Examples of addSequence()

Examples of com.topologi.diffx.sequence.EventSequence.addSequence()

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        for (int k = rdi.leftStart() ; k< rdi.leftEnd() ; k++) {

          if (rdi.kind()==rdi.CHANGE) {
            // This we need to diff
            //leftReport.append( "#" );
            seq1.addSequence(leftESC.getItem(k));

            // Don't forget our existing prefix mappings!
            PrefixMapping existingPM = leftESC.getItem(k).getPrefixMapping();
            addToPrefixMapping(seq1.getPrefixMapping(), existingPM);
          } else {
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Examples of com.volantis.mcs.dom2theme.impl.generator.rule.builder.RuleBuilder.addSequence()

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        // ==================================================================
        // Do the test.
        // ==================================================================

        RuleBuilder ruleBuilder = new RuleBuilder();
        ruleBuilder.addSequence(sequenceBuilderMock);
        ruleBuilder.setProperties(stylePropertiesMock);
        Rule rule = ruleBuilder.getRule();

        assertEquals("", rule.getSelectors().size(), 1);
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Examples of com.volantis.mcs.dom2theme.impl.generator.rule.builder.RuleBuilder.addSequence()

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                        sequenceBuilder.setTypeSelector(
                                selectorSequence.getType());
                    }
                    sequenceBuilder.addPseudoSelectors(
                            selectorSequence.getPath());
                    ruleBuilder.addSequence(sequenceBuilder);
                    ruleBuilder.setProperties(commonProperties);
                    Rule rule = ruleBuilder.getRule();

                    // Add the created rule to the rule set.
                    styleSheet.addRule(rule);
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Examples of com.volantis.mcs.dom2theme.impl.generator.rule.builder.RuleBuilder.addSequence()

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        RuleBuilder ruleBuilder = ruleBuilderFactory.createRuleBuilder();
        SimpleSelectorSequenceBuilder sequenceBuilder =
                ruleBuilderFactory.createSequenceBuilder();
        sequenceBuilder.addClassSelector(className);
        sequenceBuilder.addPseudoSelectors(pseudoPath);
        ruleBuilder.addSequence(sequenceBuilder);
        ruleBuilder.setProperties(styles.getPathProperties(pseudoPath));
        Rule rule = ruleBuilder.getRule();
        styleSheet.addRule(rule);
    }
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Examples of cz.startnet.utils.pgdiff.schema.PgSchema.addSequence()

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            throw new RuntimeException(MessageFormat.format(
                    Resources.getString("CannotFindSchema"), schemaName,
                    statement));
        }

        schema.addSequence(sequence);

        while (!parser.expectOptional(";")) {
            if (parser.expectOptional("INCREMENT")) {
                parser.expectOptional("BY");
                sequence.setIncrement(parser.parseString());
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Examples of edu.msu.cme.rdp.classifier.train.validation.TreeFactory.addSequence()

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        LineageSequenceParser parser = new LineageSequenceParser(source_file);
        HashMap<String, HashSet> genusTrainSeqMap = new HashMap<String, HashSet>(); // keep the seqID for each genus

        while ( parser.hasNext() ){
            LineageSequence pSeq = parser.next();
            HierarchyTree genusNode = factory.addSequence( pSeq);
            HashSet<String> genusSeqSet = genusTrainSeqMap.get(genusNode.getName());
            if ( genusSeqSet == null){
                genusSeqSet = new HashSet<String>();
                genusTrainSeqMap.put(genusNode.getName(), genusSeqSet);
            }
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Examples of edu.msu.cme.rdp.classifier.train.validation.TreeFactory.addSequence()

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        LineageSequenceParser parser = new LineageSequenceParser(source_file);

        while ( parser.hasNext() ){
            LineageSequence pSeq = parser.next();
            if ( !selectedTestSeqIDs.contains(pSeq.getSeqName())){
              factory.addSequence( pSeq);
            }
        }
        parser.close();

        //after all the training set is being parsed, calculate the prior probability for all the words.
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Examples of edu.msu.cme.rdp.classifier.train.validation.TreeFactory.addSequence()

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        LineageSequenceParser parser = new LineageSequenceParser(new File(seqFile));
        LineageSequence seq;
        HashMap<String, String> seqMap = new HashMap<String, String>(); // seqID, desc
        while ( parser.hasNext()){
            seq = parser.next();
            factory.addSequence(seq, false); // donot check the kmers
           
            if ( seq.getSeqName().contains("|S00") ){ // rdpID
                String[] values = seq.getSeqName().split("\\|");
                seqMap.put(values[0], seq.getDesc());  
            }else if (seq.getSeqName().contains("|SH") ){  // if it's seq from UNITE, we need to do something with the seqID            
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Examples of gov.nysenate.openleg.model.Supplemental.addSequence()

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        // Handle sequences when available
        XMLSequence xmlSequence = xmlSupp.getSequence();
        if (xmlSequence != null) {
            Sequence sequence = parseSequence(storage, supplemental, xmlSequence);
            supplemental.addSequence(sequence);

            // TODO: new removal objects? how/why?
            setRemoveObject(sequence, sequence.getId());
        }
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Examples of htsjdk.samtools.SAMFileHeader.addSequence()

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    @Test(dataProvider="invalidIntervalTestData")
    public void testInvalidPicardIntervalHandling(GATKArgumentCollection argCollection, GenomeLocParser genomeLocParser,
                                                  String contig, int intervalStart, int intervalEnd ) throws Exception {

        SAMFileHeader picardFileHeader = new SAMFileHeader();
        picardFileHeader.addSequence(genomeLocParser.getContigInfo("chr1"));
        IntervalList picardIntervals = new IntervalList(picardFileHeader);
        picardIntervals.add(new Interval(contig, intervalStart, intervalEnd, true, "dummyname"));

        File picardIntervalFile = createTempFile("testInvalidPicardIntervalHandling", ".intervals");
        picardIntervals.write(picardIntervalFile);
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