From c63080556acea474d37297866cfdfc54a2a610ee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micha=C3=ABl=20Zasso?= Date: Wed, 24 Mar 2021 16:18:53 +0100 Subject: [PATCH] fix: update dependencies --- .github/workflows/lactame.yml | 11 +- .github/workflows/nodejs.yml | 39 +- .github/workflows/release.yml | 15 +- .github/workflows/typedoc.yml | 14 +- docs/assets/css/main.css | 1 - docs/assets/images/icons.png | Bin 9615 -> 0 bytes docs/assets/images/icons@2x.png | Bin 28144 -> 0 bytes docs/assets/images/widgets.png | Bin 480 -> 0 bytes docs/assets/images/widgets@2x.png | Bin 855 -> 0 bytes docs/assets/js/main.js | 51 - docs/assets/js/search.json | 1 - docs/classes/chromatogram.html | 1380 ----------------- docs/classes/chromatogramseries.html | 277 ---- docs/classes/chromatogramseries1d.html | 271 ---- docs/classes/chromatogramseries2d.html | 271 ---- docs/globals.html | 854 ---------- docs/index.html | 311 ---- docs/interfaces/addseriesoptions.html | 160 -- 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docs/interfaces/meanfilteroptions.html delete mode 100644 docs/interfaces/mergeoptions.html delete mode 100644 docs/interfaces/mergeresult.html delete mode 100644 docs/interfaces/nmfoptions.html delete mode 100644 docs/interfaces/percentagefilteroptions.html delete mode 100644 docs/interfaces/scalealignmentoptions.html delete mode 100644 docs/interfaces/spectracomparisonoptions.html delete mode 100644 docs/interfaces/spectracomparisonresult.html delete mode 100644 docs/interfaces/vectorifyoptions.html diff --git a/.github/workflows/lactame.yml b/.github/workflows/lactame.yml index 912db9c..08598ba 100644 --- a/.github/workflows/lactame.yml +++ b/.github/workflows/lactame.yml @@ -4,16 +4,19 @@ on: release: types: [published] +env: + NODE_VERSION: 14.x + jobs: deploy: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 - name: Get package name - run: echo "PACKAGENAME=$(jq .name package.json | tr -d '"')" >> $GITHUB_ENV - - uses: actions/setup-node@v2-beta + run: echo "PACKAGE_NAME=$(jq .name package.json | tr -d '"')" >> $GITHUB_ENV + - uses: actions/setup-node@v2 with: - node-version: 14.x + node-version: ${{ env.NODE_VERSION }} - name: Install dependencies run: npm install - name: Build project @@ -22,5 +25,5 @@ jobs: uses: zakodium/lactame-action@v1 with: token: ${{ secrets.LACTAME_TOKEN }} - name: "${{env.PACKAGENAME}}" + name: ${{ env.PACKAGE_NAME }} folder: dist diff --git a/.github/workflows/nodejs.yml b/.github/workflows/nodejs.yml index 06c33b7..2056e66 100644 --- a/.github/workflows/nodejs.yml +++ b/.github/workflows/nodejs.yml @@ -5,35 +5,36 @@ on: branches: master pull_request: +env: + NODE_VERSION: 14.x + jobs: lint: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v1 - - name: Use Node.js 12 - uses: actions/setup-node@v1 + - uses: actions/checkout@v2 + - uses: actions/setup-node@v2 with: - node-version: 12 - - name: npm install and test - run: | - npm install - npm run eslint - env: - CI: true + node-version: ${{ env.NODE_VERSION }} + - name: Install dependencies + run: npm install + - name: Run ESLint + run: npm run eslint test: runs-on: ubuntu-latest strategy: matrix: - node-version: [10.x, 12.x, 13.x] + node-version: [10.x, 12.x, 14.x, 15.x] + fail-fast: false steps: - - uses: actions/checkout@v1 + - uses: actions/checkout@v2 - name: Use Node.js ${{ matrix.node-version }} - uses: actions/setup-node@v1 + uses: actions/setup-node@v2 with: node-version: ${{ matrix.node-version }} - - name: npm install and test - run: | - npm install - npm run test-coverage - env: - CI: true + - name: Install dependencies + run: npm install + - name: Run tests + run: npm run test-coverage + - name: Send coverage report to Codecov + uses: codecov/codecov-action@v1 diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 9ed58e8..455b052 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -5,28 +5,33 @@ on: branches: - master +env: + NODE_VERSION: 14.x + jobs: release-please: runs-on: ubuntu-latest steps: - - uses: GoogleCloudPlatform/release-please-action@v2.5.6 + - name: Get package name + run: echo "PACKAGE_NAME=$(jq .name package.json | tr -d '"')" >> $GITHUB_ENV + - uses: GoogleCloudPlatform/release-please-action@v2 id: release with: token: ${{ secrets.BOT_TOKEN }} release-type: node - package-name: 'chromatography' + package-name: ${{ env.PACKAGE_NAME }} bump-minor-pre-major: Yes - uses: actions/checkout@v2 # These if statements ensure that a publication only occurs when a new release is created if: ${{ steps.release.outputs.release_created }} - - uses: actions/setup-node@v2-beta + - uses: actions/setup-node@v2 with: - node-version: 14.x + node-version: ${{ env.NODE_VERSION }} registry-url: 'https://registry.npmjs.org' if: ${{ steps.release.outputs.release_created }} - run: npm install if: ${{ steps.release.outputs.release_created }} - - run: npm publish + - run: npm publish --access public env: NODE_AUTH_TOKEN: ${{ secrets.NPM_BOT_TOKEN }} if: ${{ steps.release.outputs.release_created }} diff --git a/.github/workflows/typedoc.yml b/.github/workflows/typedoc.yml index 23e005b..ba5144d 100644 --- a/.github/workflows/typedoc.yml +++ b/.github/workflows/typedoc.yml @@ -1,18 +1,28 @@ name: Deploy TypeDoc on GitHub pages on: + workflow_dispatch: release: types: [published] +env: + NODE_VERSION: 14.x + ENTRY_FILE: 'chromatography.d.ts' + jobs: deploy: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 + - uses: actions/setup-node@v2 + with: + node-version: ${{ env.NODE_VERSION }} + - name: Install dependencies + run: npm install - name: Build documentation - uses: zakodium/typedoc-action@v1 + uses: zakodium/typedoc-action@v2 with: - entry: 'src/index.ts' + entry: ${{ env.ENTRY_FILE }} - name: Deploy to GitHub pages uses: JamesIves/github-pages-deploy-action@releases/v3 with: diff --git a/docs/assets/css/main.css b/docs/assets/css/main.css deleted file mode 100644 index 3c0dcab..0000000 --- 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\ No newline at end of file diff --git a/docs/classes/chromatogram.html b/docs/classes/chromatogram.html deleted file mode 100644 index d723fe3..0000000 --- a/docs/classes/chromatogram.html +++ /dev/null @@ -1,1380 +0,0 @@ - - - - - - Chromatogram | Chromatography - - - - - -
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Class Chromatogram

