTTTGA TGGTGGTTAA + 5461 CGGCGGGATA TAACATGAGC TGTCTTCGGT ATCGTCGTAT CCCACTACCG AGATGTCCGC + 5521 ACCAACGCGC AGCCCGGACT CGGTAATGGC GCGCATTGCG CCCAGCGCCA TCTGATCGTT + 5581 GGCAACCAGC ATCGCAGTGG GAACGATGCC CTCATTCAGC ATTTGCATGG TTTGTTGAAA + 5641 ACCGGACATG GCACTCCAGT CGCCTTCCCG TTCCGCTATC GGCTGAATTT GATTGCGAGT + 5701 GAGATATTTA TGCCAGCCAG CCAGACGCAG ACGCGCCGAG ACAGAACTTA ATGGGCCCGC + 5761 TAACAGCGCG ATTTGCTGGT GACCCAATGC GACCAGATGC TCCACGCCCA GTCGCGTACC + 5821 GTCTTCATGG GAGAAAATAA TACTGTTGAT GGGTGTCTGG TCAGAGACAT CAAGAAATAA + 5881 CGCCGGAACA TTAGTGCAGG CAGCTTCCAC AGCAATGGCA TCCTGGTCAT CCAGCGGATA + 5941 GTTAATGATC AGCCCACTGA CGCGTTGCGC GAGAAGATTG TGCACCGCCG CTTTACAGGC + 6001 TTCGACGCCG CTTCGTTCTA CCATCGACAC CACCACGCTG GCACCCAGTT GATCGGCGCG + 6061 AGATTTAATC GCCGCGACAA TTTGCGACGG CGCGTGCAGG GCCAGACTGG AGGTGGCAAC + 6121 GCCAATCAGC AACGACTGTT TGCCCGCCAG TTGTTGTGCC ACGCGGTTGG GAATGTAATT + 6181 CAGCTCCGCC ATCGCCGCTT CCACTTTTTC CCGCGTTTTC GCAGAAACGT GGCTGGCCTG + 6241 GTTCACCACG CGGGAAACGG TCTGATAAGA GACACCGGCA TACTCTGCGA CATCGTATAA + 6301 CGTTACTGGT TTCACATTCA CCACCCTGAA TTGACTCTCT TCCGGGCGCT ATCATGCCAT + 6361 ACCGCGAAAG GTTTTGCGCC ATTCGATGGT GTCCGGGATC TCGACGCTCT CCCTTATGCG + 6421 ACTCCTGCAT TAGGAAGCAG CCCAGTAGTA GGTTGAGGCC GTTGAGCACC GCCGCCGCAA + 6481 GGAATGGTGC ATGCAAGGAG ATGGCGCCCA ACAGTCCCCC GGCCACGGGG CCTGCCACCA + 6541 TACCCACGCC GAAACAAGCG CTCATGAGCC CGAAGTGGCG AGCCCGATCT TCCCCATCGG + 6601 TGATGTCGGC GATATAGGCG CCAGCAACCG CACCTGTGGC GCCGGTGATG CCGGCCACGA + 6661 TGCGTCCGGC GTAGAGGATC GAGATCGATC TCGATCCCGC GAAAT +// \ No 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"editor", + "dna", + "ove" + ], + "author": "tnrich", + "license": "MIT", + "devDependencies": { + "electron": "^6.0.9", + "electron-builder": "^21.2.0", + "eslint": "^6.4.0", + "eslint-config-teselagen": "^5.0.5" + }, + "dependencies": { + "bio-parsers": "5.6.1", + "open-vector-editor": "^10.1.8", + "ve-range-utils": "^2.5.5", + "ve-sequence-utils": "^3.3.50" + } +} diff --git a/src/renderer.js b/src/renderer.js new file mode 100644 index 0000000..1511ae6 --- /dev/null +++ b/src/renderer.js @@ -0,0 +1,190 @@ +const electron = require("electron"); +const currentWindow = electron.remote.getCurrentWindow(); + +const seqDataToUse = currentWindow.initialSeqJson || { circular: true }; +// export default generateSequenceData() + +const editor = window.createVectorEditor("createDomNodeForMe", { + isFullscreen: true, + // or you can pass "createDomNodeForMe" but make sure to use editor.close() to clean up the dom node! + + //you can also pass a DOM node as the first arg here + // showReadOnly: false, + // disableSetReadOnly: true, + shouldAutosave: true, + // rightClickOverrides: { + // selectionLayerRightClicked: (items /* { annotation }, props */) => { + // return [ + // ...items, + // { + // text: "Create Part", + // onClick: () => console.info("hey!