Example usage for javafx.scene.layout GridPane setHgrow

List of usage examples for javafx.scene.layout GridPane setHgrow

Introduction

In this page you can find the example usage for javafx.scene.layout GridPane setHgrow.

Prototype

public static void setHgrow(Node child, Priority value) 

Source Link

Document

Sets the horizontal grow priority for the child when contained by a gridpane.

Usage

From source file:uk.co.everywheremusic.viewcontroller.SetupScene.java

private boolean validateForm() {

    boolean valid = true;
    String errorMessage = "";

    File musicDir = new File(txtFolder.getText());
    if (!musicDir.isDirectory()) {
        valid = false;// w  w  w. j  ava2s .c  om
        errorMessage += Globals.SETUP_ERR_INVALID_FOLDER + "\n\n";
    }

    String password = txtPassword.getText();
    String confirmPassword = txtConfirmPassword.getText();
    if (!password.equals(confirmPassword)) {
        valid = false;
        errorMessage += "Passwords do not match\n\n";
    }

    if (password.equals("")) {
        valid = false;
        errorMessage += "Enter a password\n\n";
    }

    if (!valid) {
        Alert alert = new Alert(AlertType.INFORMATION);
        alert.setTitle(Globals.SETUP_ALERT_TITLE);
        alert.setHeaderText(Globals.SETUP_ALERT_HEADER_TEXT);

        TextArea text = new TextArea(errorMessage);
        text.setEditable(false);
        text.setWrapText(true);
        GridPane.setVgrow(text, Priority.NEVER);
        GridPane.setHgrow(text, Priority.NEVER);

        GridPane content = new GridPane();
        content.setMaxWidth(Double.MAX_VALUE);
        content.add(text, 0, 0);

        alert.getDialogPane().setContent(content);
        alert.showAndWait();
    }

    return valid;

}

From source file:frontend.GUIController.java

@FXML
void showAbout(ActionEvent event) {
    /*Dialogs.create()/*ww w . ja  va 2s  .com*/
    .title("About")
    .message(getLicense())
    .showInformation();*/
    Alert alert = new Alert(AlertType.INFORMATION);
    alert.initOwner(stage);
    alert.initModality(Modality.APPLICATION_MODAL);
    alert.setTitle("SAIL 1.1: About");
    alert.setHeaderText("SAIL 1.1 details");
    alert.setContentText("SAIL 1.1");
    Label label = new Label("SAIL License details:");

    TextArea textArea = new TextArea(getLicense());
    textArea.setEditable(false);
    textArea.setWrapText(true);

    textArea.setMaxWidth(Double.MAX_VALUE);
    textArea.setMaxHeight(Double.MAX_VALUE);
    GridPane.setVgrow(textArea, Priority.ALWAYS);
    GridPane.setHgrow(textArea, Priority.ALWAYS);

    GridPane expContent = new GridPane();
    expContent.setMaxWidth(Double.MAX_VALUE);
    expContent.add(label, 0, 0);
    expContent.add(textArea, 0, 1);

    // Set expandable Exception into the dialog pane.
    alert.getDialogPane().setExpandableContent(expContent);

    alert.showAndWait();

}

From source file:io.bitsquare.gui.main.overlays.Overlay.java

protected void addMessage() {
    if (message != null) {
        messageLabel = new Label(truncatedMessage);
        messageLabel.setMouseTransparent(true);
        messageLabel.setWrapText(true);// ww  w .j  a va2s.co  m
        GridPane.setHalignment(messageLabel, HPos.LEFT);
        GridPane.setHgrow(messageLabel, Priority.ALWAYS);
        GridPane.setMargin(messageLabel, new Insets(3, 0, 0, 0));
        GridPane.setRowIndex(messageLabel, ++rowIndex);
        GridPane.setColumnIndex(messageLabel, 0);
        GridPane.setColumnSpan(messageLabel, 2);
        gridPane.getChildren().add(messageLabel);
    }
}

From source file:qupath.lib.gui.panels.survival.KaplanMeierDisplay.java

@SuppressWarnings("unchecked")
private void generatePlot() {

    KaplanMeierDisplay.ScoreData newScoreData = scoreData;