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Hierarchy

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Index

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Constructors

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Accessors

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Constructors

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constructor

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  • new Chromatogram(times: number[], series: {}): Chromatogram
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Accessors

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firstTime

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lastTime

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length

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Methods

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addSeries

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applyLockMass

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calculateBpc

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    Calculate the base peak chromatogram (BPC) and save it in the "bpc" series.

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calculateEic

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    Calculate the extracted ion chromatogram (EIC) and save it in a new series.

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      targetMass: number | number[]
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      Mass or masses for which to extract the spectrum.

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      Optional options: CalculateForMassOptions
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    Returns ChromatogramSeries1D

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    • The created series.
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calculateForMF

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calculateLength

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    Calculate length (number of points of each related information) and save it in the "length" series.

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      seriesName: string
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      Name of the series to make calculation on. It must be a 2D series.

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      Optional options: CalculateOptions
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calculateTic

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copy

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deconvolution

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deleteSeries

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    Delete a series.

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      seriesName: string
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filter

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    Will filter the entries based on the index and time.

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    Parameters

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      callback: (index: number, time: number) => boolean
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          Parameters

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            index: number
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          Returns boolean

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      Optional options: FilterOptions
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    Returns Chromatogram

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getClosestData

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getClosestTime

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    Returns the index of the closest real time to the specified one.

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      time: number
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      Retention time.

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    Returns number

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    • Time index.
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getMzVsTimesMatrix

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getPeaks

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getSeries

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    Find the series from its name.

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    Parameters

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      seriesName: string
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      Name of the series.

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    Returns ChromatogramSeries<number[] | number[][][]>

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getSeries1D

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getSeries2D

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getSeriesNames

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getTimes

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hasMass

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    Returns whether the chromatogram has an "ms" series.

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    Returns boolean

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hasSeries

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    Returns whether the series exists.

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    Parameters

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      seriesName: string
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      Name of the series to check.

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integrate

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meanFilter

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merge

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percentageFilter

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requiresSeries

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    Throws an error if the series does not exist.

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    Parameters

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      Name of the series to check.

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rescaleTime

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    Modifies the time applying the conversion function.

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          Returns number

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    Returns this

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setTimes

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    Assign the time values.

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      times: number[]
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      New time values.

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toJSON

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    Returns a serializable representation of the chromatogram.

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Class ChromatogramSeries<DataType>

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getData

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is1D

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is2D

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keep

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    Specify an array of indexes to keep.

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    Parameters

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toJSON

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    Returns { data: DataType; meta?: object }

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Class ChromatogramSeries1D

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getData

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is1D

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is2D

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keep

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toJSON

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Class ChromatogramSeries2D

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getData

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is1D

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is2D

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keep

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toJSON

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Chromatography

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Type aliases

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ChromatogramSeriesData

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ChromatogramSeriesData: number[] | number[][][]
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Functions

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appendKovats

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appendMass

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cosineSimilarity

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  • cosineSimilarity(ms1x: number[], ms1y: number[], ms2x: number[], ms2y: number[]): number
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    Cosine similarity between two MS spectra. - This algorithm is optimized for missing mass values.

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    Parameters

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      ms1x: number[]
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      Array of mass values for the first spectra

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      ms1y: number[]
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      Array of weighted abundance values for the first spectra

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      ms2x: number[]
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      Array of mass values for the second spectra

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      ms2y: number[]
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      Array of weighted abundance values for the second spectra

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    Similarity between two MS spectra.

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fromJSON

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fromJcamp

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    Creates a new Chromatogram from a JCAMP string.

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    Parameters

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      jcamp: string
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      String containing the JCAMP data

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fromNetCDF

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fromText

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fromXML

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    Creates a new Chromatogram from supported XML formats.

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    Parameters

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      xml: string
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      String containing the XML chromatogram.

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    Returns Chromatogram

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getKovatsConversionFunction

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    Returns a function that can convert from time to Kovats or from Kovats to time.

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    Parameters

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    Returns (value: number) => number

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        Returns number

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kovats

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massFilter

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scaleAlignment

- -
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    Aligns the time of the sample based on the regression with his reference value

    -
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    Parameters

    -
      -
    • -
      reference: any[]
      -
      -

      Array of peaks, integrated mass spectra and weighted mass spectra for the reference chromatogram

      -
      -
      • -
    • -
      sample: any[]
      -
      -

      Array of peaks, integrated mass spectra and weighted mass spectra for the sample chromatogram

      -
      -
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      Optional options: ScaleAlignmentOptions
      -
      • -
    -

    Returns any

    -

    The scaled spectra.

    -
      -
    • scaleRegression: The regression function to make the regression
      • -
    • stringFormula: Regression equation
      • -
    • r2: R2 quality number
      • -
    • error: Vector of the difference between the spected value and the actual shift value
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spectraComparison

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vectorify

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Chromatography

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chromatography

- -

NPM version - build status - npm download

-

Tools for storing, searching and analyzing GC/MS data.

- -

Installation

- -

$ npm i chromatography

- -

Usage

- - 
import * as GCMS from 'chromatography';
-
-let gcms = GCMS.fromJcamp(jcampReferenceMixture);
-
-let kovatsConversionTable = GCMS.appendKovats(gcms); // [{time, value}]
-let conversionFunction = GCMS.getKovatsConversionFunction(
-  kovatsConversionTable,
-  {},
-);
-
-let diesel = GCMS.fromJcamp(jcampOfDiesel);
-let times = GCMS.rescaleTime(diesel.getTimes(), conversionFunction);
-diesel.setTimes(times);
-
-let peaks = GCMS.getPeaks(diesel, options);
-let dieselJSON = diesel.toJSON(options); // [{time:12, height:12, width: 3, mass: [{mass, intensity}]}]
-let gcms2 = GCMS.fromJSON(anotherDieselJSON);
-let similarity = GCMS.similarity(gcms, gcms2, options);
-
-// Get a spectrum in another reference model
-let revertConversionFunction = GCMS.getKovatsConversionFunction(
-  kovatsConversionTable,
-  { revert: true },
-);
-let mySpectrumInAnotherReference = revertConversionFunction(mySpectrum);
- -

API Documentation

- -

API discussion

- -

License

- -

MIT

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Legend

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Interface AddSeriesOptions

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Hierarchy

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Index

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Properties

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Properties

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Optional force

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force: boolean
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Force replacement of existing series. - If false, trying to add an already existing series will throw an error.

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default
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false

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Interface AppendKovatsResult

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Hierarchy

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Index

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Properties

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Properties

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from

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from: number
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kovats

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kovats: KovatsResult
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ms

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ms: MergeResult
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to

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to: number
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Legend

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Interface AppendMassOptions

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Hierarchy

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Index

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Properties

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Properties

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Optional mergeThreshold

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mergeThreshold: number
- -
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Parameter for merging the peaks

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default
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0.3

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Optional range

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range: ChromatogramRange
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Range to merge.

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Optional seriesName

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seriesName: string
- -
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Name of the mass series.

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default
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'ms'

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Legend

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Interface AppendMassResult

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Hierarchy

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Properties

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from

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from: number
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ms

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ms: MergeResult
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to

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to: number
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Legend

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Interface ApplyLockMassOptions

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Hierarchy

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Index

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Properties

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Properties

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Optional maxShift

-
maxShift: number
- -
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Maximum allowed shift

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default
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0.1

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Optional oddReference

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oddReference: boolean
- -
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Whether the reference is in the odd position.

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default
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true

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Legend

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Interface CalculateForMassOptions

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Hierarchy

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Index

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Properties

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Properties

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Optional cache

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cache: boolean
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Retrieve result from cache if it exists.

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default
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false

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Optional force

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force: boolean
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Force replacement of existing series. - If false, trying to add an already existing series will throw an error.

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default
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false

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Optional seriesName

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seriesName: string
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Name of the series where the result will be stored. - Defaults to an automatically generated name.

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Optional slotWidth

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slotWidth: number
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Width of the slot around the target mass.

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default
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1

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Legend

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Interface CalculateForMFOptions

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Hierarchy

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Index

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Properties

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Properties

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Optional cache

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cache: boolean
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Retrieve result from cache if it exists.

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false

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Optional force

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force: boolean
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Force replacement of existing series. - If false, trying to add an already existing series will throw an error.

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default
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false

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Optional ionizations

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ionizations: string
- -
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-

List of allowed ionisations.

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-
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default
-

'H+'

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Optional seriesName

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seriesName: string
- -
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Name of the series where the result will be stored. - Defaults to an automatically generated name.

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Optional slotWidth

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slotWidth: number
- -
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Width of the slot around the mass of targetMF.

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default
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1

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Optional threshold

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threshold: number
- -
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Minimal height for peaks.

-
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default
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0.5

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Legend

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- - - \ No newline at end of file diff --git a/docs/interfaces/calculateoptions.html b/docs/interfaces/calculateoptions.html deleted file mode 100644 index 9c2a30b..0000000 --- a/docs/interfaces/calculateoptions.html +++ /dev/null @@ -1,160 +0,0 @@ - - - - - - CalculateOptions | Chromatography - - - - - -
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Interface CalculateOptions

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Hierarchy

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Properties

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Force the calculation if it already exists. - If false, calling the method more than once will have no effect.

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false

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Legend

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Interface ChromatogramPeak

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Hierarchy

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Index

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Properties

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Properties

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from

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from: number
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inflectionPoints

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inflectionPoints: { from: number; to: number }
- -
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Type declaration

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intensity

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intensity: number
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retentionTime

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retentionTime: number
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to

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to: number
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toIndex

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toIndex: number
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Legend

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Interface ChromatogramRange

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Hierarchy

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Properties

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from

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Legend

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Interface DeconvolutionOptions

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Hierarchy

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  • - DeconvolutionOptions -
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Index

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Properties

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Properties

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nmfOptions

-
nmfOptions: nmfOptions
- -
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range

-
range: ChromatogramRange
- -
-
- -

rank

-
rank: number
- -
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Number of pure components

-
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Legend

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Interface DeconvolutionResult

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Hierarchy

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Properties

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component

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component: number[][]
- -
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Matrix with row as estimated pure components

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matrix

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matrix: number[][]
- -
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submatrix, times and m/z axis of the range

-
-
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mzAxis

-
mzAxis: number[]
- -
-
-

vector with m/z value of the range

-
-
-
-
- -

profile

-
profile: number[][]
- -
-
-

Matrix with columns as composition profile

-
-
-
-
- -

rank

-
rank: number
- -
-
-

number of pure components

-
-
-
-
- -

times

-
times: number[]
- -
-
-

vector with retention times of the range

-
-
-
-
-
-
- - -
-
-
-
-
-

Legend

-
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    -
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- - - \ No newline at end of file diff --git a/docs/interfaces/filteroptions.html b/docs/interfaces/filteroptions.html deleted file mode 100644 index 43eb5d4..0000000 --- a/docs/interfaces/filteroptions.html +++ /dev/null @@ -1,159 +0,0 @@ - - - - - - FilterOptions | Chromatography - - - - - -
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Interface FilterOptions

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-
-
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-
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Hierarchy

-
    -
  • - FilterOptions -
    • -
-
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Index

-
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-

Properties

- -
-
-
-
-
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Properties

-
- -

Optional copy

-
copy: boolean
- -
-
-

Whether the method should return a copy of the chromatogram or modify it in-place.

-
-
-
default
-

false

-
-
-
-
-
-
-
- - -
-
-
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Legend

-
-
    -
  • Constructor
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    • -
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  • Inherited method
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- - - \ No newline at end of file diff --git a/docs/interfaces/fromjsonobject.html b/docs/interfaces/fromjsonobject.html deleted file mode 100644 index 313a971..0000000 --- a/docs/interfaces/fromjsonobject.html +++ /dev/null @@ -1,163 +0,0 @@ - - - - - - FromJSONObject | Chromatography - - - - - -
-
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    -
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  • Public/Protected
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- -

Interface FromJSONObject

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Hierarchy

-
    -
  • - FromJSONObject -
    • -
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Index

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Properties

- -
-
-
-
-
-

Properties

-
- -

series

-
series: { data: ChromatogramSeriesData; name: string }[] | {}
- -
-
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times

-
times: number[]
- -
-
-
-
- - -
-
-
-
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-

Legend

-
-
    -
  • Constructor
    • -
  • Method
    • -
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  • Property
    • -
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  • Inherited method
    • -
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- - - \ No newline at end of file diff --git a/docs/interfaces/fromtextoptions.html b/docs/interfaces/fromtextoptions.html deleted file mode 100644 index a82ee93..0000000 --- a/docs/interfaces/fromtextoptions.html +++ /dev/null @@ -1,233 +0,0 @@ - - - - - - FromTextOptions | Chromatography - - - - - -
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Interface FromTextOptions

-
-
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Hierarchy

-
    -
  • - FromTextOptions -
    • -
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Index

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Properties

- -
-
-
-
-
-

Properties

-
- -

keepInfo

-
keepInfo: boolean
- -
-
- -

maxNumberColumns

-
maxNumberColumns: number
- -
-
- -

minNumberColumns

-
minNumberColumns: number
- -
-
- -

rescale

-
rescale: boolean
- -
-
- -

uniqueX

-
uniqueX: boolean
- -
-
- -

xColumn

-
xColumn: number
- -
-
- -

yColumn

-
yColumn: number
- -
-
-
-
- - -
-
-
-
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-

Legend

-
-
    -
  • Constructor
    • -
  • Method
    • -
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  • Property
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  • Inherited method
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- - - \ No newline at end of file diff --git a/docs/interfaces/getclosestdataoptions.html b/docs/interfaces/getclosestdataoptions.html deleted file mode 100644 index f20c835..0000000 --- a/docs/interfaces/getclosestdataoptions.html +++ /dev/null @@ -1,159 +0,0 @@ - - - - - - GetClosestDataOptions | Chromatography - - - - - -
-
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- -

