Examples of TagFilter

htsjdk.samtools.filter.TagFilter
org.apache.derby.iapi.sql.compile.TagFilter
Filter which passes Visitables which have been marked with a given tag.
org.watermint.sourcecolon.org.opensolaris.opengrok.analysis.TagFilter
A reader that reads only plain text from a HTML or XML file @author Chandan

Examples of htsjdk.samtools.filter.TagFilter

    public void writeBfqFiles() {


        final Iterator<SAMRecord> iterator = (new SAMFileReader(IOUtil.openFileForReading(this.bamFile))).iterator();


        // Filter out noise reads and reads that fail the quality filter
        final TagFilter tagFilter = new TagFilter(ReservedTagConstants.XN, 1);
        final FailsVendorReadQualityFilter qualityFilter = new FailsVendorReadQualityFilter();
        final WholeReadClippedFilter clippedFilter = new WholeReadClippedFilter();




        if (!pairedReads) {

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Examples of htsjdk.samtools.filter.TagFilter

        }
        final PeekableIterator<SAMRecord> it = new PeekableIterator<SAMRecord>(reader.iterator());
        if (!this.pairedReads) {
            // Filter out noise reads and reads that fail the quality filter
            final List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>();
            filters.add(new TagFilter(ReservedTagConstants.XN, 1));
            if (!this.includeNonPfReads) {
                filters.add(new FailsVendorReadQualityFilter());
            }
            final FilteringIterator itr = new FilteringIterator(it, new AggregateFilter(filters));
            while (itr.hasNext()) {

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Examples of org.apache.derby.iapi.sql.compile.TagFilter

        ArrayList<String>   explicitlySetColumns = getExplicitlySetColumns();
        List<CastNode> allCastNodes = collectAllCastNodes();
        tagPrivilegedNodes();


        // tell the compiler to only add privilege checks for nodes which have been tagged
        TagFilter   tagFilter = new TagFilter( TagFilter.NEED_PRIVS_FOR_UPDATE_STMT );
        getCompilerContext().addPrivilegeFilter( tagFilter );
    
    bindTables(dataDictionary);


    // wait to bind named target table until the cursor

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Examples of org.watermint.sourcecolon.org.opensolaris.opengrok.analysis.TagFilter

        // Why? Is it CS sensible?
        try {
            if (compressed) {
                fis = new FileInputStream(new File(basedir, path + ".gz"));
                gis = new GZIPInputStream(fis);
                r = new TagFilter(new BufferedReader(new InputStreamReader(gis)));
            } else {
                fr = new FileReader(new File(basedir, path));
                r = new TagFilter(new BufferedReader(fr));
            }
            int len = r.read(content);
            return new String(content, 0, len);
        } catch (Exception e) {
            log.log(Level.WARNING, "An error reading tags from " + basedir + path + (compressed ? ".gz" : ""), e);

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Examples of org.watermint.sourcecolon.org.opensolaris.opengrok.analysis.TagFilter

    private ConstantPool cp;


    @Override
    public TokenStream tokenStream(String fieldName, Reader reader) {
        if ("full".equals(fieldName)) {
            return new PlainFullTokenizer(new TagFilter(reader));
        }
        return super.tokenStream(fieldName, reader);
    }

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Examples of org.watermint.sourcecolon.org.opensolaris.opengrok.analysis.TagFilter

                                    tags, nhits > 100, ret);
                        } else if (Genre.XREFABLE == genre && data != null && summarizer != null) {
                            int l = 0;
                            Reader r = null;
                            if (RuntimeEnvironment.getInstance().isCompressXref()) {
                                r = new TagFilter(new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(data + "/xref" + filename + ".gz")))));
                            } else {
                                r = new TagFilter(new BufferedReader(new FileReader(data + "/xref" + filename)));
                            }
                            try {
                                l = r.read(content);
                            } finally {
                                IOUtils.close(r);

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