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fix: remove shape from gsd peaks (#111)
1 parent b23d382 commit 926ca69

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8 files changed

+2
-76
lines changed

8 files changed

+2
-76
lines changed

‎package.json‎

Lines changed: 1 addition & 4 deletions
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@@ -10,9 +10,6 @@
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"src",
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"lib-esm"
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],
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"env": {
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"jest": true
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},
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"scripts": {
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"build": "npm run tsc-esm && cheminfo-build --entry lib-esm/index.js --root GSD",
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"check-types": "tsc --noEmit",
@@ -43,7 +40,7 @@
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"author": "Andres Castillo",
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"contributors": [
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"Miguel Asencio <[email protected]> (https://github.com/maasencioh)",
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"Alejandro Bolaños <[email protected]> (https://github.com/jobo322)"
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"J. Alejandro Bolaños A. <[email protected]> (https://github.com/jobo322)"
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],
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"license": "MIT",
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"bugs": {

‎src/__tests__/gaussian-overlapping.test.ts‎

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Original file line numberDiff line numberDiff line change
@@ -49,13 +49,11 @@ describe('gaussian overlapping', () => {
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x: -0.1,
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y: 1,
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width: 0.1,
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shape: { kind: 'gaussian', fwhm: 0.11774128880591818 },
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},
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{
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x: 0.1,
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y: 1,
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width: 0.1,
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shape: { kind: 'gaussian', fwhm: 0.11774128880591818 },
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},
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]);
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});

‎src/__tests__/gaussian-smooth.test.ts‎

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Original file line numberDiff line numberDiff line change
@@ -39,10 +39,6 @@ describe('gaussian simulated peaks', () => {
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ddY: -259.83290100626783,
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width: 0.08,
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index: 25,
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shape: {
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fwhm: 0.09419280180123805,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { x: -0.54, index: 23 },
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to: { x: -0.46, index: 27 },
@@ -55,10 +51,6 @@ describe('gaussian simulated peaks', () => {
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ddY: -259.83290100626783,
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width: 0.08,
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index: 75,
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shape: {
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fwhm: 0.09419280180123805,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { x: 0.46, index: 73 },
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to: { x: 0.54, index: 77 },

‎src/__tests__/gaussian.test.ts‎

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Original file line numberDiff line numberDiff line change
@@ -38,10 +38,6 @@ describe('smooth:false option', () => {
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ddY: -259.83290100626783,
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width: 0.08,
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index: 25,
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shape: {
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fwhm: 0.09419280180123805,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { index: 23, x: -0.54 },
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to: { index: 27, x: -0.46 },
@@ -53,10 +49,6 @@ describe('smooth:false option', () => {
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ddY: -259.83290100626783,
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width: 0.08,
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index: 75,
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shape: {
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fwhm: 0.09419280180123805,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { index: 73, x: 0.46 },
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to: { index: 77, x: 0.54 },
@@ -76,10 +68,6 @@ describe('smooth:false option', () => {
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ddY: -259.83290100626783,
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width: 0.08,
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index: 25,
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shape: {
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fwhm: 0.09419280180123805,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { index: 23, x: -0.54 },
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to: { index: 27, x: -0.46 },
@@ -91,10 +79,6 @@ describe('smooth:false option', () => {
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ddY: -259.83290100626783,
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width: 0.08,
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index: 75,
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shape: {
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fwhm: 0.09419280180123805,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { index: 73, x: 0.46 },
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to: { index: 77, x: 0.54 },
@@ -117,10 +101,6 @@ describe('smooth:false option', () => {
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ddY: 259.83290100626783,
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width: 0.08,
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index: 25,
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shape: {
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fwhm: 0.09419280180123805,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { index: 23, x: -0.54 },
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to: { index: 27, x: -0.46 },
@@ -132,10 +112,6 @@ describe('smooth:false option', () => {
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ddY: 259.83290100626783,
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width: 0.08,
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index: 75,
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shape: {
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fwhm: 0.09419280180123805,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { index: 73, x: 0.46 },
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to: { index: 77, x: 0.54 },
@@ -159,10 +135,6 @@ describe('smooth:false option', () => {
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ddY: 259.83290100626783,
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width: 0.08,
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index: 25,
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shape: {
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fwhm: 0.09419280180123805,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { index: 23, x: -0.54 },
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to: { index: 27, x: -0.46 },
@@ -174,10 +146,6 @@ describe('smooth:false option', () => {
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ddY: 259.83290100626783,
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width: 0.08,
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index: 75,
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shape: {
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fwhm: 0.09419280180123805,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { index: 73, x: 0.46 },
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to: { index: 77, x: 0.54 },

