sequenceserver 2.0.0.rc8 → 2.1.0
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- checksums.yaml +4 -4
- data/bin/sequenceserver +22 -30
- data/lib/sequenceserver/api_errors.rb +29 -3
- data/lib/sequenceserver/blast/constants.rb +1 -1
- data/lib/sequenceserver/blast/hit.rb +5 -16
- data/lib/sequenceserver/blast/job.rb +49 -24
- data/lib/sequenceserver/blast/report.rb +38 -30
- data/lib/sequenceserver/config.rb +52 -27
- data/lib/sequenceserver/database.rb +69 -9
- data/lib/sequenceserver/job.rb +14 -4
- data/lib/sequenceserver/job_remover.rb +25 -29
- data/lib/sequenceserver/makeblastdb.rb +40 -45
- data/lib/sequenceserver/refinements.rb +15 -0
- data/lib/sequenceserver/routes.rb +70 -4
- data/lib/sequenceserver/sequence.rb +8 -7
- data/lib/sequenceserver/sys.rb +2 -2
- data/lib/sequenceserver/version.rb +1 -1
- data/lib/sequenceserver/zip_file_generator.rb +56 -0
- data/lib/sequenceserver.rb +16 -11
- data/public/config.js +62 -55
- data/public/css/fonts.css +23 -22
- data/public/css/grapher.css +598 -594
- data/public/css/sequenceserver.css +130 -27
- data/public/css/sequenceserver.min.css +3 -3
- data/public/js/alignment_exporter.js +30 -22
- data/public/js/circos.js +370 -234
- data/public/js/cloud_share_modal.js +216 -0
- data/public/js/databases.js +144 -0
- data/public/js/databases_tree.js +144 -0
- data/public/js/dnd.js +164 -0
- data/public/js/download_fasta.js +1 -1
- data/public/js/error_modal.js +4 -11
- data/public/js/exporter.js +7 -3
- data/public/js/form.js +260 -0
- data/public/js/grapher.js +113 -106
- data/public/js/hit.js +84 -67
- data/public/js/hits_overview.js +3 -3
- data/public/js/hsp.js +343 -288
- data/public/js/jquery_world.js +4 -4
- data/public/js/length_distribution.js +5 -5
- data/public/js/mailto.js +36 -0
- data/public/js/options.js +84 -0
- data/public/js/query.js +321 -64
- data/public/js/report.js +322 -288
- data/public/js/report_root.js +75 -0
- data/public/js/search.js +28 -992
- data/public/js/search_button.js +195 -0
- data/public/js/sequence.js +2409 -2411
- data/public/js/sequence_modal.js +152 -159
- data/public/js/share_url.js +23 -0
- data/public/js/sidebar.js +265 -86
- data/public/js/svgExporter.js +12 -12
- data/public/js/tests/database.spec.js +60 -0
- data/public/js/tests/mock_data/databases.json +91 -0
- data/public/js/tests/mock_data/long_response.json +269 -0
- data/public/js/tests/mock_data/short_response.json +2240 -0
- data/public/js/tests/report.spec.js +99 -0
- data/public/js/tests/search_button.spec.js +14 -0
- data/public/js/tests/search_query.spec.js +41 -0
- data/public/js/visualisation_helpers.js +4 -5
- data/public/packages/circosJS@1.7.0.js +1640 -0
- data/public/packages/jquery-ui@1.11.4.js +16624 -0
- data/public/sequenceserver-report.min.js +2425 -19
- data/public/sequenceserver-search.min.js +2337 -11
- data/public/vendor/github/jspm/nodelibs-assert@0.1.0/index.js +2 -0
- data/public/vendor/github/jspm/{nodelibs-buffer@0.1.0 → nodelibs-assert@0.1.0}/package.json +1 -1
- data/public/vendor/github/jspm/nodelibs-assert@0.1.0.js +1 -0
- data/public/vendor/github/jspm/nodelibs-buffer@0.1.1/package.json +6 -0
- data/public/vendor/github/jspm/nodelibs-buffer@0.1.1.js +1 -0
- data/public/vendor/github/jspm/{nodelibs-process@0.1.1 → nodelibs-process@0.1.2}/package.json +2 -2
- data/public/vendor/github/jspm/nodelibs-process@0.1.2.js +1 -0
- data/public/vendor/github/jspm/nodelibs-vm@0.1.0/index.js +2 -0
- data/public/vendor/github/jspm/nodelibs-vm@0.1.0/package.json +6 -0
- data/public/vendor/github/jspm/nodelibs-vm@0.1.0.js +1 -0
- data/public/vendor/github/vakata/jstree@3.3.8/LICENSE-MIT +22 -0
- data/public/vendor/github/vakata/jstree@3.3.8/README.md +663 -0
- data/public/vendor/github/vakata/jstree@3.3.8/bower.json +33 -0
- data/public/vendor/github/vakata/jstree@3.3.8/component.json +28 -0
- data/public/vendor/github/vakata/jstree@3.3.8/composer.json +46 -0
- data/public/vendor/github/vakata/jstree@3.3.8/demo/README.md +2 -0
- data/public/vendor/github/vakata/jstree@3.3.8/demo/basic/index.html +146 -0
- data/public/vendor/github/vakata/jstree@3.3.8/demo/basic/root.json +1 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/jstree.js +8612 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/jstree.min.js +6 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/32px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/40px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/style.css +1102 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/style.min.css +1 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/throbber.gif +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/32px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/40px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/style.css +1146 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/style.min.css +1 -0
