Examples of Locus

Examples of mondrian.server.Locus

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            } while (phase());

            evaluator.restore(savepoint);

            // Get value for each Cell
            final Locus locus = new Locus(execution, null, "Loading cells");
            Locus.push(locus);
            try {
                executeBody(slicerEvaluator, query, new int[axes.length]);
            } finally {
                Locus.pop(locus);
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Examples of mondrian.server.Locus

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                "coordinates should have dimension " + point.size());
        }

        for (int i = 0; i < pos.length; i++) {
            if (positionsHighCardinality.get(i)) {
                final Locus locus = new Locus(execution, null, "Loading cells");
                Locus.push(locus);
                try {
                    executeBody(evaluator, statement.getQuery(), pos);
                } finally {
                    Locus.pop(locus);
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Examples of mondrian.server.Locus

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                if (connection == null) {
                    throw new IllegalArgumentException("Connection required");
                }
                execution = new Execution(connection.getInternalStatement(), 0);
            }
            final Locus locus = new Locus(
                execution,
                "CacheControlImpl.execute",
                "when modifying the member cache.");
            Locus.push(locus);
            try {
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Examples of mondrian.server.Locus

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        final String sql = buf.toString();
        SqlStatement stmt =
            RolapUtil.executeQuery(
                dataSource,
                sql,
                new Locus(
                    execution,
                    "SqlStatisticsProvider.getTableCardinality",
                    "Reading row count from table "
                    + Arrays.asList(catalog, schema, table)));
        try {
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Examples of mondrian.server.Locus

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        final String countSql = buf.toString();
        SqlStatement stmt =
            RolapUtil.executeQuery(
                dataSource,
                countSql,
                new Locus(
                    execution,
                    "SqlStatisticsProvider.getQueryCardinality",
                    "Reading row count from query [" + sql + "]"));
        try {
            ResultSet resultSet = stmt.getResultSet();
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Examples of mondrian.server.Locus

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        }
        SqlStatement stmt =
            RolapUtil.executeQuery(
                dataSource,
                sql,
                new Locus(
                    execution,
                    "SqlStatisticsProvider.getColumnCardinality",
                    "Reading cardinality for column "
                    + Arrays.asList(catalog, schema, table, column)));
        try {
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Examples of org.broad.igv.feature.Locus

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    private List<LocusScore> scores;
    int zoom;

    public LoadedDataInterval(String chr, int start, int end, int zoom, List<LocusScore> scores) {

        range = new Locus(chr, start, end);
        this.zoom = zoom;
        this.scores = scores;
    }
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Examples of org.broad.igv.feature.Locus

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        }
        if (tokens.length >= sigColumn) {
            String locusString = tokens[locusColumn];
            if (locusString == null) return null;

            Locus locus = Locus.fromString(locusString);
            if (locus == null || locus.getChr() == null) return null;

            String logRatioStr = tokens[logRatioColumn];
            float logRatio = Float.parseFloat(logRatioStr);

            if (Float.isInfinite(logRatio) || Float.isNaN(logRatio)) {
                log.info("LogRatio " + logRatioStr + " cannot be parsed as a float");
                logRatio = Float.NaN;
            }

            float fpkmX = Float.parseFloat(tokens[xColumn]);
            float fpkmY = Float.parseFloat(tokens[yColumn]);
            String gene = tokens[geneColumn];
            String significant = tokens[sigColumn];
            return new ExpDiffValue(locus.getChr(), locus.getStart() - 1, locus.getEnd(), gene,
                    logRatio, fpkmX, fpkmY, significant);
        } else {
            log.info("Unexpected # of columns.  Expected at least 12,  found " + tokens.length);
            return null;
        }
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Examples of org.broad.igv.feature.Locus

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        }
        if (tokens.length >= (startfpkmCol + numSamples*colsPerSample)) {
            String locusString = tokens[locusColumn];
            if (locusString == null) return null;

            Locus locus = Locus.fromString(locusString);
            if(locus == null || locus.getChr() == null) return null;

            String gene = tokens[geneColumn];
            float[] fpkm = new float[numSamples];
            float[] confLo = new float[numSamples];
            float[] confHi = new float[numSamples];

            for(int sampNum = 0; sampNum < numSamples; sampNum++){
                int startCol = startfpkmCol + sampNum*colsPerSample;
                fpkm[sampNum] = Float.parseFloat(tokens[startCol]);
                confLo[sampNum] = Float.parseFloat(tokens[startCol+1]);
                confHi[sampNum] = Float.parseFloat(tokens[startCol+2]);
            }

            return new FPKMValue(locus.getChr(), locus.getStart() - 1, locus.getEnd(), gene,
                    fpkm, confLo, confHi);
        } else {
            log.info("Unexpected # of columns.  Expected at least 12,  found " + tokens.length);
            return null;
        }
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Examples of org.broad.igv.feature.Locus

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    @BeforeClass
    public static void setup() throws IOException {
        Map<String, List<Feature>> allFeatures = loadTestFeatures();

        frame = new ExomeReferenceFrame(new ReferenceFrame("test"), allFeatures);
        frame.jumpTo(new Locus("chr6", 1, 100));
    }
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