    // If we have a hierarchy, update the scores with the most recent data
    if (hierarchy != null) {
        List<TMACoreObject> cores = PathObjectTools.getTMACoreObjects(hierarchy, false);
        double[] survival = new double[cores.size()];
        boolean[] censored = new boolean[cores.size()];
        double[] scores = new double[cores.size()];

        //            // Optionally sort by scores... helps a bit when debugging e.g. p-values, Hazard ratios etc.
        //            cores.sort((c1, c2) -> Double.compare(c1.getMeasurementList().getMeasurementValue(scoreColumn), c2.getMeasurementList().getMeasurementValue(scoreColumn)));

        //            scoreColumn = "Positive %";
        //         scoreColumn = "RoughScore";
        for (int i = 0; i < cores.size(); i++) {
            TMACoreObject core = cores.get(i);
            MeasurementList ml = core.getMeasurementList();
            survival[i] = core.getMeasurementList().getMeasurementValue(survivalColumn);
            double censoredValue = core.getMeasurementList().getMeasurementValue(censoredColumn);
            boolean hasCensoredValue = !Double.isNaN(censoredValue)
                    && (censoredValue == 0 || censoredValue == 1);
            censored[i] = censoredValue != 0;
            if (!hasCensoredValue) {
                // If we don't have a censored value, ensure we mask out everything else
                scores[i] = Double.NaN;
                survival[i] = Double.NaN;
            } else if (ml.containsNamedMeasurement(scoreColumn))
                // Get the score if we can
                scores[i] = ml.getMeasurementValue(scoreColumn);
            else {
                //               // Try to compute score if we need to
                //               Map<String, Number> map = ROIMeaningfulMeasurements.getPathClassSummaryMeasurements(core.getChildObjects(), true);
                //               Number value = map.get(scoreColumn);
                //               if (value == null)
                scores[i] = Double.NaN;
                //               else
                //                  scores[i] = value.doubleValue();
            }//from  w  w w  .  j av  a2s  . co  m
        }
        // Mask out any scores that don't have associated survival data
        for (int i = 0; i < survival.length; i++) {
            if (Double.isNaN(survival[i]))
                scores[i] = Double.NaN;
        }

        newScoreData = new ScoreData(scores, survival, censored);

    }

    if (newScoreData == null || newScoreData.scores.length == 0)
        return;

    //         KaplanMeier kmHigh = new KaplanMeier("Above threshold");
    //         KaplanMeier kmLow = new KaplanMeier("Below threshold");

    double[] quartiles = StatisticsHelper.getQuartiles(newScoreData.scores);
    double q1 = quartiles[0];
    double median = quartiles[1];
    double q3 = quartiles[2];
    double[] thresholds;
    if (params != null) {
        Object thresholdMethod = params.getChoiceParameterValue("scoreThresholdMethod");
        if (thresholdMethod.equals("Median")) {
            //               panelParams.setNumericParameterValue("scoreThreshold", median);
            //               ((DoubleParameter)params.getParameters().get("scoreThreshold")).setValue(median); // TODO: UPDATE DIALOG!
            thresholds = new double[] { median };
        } else if (thresholdMethod.equals("Tertiles")) {
            //                  ((DoubleParameter)params.getParameters().get("scoreThreshold")).setValue(median); // TODO: UPDATE DIALOG!
            thresholds = StatisticsHelper.getTertiles(newScoreData.scores);
        } else if (thresholdMethod.equals("Quartiles")) {
            //               ((DoubleParameter)params.getParameters().get("scoreThreshold")).setValue(median); // TODO: UPDATE DIALOG!
            thresholds = new double[] { q1, median, q3 };
        } else if (thresholdMethod.equals("Manual (1)")) {
            thresholds = new double[] { params.getDoubleParameterValue("threshold1") };
        } else if (thresholdMethod.equals("Manual (2)")) {
            thresholds = new double[] { params.getDoubleParameterValue("threshold1"),
                    params.getDoubleParameterValue("threshold2") };
        } else //if (thresholdMethod.equals("Manual (3)")) {
            thresholds = new double[] { params.getDoubleParameterValue("threshold1"),
                    params.getDoubleParameterValue("threshold2"),
                    params.getDoubleParameterValue("threshold3") };
    } else
        thresholds = new double[] { median };