- data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/throbber.gif +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/gruntfile.js +242 -0
- data/public/vendor/github/vakata/jstree@3.3.8/jstree.jquery.json +28 -0
- data/public/vendor/github/vakata/jstree@3.3.8/package.json +58 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/intro.js +14 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.changed.js +69 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.checkbox.js +976 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.conditionalselect.js +38 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.contextmenu.js +661 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.dnd.js +669 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.js +4931 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.massload.js +137 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.search.js +421 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.sort.js +74 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.state.js +138 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.types.js +372 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.unique.js +164 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.wholerow.js +122 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/misc.js +656 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/outro.js +1 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/sample.js +93 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/base.less +93 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/32px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/40px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/style.css +1102 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/style.less +22 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/throbber.gif +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/32px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/40px.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/style.css +1146 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/style.less +50 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/throbber.gif +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/main.less +77 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/mixins.less +104 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/themes/responsive.less +67 -0
- data/public/vendor/github/vakata/jstree@3.3.8/src/vakata-jstree.js +38 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/unit/index.html +16 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/unit/libs/qunit.css +244 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/unit/libs/qunit.js +2212 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/unit/test.js +11 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/desktop/index.html +44 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/mobile/index.html +42 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/desktop/desktop.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/desktop/home.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/mobile/home.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/mobile/mobile.png +0 -0
- data/public/vendor/github/vakata/jstree@3.3.8.js +3 -0
- data/public/vendor/npm/assert@1.5.0/CHANGELOG.md +8 -0
- data/public/vendor/npm/assert@1.5.0/README.md +105 -0
- data/public/vendor/npm/assert@1.5.0/assert.js +327 -0
- data/public/vendor/npm/assert@1.5.0/package.json +32 -0
- data/public/vendor/npm/assert@1.5.0/test.js +288 -0
- data/public/vendor/npm/assert@1.5.0.js +1 -0
- data/public/vendor/npm/{base64-js@0.0.8/LICENSE.MIT → base64-js@1.5.1/LICENSE} +1 -1
- data/public/vendor/npm/{base64-js@0.0.8 → base64-js@1.5.1}/README.md +10 -7
- data/public/vendor/npm/base64-js@1.5.1/base64js.min.js +3 -0
- data/public/vendor/npm/base64-js@1.5.1/index.d.ts +3 -0
- data/public/vendor/npm/base64-js@1.5.1/index.js +151 -0
- data/public/vendor/npm/base64-js@1.5.1/package.json +47 -0
- data/public/vendor/npm/base64-js@1.5.1.js +1 -0
- data/public/vendor/npm/buffer@5.7.1/AUTHORS.md +70 -0
- data/public/vendor/npm/{buffer@3.4.3 → buffer@5.7.1}/README.md +111 -41
- data/public/vendor/npm/buffer@5.7.1/index.d.ts +186 -0
- data/public/vendor/npm/buffer@5.7.1/index.js +1817 -0
- data/public/vendor/npm/buffer@5.7.1/package.json +96 -0
- data/public/vendor/npm/buffer@5.7.1.js +1 -0
- data/public/vendor/npm/core-util-is@1.0.3/LICENSE +19 -0
