Examples with TableView javafx.scene.control.TableView used on opensource projects

Example 21 with TableView

use of javafx.scene.control.TableView in project jvarkit by lindenb.

the class BamStage method createSamFlagTable.

private TableView<SamFlagRow> createSamFlagTable() {
    final TableView<SamFlagRow> table = new TableView<>();
    table.getColumns().add(makeColumn("Flag", O -> O.flag.name()));
    table.getColumns().add(makeColumn("Status", param -> param.flag.isSet(param.record.getFlags()) ? "\u2611" : "\u2610"));
    table.setPlaceholder(new Label("No SAM flag."));
    return table;
}

Example 22 with TableView

use of javafx.scene.control.TableView in project jvarkit by lindenb.

the class BamStage method createReadGroupPane.

private Tab createReadGroupPane(final SAMFileHeader header) {
    final TableView<SAMReadGroupRecord> table = new TableView<>(header == null ? FXCollections.observableArrayList() : FXCollections.observableArrayList(header.getReadGroups()));
    table.getColumns().add(makeColumn("ID", G -> G.getId()));
    table.getColumns().add(makeColumn("Sample", G -> G.getSample()));
    table.getColumns().add(makeColumn("Center", G -> G.getSequencingCenter()));
    table.getColumns().add(makeColumn("Platform", G -> G.getPlatform()));
    table.getColumns().add(makeColumn("PlatformModel", G -> G.getPlatformModel()));
    table.getColumns().add(makeColumn("PlatformUnit", G -> G.getPlatformUnit()));
    table.getColumns().add(makeColumn("MedianInsertSize", G -> G.getPredictedMedianInsertSize()));
    table.getColumns().add(makeColumn("Desc", G -> G.getDescription()));
    table.getColumns().add(makeColumn("PU", G -> G.getPlatformUnit()));
    table.getColumns().add(makeColumn("Lib", G -> G.getLibrary()));
    table.getColumns().add(makeColumn("Run-Date", G -> G.getRunDate()));
    final Tab tab = new Tab("ReadGroups", table);
    tab.setClosable(false);
    table.setPlaceholder(new Label("No BAM read-greoup."));
    return tab;
}

Example 23 with TableView

use of javafx.scene.control.TableView in project jvarkit by lindenb.

the class VcfStage method buildVepTableRow.

private TableView<VepPredictionParser.VepPrediction> buildVepTableRow(final VepPredictionParser parser) {
    final TableView<VepPredictionParser.VepPrediction> table = new TableView<>();
    if (parser.isValid()) {
        for (final String col : parser.getCategories()) {
            table.getColumns().add(makeColumn(col, P -> P.get(col)));
        }
    }
    table.setPlaceholder(new Label("No VEP prediction available"));
    return table;
}

Example 24 with TableView

use of javafx.scene.control.TableView in project jvarkit by lindenb.

the class VcfStage method buildVariantTable.

/**
 * build table of variants
 */
private TableView<VariantContext> buildVariantTable() {
    final TableView<VariantContext> table = new TableView<>();
    table.getColumns().add(makeColumn("CHROM", V -> V.getContig()));
    table.getColumns().add(formatIntegerColumn(makeColumn("POS", V -> V.getStart())));
    table.getColumns().add(makeColumn("ID", V -> V.hasID() ? V.getID() : null));
    table.getColumns().add(makeColumn("REF", V -> allele2stringConverter.apply(V.getReference())));
    table.getColumns().add(makeColumn("ALT", V -> V.getAlternateAlleles().stream().map(A -> allele2stringConverter.apply(A)).collect(Collectors.joining(","))));
    table.getColumns().add(makeColumn("FILTER", V -> V.getFilters().stream().collect(Collectors.joining(","))));
    table.getColumns().add(makeColumn("QUAL", V -> V.hasLog10PError() ? V.getPhredScaledQual() : null));
    table.setPlaceholder(new Label("No Variant."));
    final ContextMenu ctxMenu = new ContextMenu();
    MenuItem menuItem = new MenuItem("dbSNP...");
    menuItem.setOnAction(AE -> {
        final VariantContext ctx = table.getSelectionModel().getSelectedItem();
        if (ctx == null || !ctx.hasID() || !ctx.getID().matches("rs[0-9]+"))
            return;
        // http://stackoverflow.com/questions/16604341
        VcfStage.this.owner.getHostServices().showDocument("https://www.ncbi.nlm.nih.gov/snp/" + ctx.getID().substring(2));
    });
    ctxMenu.getItems().add(menuItem);
    ctxMenu.getItems().addAll(super.buildItemsForContextMenu());
    for (final String build : new String[] { "human" }) {
        menuItem = new MenuItem("Prediction Ensembl REST [" + build + "]");
        menuItem.setOnAction(AE -> {
            final VariantContext ctx = table.getSelectionModel().getSelectedItem();
            if (ctx == null)
                return;
            for (final Allele a : ctx.getAlternateAlleles()) {
                if (a.isReference())
                    continue;
                if (a.isSymbolic())
                    continue;
                if (a.isNoCall())
                    continue;
                VcfStage.this.owner.getHostServices().showDocument("http://rest.ensembl.org/vep/" + build + "/region/" + JfxNgs.ContigToEnseml.apply(ctx.getContig()) + "%3A" + ctx.getStart() + "-" + ctx.getEnd() + "%3A1%2F" + a.getDisplayString() + "?content-type=text%2Fxml");
            }
        });
        ctxMenu.getItems().add(menuItem);
    }
    for (final String database : new String[] { "Exac", "gnomAD" }) {
        menuItem = new MenuItem("Open Variant (ALT) in " + database + " ... ");
        menuItem.setOnAction(AE -> {
            final VariantContext ctx = table.getSelectionModel().getSelectedItem();
            if (ctx == null)
                return;
            for (final Allele a : ctx.getAlternateAlleles()) {
                if (a.isReference())
                    continue;
                if (a.isSymbolic())
                    continue;
                if (a.isNoCall())
                    continue;
                VcfStage.this.owner.getHostServices().showDocument("http://" + database.toLowerCase() + ".broadinstitute.org/variant/" + JfxNgs.ContigToEnseml.apply(ctx.getContig()) + "-" + ctx.getStart() + "-" + ctx.getReference().getDisplayString() + "-" + a.getDisplayString());
            }
        });
        ctxMenu.getItems().add(menuItem);
    }
    table.setContextMenu(ctxMenu);
    return table;
}

Example 25 with TableView

use of javafx.scene.control.TableView in project jvarkit by lindenb.

the class VcfStage method buildInfoHeaderTab.

/**
 * build a table describing the INFO column
 */
private Tab buildInfoHeaderTab(final VCFHeader header) {
    final TableView<VCFInfoHeaderLine> table = new TableView<>(FXCollections.observableArrayList(header.getInfoHeaderLines()));
    table.getColumns().add(makeColumn("ID", F -> F.getID()));
    table.getColumns().add(makeColumn("Type", F -> F.getType() == null ? null : F.getType().name()));
    table.getColumns().add(makeColumn("Count", F -> F.isFixedCount() ? F.getCount() : null));
    table.getColumns().add(makeColumn("Description", F -> F.getDescription()));
    final Tab tab = new Tab("INFO", table);
    tab.setClosable(false);
    table.setPlaceholder(new Label("No INFO defined."));
    return tab;
}