    double minVal = Double.POSITIVE_INFINITY;
    double maxVal = Double.NEGATIVE_INFINITY;
    int numNonNaN = 0;
    for (double d : newScoreData.scores) {
        if (Double.isNaN(d))
            continue;
        if (d < minVal)
            minVal = d;
        if (d > maxVal)
            maxVal = d;
        numNonNaN++;
    }
    boolean scoresValid = maxVal > minVal; // If not this, we don't have valid scores that we can work with

    double maxTimePoint = 0;
    for (double d : newScoreData.survival) {
        if (Double.isNaN(d))
            continue;
        if (d > maxTimePoint)
            maxTimePoint = d;
    }
    if (panelParams != null
            && maxTimePoint > ((IntParameter) params.getParameters().get("censorTimePoints")).getUpperBound()) {
        panelParams.setNumericParameterValueRange("censorTimePoints", 0, Math.ceil(maxTimePoint));
    }

    // Optionally censor at specified time
    double censorThreshold = params == null ? maxTimePoint : params.getIntParameterValue("censorTimePoints");

    // Compute log-rank p-values for *all* possible thresholds
    // Simultaneously determine the threshold that yields the lowest p-value, 
    // resolving ties in favour of a more even split between high/low numbers of events
    boolean pValuesChanged = false;
    if (calculateAllPValues) {
        if (!(pValues != null && pValueThresholds != null && newScoreData.equals(scoreData)
                && censorThreshold == lastPValueCensorThreshold)) {
            Map<Double, Double> mapLogRank = new TreeMap<>();
            Set<Double> setObserved = new HashSet<>();
            for (int i = 0; i < newScoreData.scores.length; i++) {
                Double d = newScoreData.scores[i];
                boolean observed = !newScoreData.censored[i] && newScoreData.survival[i] < censorThreshold;
                if (observed)
                    setObserved.add(d);
                if (mapLogRank.containsKey(d))
                    continue;
                List<KaplanMeierData> kmsTemp = splitByThresholds(newScoreData, new double[] { d },
                        censorThreshold, false);
                //               if (kmsTemp.get(1).nObserved() == 0 || kmsTemp.get(1).nObserved() == 0)
                //                  continue;
                LogRankResult test = LogRankTest.computeLogRankTest(kmsTemp.get(0), kmsTemp.get(1));
                double pValue = test.getPValue();
                //                  double pValue = test.hazardRatio < 1 ? test.hazardRatio : 1.0/test.hazardRatio; // Checking usefulness of Hazard ratios...
                if (!Double.isFinite(pValue))
                    continue;
                //               if (!Double.isFinite(test.getHazardRatio())) {
                ////                  continue;
                //                  pValue = Double.NaN;
                //               }
                mapLogRank.put(d, pValue);
            }
            pValueThresholds = new double[mapLogRank.size()];
            pValues = new double[mapLogRank.size()];
            pValueThresholdsObserved = new boolean[mapLogRank.size()];
            int count = 0;
            for (Entry<Double, Double> entry : mapLogRank.entrySet()) {
                pValueThresholds[count] = entry.getKey();
                pValues[count] = entry.getValue();
                if (setObserved.contains(entry.getKey()))
                    pValueThresholdsObserved[count] = true;
                count++;
            }

            // Find the longest 'significant' stretch
            int maxSigCount = 0;
            int maxSigInd = -1;
            int sigCurrent = 0;
            int[] sigCount = new int[pValues.length];
            for (int i = 0; i < pValues.length; i++) {
                if (pValues[i] < 0.05) {
                    sigCurrent++;
                    sigCount[i] = sigCurrent;
                    if (sigCurrent > maxSigCount) {
                        maxSigCount = sigCurrent;
                        maxSigInd = i;
                    }
                } else
                    sigCurrent = 0;
            }
            if (maxSigCount == 0) {
                logger.info("No p-values < 0.05");
            } else {
                double minThresh = maxSigInd - maxSigCount < 0 ? pValueThresholds[0] - 0.0000001
                        : pValueThresholds[maxSigInd - maxSigCount];
                double maxThresh = pValueThresholds[maxSigInd];
                int nBetween = 0;
                int nBetweenObserved = 0;
                for (int i = 0; i < newScoreData.scores.length; i++) {
                    if (newScoreData.scores[i] > minThresh && newScoreData.scores[i] <= maxThresh) {
                        nBetween++;
                        if (newScoreData.survival[i] < censorThreshold && !newScoreData.censored[i])
                            nBetweenObserved++;
                    }
                }
                logger.info("Longest stretch of p-values < 0.05: {} - {} ({} entries, {} observed)", minThresh,
                        maxThresh, nBetween, nBetweenObserved);
            }