- data/public/vendor/npm/core-util-is@1.0.3/lib/util.js +64 -0
- data/public/vendor/npm/{core-util-is@1.0.1 → core-util-is@1.0.3}/package.json +13 -1
- data/public/vendor/npm/core-util-is@1.0.3.js +1 -0
- data/public/vendor/npm/events@1.0.2/tests/add-listeners.js +2 -2
- data/public/vendor/npm/events@1.0.2/tests/check-listener-leaks.js +3 -3
- data/public/vendor/npm/events@1.0.2/tests/common.js +1 -1
- data/public/vendor/npm/events@1.0.2/tests/index.js +13 -13
- data/public/vendor/npm/events@1.0.2/tests/listeners-side-effects.js +2 -2
- data/public/vendor/npm/events@1.0.2/tests/listeners.js +2 -2
- data/public/vendor/npm/events@1.0.2/tests/max-listeners.js +2 -2
- data/public/vendor/npm/events@1.0.2/tests/modify-in-emit.js +2 -2
- data/public/vendor/npm/events@1.0.2/tests/num-args.js +2 -2
- data/public/vendor/npm/events@1.0.2/tests/once.js +2 -2
- data/public/vendor/npm/events@1.0.2/tests/remove-all-listeners.js +3 -3
- data/public/vendor/npm/events@1.0.2/tests/remove-listeners.js +3 -3
- data/public/vendor/npm/events@1.0.2/tests/set-max-listeners-side-effects.js +2 -2
- data/public/vendor/npm/events@1.0.2/tests/subclass.js +3 -3
- data/public/vendor/npm/events@1.0.2.js +1 -1
- data/public/vendor/npm/ieee754@1.2.1/LICENSE +11 -0
- data/public/vendor/npm/{ieee754@1.1.6 → ieee754@1.2.1}/README.md +12 -8
- data/public/vendor/npm/ieee754@1.2.1/index.d.ts +10 -0
- data/public/vendor/npm/{ieee754@1.1.6 → ieee754@1.2.1}/index.js +6 -6
- data/public/vendor/npm/ieee754@1.2.1/package.json +52 -0
- data/public/vendor/npm/ieee754@1.2.1.js +1 -0
- data/public/vendor/npm/{is-array@1.0.1 → indexof@0.0.1}/Makefile +3 -3
- data/public/vendor/npm/indexof@0.0.1/Readme.md +15 -0
- data/public/vendor/npm/indexof@0.0.1/component.json +10 -0
- data/public/vendor/npm/indexof@0.0.1/index.js +11 -0
- data/public/vendor/npm/indexof@0.0.1/package.json +12 -0
- data/public/vendor/npm/indexof@0.0.1.js +1 -0
- data/public/vendor/npm/inherits@2.0.1/inherits.js +1 -1
- data/public/vendor/npm/inherits@2.0.1.js +1 -1
- data/public/vendor/npm/isarray@0.0.1.js +1 -1
- data/public/vendor/npm/js-tokens@4.0.0/index.js +23 -0
- data/public/vendor/npm/js-tokens@4.0.0/package.json +30 -0
- data/public/vendor/npm/js-tokens@4.0.0.js +1 -0
- data/public/vendor/npm/loose-envify@1.4.0/LICENSE +21 -0
- data/public/vendor/npm/loose-envify@1.4.0/README.md +45 -0
- data/public/vendor/npm/loose-envify@1.4.0/cli.js +12 -0
- data/public/vendor/npm/loose-envify@1.4.0/custom.js +3 -0
- data/public/vendor/npm/loose-envify@1.4.0/index.js +5 -0
- data/public/vendor/npm/loose-envify@1.4.0/loose-envify.js +33 -0
- data/public/vendor/npm/loose-envify@1.4.0/package.json +36 -0
- data/public/vendor/npm/loose-envify@1.4.0/replace.js +52 -0
- data/public/vendor/npm/loose-envify@1.4.0.js +1 -0
- data/public/vendor/npm/object-assign@4.1.1/index.js +90 -0
- data/public/vendor/npm/object-assign@4.1.1/package.json +42 -0
- data/public/vendor/npm/object-assign@4.1.1.js +1 -0
- data/public/vendor/npm/path-browserify@0.0.0/index.js +1 -1
- data/public/vendor/npm/path-browserify@0.0.0.js +1 -1
- data/public/vendor/npm/{process@0.10.1 → process@0.11.10}/README.md +4 -1
- data/public/vendor/npm/process@0.11.10/browser.js +184 -0
- data/public/vendor/npm/{process@0.10.1 → process@0.11.10}/package.json +10 -1
- data/public/vendor/npm/process@0.11.10/test.js +185 -0
- data/public/vendor/npm/process@0.11.10.js +1 -0
- data/public/vendor/npm/react-dom@18.0.0/LICENSE +21 -0
- data/public/vendor/npm/react-dom@18.0.0/README.md +50 -0
- data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server-legacy.browser.development.js +4771 -0
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# buffer [![travis][travis-image]][travis-url] [![npm][npm-image]][npm-url] [![downloads][downloads-image]][downloads-url] [![javascript style guide][standard-image]][standard-url]
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#### The buffer module from [node.js](https://nodejs.org/), for the browser.
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[travis-image]: https://img.shields.io/travis/feross/buffer.svg?style=flat
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[travis-url]: https://travis-ci.org/feross/buffer
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[downloads-image]: https://img.shields.io/npm/dm/buffer.svg?style=flat
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[saucelabs-image]: https://saucelabs.com/browser-matrix/buffer.svg
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[saucelabs-url]: https://saucelabs.com/u/buffer
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With [browserify](http://browserify.org), simply `require('buffer')` or use the `Buffer` global and you will get this module.
