exfilms - npm Package Compare versions

Comparing version 1.0.3 to 1.1.0

CHANGELOG.md

@@ -0,1 +1,8 @@
+# [1.1.0](https://github.com/vmalnathnambiar/exfilms/compare/v1.0.3...v1.1.0) (2024-03-28)
+
+
+### Features
+
+* **chromatogram extraction:** fix and update isolation window target extraction ([1439919](https://github.com/vmalnathnambiar/exfilms/commit/14399197fdc7e82bb2bc3064480de9e402cd02b7)), closes [#3](https://github.com/vmalnathnambiar/exfilms/issues/3)
+
 ## [1.0.3](https://github.com/vmalnathnambiar/exfilms/compare/v1.0.2...v1.0.3) (2024-03-28)
@@ -2,0 +9,0 @@

package.json

 {
   "name": "exfilms",
-  "version": "1.0.3",
+  "version": "1.1.0",
   "description": "A cross-platform, command line interface (CLI) tool to extract mass spectrometry (MS) data from mzML formatted files, with spectrum filtering capabilities.",
@@ -5,0 +5,0 @@ "bin": {

README.md

@@ -42,12 +42,20 @@ ![ExfilMS](./img/logo.png)\
       <th>MS Platform</th>
+      <th>Status</th>
    </tr>
    <tr>
-      <td rowspan="3">Bruker</td>
+      <td rowspan="4">Bruker</td>
+      <td>EVOQ TQ-MS</td>
+      <td>Not Working</td>
+   </tr>
+   <tr>
       <td>ImpactII QToF-MS</td>
+      <td>Working</td>
    </tr>
    <tr>
       <td>solariX MRMS</td>
+      <td>Working</td>
    </tr>
-      <tr>
+   <tr>
       <td>timsTOFPro TIMS-ToF-MS</td>
+      <td>Not Working</td>
    </tr>
@@ -57,8 +65,11 @@ <tr>
       <td>XEVOTQXS TQ-MS</td>
+      <td>Working</td>
    </tr>
    <tr>
-      <td>XEVOTQXS DESI-MS</td>
+      <td>XEVOG2XSQTOF DESI-MS</td>
+      <td>Working</td>
    </tr>
       <tr>
       <td>XEVOG2XSQTOF REIMS</td>
+      <td>Working</td>
    </tr>
@@ -68,2 +79,3 @@ <tr>
       <td>QTRAP6500+ TQ-MS</td>
+      <td>Working</td>
    </tr>
@@ -70,0 +82,0 @@ </table>

src/utils/extractChromatogram.js

@@ -26,2 +26,3 @@ /* eslint-disable no-await-in-loop */
     const precursorMap = chromatogramData.precursor;
+    const productMap = chromatogramData.product;
     const binaryDataArrayMap =
@@ -38,5 +39,6 @@ chromatogramData.binaryDataArrayList.binaryDataArray;
       dwellTime: null,
-      isolationWindowTarget: null,
+      precursorIsolationWindowTarget: null,
       collisionType: null,
       collisionEnergy: null,
+      productIsolationWindowTarget: null,
       timeArray: [],
@@ -54,4 +56,4 @@ intensityArray: [],
       const mappedKey = keyMap[cvParam.$name];
-      let paramValue = cvParam.$value;
       const mappedValue = valueMap[cvParam.$name];
+      const paramValue = cvParam.$value;
       if (mappedKey) {
@@ -69,4 +71,5 @@ data[mappedKey] = mappedValue || paramValue;
         const mappedKey = keyMap[cvParam.$name];
+        const paramValue = cvParam.$value;
         if (mappedKey) {
-          data[mappedKey] = cvParam.$value;
+          data[mappedKey] = paramValue;
         }
@@ -87,4 +90,9 @@ }
         const mappedKey = keyMap[cvParam.$name];
+        const paramValue = cvParam.$value;
         if (mappedKey) {
-          data[mappedKey] = cvParam.$value;
+          if (mappedKey === 'isolationWindowTarget') {
+            data.precursorIsolationWindowTarget = paramValue;
+          } else {
+            data[mappedKey] = paramValue;
+          }
         }
@@ -100,4 +108,5 @@ }
         const mappedValue = valueMap[cvParam.$name];
+        const paramValue = cvParam.$value;
         if (mappedKey) {
-          data[mappedKey] = mappedValue || cvParam.$value;
+          data[mappedKey] = mappedValue || paramValue;
         }
@@ -107,2 +116,23 @@ }
 
