Changes between Version 2 and Version 3 of DeterimingIonSets


Ignore:
Timestamp:
07/06/2018 09:41:40 PM (3 years ago)
Author:
dbrentw
Comment:

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  • DeterimingIonSets

    v2 v3  
    11= Tutorial for Determining Parameter Sets for Glycan Annotation=
    22This page contains source code for determining parameter sets when the user specifies adducts, ion exchanges, and neutral loss or gains (see GELATO wizard).
     3{{{
     4        /**
     5         * Initializes all the data structures with the varius adducts, loss/gain, exchnanges, and their counts.<br>
     6         * <i>Technically, we should have different adducts, exchanges, etc
     7         * per analyte settings object, but this isn't implemented yet!</i>
     8         *
     9         * @param _analayteSettings - the current AnalyteSettings object to use for GELATO annotation of the MS file
     10         *
     11         */
     12        protected void initializeAdductsAndExchanges( AnalyteSettings _analayteSettings ) {
     13                lPosModeSettingsToAnalyze = new ArrayList<>();
     14                lPosModeSettingsToAnalyzeCounts = new ArrayList<>();
     15                GlycanStructureAnnotation.determineIonSettingSets(true, method.getIons(), method.getMaxIonCount(), lPosModeSettingsToAnalyze, lPosModeSettingsToAnalyzeCounts);
     16
     17                lNegModeSettingsToAnalyze = new ArrayList<>();
     18                lNegModeSettingsToAnalyzeCounts = new ArrayList<>();
     19                GlycanStructureAnnotation.determineIonSettingSets(false, method.getIons(), method.getMaxIonCount(), lNegModeSettingsToAnalyze, lNegModeSettingsToAnalyzeCounts);
     20
     21                lExchangesoAnalyze = new ArrayList<>();
     22                lExchangesToAnalyzeCounts = new ArrayList<>();
     23                GlycanStructureAnnotation.determineIonSettingSets(null, method.getIonExchanges(), method.getMaxIonCount(), lExchangesoAnalyze, lExchangesToAnalyzeCounts);
     24
     25                lNeutralLossesToAnalyze = new ArrayList<>();
     26                lNeutralLossesToAnalyzeCounts = new ArrayList<>();
     27                GlycanStructureAnnotation.determineIonSettingSets(null, method.getNeutralLoss(), -1, lNeutralLossesToAnalyze, lNeutralLossesToAnalyzeCounts);
     28        }
     29}}}
    330
    431{{{