Interface GetClosestDataOptions

-
-
-
-
-
-
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Hierarchy

-
    -
  • - GetClosestDataOptions -
    • -
-
-
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Index

-
-
-
-

Properties

- -
-
-
-
-
-

Properties

-
- -

Optional seriesName

-
seriesName: string
- -
-
-

Name of the mass series

-
-
-
default
-

'ms'

-
-
-
-
-
-
-
- - -
-
-
-
-
-

Legend

-
-
    -
  • Constructor
    • -
  • Method
    • -
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    -
  • Property
    • -
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  • Inherited method
    • -
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- - - \ No newline at end of file diff --git a/docs/interfaces/getclosestdataresult.html b/docs/interfaces/getclosestdataresult.html deleted file mode 100644 index 4b49323..0000000 --- a/docs/interfaces/getclosestdataresult.html +++ /dev/null @@ -1,185 +0,0 @@ - - - - - - GetClosestDataResult | Chromatography - - - - - -
-
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-
- -

Interface GetClosestDataResult<DataType>

-
-
-
-
-
-
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-

Type parameters

-
    -
  • -

    DataType

    -
    • -
-
-
-

Hierarchy

-
    -
  • - GetClosestDataResult -
    • -
-
-
-

Index

-
-
-
-

Properties

- -
-
-
-
-
-

Properties

-
- -

data

-
data: DataType
- -
-
- -

index

-
index: number
- -
-
- -

rt

-
rt: number
- -
-
-
-
- - -
-
-
-
-
-

Legend

-
-
    -
  • Constructor
    • -
  • Method
    • -
-
    -
  • Property
    • -
-
    -
  • Inherited method
    • -
-
-
-
-
- - - \ No newline at end of file diff --git a/docs/interfaces/getkovatsconversionfunctionoptions.html b/docs/interfaces/getkovatsconversionfunctionoptions.html deleted file mode 100644 index 0470494..0000000 --- a/docs/interfaces/getkovatsconversionfunctionoptions.html +++ /dev/null @@ -1,160 +0,0 @@ - - - - - - GetKovatsConversionFunctionOptions | Chromatography - - - - - -
-
-
-
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-
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- -

Interface GetKovatsConversionFunctionOptions

-
-
-
-
-
-
-
-

Hierarchy

-
    -
  • - GetKovatsConversionFunctionOptions -
    • -
-
-
-

Index

-
-
-
-

Properties

- -
-
-
-
-
-

Properties

-
- -

Optional revert

-
revert: boolean
- -
-
-

If true, the function will convert from Kovats to time. - If false, the function will convert from time to Kovats.

-
-
-
default
-

false

-
-
-
-
-
-
-
- - -
-
-
-
-
-

Legend

-
-
    -
  • Constructor
    • -
  • Method
    • -
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  • Property
    • -
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  • Inherited method
    • -
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- - - \ No newline at end of file diff --git a/docs/interfaces/getpeaksoptions.html b/docs/interfaces/getpeaksoptions.html deleted file mode 100644 index a6d1e2a..0000000 --- a/docs/interfaces/getpeaksoptions.html +++ /dev/null @@ -1,183 +0,0 @@ - - - - - - GetPeaksOptions | Chromatography - - - - - -
-
-
-
- -
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- Options -
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    -
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  • Public/Protected
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- -

Interface GetPeaksOptions

-
-
-
-
-
-
-
-

Hierarchy

-
    -
  • - GetPeaksOptions -
    • -
-
-
-

Index

-
-
-
-

Properties

- -
-
-
-
-
-

Properties

-
- -

Optional heightFilter

-
heightFilter: number
- -
-
-

Filter all objects that are below heightFilter times the median of the height.

-
-
-
default:
-

2

-
-
-
-
-
- -

Optional seriesName

-
seriesName: string
- -
-
-

Series to do the peak picking on

-
-
-
default
-

'tic'

-
-
-
-
-
-
-
- - -
-
-
-
-
-

Legend

-
-
    -
  • Constructor
    • -
  • Method
    • -
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  • Property
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  • Inherited method
    • -
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-
- - - \ No newline at end of file diff --git a/docs/interfaces/integrateoptions.html b/docs/interfaces/integrateoptions.html deleted file mode 100644 index b486935..0000000 --- a/docs/interfaces/integrateoptions.html +++ /dev/null @@ -1,178 +0,0 @@ - - - - - - IntegrateOptions | Chromatography - - - - - -
-
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Interface IntegrateOptions

-
-
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-
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-

Hierarchy

-
    -
  • - IntegrateOptions -
    • -
-
-
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Index

-
-
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-

Properties

- -
-
-
-
-
-

Properties

-
- -

Optional baseline

-
baseline: "trapezoid" | "min"
- -
-
-

Apply the specified baseline correction.

-
-
-
-
- -

Optional seriesName

-
seriesName: string
- -
-
-

Name of the chromatogram series to use.

-
-
-
default
-

'tic'

-
-
-
-
-
-
-
- - -
-
-
-
-
-

Legend

-
-
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  • Constructor
    • -
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    • -
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    • -
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- - - \ No newline at end of file diff --git a/docs/interfaces/integrateresult.html b/docs/interfaces/integrateresult.html deleted file mode 100644 index 0bf5e6e..0000000 --- a/docs/interfaces/integrateresult.html +++ /dev/null @@ -1,205 +0,0 @@ - - - - - - IntegrateResult | Chromatography - - - - - -
-
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Interface IntegrateResult

-
-
-
-
-
-
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-

Hierarchy

-
    -
  • - IntegrateResult -
    • -
-
-
-

Index

-
-
-
-

Properties

- -
-
-
-
-
-

Properties

-
- -

from

-
from: { baseline: number; index: number; time: number }
- -
-

Type declaration

-
    -
  • -
    baseline: number
    -
    • -
  • -
    index: number
    -
    • -
  • -
    time: number
    -
    • -
-
-
-
- -

integration

-
integration: number
- -
-
- -

to

-
to: { baseline: number; index: number; time: number }
- -
-

Type declaration

-
    -
  • -
    baseline: number
    -
    • -
  • -
    index: number
    -
    • -
  • -
    time: number
    -
    • -
-
-
-
-
-
- - -
-
-
-
-
-

Legend

-
-
    -
  • Constructor
    • -
  • Method
    • -
-
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  • Property
    • -
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  • Inherited method
    • -
-
-
-
-
- - - \ No newline at end of file diff --git a/docs/interfaces/kovatsoptions.html b/docs/interfaces/kovatsoptions.html deleted file mode 100644 index 2386a73..0000000 --- a/docs/interfaces/kovatsoptions.html +++ /dev/null @@ -1,156 +0,0 @@ - - - - - - KovatsOptions | Chromatography - - - - - -
-
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    -
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    • -
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    • -
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- - - - -
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-
-
-
-
-
- -

Interface KovatsOptions

-
-
-
-
-
-
-
-

Hierarchy

-
    -
  • - KovatsOptions -
    • -
-
-
-

Index

-
-
-
-

Properties

- -
-
-
-
-
-

Properties

-
- -

Optional threshold

-
threshold: number
- -
-
-
default
-

0.01

-
-
-
-
-
-
-
- - -
-
-
-
-
-

Legend

-
-
    -
  • Constructor
    • -
  • Method
    • -
-
    -
  • Property
    • -
-
    -
  • Inherited method
    • -
-
-
-
-
- - - \ No newline at end of file diff --git a/docs/interfaces/kovatsresult.html b/docs/interfaces/kovatsresult.html deleted file mode 100644 index 80e3006..0000000 --- a/docs/interfaces/kovatsresult.html +++ /dev/null @@ -1,177 +0,0 @@ - - - - - - KovatsResult | Chromatography - - - - - -
-
-
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-
- Options -
-
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    -
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    • -
  • Public/Protected
    • -
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    • -
-
- - - - -
-
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-
-
-
-
-
- -

Interface KovatsResult

-
-
-
-
-
-
-
-

Hierarchy

-
    -
  • - KovatsResult -
    • -
-
-
-

Index

-
-
-
-

Properties

- -
-
-
-
-
-

Properties

-
- -

index

-
index: number
- -
-
- -

numberFragments

-
numberFragments: number
- -
-
- -

percentFragments

-
percentFragments: number
- -
-
-
-
- - -
-
-
-
-
-

Legend

-
-
    -
  • Constructor
    • -
  • Method
    • -
-
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  • Property
    • -
-
    -
  • Inherited method
    • -
-
-
-
-
- - - \ No newline at end of file diff --git a/docs/interfaces/lockmassreferenceused.html b/docs/interfaces/lockmassreferenceused.html deleted file mode 100644 index 8f038e1..0000000 --- a/docs/interfaces/lockmassreferenceused.html +++ /dev/null @@ -1,199 +0,0 @@ - - - - - - LockMassReferenceUsed | Chromatography - - - - - -
-
-
-
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-
- Options -
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- All -
    -
  • Public
    • -
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    • -
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-
- -

Interface LockMassReferenceUsed

-
-
-
-
-
-
-
-

Hierarchy

-
    -
  • - LockMassReferenceUsed -
    • -
-
-
-

Index

-
-
-
-

Properties

- -
-
-
-
-
-

Properties

-
- -

mfs

-
mfs: {}
- -
-

Type declaration

-
    -
  • -
    [mf: string]: number
    -
    • -
-
-
-
- -

percent

-
percent: number
- -
-
- -

total

-
total: number
- -
-
- -

totalFound

-
totalFound: number
- -
-
-
-
- - -
-
-
-
-
-

Legend

-
-
    -
  • Constructor
    • -
  • Method
    • -
-
    -
  • Property
    • -
-
    -
  • Inherited method
    • -
-
-
-
-
- - - \ No newline at end of file diff --git a/docs/interfaces/massfilteroptions.html b/docs/interfaces/massfilteroptions.html deleted file mode 100644 index eaf51d2..0000000 --- a/docs/interfaces/massfilteroptions.html +++ /dev/null @@ -1,207 +0,0 @@ - - - - - - MassFilterOptions | Chromatography - - - - - -
-
-
-
- -
-
- Options -
-
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    -
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    • -
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    • -
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-
-
- -

Interface MassFilterOptions

-
-
-
-
-
-
-
-

Hierarchy

-
    -
  • - MassFilterOptions -
    • -
-
-
-

Index

-
-
-
-

Properties

- -
-
-
-
-
-

Properties

-
- -

Optional groupWidth

-
groupWidth: number
- -
-
-

When find a max can't be another max in a radius of this size.

-
-
-
default
-

0

-
-
-
-
-
- -

Optional maxNumberPeaks

-
maxNumberPeaks: number
- -
-
-

Maximum number of peaks for each mass spectrum (when it is Number.MAX_VALUE, there's no filter).

-
-
-
default
-

Number.MAX_VALUE

-
-
-
-
-
- -

Optional thresholdFactor

-
thresholdFactor: number
- -
-
-

Every peak that is below the main peak times this factor fill be removed (when it is 0, there's no filter).

-
-
-
default
-

0

-
-
-
-
-
-
-
- - -
-
-
-
-
-

Legend

-
-
    -
  • Constructor
    • -
  • Method
    • -
-
    -
  • Property
    • -
-
    -
  • Inherited method
    • -
-
-
-
-
- - - \ No newline at end of file diff --git a/docs/interfaces/massspectrum.html b/docs/interfaces/massspectrum.html deleted file mode 100644 index 23da1f3..0000000 --- a/docs/interfaces/massspectrum.html +++ /dev/null @@ -1,173 +0,0 @@ - - - - - - MassSpectrum | Chromatography - - - - - -
-
-
-
- -
-
- Options -
-
- All -
    -
  • Public
    • -
  • Public/Protected
    • -
  • All
    • -
-
- - - - -
-
- Menu -
-
-
-
-
-
- -

Interface MassSpectrum

-
-
-
-
-
-
-
-

Hierarchy

-
    -
  • - MassSpectrum -
    • -
-
-
-

Index

-
-
-
-

Properties

-
    -
  • x
    • -
  • y
    • -
-
-
-
-
-
-

Properties

-
- -

x

-
x: number[]
- -
-
-

Array of mass values.

-
-
-
-
- -

y

-
y: number[]
- -
-
-

Array of abundance values.

-
-
-
-
-
-
- - -
-
-
-
-
-

Legend

-
-
    -
  • Constructor
    • -
  • Method
    • -
-
    -
  • Property
    • -
-
    -
  • Inherited method
    • -
-
-
-
-
- - - \ No newline at end of file diff --git a/docs/interfaces/meanfilteroptions.html b/docs/interfaces/meanfilteroptions.html deleted file mode 100644 index 7480b6a..0000000 --- a/docs/interfaces/meanfilteroptions.html +++ /dev/null @@ -1,208 +0,0 @@ - - - - - - MeanFilterOptions | Chromatography - - - - - -
-
-
-
- -
-
- Options -
-
- All -
    -
  • Public
    • -
  • Public/Protected
    • -
  • All
    • -
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factor: number
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The values under the median times this factor are removed.

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2

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force: boolean
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Force replacement of existing series. - If false, trying to add an already existing series will throw an error.

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false

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seriesName: string
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Name of the created series.

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'msMean'

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Optional mergeThreshold

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mergeThreshold: number
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Parameter for merging the peaks

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0.3

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Optional range

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range: ChromatogramRange
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Range to merge.

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Optional seriesName

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seriesName: string
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Name of the mass series.

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'ms'

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from

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Type declaration

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to

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Type declaration

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y

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y: number[]
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maxFBIteration

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maxFBIteration: number
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Maximum number of iterations of the Forward-Backward subroutine.

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80

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maximumIteration

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maximumIteration: number
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Maximum number of iterations

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500

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phaseRatio

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phaseRatio: number
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Transition between decreasing thresholding phase and refinement phase in percent of the iterations.

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0.8

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toleranceFB

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toleranceFB: number
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Relative difference tolerance for convergence of the Forward-Backward sub-iterations.

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1e-5

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useTranspose

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useTranspose: boolean
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If true the originalMatrix is transposed.

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false

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- - - \ No newline at end of file diff --git a/docs/interfaces/percentagefilteroptions.html b/docs/interfaces/percentagefilteroptions.html deleted file mode 100644 index f225709..0000000 --- a/docs/interfaces/percentagefilteroptions.html +++ /dev/null @@ -1,205 +0,0 @@ - - - - - - PercentageFilterOptions | Chromatography - - - - - -
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Optional force

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force: boolean
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Force replacement of existing series. - If false, trying to add an already existing series will throw an error.

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false

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Optional percentage

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percentage: number
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0.1

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Optional seriesName

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seriesName: string
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Name of the created series.

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'msPercentage'

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Interface ScaleAlignmentOptions

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computeQuality

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computeQuality: boolean
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Calculate the quality of the regression.

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false

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polynomialDegree

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polynomialDegree: number
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Degree of the polynomial regression.

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3

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Optional groupWidth

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groupWidth: number
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When find a max can't be another max in a radius of this size.

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0

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Optional heightFilter

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heightFilter: number
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Filter all objects that are below heightFilter times the median of the height.

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default:
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2

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Optional intPower

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intPower: number
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Power applied to the abundance values.

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0.6

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Optional massPower

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massPower: number
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Power applied to the mass values.

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3

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Optional maxNumberPeaks

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maxNumberPeaks: number
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Maximum number of peaks for each mass spectrum (when it is Number.MAX_VALUE, there's no filter).

