emdb - npm Package Compare versions

Comparing version 0.13.0 to 0.13.1

package.json

 {
   "name": "emdb",
-  "version": "0.13.0",
+  "version": "0.13.1",
   "description": "Database manager for exact mass query",
@@ -25,19 +25,20 @@ "browser": {
   "dependencies": {
-    "isotopic-distribution": "^0.12.0",
+    "isotopic-distribution": "^0.12.1",
     "jszip": "^3.2.2",
-    "mf-finder": "^0.12.0",
-    "mf-from-google-sheet": "^0.12.0",
-    "mf-generator": "^0.12.0",
-    "mf-matcher": "^0.12.0",
-    "mf-parser": "^0.13.0",
-    "mf-utilities": "^0.12.0",
+    "mf-finder": "^0.12.1",
+    "mf-from-google-sheet": "^0.12.1",
+    "mf-generator": "^0.12.1",
+    "mf-matcher": "^0.12.1",
+    "mf-parser": "^0.13.1",
+    "mf-utilities": "^0.12.1",
     "ml-array-max": "^1.1.2",
     "ml-array-min": "^1.1.2",
     "ml-regression-theil-sen": "^2.0.0",
-    "ms-spectrum": "^0.12.0",
-    "nucleotide": "^0.12.0",
+    "ms-spectrum": "^0.12.1",
+    "nucleotide": "^0.12.1",
     "peaks-similarity": "^2.3.1",
     "peptide": "^1.10.1",
     "request-promise-native": "^1.0.8"
-  }
+  },
+  "gitHead": "cc0873275c6a22fafb6babe866e8164ee25e0d30"
 }

src/fromArray.js

@@ -8,3 +8,4 @@ 'use strict';
  * @param {array} mfsArray - Array of string or Array of array containing the parts to combine
- * @param {*} options
+ * @param {obejct} [options={}]
+ * @param {boolean} [options.estimate=false] - estimate the number of MF without filters
  * @param {string} [options.databaseName='generated']
@@ -11,0 +12,0 @@ * @param {number} [options.limit=10000000] - Maximum number of results

src/fromNucleicSequence.js

@@ -11,2 +11,3 @@ 'use strict';
  * @param {object} [options={}]
+ * @param {boolean}       [options.estimate=false] - estimate the number of MF without filters
  * @param {string} [options.ionizations='']
@@ -54,2 +55,3 @@ * @param {object} [options.info={}]
     info = {},
+    estimate = false,
   } = options;
@@ -78,4 +80,5 @@
     ionizations,
-    filter: filter,
+    filter,
     uniqueMFs: false,
+    estimate,
   });
@@ -82,0 +85,0 @@