‎src/__tests__/power.test.ts‎

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@@ -57,10 +57,6 @@ describe('power', () => {
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width: 0.3,
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index: 100,
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ddY: -33832.03463203485,
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shape: {
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fwhm: 0.35322300675464324,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { x: 4.85, index: 97 },
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to: { x: 5.15, index: 103 },
@@ -84,10 +80,6 @@ describe('power', () => {
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width: 0.05,
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index: 89,
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ddY: 800,
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shape: {
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fwhm: 0.05887050112577352,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { x: 4.4, index: 88 },
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to: { x: 4.45, index: 89 },
@@ -100,10 +92,6 @@ describe('power', () => {
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width: 0.2,
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index: 100,
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ddY: -44914.28571428623,
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shape: {
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fwhm: 0.2354820045030941,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { x: 4.9, index: 98 },
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to: { x: 5.1, index: 102 },
@@ -116,10 +104,6 @@ describe('power', () => {
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width: 0.05,
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index: 111,
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ddY: 800,
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shape: {
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fwhm: 0.05887050112577352,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { x: 5.55, index: 111 },
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to: { x: 5.6, index: 112 },

‎src/__tests__/ubiquitin.test.ts‎

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Original file line numberDiff line numberDiff line change
@@ -30,10 +30,6 @@ describe('Global spectra deconvolution ubiquitin', () => {
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ddY: -15468134.039875854,
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width: 0.002420000000000755,
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index: 11,
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shape: {
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fwhm: 0.0028493322544883375,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { x: 200.054133, index: 9 },
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to: { x: 200.056553, index: 13 },

‎src/gsd.ts‎

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Original file line numberDiff line numberDiff line change
@@ -1,6 +1,5 @@
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import { v4 as generateID } from '@lukeed/uuid';
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import type { DataXY } from 'cheminfo-types';
3-
import { Shape1D } from 'ml-peak-shape-generator';
43
import { sgg, SGGOptions } from 'ml-savitzky-golay-generalized';
54
import {
65
xIsEquallySpaced,
@@ -14,7 +13,6 @@ import { GSDPeak } from './GSDPeak';
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import { MakeMandatory } from './utils/MakeMandatory';
1514
import { MakeOptional } from './utils/MakeOptional';
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import { optimizeTop } from './utils/optimizeTop';
17-
import { setShape } from './utils/setShape';
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1917
export interface GSDOptions {
2018
/**
@@ -49,11 +47,6 @@ export interface GSDOptions {
4947
* @default false
5048
*/
5149
realTopDetection?: boolean;
52-
/**
53-
* Shape used to add FWHM property in the peaks
54-
* @default {kind:'gaussian'}
55-
*/
56-
shape?: Shape1D;
5750
}
5851
export type GSDPeakID = MakeMandatory<GSDPeak, 'id'>;
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export type GSDPeakIDOptionalShape = MakeOptional<GSDPeak, 'shape'>;
@@ -71,7 +64,6 @@ export function gsd(data: DataXY, options: GSDOptions = {}): GSDPeakID[] {
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windowSize: 9,
7265
polynomial: 3,
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},
74-
shape,
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noiseLevel,
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smoothY = false,
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maxCriteria = true,
@@ -279,5 +271,5 @@ export function gsd(data: DataXY, options: GSDOptions = {}): GSDPeakID[] {
279271
return a.x - b.x;
280272
});
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282-
return setShape(peaks, { shape }) as GSDPeakID[];
274+
return peaks as GSDPeakID[];
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}

‎src/utils/setShape.ts‎

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@@ -22,7 +22,6 @@ export function setShape<T extends { width: number }>(
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output = parse(stringify(peaks)) as T[],
2323
} = options;
2424
let shapeInstance = getShape1D(shape);
25-
2625
return output.map((peak) => ({
2726
...peak,
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shape: { fwhm: shapeInstance.widthToFWHM(peak.width), ...shape },

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