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Number.MAX_VALUE

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Optional similarityThreshold

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similarityThreshold: number
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Minimum similarity value to consider them similar.

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0.7

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Optional thresholdFactor

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thresholdFactor: number
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-
-

Every peak that is below the main peak times this factor fill be removed (when it is 0, there's no filter).

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default
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0

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Legend

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- - - \ No newline at end of file diff --git a/docs/interfaces/spectracomparisonresult.html b/docs/interfaces/spectracomparisonresult.html deleted file mode 100644 index bbcb36d..0000000 --- a/docs/interfaces/spectracomparisonresult.html +++ /dev/null @@ -1,192 +0,0 @@ - - - - - - SpectraComparisonResult | Chromatography - - - - - -
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peaksFirst

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peaksFirst: ChromatogramPeak[]
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Array of peaks, integrated mass spectra and weighted mass spectra for the first chromatogram.

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peaksSecond

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peaksSecond: ChromatogramPeak[]
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-

Array of peaks, integrated mass spectra and weighted mass spectra for the second chromatogram.

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peaksSimilarity

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peaksSimilarity: number[]
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Array of similarities.

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- - - \ No newline at end of file diff --git a/docs/interfaces/vectorifyoptions.html b/docs/interfaces/vectorifyoptions.html deleted file mode 100644 index f6fcba6..0000000 --- a/docs/interfaces/vectorifyoptions.html +++ /dev/null @@ -1,255 +0,0 @@ - - - - - - VectorifyOptions | Chromatography - - - - - -
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Interface VectorifyOptions

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Hierarchy

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Properties

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Optional groupWidth

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groupWidth: number
- -
-
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When find a max can't be another max in a radius of this size.

-
-
-
default
-

0

-
-
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-
- -

Optional intPower

-
intPower: number
- -
-
-

Power applied to the abundance values.

-
-
-
default
-

0.6

-
-
-
-
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Optional massPower

-
massPower: number
- -
-
-

Power applied to the mass values.

-
-
-
default
-

3

-
-
-
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-
- -

Optional maxNumberPeaks

-
maxNumberPeaks: number
- -
-
-

Maximum number of peaks for each mass spectrum (when it is Number.MAX_VALUE, there's no filter).

-
-
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default
-

Number.MAX_VALUE

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-
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Optional thresholdFactor

-
thresholdFactor: number
- -
-
-

Every peak that is below the main peak times this factor fill be removed (when it is 0, there's no filter).

-
-
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default
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0

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Legend

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- - - \ No newline at end of file diff --git a/package.json b/package.json index 9e7f3dc..5ce8417 100644 --- a/package.json +++ b/package.json @@ -23,7 +23,6 @@ ], "scripts": { "build": "cheminfo-build --entry src/index.js --root Chromatography", - "build-docs": "typedoc --out docs --name \"Chromatography\" --mode file --includeDeclarations --excludeExternals --hideGenerator --excludePrivate --moduleResolution node --target ESNext chromatography.d.ts", "eslint": "eslint src --cache", "eslint-fix": "npm run eslint -- --fix", "prepublishOnly": "rollup -c", @@ -50,37 +49,36 @@ "homepage": "https://github.com/cheminfo/chromatography#readme", "devDependencies": { "@babel/plugin-transform-modules-commonjs": "^7.13.8", - "@types/jest": "^26.0.20", + "@types/jest": "^26.0.21", "cheminfo-build": "^1.1.10", - "eslint": "^7.21.0", + "eslint": "^7.22.0", "eslint-config-cheminfo": "^5.2.3", "esm": "^3.2.25", "jest": "^26.6.3", "jest-matcher-deep-close-to": "^2.0.1", "prettier": "^2.2.1", - "rollup": "^2.41.0", - "spectrum-generator": "^4.7.0", - "typedoc": "^0.20.30", + "rollup": "^2.42.4", + "spectrum-generator": "^4.7.1", "typescript": "^4.2.3" }, "dependencies": { "binary-search": "^1.3.6", - "is-any-array": "0.1.1", - "isotopic-distribution": "^1.1.9", - "jcampconverter": "^7.7.0", - "mf-parser": "^1.1.6", - "ml-array-max": "^1.2.2", - "ml-array-mean": "^1.1.4", - "ml-array-median": "^1.1.4", - "ml-array-sum": "^1.1.4", - "ml-gsd": "^6.6.0", - "ml-matrix": "^6.6.0", - "ml-ngmca": "^0.2.2", + "is-any-array": "^1.0.0", + "isotopic-distribution": "^1.1.13", + "jcampconverter": "^7.8.0", + "mf-parser": "^1.1.10", + "ml-array-max": "^1.2.3", + "ml-array-mean": "^1.1.5", + "ml-array-median": "^1.1.5", + "ml-array-sum": "^1.1.5", + "ml-gsd": "^6.6.1", + "ml-matrix": "^6.7.0", + "ml-ngmca": "^1.0.0", "ml-pca": "^4.0.1", "ml-regression-polynomial": "^2.1.0", - "ml-spectra-processing": "^5.7.2", + "ml-spectra-processing": "^5.8.0", "mzdata": "^2.1.0", "netcdf-gcms": "^1.4.0", - "xy-parser": "^3.0.0" + "xy-parser": "^3.1.1" } }