extension of the DatabaseIsotopeRefiner #1507
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…opesDifferentResolutions" based on the IsotopePatternFinder: - Calculation of isotope patterns at different resolutions - comparison of these with the found isotope pattern - highest isotope pattern score is output
SteffenHeu
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Sep 28, 2023
.../github/mzmine/modules/dataprocessing/id_localcsvsearch/DatabaseIsotopeRefinerScanBased.java
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.../github/mzmine/modules/dataprocessing/id_localcsvsearch/DatabaseIsotopeRefinerScanBased.java
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| @@ -208,6 +320,35 @@ private static IsotopePattern getCalculateIsotopePattern(final MZTolerance mzTol | |||
| return pattern; | |||
| } | |||
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| private static Map<Double, IsotopePattern> getCalculateIsotopePatternDifferentResolutions( | |||
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you can remove the get from the name
| final double minIntensity, final IonType adductType, final IMolecularFormula ionFormula) { | ||
| // TODO Predict pattern - Do this in the IsotopePatternCalculator.calculateIsotopePatternForResolutions | ||
| // return Map<Integer, IsotopePattern> (use HashMap<>) | ||
| var patterns = IsotopePatternCalculator.calculateIsotopePatternForResolutions(ionFormula, minIntensity, |
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if you just call this method, why even wrap it in another method?
.../github/mzmine/modules/dataprocessing/id_localcsvsearch/DatabaseIsotopeRefinerScanBased.java
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src/main/java/io/github/mzmine/modules/tools/isotopeprediction/IsotopePatternCalculator.java
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robinschmid
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Oct 3, 2023
.../github/mzmine/modules/dataprocessing/id_localcsvsearch/DatabaseIsotopeRefinerScanBased.java
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robinschmid
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Oct 3, 2023
| // no isotope pattern and no default MS1 scan. e.g., if just a feature list loaded | ||
| return false; | ||
| } | ||
| var score = calculateIsotopeScoreDifferentResolutions(annotation, measuredIsotopes, minIntensity, |
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Maybe we should save this score somehow in the final annotation so that we can reuse it?
robinschmid
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Oct 3, 2023
| return finalScore; | ||
| } | ||
| private static double[] getDoubleResolutions(){ | ||
| return new double[]{0.0001,0.001,0.01,0.1}; |
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we can finalize those later but maybe the smallest shoudl be something like 0.00025 or a bit higher?
would be interesting to know what you need to separate N O C S ...
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see comment below. Maybe just creating a global MZtolerance[] might be best
robinschmid
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Oct 3, 2023
.../github/mzmine/modules/dataprocessing/id_localcsvsearch/DatabaseIsotopeRefinerScanBased.java
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robinschmid
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Oct 3, 2023
.../github/mzmine/modules/dataprocessing/id_localcsvsearch/DatabaseIsotopeRefinerScanBased.java
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…otope_pattern_matcher # Conflicts: # src/main/java/io/github/mzmine/modules/dataprocessing/id_localcsvsearch/LocalCSVDatabaseSearchTask.java
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looks good to me |
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with "refineAnnotationsByIsotopesDifferentResolutions" based on the IsotopePatternFinder: