Examples of IdFilter

com.compomics.util.preferences.IdFilter
net.sf.saxon.event.IDFilter
IDFilter is a ProxyReceiver that extracts the subtree of a document rooted at the element with a given ID value. Namespace declarations outside this subtree are treated as if they were present on the identified element.
nu.validator.xml.IdFilter
Supports XML 1.0 only! String interning must be on! @version $Id$ @author hsivonen
org.pdf4j.saxon.event.IDFilter
IDFilter is a ProxyReceiver that extracts the subtree of a document rooted at the element with a given ID value. Namespace declarations outside this subtree are treated as if they were present on the identified element.
org.waveprotocol.wave.model.id.IdFilter
An immutable filter representing a (possibly infinite) subset of all possible WaveletIds. A filter comprises a (possibly empty) set of ids to explicitly accept, plus a (possibly empty) set of id prefixes to accept. Matches against WaveletIds must be exact, but when matching a prefix, only the {@link WaveletId#getId() local id} part of the WaveletId is considered.Thus a WaveletId is accepted by an IdFilter if it exactly equals one of the specified WaveletIds, or if its local id part starts with one of the specified prefixes. An IdFilter with prefix "" accepts everything. An IdFilter with no prefix and no id accepts nothing. IdFilter is a value class. Use {@link #accepts(IdFilter,WaveletId)} todetermine if a filter accepts an id. @author anorth@google.com (Alex North)

Examples of com.compomics.util.preferences.IdFilter

                }
            }
        }


        // set the filtering import settings
        idFilter = new IdFilter();
        idFilter.setMinPepLength(cliInputBean.getMinPepLength());
        idFilter.setMaxPepLength(cliInputBean.getMaxPepLength());
        idFilter.setMaxMzDeviation(cliInputBean.getMaxMzDeviation());
        idFilter.setIsPpm(cliInputBean.isMaxMassDeviationPpm());
        idFilter.setRemoveUnknownPTMs(cliInputBean.excludeUnknownPTMs());

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Examples of com.compomics.util.preferences.IdFilter

     *
     * @param evt
     */
    private void importFilterMenuActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_importFilterMenuActionPerformed
        ImportSettingsDialog importSettingsDialog = new ImportSettingsDialog(this, getIdFilter(), true);
        IdFilter newFilter = importSettingsDialog.getFilter();
        if (newFilter != null) {
            setIdFilter(newFilter);
        }
    }//GEN-LAST:event_importFilterMenuActionPerformed

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Examples of com.compomics.util.preferences.IdFilter

     *
     * @param evt
     */
    private void editImportFilterButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_editImportFilterButtonActionPerformed
        ImportSettingsDialog importSettingsDialog = new ImportSettingsDialog(this, peptideShakerGUI.getIdFilter(), true);
        IdFilter newFilter = importSettingsDialog.getFilter();
        if (newFilter != null) {
            importFilterTxt.setText("User Defined");
            idFilter = newFilter;
        }
    }//GEN-LAST:event_editImportFilterButtonActionPerformed

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Examples of com.compomics.util.preferences.IdFilter


            experimentSettings = new PeptideShakerSettings(tempSettings.getSearchParameters(), tempSettings.getAnnotationPreferences(),
                    tempSettings.getSpectrumCountingPreferences(), tempSettings.getProjectDetails(), tempSettings.getFilterPreferences(),
                    tempSettings.getDisplayPreferences(),
                    tempSettings.getMetrics(), tempProcessingPreferences, tempSettings.getIdentificationFeaturesCache(),
                    tempPTMScoringPreferences, new GenePreferences(), new IdFilter(), SequenceMatchingPreferences.getDefaultSequenceMatching(tempSettings.getSearchParameters()));


        } else {
            experimentSettings = (PeptideShakerSettings) experiment.getUrParam(experimentSettings);
        }

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Examples of com.compomics.util.preferences.IdFilter

        displayPreferences = new DisplayPreferences();
        searchParameters = new SearchParameters();
        processingPreferences = new ProcessingPreferences();
        genePreferences = new GenePreferences();
        sequenceMatchingPreferences = null;
        idFilter = new IdFilter();
    }

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Examples of com.compomics.util.preferences.IdFilter

        spectrumCountingPreferences.setValidatedHits(true);
        processingPreferences = new ProcessingPreferences();
        ptmScoringPreferences = new PTMScoringPreferences();
        genePreferences = new GenePreferences();
        sequenceMatchingPreferences = SequenceMatchingPreferences.getDefaultSequenceMatching(searchParameters);
        idFilter = new IdFilter();
    }

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Examples of com.compomics.util.preferences.IdFilter

     * @throws Exception exception thrown whenever a problem occurred while
     * deserializing a match
     */
    public void scoreProteinPtms(Identification identification, Metrics metrics, WaitingHandler waitingHandler, SearchParameters searchParameters,
            AnnotationPreferences annotationPreferences, PTMScoringPreferences ptmScoringPreferences, SequenceMatchingPreferences sequenceMatchingPreferences) throws Exception {
        scoreProteinPtms(identification, metrics, waitingHandler, searchParameters, annotationPreferences, ptmScoringPreferences, new IdFilter(), null, sequenceMatchingPreferences);
    }

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Examples of net.sf.saxon.event.IDFilter

                    ((AugmentedSource)source).setStripSpace(stripSpace);
            }
        }


        if (id != null) {
            IDFilter filter = new IDFilter(id);
            source = AugmentedSource.makeAugmentedSource(source);
            ((AugmentedSource)source).addFilter(filter);
        }


        if (params != null) {

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Examples of net.sf.saxon.event.IDFilter

            if (source==null) {
                source = config.getSystemURIResolver().resolve(relative, getBaseURI());
            }


            if (fragment != null) {
                IDFilter filter = new IDFilter(fragment);
                source = AugmentedSource.makeAugmentedSource(source);
                ((AugmentedSource)source).addFilter(filter);
            }


            // check for recursion

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Examples of net.sf.saxon.event.IDFilter

                    ((AugmentedSource)source).setStripSpace(stripSpace);
            }
        }


        if (id != null) {
            IDFilter filter = new IDFilter(id);
            source = AugmentedSource.makeAugmentedSource(source);
            ((AugmentedSource)source).addFilter(filter);
        }


        if (params != null) {

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