src/fromPeptidicSequence.js

@@ -9,44 +9,48 @@ 'use strict';
  *
- * @param {string} [sequence] Sequence as a string of 1 letter or 3 letters code. Could also be a correct molecular formula respecting uppercase, lowercase
- * @param {object} [options={}]
- * @param {string} [options.ionizations='']
- * @param {array} [options.mfsArray=[]]
- *  * @param {boolean} [options.protonation=false]
- * @param {number} [options.protonationPH=7]
- * @param {boolean} [options.allowNeutralLoss=false]
- * @param {object} [options.digestion={}] Object defining options for digestion
- * @param {number} [options.digestion.minMissed=0] Minimal number of allowed missed cleavage
- * @param {number} [options.digestion.maxMissed=0] Maximal number of allowed missed cleavage
- * @param {number} [options.digestion.minResidue=0] Minimal number of residues
- * @param {number} [options.digestion.maxResidue=+Infinity] Maximal number of residues
- * @param {string} [options.digestion.enzyme] Mandatory field containing the name of the enzyme among: chymotrypsin, trypsin, glucph4, glucph8, thermolysin, cyanogenbromide
+ * @param {string}         [sequence] Sequence as a string of 1 letter or 3 letters code. Could also be a correct molecular formula respecting uppercase, lowercase
+ * @param {object}         [options={}]
+ * @param {boolean}        [options.estimate=false] - estimate the number of MF without filters
+ * @param {string}         [options.ionizations='']
+ * @param {array}          [options.mfsArray=[]]
+ * @param {boolean}        [options.protonation=false]
+ * @param {number}         [options.protonationPH=7]
+ * @param {boolean}        [options.allowNeutralLoss=false]
  *
- * @param {object} [options.fragmentation={}] Object defining options for fragmentation
- * @param {boolean} [options.fragmentation.a=false] If true allow fragments of type 'a'
- * @param {boolean} [options.fragmentation.b=false] If true allow fragments of type 'b'
- * @param {boolean} [options.fragmentation.c=false] If true allow fragments of type 'c'
- * @param {boolean} [options.fragmentation.x=false] If true allow fragments of type 'x'
- * @param {boolean} [options.fragmentation.y=false] If true allow fragments of type 'y'
- * @param {boolean} [options.fragmentation.z=false] If true allow fragments of type 'z'
- * @param {boolean} [options.fragmentation.ya=false] If true allow fragments of type 'ya'
- * @param {boolean} [options.fragmentation.yb=false] If true allow fragments of type 'yb'
- * @param {boolean} [options.fragmentation.yc=false] If true allow fragments of type 'yc'
- * @param {boolean} [options.fragmentation.zc=false] If true allow fragments of type 'zc'
- * @param {number} [options.fragmentation.minInternal=0] Minimal internal fragment length
- * @param {number} [options.fragmentation.maxInternal=+Infinity] Maximal internal fragment length
+ * @param {object}         [options.digestion={}] Object defining options for digestion
+ * @param {number}         [options.digestion.minMissed=0] Minimal number of allowed missed cleavage
+ * @param {number}         [options.digestion.maxMissed=0] Maximal number of allowed missed cleavage
+ * @param {number}         [options.digestion.minResidue=0] Minimal number of residues
+ * @param {number}         [options.digestion.maxResidue=+Infinity] Maximal number of residues
+ * @param {string}         [options.digestion.enzyme] Mandatory field containing the name of the enzyme among: chymotrypsin, trypsin, glucph4, glucph8, thermolysin, cyanogenbromide
  *
- * @param {object} [options.filter={}] Object defining options for molecular formula filter
- * @param {number} [options.filter.minMass=0] - Minimal monoisotopic mass
- * @param {number} [options.filter.maxMass=+Infinity] - Maximal monoisotopic mass
- * @param {number} [options.filter.minEM=0] - Minimal neutral monoisotopic mass
- * @param {number} [options.filter.maxEM=+Infinity] - Maximal neutral monoisotopic mass
- * @param {number} [options.filter.minMSEM=0] - Minimal observed monoisotopic mass
- * @param {number} [options.filter.maxMSEM=+Infinity] - Maximal observed monoisotopic mass
- * @param {number} [options.filter.minCharge=-Infinity] - Minimal charge
- * @param {number} [options.filter.maxCharge=+Infinity] - Maximal charge
- * @param {number} [options.filter.unsaturation={}]
- * @param {number} [options.filter.unsaturation.min=-Infinity] - Minimal unsaturation
- * @param {number} [options.filter.unsaturation.max=+Infinity] - Maximal unsaturation
- * @param {number} [options.filter.unsaturation.onlyInteger=false] - Integer unsaturation
- * @param {number} [options.filter.unsaturation.onlyNonInteger=false] - Non integer unsaturation
+ * @param {object}         [options.fragmentation={}] Object defining options for fragmentation
+ * @param {boolean}        [options.fragmentation.a=false] If true allow fragments of type 'a'
+ * @param {boolean}        [options.fragmentation.b=false] If true allow fragments of type 'b'
+ * @param {boolean}        [options.fragmentation.c=false] If true allow fragments of type 'c'
+ * @param {boolean}        [options.fragmentation.x=false] If true allow fragments of type 'x'
+ * @param {boolean}        [options.fragmentation.y=false] If true allow fragments of type 'y'
+ * @param {boolean}        [options.fragmentation.z=false] If true allow fragments of type 'z'
+ * @param {boolean}        [options.fragmentation.ya=false] If true allow fragments of type 'ya'
+ * @param {boolean}        [options.fragmentation.yb=false] If true allow fragments of type 'yb'
+ * @param {boolean}        [options.fragmentation.yc=false] If true allow fragments of type 'yc'
+ * @param {boolean}        [options.fragmentation.zc=false] If true allow fragments of type 'zc'
+ * @param {number}         [options.fragmentation.minInternal=0] Minimal internal fragment length
+ * @param {number}         [options.fragmentation.maxInternal=+Infinity] Maximal internal fragment length
+ *
+ * @param {object}         [options.filter={}] Object defining options for molecular formula filter
+ * @param {number}         [options.filter.precision=1000] - The precision on the experimental mass
+ * @param {number}         [options.filter.targetMass] - Target mass, allows to calculate error and filter results
+ * @param {Array<number>}  [options.filter.targetMasses] - Target masses: SORTED array of numbers
+ * @param {Array<number>}  [options.filter.targetIntensities] - Target intensities: SORTED array of numbers
+ * @param {number}         [options.filter.minEM=0] - Minimal neutral monoisotopic mass
+ * @param {number}         [options.filter.maxEM=+Infinity] - Maximal neutral monoisotopic mass
+ * @param {number}         [options.filter.minMSEM=0] - Minimal observed monoisotopic mass
+ * @param {number}         [options.filter.maxMSEM=+Infinity] - Maximal observed monoisotopic mass
+ * @param {number}         [options.filter.minCharge=-Infinity] - Minimal charge
+ * @param {number}         [options.filter.maxCharge=+Infinity] - Maximal charge
+ * @param {number}         [options.filter.unsaturation={}]
+ * @param {number}         [options.filter.unsaturation.min=-Infinity] - Minimal unsaturation
+ * @param {number}         [options.filter.unsaturation.max=+Infinity] - Maximal unsaturation
+ * @param {number}         [options.filter.unsaturation.onlyInteger=false] - Integer unsaturation
+ * @param {number}         [options.filter.unsaturation.onlyNonInteger=false] - Non integer unsaturation
  */
@@ -64,2 +68,3 @@
     ionizations = '',
+    estimate = false,
   } = options;
@@ -99,3 +104,4 @@
     ionizations,
-    filter: filter,
+    filter,
+    estimate,
   });
@@ -102,0 +108,0 @@

