Examples of org.broadinstitute.gatk.tools.walkers.varianteval.util.AnalysisModuleScanner

            final EvaluationContext nec = stratManager.get(key);


            for ( final VariantEvaluator ve : nec.getVariantEvaluators() ) {
                final GATKReportTable table = report.getTable(ve.getSimpleName());


                final AnalysisModuleScanner scanner = new AnalysisModuleScanner(ve);
                final Map<Field, DataPoint> datamap = scanner.getData();
                try {
                    if ( scanner.hasMoltenField() ) {
                        final Field field = scanner.getMoltenField();
                        final Object fieldValue = field.get(ve);


                        if ( fieldValue == null || ! (fieldValue instanceof Map) )
                            throw new ReviewedGATKException("BUG field " + field.getName() + " must be a non-null instance of Map in " + scanner.getAnalysis().name());
                        final Map<Object, Object> map = (Map<Object, Object>)fieldValue;
                        if ( map.isEmpty() )
                            throw new ReviewedGATKException("BUG: map is null or empty in analysis " + scanner.getAnalysis());
                        
                        int counter = 0; // counter is used to ensure printing order is as defined by entrySet
                        for ( Map.Entry<Object, Object> keyValue : map.entrySet() ) {
                            // "%05d" is a terrible hack to ensure sort order
                            final String moltenStratStateString = stratStateString + String.format("%05d", counter++);
                            setStratificationColumns(table, moltenStratStateString, stratsAndStates);
                            table.set(moltenStratStateString, scanner.getMoltenAnnotation().variableName(), keyValue.getKey());
                            table.set(moltenStratStateString, scanner.getMoltenAnnotation().valueName(), keyValue.getValue());
                        }
                    } else {
                        setStratificationColumns(table, stratStateString, stratsAndStates);
                        for ( final Field field : datamap.keySet()) {
                            table.set(stratStateString, field.getName(), field.get(ve));

    private static GATKReport initializeGATKReport(final Collection<VariantStratifier> stratifiers,
                                                   final Collection<VariantEvaluator> evaluators) {
        final GATKReport report = new GATKReport();


        for (final VariantEvaluator ve : evaluators) {
            final AnalysisModuleScanner scanner = new AnalysisModuleScanner(ve);
            final Map<Field, DataPoint> datamap = scanner.getData();


            // create the table
            final String tableName = ve.getSimpleName();
            final String tableDesc = ve.getClass().getAnnotation(Analysis.class).description();
            report.addTable(tableName, tableDesc, 1 + stratifiers.size() + (scanner.hasMoltenField() ? 2 : datamap.size()), GATKReportTable.TableSortingWay.SORT_BY_ROW);


            // grab the table, and add the columns we need to it
            final GATKReportTable table = report.getTable(tableName);
            table.addColumn(tableName, tableName);


            // first create a column to hold each stratifier state
            for (final VariantStratifier vs : stratifiers) {
                final String columnName = vs.getName();
                table.addColumn(columnName, vs.getFormat());
            }


            if ( scanner.hasMoltenField() ) {
                // deal with molten data
                table.addColumn(scanner.getMoltenAnnotation().variableName(), scanner.getMoltenAnnotation().variableFormat());
                table.addColumn(scanner.getMoltenAnnotation().valueName(), scanner.getMoltenAnnotation().valueFormat());
            } else {
                if ( datamap.isEmpty() )
                    throw new ReviewedGATKException("Datamap is empty for analysis " + scanner.getAnalysis());
                
                // add DataPoint's for each field marked as such
                for (final Map.Entry<Field, DataPoint> field : datamap.entrySet()) {
                    try {
                        field.getKey().setAccessible(true);

Examples of org.broadinstitute.gatk.tools.walkers.varianteval.util.AnalysisModuleScanner

Related Classes of org.broadinstitute.gatk.tools.walkers.varianteval.util.AnalysisModuleScanner