Examples of TagMatcher

Examples of com.compomics.util.experiment.identification.tags.matchers.TagMatcher

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        HashMap<String, LinkedList<SpectrumMatch>> tagMap = idfileReader.getTagsMap();
        if (tagMap != null && !tagMap.isEmpty()) {
            waitingHandler.setMaxSecondaryProgressCounter(tagMap.size());
            waitingHandler.appendReport("Mapping de novo tags to peptides.", true, true);
            for (String key : tagMap.keySet()) {
            TagMatcher tagMatcher = new TagMatcher(searchParameters.getModificationProfile().getFixedModifications(), searchParameters.getModificationProfile().getAllNotFixedModifications(), sequenceMatchingPreferences);
                Iterator<SpectrumMatch> matchIterator = tagMap.get(key).iterator();
                while (matchIterator.hasNext()) {
                    SpectrumMatch spectrumMatch = matchIterator.next();
                    mapTagsForSpectrumMatch(spectrumMatch, tagMatcher, key, waitingHandler, !matchIterator.hasNext());
                }
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Examples of com.compomics.util.experiment.identification.tags.matchers.TagMatcher

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        HashMap<String, LinkedList<SpectrumMatch>> tagMap = idfileReader.getTagsMap();
        if (tagMap != null && !tagMap.isEmpty()) {
            waitingHandler.setMaxSecondaryProgressCounter(tagMap.size());
            waitingHandler.appendReport("Mapping de novo tags to peptides.", true, true);
            for (String key : tagMap.keySet()) {
            TagMatcher tagMatcher = new TagMatcher(searchParameters.getModificationProfile().getFixedModifications(), searchParameters.getModificationProfile().getAllNotFixedModifications(), sequenceMatchingPreferences);
            tagMatcher.setSynchronizedIndexing(true);
                Iterator<SpectrumMatch> matchIterator = tagMap.get(key).iterator();
                while (matchIterator.hasNext()) {
                    SpectrumMatch spectrumMatch = matchIterator.next();
                    SpectrumMatchTagMapperRunnable tagMapperRunnable = new SpectrumMatchTagMapperRunnable(spectrumMatch, tagMatcher, key, waitingHandler, !matchIterator.hasNext());
                    pool.submit(tagMapperRunnable);
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Examples of com.compomics.util.experiment.identification.tags.matchers.TagMatcher

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         */
        public KeyTagMapperRunnable(LinkedList<SpectrumMatch> spectrumMatches, ArrayList<String> fixedModifications, ArrayList<String> variableModifications, SequenceMatchingPreferences sequenceMatchingPreferences, String key, WaitingHandler waitingHandler) {
            this.spectrumMatches = spectrumMatches;
            this.key = key;
            this.waitingHandler = waitingHandler;
            this.tagMatcher = new TagMatcher(fixedModifications, variableModifications, sequenceMatchingPreferences);
        }
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