src/fromRange.js

@@ -8,3 +8,4 @@ 'use strict';
  * @param {string} range - a string representing the range to search
- * @param {*} options
+ * @param {object} [options={}]
+ * @param {boolean} [options.estimate=false] - estimate the number of MF without filters
  * @param {string} [options.databaseName='generated']
@@ -11,0 +12,0 @@ * @param {number} [options.limit=10000000] - Maximum number of results

src/index.js

@@ -93,4 +93,5 @@ 'use strict';
 DBManager.prototype.fromArray = function fromArray(sequence, options = {}) {
-  const { databaseName = 'generated', append = false } = options;
+  const { databaseName = 'generated', append = false, estimate } = options;
   const results = require('./fromArray')(sequence, options);
+  if (estimate) return results;
   replaceOrAppend(this, databaseName, results, append);
@@ -100,4 +101,5 @@ };
 DBManager.prototype.fromRange = function fromRange(sequence, options = {}) {
-  const { databaseName = 'generated', append = false } = options;
+  const { databaseName = 'generated', append = false, estimate } = options;
   const results = require('./fromRange')(sequence, options);
+  if (estimate) return results;
   replaceOrAppend(this, databaseName, results, append);
@@ -110,4 +112,5 @@ };
 ) {
-  const { databaseName = 'peptidic', append = false } = options;
+  const { databaseName = 'peptidic', append = false, estimate } = options;
   const results = require('./fromPeptidicSequence')(sequence, options);
+  if (estimate) return results;
   replaceOrAppend(this, databaseName, results, append);
@@ -120,4 +123,5 @@ };
 ) {
-  const { databaseName = 'nucleic', append = false } = options;
+  const { databaseName = 'nucleic', append = false, estimate } = options;
   const results = require('./fromNucleicSequence')(sequence, options);
+  if (estimate) return results;
   replaceOrAppend(this, databaseName, results, append);
@@ -124,0 +128,0 @@ };

src/searchMSEM.js

@@ -12,16 +12,19 @@ 'use strict';
 * @param {boolean}  [options.flatten=false] - should we return the array as a flat result
-
 * @param {object}   [options.filter={}]
 * @param {string}   [options.ionizations] - list the allowed ionizations possibilities
-* @param {boolean}  [options.filter.forceIonization=false] - If true ignore existing ionizations
-* @param {number}   [options.filter.precision=1000] - The precision on the experimental mass
-* @param {number}   [options.filter.minCharge=-Infinity] - Minimal charge
-* @param {number}   [options.filter.maxCharge=+Infinity] - Maximal charge
-* @param {object}   [options.filter.unsaturation={}}]
-* @param {number}   [options.filter.unsaturation.min=-Infinity] - Minimal unsaturation
-* @param {number}   [options.filter.unsaturation.max=+Infinity] - Maximal unsaturation
-* @param {number}   [options.filter.unsaturation.onlyInteger=false] - Integer unsaturation
-* @param {number}   [options.filter.unsaturation.onlyNonInteger=false] - Non integer unsaturation
-* @param {object}   [options.filter.atoms] - object of atom:{min, max}
-
+ * @param {number}         [options.filter.targetMass] - Target mass, allows to calculate error and filter results
+ * @param {Array<number>}  [options.filter.targetMasses] - Target masses: SORTED array of numbers
+ * @param {Array<number>}  [options.filter.targetIntensities] - Target intensities: SORTED array of numbers
+ * @param {number}         [options.filter.minEM=0] - Minimal monoisotopic mass
+ * @param {number}         [options.filter.maxEM=+Infinity] - Maximal monoisotopic mass
+ * @param {number}         [options.filter.minMSEM=0] - Minimal monoisotopic mass observed by mass
+ * @param {number}         [options.filter.maxMSEM=+Infinity] - Maximal monoisotopic mass observed by mass
+ * @param {number}         [options.filter.minCharge=-Infinity] - Minimal charge
+ * @param {number}         [options.filter.maxCharge=+Infinity] - Maximal charge
+ * @param {object}         [options.filter.unsaturation={}}]
+ * @param {number}         [options.filter.unsaturation.min=-Infinity] - Minimal unsaturation
+ * @param {number}         [options.filter.unsaturation.max=+Infinity] - Maximal unsaturation
+ * @param {number}         [options.filter.unsaturation.onlyInteger=false] - Integer unsaturation
+ * @param {number}         [options.filter.unsaturation.onlyNonInteger=false] - Non integer unsaturation
+ * @param {object}         [options.filter.atoms] - object of atom:{min, max}
 */
@@ -28,0 +31,0 @@

No alert changes

Improved metrics

Total package byte prevSize

1508202

increased by4.49%

Number of package files

50

increased by4.17%

Lines of code

1603

increased by1.26%

Dependency changes

• Updatedisotopic-distribution@^0.12.1

• Updatedmf-finder@^0.12.1

• Updatedmf-from-google-sheet@^0.12.1

• Updatedmf-generator@^0.12.1

• Updatedmf-matcher@^0.12.1

• Updatedmf-parser@^0.13.1

• Updatedmf-utilities@^0.12.1

• Updatedms-spectrum@^0.12.1

• Updatednucleotide@^0.12.1