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The goal is to provide an API that is 100% identical to
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[node's Buffer API](
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[official docs](
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[node's Buffer API](https://nodejs.org/api/buffer.html). Read the
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[official docs](https://nodejs.org/api/buffer.html) for the full list of properties,
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instance methods, and class methods that are supported.
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## features
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- Manipulate binary data like a boss, in all browsers
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- Manipulate binary data like a boss, in all browsers!
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- Super fast. Backed by Typed Arrays (`Uint8Array`/`ArrayBuffer`, not `Object`)
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- Extremely small bundle size (**
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- Excellent browser support (
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- Preserves Node API exactly, with one
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- Extremely small bundle size (**6.75KB minified + gzipped**, 51.9KB with comments)
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- Excellent browser support (Chrome, Firefox, Edge, Safari 9+, IE 11, iOS 9+, Android, etc.)
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- Preserves Node API exactly, with one minor difference (see below)
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- Square-bracket `buf[4]` notation works!
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- Does not modify any browser prototypes or put anything on `window`
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- Comprehensive test suite (including all buffer tests from node.js core)
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## install
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To use this module directly (without browserify), install it:
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This module was previously called **native-buffer-browserify**, but please use **buffer**
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from now on.
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If you do not use a bundler, you can use the [standalone script](https://bundle.run/buffer).
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## usage
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[official docs](
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[official docs](https://nodejs.org/api/buffer.html) for the full list of properties,
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instance methods, and class methods that are supported.
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As mentioned above, `require('buffer')` or use the `Buffer` global with
|
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## how does it work?
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The
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changed to `Buffer.prototype`. Furthermore, `Buffer` is a subclass of `Uint8Array`,
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so the returned instances will have all the node `Buffer` methods and the
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`Uint8Array` methods. Square bracket notation works as expected -- it returns a
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single octet.
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The `Uint8Array` prototype remains unmodified.
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## differences
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node
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This module tracks the Buffer API in the latest (unstable) version of node.js. The Buffer
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API is considered **stable** in the
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[node stability index](https://nodejs.org/docs/latest/api/documentation.html#documentation_stability_index),
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so it is unlikely that there will ever be breaking changes.
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Nonetheless, when/if the Buffer API changes in node, this module's API will change
|
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accordingly.