            pValuesSmoothed = new double[pValues.length];
            Arrays.fill(pValuesSmoothed, Double.NaN);
            int n = (pValues.length / 20) * 2 + 1;
            logger.info("Smoothing log-rank test p-values by " + n);
            for (int i = n / 2; i < pValues.length - n / 2; i++) {
                double sum = 0;
                for (int k = i - n / 2; k < i - n / 2 + n; k++) {
                    sum += pValues[k];
                }
                pValuesSmoothed[i] = sum / n;
            }
            //               for (int i = 0; i < pValues.length; i++) {
            //                  double sum = 0;
            //                  for (int k = Math.max(0, i-n/2); k < Math.min(pValues.length, i-n/2+n); k++) {
            //                     sum += pValues[k];
            //                  }
            //                  pValuesSmoothed[i] = sum/n;
            //               }
            //               pValues = pValuesSmoothed;

            lastPValueCensorThreshold = censorThreshold;
            pValuesChanged = true;
        }
    } else {
        lastPValueCensorThreshold = Double.NaN;
        pValueThresholds = null;
        pValues = null;
    }

    //            if (params != null && !Double.isNaN(bestThreshold) && (params.getChoiceParameterValue("scoreThresholdMethod").equals("Lowest p-value")))
    if (params != null && (params.getChoiceParameterValue("scoreThresholdMethod").equals("Lowest p-value"))) {
        int bestIdx = -1;
        double bestPValue = Double.POSITIVE_INFINITY;
        for (int i = pValueThresholds.length / 10; i < pValueThresholds.length * 9 / 10; i++) {
            if (pValues[i] < bestPValue) {
                bestIdx = i;
                bestPValue = pValues[i];
            }
        }
        thresholds = bestIdx >= 0 ? new double[] { pValueThresholds[bestIdx] } : new double[0];
    } else if (params != null
            && (params.getChoiceParameterValue("scoreThresholdMethod").equals("Lowest smoothed p-value"))) {
        int bestIdx = -1;
        double bestPValue = Double.POSITIVE_INFINITY;
        for (int i = pValueThresholds.length / 10; i < pValueThresholds.length * 9 / 10; i++) {
            if (pValuesSmoothed[i] < bestPValue) {
                bestIdx = i;
                bestPValue = pValuesSmoothed[i];
            }
        }
        thresholds = bestIdx >= 0 ? new double[] { pValueThresholds[bestIdx] } : new double[0];
    }

    // Split into different curves using the provided thresholds
    List<KaplanMeierData> kms = splitByThresholds(newScoreData, thresholds, censorThreshold,
            params != null && "Quartiles".equals(params.getChoiceParameterValue("scoreThresholdMethod")));

    //         for (KaplanMeier km : kms)
    //            km.censorAtTime(censorThreshold);
    ////         kmHigh.censorAtTime(censorThreshold);
    ////         kmLow.censorAtTime(censorThreshold);

    //         logger.info("High: " + kmHigh.toString());
    //         logger.info("Low: " + kmLow.toString());
    //         logger.info("Log rank comparison: {}", LogRankTest.computeLogRankTest(kmLow, kmHigh));

    if (plotter == null) {
        plotter = new KaplanMeierChartWrapper(survivalColumn + " time");
        //            plotter.setBorder(BorderFactory.createTitledBorder("Survival plot"));
        //            plotter.getCanvas().setWidth(300);
        //            plotter.getCanvas().setHeight(300);
    }
    KaplanMeierData[] kmArray = new KaplanMeierData[kms.size()];
    plotter.setKaplanMeierCurves(survivalColumn + " time", kms.toArray(kmArray));
    tableModel.setSurvivalCurves(thresholds,
            params != null && params.getChoiceParameterValue("scoreThresholdMethod").equals("Lowest p-value"),
            kmArray);