+    // Product data
+    if (productMap) {
+      const isolationWindowMap = productMap.isolationWindow;
+
+      // Isolation window parameters
+      const isolationWindowCvParam = Array.isArray(isolationWindowMap.cvParam)
+        ? isolationWindowMap.cvParam
+        : [isolationWindowMap.cvParam];
+      for (const cvParam of isolationWindowCvParam) {
+        const mappedKey = keyMap[cvParam.$name];
+        const paramValue = cvParam.$value;
+        if (mappedKey) {
+          if (mappedKey === 'isolationWindowTarget') {
+            data.productIsolationWindowTarget = paramValue;
+          } else {
+            data[mappedKey] = paramValue;
+          }
+        }
+      }
+    }
+
     // Chromatogram binary data array
@@ -109,0 +139,0 @@ for (const binaryData of binaryDataArrayMap) {

src/utils/extractSpectrum.js

@@ -72,4 +72,4 @@ /* eslint-disable no-await-in-loop */
       const mappedKey = keyMap[cvParam.$name];
+      const mappedValue = valueMap[cvParam.$name];
       let paramValue = cvParam.$value;
-      const mappedValue = valueMap[cvParam.$name];
 
@@ -111,4 +111,5 @@ if (mappedKey) {
       const mappedKey = keyMap[cvParam.$name];
+      const paramValue = cvParam.$value;
       if (mappedKey) {
-        data[mappedKey] = cvParam.$value;
+        data[mappedKey] = paramValue;
       }
@@ -130,4 +131,5 @@ }
         const mappedKey = keyMap[cvParam.$name];
+        const paramValue = cvParam.$value;
         if (mappedKey) {
-          data[mappedKey] = cvParam.$value;
+          data[mappedKey] = paramValue;
         }
@@ -142,4 +144,5 @@ }
         const mappedKey = keyMap[cvParam.$name];
+        const paramValue = cvParam.$value;
         if (mappedKey) {
-          data[mappedKey] = cvParam.$value;
+          data[mappedKey] = paramValue;
         }
@@ -155,4 +158,5 @@ }
         const mappedValue = valueMap[cvParam.$name];
+        const paramValue = cvParam.$value;
         if (mappedKey) {
-          data[mappedKey] = mappedValue || cvParam.$value;
+          data[mappedKey] = mappedValue || paramValue;
         }
@@ -159,0 +163,0 @@ }

src/utils/initChromatogramArray.js

@@ -22,5 +22,6 @@ /**
       dwellTime: null,
-      isolationWindowTarget: null,
+      precursorIsolationWindowTarget: null,
       collisionType: null,
       collisionEnergy: null,
+      productIsolationWindowTarget: null,
       timeArray: [],
@@ -38,5 +39,6 @@ intensityArray: [],
       dwellTime: null,
-      isolationWindowTarget: null,
+      precursorIsolationWindowTarget: null,
       collisionType: null,
       collisionEnergy: null,
+      productIsolationWindowTarget: null,
       timeArray: [],
@@ -60,5 +62,6 @@ intensityArray: [],
         dwellTime: null,
-        isolationWindowTarget: null,
+        precursorIsolationWindowTarget: null,
         collisionType: null,
         collisionEnergy: null,
+        productIsolationWindowTarget: null,
         timeArray: [],
@@ -65,0 +68,0 @@ intensityArray: [],

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Improved metrics

Total package byte prevSize

2255911

increased by0.09%

Lines of code

2046

increased by1.79%

Number of lines in readme file

211

increased by6.03%

No dependency changes