≈") + // } + // ]; + // } + // }, + // handleFullscreenClose: () => { //comment this function in to make the editor fullscreen by default + // editor.close() //this calls reactDom.unmountComponent at the node you passed as the first arg + // }, + // onRename: () => {}, //this option should be shown by default + // onNew: () => {}, //unless this callback is defined, don't show the option to create a new seq + // onDuplicate: () => {}, //unless this callback is defined, don't show the option to create a new seq + // onSave: function( + // event, + // sequenceDataToSave, + // editorState, + // onSuccessCallback + // ) { + // console.info("event:", event); + // console.info("sequenceData:", sequenceDataToSave); + // console.info("editorState:", editorState); + // // To disable the save button after successful saving + // // either call the onSuccessCallback or return a successful promise :) + // onSuccessCallback(); + // //or + // // return myPromiseBasedApiCall() + // }, + // onDelete: data => { + // console.warn("would delete", data); + // }, + // onCopy: function(event, copiedSequenceData /* , editorState */) { + // //the copiedSequenceData is the subset of the sequence that has been copied in the teselagen sequence format + // const clipboardData = event.clipboardData; + // clipboardData.setData("text/plain", copiedSequenceData.sequence); + // clipboardData.setData( + // "application/json", + // //for example here you could change teselagen parts into jbei parts + // JSON.stringify(copiedSequenceData) + // ); + // event.preventDefault(); + // //in onPaste in your app you can do: + // // e.clipboardData.getData('application/json') + // }, + // onPaste: function(event /* , editorState */) { + // //the onPaste here must return sequenceData in the teselagen data format + // const clipboardData = event.clipboardData; + // let jsonData = clipboardData.getData("application/json"); + // if (jsonData) { + // jsonData = JSON.parse(jsonData); + // if (jsonData.isJbeiSeq) { + // jsonData = convertJbeiToTeselagen(jsonData); + // } + // } + // const sequenceData = jsonData || { + // sequence: clipboardData.getData("text/plain") + // }; + // return sequenceData; + // }, + // getSequenceAtVersion: versionId => { + // if (versionId === 2) { + // return { + // sequence: "thomaswashere" + // }; + // } else if ((versionId = 3)) { + // return { + // features: [{ start: 4, end: 6 }], + // sequence: + // "GGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacacccccc" + // }; + // } else { + // console.error("we shouldn't be here..."); + // return { + // sequence: "taa" + // }; + // } + // }, + // getVersionList: () => { + // return [ + // { + // dateChanged: "12/30/2211", + // editedBy: "Nara", + // // revisionType: "Sequence Deletion", + // versionId: 2 + // }, + // { + // dateChanged: "8/30/2211", + // editedBy: "Ralph", + // // revisionType: "Feature Edit", + // versionId: 3 + // } + // ]; + // }, + showMenuBar: true, + PropertiesProps: { + propertiesList: [ + "general", + "features", + "parts", + "primers", + "translations", + "cutsites", + "orfs", + "genbank" + ] + }, + ToolBarProps: { + toolList: [ + "saveTool", + "downloadTool", + "importTool", + "undoTool", + "redoTool", + "cutsiteTool", + "featureTool", + "alignmentTool", + "versionHistoryTool", + // "oligoTool", + "orfTool", + // "viewTool", + "editTool", + "findTool", + "visibilityTool" + // "propertiesTool" + ] + } +}); /* createDomNodeForMe will make a dom node for you and append it to the document.body*/ + +editor.updateEditor({ + sequenceData: seqDataToUse, + sequenceDataHistory: {}, //clear the sequenceDataHistory if there is any left over from a previous sequence + annotationVisibility: { + // features: false, + orfTranslations: false + }, + readOnly: false, + panelsShown: [ + [ + { + // fullScreen: true, + active: true, + id: "circular", + name: "Circular Map" + }, + { + id: "rail", + name: "Linear Map" + } + ], + [ + { + id: "sequence", + name: "Sequence Map", + active: true + }, + + { + id: "properties", + name: "Properties" + } + ] + ], + annotationsToSupport: { + //these are the defaults, change to false to exclude + features: true, + translations: true, + parts: true, + orfs: true, + cutsites: true, + primers: false + } +}); diff --git a/src/utils/menu.js b/src/utils/menu.js new file mode 100644 index 0000000..1234fbc --- /dev/null +++ b/src/utils/menu.js @@ -0,0 +1,138 @@ +const { Menu } = require("electron"); + +const { dialog } = require("electron"); + +const { BrowserWindow } = require("electron"); + +const isMac = process.platform === "darwin"; + +module.exports = function createMenu({ createWindow, getSeqJsonFromPath }) { + const template = [ + // { role: 'appMenu' } + ...(isMac + ? [ + { + label: "OVE", + submenu: [ + { role: "about" }, + { type: "separator" }, + { role: "services" }, + { type: "separator" }, + { role: "hide" }, + { role: "hideothers" }, + { role: "unhide" }, + { type: "separator" }, + { role: "quit" } + ] + } + ] + : []), + // { role: 'fileMenu' } + { + label: "File", + submenu: [ + { + label: "New File", + accelerator: "CmdOrCtrl+N", + click: () => { + createWindow({ + initialSeqJson: {} + }); + } + }, + { + label: "Open", + accelerator: "CmdOrCtrl+O", + click: async () => { + const { filePaths } = await dialog.showOpenDialog({ + filters: [ + { name: "Sequence Files", extensions: ["gb", "gbk", "fasta"] } + ], + properties: ["openFile", "multiSelections"] + }); + + filePaths.forEach(async p => { + let browserWindow = BrowserWindow.getFocusedWindow() + if (browserWindow) { + browserWindow.close(); + browserWindow = null; + } + + const initialSeqJson = await getSeqJsonFromPath(p); + createWindow({ + initialSeqJson + }); + }); + } + }, + isMac ? { role: "close" } : { role: "quit" } + ] + }, + // { role: 'editMenu' } + { + label: 'Edit', + submenu: [ + // { role: 'undo' }, + // { role: 'redo' }, + // { type: 'separator' }, + { role: 'cut' }, + { role: 'copy' }, + { role: 'paste' }, + // ...(isMac ? [ + // { role: 'pasteAndMatchStyle' }, + // { role: 'delete' }, + // { role: 'selectAll' }, + // { type: 'separator' }, + // { + // label: 'Speech', + // submenu: [ + // { role: 'startspeaking' }, + // { role: 'stopspeaking' } + // ] + // } + // ] : [ + // { role: 'delete' }, + // { type: 'separator' }, + // { role: 'selectAll' } + // ]) + ] + }, + // { role: 'viewMenu' } + { + label: "View", + submenu: [ + { role: "reload" }, + { role: "forcereload" }, + { role: "toggledevtools" }, + { type: "separator" }, + { role: "resetzoom" }, + { role: "zoomin" }, + { role: "zoomout" }, + { type: "separator" }, + { role: "togglefullscreen" } + ] + }, + // { role: 'windowMenu' } + { + label: "Window", + submenu: [ + { role: "minimize" }, + { role: "zoom" }, + ...(isMac + ? [ + { type: "separator" }, + { role: "front" }, + { type: "separator" }, + { role: "window" } + ] + : [{ role: "close" }]) + ] + } + ]; + + // const menu = Menu.buildFromTemplate([ + // {label: "a", click: } + // ]) + const menu = Menu.buildFromTemplate(template); + Menu.setApplicationMenu(menu); +};