    // Bar width determined using 'Freedman and Diaconis' rule' (but overridden if this gives < 16 bins...)
    double barWidth = (2 * q3 - q1) * Math.pow(numNonNaN, -1.0 / 3.0);
    int nBins = 100;
    if (!Double.isNaN(barWidth))
        barWidth = (int) Math.max(16, Math.ceil((maxVal - minVal) / barWidth));
    Histogram histogram = scoresValid ? new Histogram(newScoreData.scores, nBins) : null;
    if (histogramPanel == null) {
        GridPane paneHistogram = new GridPane();
        histogramPanel = new HistogramPanelFX();
        histogramPanel.getChart().setAnimated(false);
        histogramWrapper = new ThresholdedChartWrapper(histogramPanel.getChart());
        for (ObservableNumberValue val : threshProperties)
            histogramWrapper.addThreshold(val, ColorToolsFX.getCachedColor(240, 0, 0, 128));
        histogramWrapper.getPane().setPrefHeight(150);
        paneHistogram.add(histogramWrapper.getPane(), 0, 0);
        Tooltip.install(histogramPanel.getChart(), new Tooltip("Distribution of scores"));
        GridPane.setHgrow(histogramWrapper.getPane(), Priority.ALWAYS);
        GridPane.setVgrow(histogramWrapper.getPane(), Priority.ALWAYS);

        NumberAxis xAxis = new NumberAxis();
        xAxis.setLabel("Score threshold");
        NumberAxis yAxis = new NumberAxis();
        yAxis.setLowerBound(0);
        yAxis.setUpperBound(1);
        yAxis.setTickUnit(0.1);
        yAxis.setAutoRanging(false);
        yAxis.setLabel("P-value");
        chartPValues = new LineChart<>(xAxis, yAxis);
        chartPValues.setAnimated(false);
        chartPValues.setLegendVisible(false);

        // Make chart so it can be navigated
        ChartToolsFX.makeChartInteractive(chartPValues, xAxis, yAxis);
        pValuesChanged = true;
        Tooltip.install(chartPValues, new Tooltip(
                "Distribution of p-values (log-rank test) comparing low vs. high for all possible score thresholds"));
        //            chartPValues.getYAxis().setAutoRanging(false);
        pValuesWrapper = new ThresholdedChartWrapper(chartPValues);
        for (ObservableNumberValue val : threshProperties)
            pValuesWrapper.addThreshold(val, ColorToolsFX.getCachedColor(240, 0, 0, 128));

        pValuesWrapper.getPane().setPrefHeight(150);
        paneHistogram.add(pValuesWrapper.getPane(), 0, 1);
        GridPane.setHgrow(pValuesWrapper.getPane(), Priority.ALWAYS);
        GridPane.setVgrow(pValuesWrapper.getPane(), Priority.ALWAYS);

        ContextMenu popup = new ContextMenu();
        ChartToolsFX.addChartExportMenu(chartPValues, popup);

        RadioMenuItem miZoomY1 = new RadioMenuItem("0-1");
        miZoomY1.setOnAction(e -> {
            yAxis.setAutoRanging(false);
            yAxis.setUpperBound(1);
            yAxis.setTickUnit(0.2);
        });
        RadioMenuItem miZoomY05 = new RadioMenuItem("0-0.5");
        miZoomY05.setOnAction(e -> {
            yAxis.setAutoRanging(false);
            yAxis.setUpperBound(0.5);
            yAxis.setTickUnit(0.1);
        });
        RadioMenuItem miZoomY02 = new RadioMenuItem("0-0.2");
        miZoomY02.setOnAction(e -> {
            yAxis.setAutoRanging(false);
            yAxis.setUpperBound(0.2);
            yAxis.setTickUnit(0.05);
        });
        RadioMenuItem miZoomY01 = new RadioMenuItem("0-0.1");
        miZoomY01.setOnAction(e -> {
            yAxis.setAutoRanging(false);
            yAxis.setUpperBound(0.1);
            yAxis.setTickUnit(0.05);
        });
        RadioMenuItem miZoomY005 = new RadioMenuItem("0-0.05");
        miZoomY005.setOnAction(e -> {
            yAxis.setAutoRanging(false);
            yAxis.setUpperBound(0.05);
            yAxis.setTickUnit(0.01);
        });
        RadioMenuItem miZoomY001 = new RadioMenuItem("0-0.01");
        miZoomY001.setOnAction(e -> {
            yAxis.setAutoRanging(false);
            yAxis.setUpperBound(0.01);
            yAxis.setTickUnit(0.005);
        });
        ToggleGroup tgZoom = new ToggleGroup();
        miZoomY1.setToggleGroup(tgZoom);
        miZoomY05.setToggleGroup(tgZoom);
        miZoomY02.setToggleGroup(tgZoom);
        miZoomY01.setToggleGroup(tgZoom);
        miZoomY005.setToggleGroup(tgZoom);
        miZoomY001.setToggleGroup(tgZoom);
        Menu menuZoomY = new Menu("Set y-axis range");
        menuZoomY.getItems().addAll(miZoomY1, miZoomY05, miZoomY02, miZoomY01, miZoomY005, miZoomY001);

        MenuItem miCopyData = new MenuItem("Copy chart data");
        miCopyData.setOnAction(e -> {
            String dataString = ChartToolsFX.getChartDataAsString(chartPValues);
            ClipboardContent content = new ClipboardContent();
            content.putString(dataString);
            Clipboard.getSystemClipboard().setContent(content);
        });

        popup.getItems().addAll(miCopyData, menuZoomY);
        chartPValues.setOnContextMenuRequested(e -> {
            popup.show(chartPValues, e.getScreenX(), e.getScreenY());
        });

        for (int col = 0; col < tableModel.getColumnCount(); col++) {
            TableColumn<Integer, String> column = new TableColumn<>(tableModel.getColumnName(col));
            int colNumber = col;
            column.setCellValueFactory(
                    new Callback<CellDataFeatures<Integer, String>, ObservableValue<String>>() {
                        @Override
                        public ObservableValue<String> call(CellDataFeatures<Integer, String> p) {
                            return new SimpleStringProperty(
                                    (String) tableModel.getValueAt(p.getValue(), colNumber));
                        }
                    });

            column.setCellFactory(new Callback<TableColumn<Integer, String>, TableCell<Integer, String>>() {

                @Override
                public TableCell<Integer, String> call(TableColumn<Integer, String> param) {
                    TableCell<Integer, String> cell = new TableCell<Integer, String>() {
                        @Override
                        protected void updateItem(String item, boolean empty) {
                            super.updateItem(item, empty);
                            setText(item);
                            setTooltip(new Tooltip(item));
                        }
                    };
                    return cell;
                }
            });

            table.getColumns().add(column);
        }
        table.setPrefHeight(250);
        table.setColumnResizePolicy(TableView.CONSTRAINED_RESIZE_POLICY);
        table.maxHeightProperty().bind(table.prefHeightProperty());