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## related packages
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- [`buffer-reverse`](https://www.npmjs.com/package/buffer-reverse) - Reverse a buffer
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- [`buffer-xor`](https://www.npmjs.com/package/buffer-xor) - Bitwise xor a buffer
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- [`is-buffer`](https://www.npmjs.com/package/is-buffer) - Determine if an object is a Buffer without including the whole `Buffer` package
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-
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the original Buffer. When you modify one buffer, you modify the other. [Read more.](http://iojs.org/api/buffer.html#buffer_buf_slice_start_end)
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## conversion packages
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### convert typed array to buffer
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bug](https://bugzilla.mozilla.org/show_bug.cgi?id=952403) (now fixed!) that made it impossible to add properties to a typed array.*
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Use [`typedarray-to-buffer`](https://www.npmjs.com/package/typedarray-to-buffer) to convert any kind of typed array to a `Buffer`. Does not perform a copy, so it's super fast.
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### convert buffer to typed array
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`Buffer` is a subclass of `Uint8Array` (which is a typed array). So there is no need to explicitly convert to typed array. Just use the buffer as a `Uint8Array`.
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[
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### convert blob to buffer
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Use [`blob-to-buffer`](https://www.npmjs.com/package/blob-to-buffer) to convert a `Blob` to a `Buffer`.
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### convert buffer to blob
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To convert a `Buffer` to a `Blob`, use the `Blob` constructor:
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```js
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var blob = new Blob([ buffer ])
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```
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Optionally, specify a mimetype:
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```js
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var blob = new Blob([ buffer ], { type: 'text/html' })
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+
```
|
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+
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### convert arraybuffer to buffer
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To convert an `ArrayBuffer` to a `Buffer`, use the `Buffer.from` function. Does not perform a copy, so it's super fast.
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```js
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var buffer = Buffer.from(arrayBuffer)
|
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```
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+
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### convert buffer to arraybuffer
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To convert a `Buffer` to an `ArrayBuffer`, use the `.buffer` property (which is present on all `Uint8Array` objects):
|
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+
|
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+
```js
|
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var arrayBuffer = buffer.buffer.slice(
|
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buffer.byteOffset, buffer.byteOffset + buffer.byteLength
|
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+
)
|
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+
```
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+
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+
Alternatively, use the [`to-arraybuffer`](https://www.npmjs.com/package/to-arraybuffer) module.
|
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|
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## performance
|
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|
@@ -113,6 +152,8 @@ sanity check (since `BrowserBuffer` uses `Uint8Array` under the hood, `Uint8Arra
|
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always be at least a bit faster). Finally, `NodeBuffer` is the node.js buffer module,
|
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which is included to compare against.
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NOTE: Performance has improved since these benchmarks were taken. PR welcome to update the README.
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### Chrome 38
|
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|
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|
| Method | Operations | Accuracy | Sampled | Fastest |
|
@@ -323,17 +364,46 @@ which is included to compare against.
|
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| NodeBuffer#writeFloatBE | 135,763 ops/sec | ±0.65% | 96 | |
|
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|
| | | | |
|
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|
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+
## Testing the project
|
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|
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+
First, install the project:
|
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+
|
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|
+
npm install
|
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+
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+
Then, to run tests in Node.js, run:
|
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|
+
|
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|
+
npm run test-node
|
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|
+
|
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|
+
To test locally in a browser, you can run:
|
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|
+
|
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|
+
npm run test-browser-es5-local # For ES5 browsers that don't support ES6
|
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|
+
npm run test-browser-es6-local # For ES6 compliant browsers
|
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|
+
|
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|
+
This will print out a URL that you can then open in a browser to run the tests, using [airtap](https://www.npmjs.com/package/airtap).
|
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|
+
|
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|
+
To run automated browser tests using Saucelabs, ensure that your `SAUCE_USERNAME` and `SAUCE_ACCESS_KEY` environment variables are set, then run:
|
385
|
+
|
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|
+
npm test
|
387
|
+
|
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|
+
This is what's run in Travis, to check against various browsers. The list of browsers is kept in the `bin/airtap-es5.yml` and `bin/airtap-es6.yml` files.
|
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|
+
|
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|
## JavaScript Standard Style
|
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|
|
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|
This module uses [JavaScript Standard Style](https://github.com/feross/standard).
|
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393
|
|
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|
-
[![
|
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|
+
[![JavaScript Style Guide](https://cdn.rawgit.com/feross/standard/master/badge.svg)](https://github.com/feross/standard)
|
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|
+
|
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|
+
To test that the code conforms to the style, `npm install` and run:
|
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397
|
|
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|
+
./node_modules/.bin/standard
|
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|
|
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|
## credit
|
334
401
|
|
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402
|
This was originally forked from [buffer-browserify](https://github.com/toots/buffer-browserify).
|
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403
|
|
404
|
+
## Security Policies and Procedures
|
405
|
+
|
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|
+
The `buffer` team and community take all security bugs in `buffer` seriously. Please see our [security policies and procedures](https://github.com/feross/security) document to learn how to report issues.
|
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|
|
338
408
|
## license
|
339
409
|
|
@@ -0,0 +1,186 @@
|
|
1
|
+
export class Buffer extends Uint8Array {
|
2
|
+
length: number
|
3
|
+
write(string: string, offset?: number, length?: number, encoding?: string): number;
|
4
|
+
toString(encoding?: string, start?: number, end?: number): string;
|
5
|
+
toJSON(): { type: 'Buffer', data: any[] };
|
6
|
+
equals(otherBuffer: Buffer): boolean;
|
7
|
+
compare(otherBuffer: Buffer, targetStart?: number, targetEnd?: number, sourceStart?: number, sourceEnd?: number): number;
|
8
|
+
copy(targetBuffer: Buffer, targetStart?: number, sourceStart?: number, sourceEnd?: number): number;
|
9
|
+
slice(start?: number, end?: number): Buffer;
|
10
|
+
writeUIntLE(value: number, offset: number, byteLength: number, noAssert?: boolean): number;
|
11
|
+
writeUIntBE(value: number, offset: number, byteLength: number, noAssert?: boolean): number;
|
12
|
+
writeIntLE(value: number, offset: number, byteLength: number, noAssert?: boolean): number;
|
13
|
+
writeIntBE(value: number, offset: number, byteLength: number, noAssert?: boolean): number;
|
14
|
+
readUIntLE(offset: number, byteLength: number, noAssert?: boolean): number;
|
15
|
+
readUIntBE(offset: number, byteLength: number, noAssert?: boolean): number;
|
16
|
+
readIntLE(offset: number, byteLength: number, noAssert?: boolean): number;
|
17
|
+
readIntBE(offset: number, byteLength: number, noAssert?: boolean): number;
|
18
|
+
readUInt8(offset: number, noAssert?: boolean): number;
|
19
|
+
readUInt16LE(offset: number, noAssert?: boolean): number;
|
20
|
+
readUInt16BE(offset: number, noAssert?: boolean): number;
|
21
|
+
readUInt32LE(offset: number, noAssert?: boolean): number;
|
22
|
+
readUInt32BE(offset: number, noAssert?: boolean): number;
|
23
|
+
readInt8(offset: number, noAssert?: boolean): number;
|
24
|
+
readInt16LE(offset: number, noAssert?: boolean): number;
|
25
|
+
readInt16BE(offset: number, noAssert?: boolean): number;
|
26
|
+
readInt32LE(offset: number, noAssert?: boolean): number;
|
27
|
+
readInt32BE(offset: number, noAssert?: boolean): number;
|
28
|
+
readFloatLE(offset: number, noAssert?: boolean): number;
|
29
|
+
readFloatBE(offset: number, noAssert?: boolean): number;
|
30
|
+
readDoubleLE(offset: number, noAssert?: boolean): number;
|
31
|
+
readDoubleBE(offset: number, noAssert?: boolean): number;
|
32
|
+
reverse(): this;
|
33
|
+
swap16(): Buffer;
|
34
|
+
swap32(): Buffer;
|
35
|
+
swap64(): Buffer;
|
36
|
+
writeUInt8(value: number, offset: number, noAssert?: boolean): number;
|
37
|
+
writeUInt16LE(value: number, offset: number, noAssert?: boolean): number;
|
38
|
+
writeUInt16BE(value: number, offset: number, noAssert?: boolean): number;
|
39
|
+
writeUInt32LE(value: number, offset: number, noAssert?: boolean): number;
|
40
|
+
writeUInt32BE(value: number, offset: number, noAssert?: boolean): number;
|
41
|
+
writeInt8(value: number, offset: number, noAssert?: boolean): number;
|
42
|
+
writeInt16LE(value: number, offset: number, noAssert?: boolean): number;
|
43
|
+
writeInt16BE(value: number, offset: number, noAssert?: boolean): number;
|
44
|
+
writeInt32LE(value: number, offset: number, noAssert?: boolean): number;
|
45
|
+
writeInt32BE(value: number, offset: number, noAssert?: boolean): number;
|
46
|
+
writeFloatLE(value: number, offset: number, noAssert?: boolean): number;
|
47
|
+
writeFloatBE(value: number, offset: number, noAssert?: boolean): number;
|
48
|
+
writeDoubleLE(value: number, offset: number, noAssert?: boolean): number;
|
49
|
+
writeDoubleBE(value: number, offset: number, noAssert?: boolean): number;
|
50
|
+
fill(value: any, offset?: number, end?: number): this;
|
51
|
+
indexOf(value: string | number | Buffer, byteOffset?: number, encoding?: string): number;
|
52
|
+
lastIndexOf(value: string | number | Buffer, byteOffset?: number, encoding?: string): number;
|
53
|
+
includes(value: string | number | Buffer, byteOffset?: number, encoding?: string): boolean;
|
54
|
+
|
55
|
+
/**
|
56
|
+
* Allocates a new buffer containing the given {str}.
|
57
|
+
*
|
58
|
+
* @param str String to store in buffer.
|
59
|
+
* @param encoding encoding to use, optional. Default is 'utf8'
|
60
|
+
*/
|
61
|
+
constructor (str: string, encoding?: string);
|
62
|
+
/**
|
63
|
+
* Allocates a new buffer of {size} octets.
|
64
|
+
*
|
65
|
+
* @param size count of octets to allocate.
|
66
|
+
*/
|
67
|
+
constructor (size: number);
|
68
|
+
/**
|
69
|
+
* Allocates a new buffer containing the given {array} of octets.
|
70
|
+
*
|
71
|
+
* @param array The octets to store.
|
72
|
+
*/
|
73
|
+
constructor (array: Uint8Array);
|
74
|
+
/**
|
75
|
+
* Produces a Buffer backed by the same allocated memory as
|
76
|
+
* the given {ArrayBuffer}.
|
77
|
+
*
|
78
|
+
*
|
79
|
+
* @param arrayBuffer The ArrayBuffer with which to share memory.
|
80
|
+
*/
|
81
|
+
constructor (arrayBuffer: ArrayBuffer);
|
82
|
+
/**
|
83
|
+
* Allocates a new buffer containing the given {array} of octets.
|
84
|
+
*
|
85
|
+
* @param array The octets to store.
|
86
|
+
*/
|
87
|
+
constructor (array: any[]);
|
88
|
+
/**
|
89
|
+
* Copies the passed {buffer} data onto a new {Buffer} instance.
|
90
|
+
*
|
91
|
+
* @param buffer The buffer to copy.
|
92
|
+
*/
|
93
|
+
constructor (buffer: Buffer);
|
94
|
+
prototype: Buffer;
|
95
|
+
/**
|
96
|
+
* Allocates a new Buffer using an {array} of octets.
|
97
|
+
*
|
98
|
+
* @param array
|
99
|
+
*/
|
100
|
+
static from(array: any[]): Buffer;
|
101
|
+
/**
|
102
|
+
* When passed a reference to the .buffer property of a TypedArray instance,
|
103
|
+
* the newly created Buffer will share the same allocated memory as the TypedArray.
|
104
|
+
* The optional {byteOffset} and {length} arguments specify a memory range
|
105
|
+
* within the {arrayBuffer} that will be shared by the Buffer.
|
106
|
+
*
|
107
|
+
* @param arrayBuffer The .buffer property of a TypedArray or a new ArrayBuffer()
|
108
|
+
* @param byteOffset
|
109
|
+
* @param length
|
110
|
+
*/
|
111
|
+
static from(arrayBuffer: ArrayBuffer, byteOffset?: number, length?: number): Buffer;
|
112
|
+
/**
|
113
|
+
* Copies the passed {buffer} data onto a new Buffer instance.
|
114
|
+
*
|
115
|
+
* @param buffer
|
116
|
+
*/
|
117
|
+
static from(buffer: Buffer | Uint8Array): Buffer;
|
118
|
+
/**
|
119
|
+
* Creates a new Buffer containing the given JavaScript string {str}.
|
120
|
+
* If provided, the {encoding} parameter identifies the character encoding.
|
121
|
+
* If not provided, {encoding} defaults to 'utf8'.
|
122
|
+
*
|
123
|
+
* @param str
|
124
|
+
*/
|
125
|
+
static from(str: string, encoding?: string): Buffer;
|
126
|
+
/**
|
127
|
+
* Returns true if {obj} is a Buffer
|
128
|
+
*
|
129
|
+
* @param obj object to test.
|
130
|
+
*/
|
131
|
+
static isBuffer(obj: any): obj is Buffer;
|
132
|
+
/**
|
133
|
+
* Returns true if {encoding} is a valid encoding argument.
|
134
|
+
* Valid string encodings in Node 0.12: 'ascii'|'utf8'|'utf16le'|'ucs2'(alias of 'utf16le')|'base64'|'binary'(deprecated)|'hex'
|
135
|
+
*
|
136
|
+
* @param encoding string to test.
|
137
|
+
*/
|
138
|
+
static isEncoding(encoding: string): boolean;
|
139
|
+
/**
|
140
|
+
* Gives the actual byte length of a string. encoding defaults to 'utf8'.
|
141
|
+
* This is not the same as String.prototype.length since that returns the number of characters in a string.
|
142
|
+
*
|
143
|
+
* @param string string to test.
|
144
|
+
* @param encoding encoding used to evaluate (defaults to 'utf8')
|
145
|
+
*/
|
146
|
+
static byteLength(string: string, encoding?: string): number;
|
147
|
+
/**
|
148
|
+
* Returns a buffer which is the result of concatenating all the buffers in the list together.
|
149
|
+
*
|
150
|
+
* If the list has no items, or if the totalLength is 0, then it returns a zero-length buffer.
|
151
|
+
* If the list has exactly one item, then the first item of the list is returned.
|
152
|
+
* If the list has more than one item, then a new Buffer is created.
|
153
|
+
*
|
154
|
+
* @param list An array of Buffer objects to concatenate
|
155
|
+
* @param totalLength Total length of the buffers when concatenated.
|
156
|
+
* If totalLength is not provided, it is read from the buffers in the list. However, this adds an additional loop to the function, so it is faster to provide the length explicitly.
|
157
|
+
*/
|
158
|
+
static concat(list: Buffer[], totalLength?: number): Buffer;
|
159
|
+
/**
|
160
|
+
* The same as buf1.compare(buf2).
|
161
|
+
*/
|
162
|
+
static compare(buf1: Buffer, buf2: Buffer): number;
|
163
|
+
/**
|
164
|
+
* Allocates a new buffer of {size} octets.
|
165
|
+
*
|
166
|
+
* @param size count of octets to allocate.
|
167
|
+
* @param fill if specified, buffer will be initialized by calling buf.fill(fill).
|
168
|
+
* If parameter is omitted, buffer will be filled with zeros.
|
169
|
+
* @param encoding encoding used for call to buf.fill while initializing
|
170
|
+
*/
|
171
|
+
static alloc(size: number, fill?: string | Buffer | number, encoding?: string): Buffer;
|
172
|
+
/**
|
173
|
+
* Allocates a new buffer of {size} octets, leaving memory not initialized, so the contents
|
174
|
+
* of the newly created Buffer are unknown and may contain sensitive data.
|
175
|
+
*
|
176
|
+
* @param size count of octets to allocate
|
177
|
+
*/
|
178
|
+
static allocUnsafe(size: number): Buffer;
|
179
|
+
/**
|
180
|
+
* Allocates a new non-pooled buffer of {size} octets, leaving memory not initialized, so the contents
|
181
|
+
* of the newly created Buffer are unknown and may contain sensitive data.
|
182
|
+
*
|
183
|
+
* @param size count of octets to allocate
|
184
|
+
*/
|
185
|
+
static allocUnsafeSlow(size: number): Buffer;
|
186
|
+
}
|