        params = new ParameterList();
        //         maxTimePoint = 0;
        //         for (TMACoreObject core : hierarchy.getTMAGrid().getTMACoreList()) {
        //            double os = core.getMeasurementList().getMeasurementValue(TMACoreObject.KEY_OVERALL_SURVIVAL);
        //            double rfs = core.getMeasurementList().getMeasurementValue(TMACoreObject.KEY_RECURRENCE_FREE_SURVIVAL);
        //            if (os > maxTimePoint)
        //               maxTimePoint = os;
        //            if (rfs > maxTimePoint)
        //               maxTimePoint = rfs;
        //         }
        params.addIntParameter("censorTimePoints", "Max censored time", (int) (censorThreshold + 0.5), null, 0,
                (int) Math.ceil(maxTimePoint), "Latest time point beyond which data will be censored");
        //            params.addChoiceParameter("scoreThresholdMethod", "Threshold method", "Manual", Arrays.asList("Manual", "Median", "Log-rank test"));
        if (calculateAllPValues)
            // Don't include "Lowest smoothed p-value" - it's not an established method and open to misinterpretation...
            params.addChoiceParameter("scoreThresholdMethod", "Threshold method", "Median",
                    Arrays.asList("Manual (1)", "Manual (2)", "Manual (3)", "Median", "Tertiles", "Quartiles",
                            "Lowest p-value"));
        //            params.addChoiceParameter("scoreThresholdMethod", "Threshold method", "Median", Arrays.asList("Manual (1)", "Manual (2)", "Manual (3)", "Median", "Tertiles", "Quartiles", "Lowest p-value", "Lowest smoothed p-value"));
        else
            params.addChoiceParameter("scoreThresholdMethod", "Threshold method", "Median",
                    Arrays.asList("Manual (1)", "Manual (2)", "Manual (3)", "Median", "Tertiles", "Quartiles"));
        params.addDoubleParameter("threshold1", "Threshold 1",
                thresholds.length > 0 ? thresholds[0] : (minVal + maxVal) / 2, null,
                "Threshold to distinguish between patient groups");
        params.addDoubleParameter("threshold2", "Threshold 2",
                thresholds.length > 1 ? thresholds[1] : (minVal + maxVal) / 2, null,
                "Threshold to distinguish between patient groups");
        params.addDoubleParameter("threshold3", "Threshold 3",
                thresholds.length > 2 ? thresholds[2] : (minVal + maxVal) / 2, null,
                "Threshold to distinguish between patient groups");
        params.addBooleanParameter("showAtRisk", "Show at risk", plotter.getShowAtRisk(),
                "Show number of patients at risk below the plot");
        params.addBooleanParameter("showTicks", "Show censored ticks", plotter.getShowCensoredTicks(),
                "Show ticks to indicate censored data");
        params.addBooleanParameter("showKey", "Show key", plotter.getShowKey(),
                "Show key indicating display of each curve");
        //            params.addBooleanParameter("useColor", "Use color", plotter.getUseColor(), "Show each curve in a different color");
        //         params.addBooleanParameter("useStrokes", "Use strokes", plotter.getUseStrokes(), "Show each curve with a differed line stroke");
        // Hide threshold parameters if threshold can't be used
        if (!scoresValid) {
            //               params.setHiddenParameters(true, "scoreThresholdMethod", "scoreThreshold");
            histogramPanel.getChart().setVisible(false);
        }
        panelParams = new ParameterPanelFX(params);
        panelParams.addParameterChangeListener(this);
        updateThresholdsEnabled();

        for (int i = 0; i < threshProperties.length; i++) {
            String p = "threshold" + (i + 1);
            threshProperties[i].addListener((v, o, n) -> {
                if (interactiveThresholds()) {
                    // Need to do a decent double check with tolerance to text field value changing while typing
                    if (!GeneralTools.almostTheSame(params.getDoubleParameterValue(p), n.doubleValue(), 0.0001))
                        panelParams.setNumericParameterValue(p, n);
                }
            });
        }

        BorderPane paneBottom = new BorderPane();
        TitledPane paneOptions = new TitledPane("Options", panelParams.getPane());
        //            paneOptions.setCollapsible(false);
        Pane paneCanvas = new StackPane();
        paneCanvas.getChildren().add(plotter.getCanvas());

        GridPane paneLeft = new GridPane();
        paneLeft.add(paneOptions, 0, 0);
        paneLeft.add(table, 0, 1);
        GridPane.setHgrow(paneOptions, Priority.ALWAYS);
        GridPane.setHgrow(table, Priority.ALWAYS);
        paneBottom.setLeft(paneLeft);
        paneBottom.setCenter(paneHistogram);

        paneMain.setCenter(paneCanvas);
        paneMain.setBottom(paneBottom);

        paneMain.setPadding(new Insets(10, 10, 10, 10));
    } else if (thresholds.length > 0) {
        // Ensure the sliders/text fields are set sensibly
        if (!GeneralTools.almostTheSame(thresholds[0], params.getDoubleParameterValue("threshold1"), 0.0001)) {
            panelParams.setNumericParameterValue("threshold1", thresholds[0]);
        }
        if (thresholds.length > 1 && !GeneralTools.almostTheSame(thresholds[1],
                params.getDoubleParameterValue("threshold2"), 0.0001)) {
            panelParams.setNumericParameterValue("threshold2", thresholds[1]);
        }
        if (thresholds.length > 2 && !GeneralTools.almostTheSame(thresholds[2],
                params.getDoubleParameterValue("threshold3"), 0.0001)) {
            panelParams.setNumericParameterValue("threshold3", thresholds[2]);
        }
    }

    if (histogram != null) {
        histogramPanel.getHistogramData()
                .setAll(HistogramPanelFX.createHistogramData(histogram, false, (Color) null));
        histogramPanel.getChart().getXAxis().setLabel(scoreColumn);
        histogramPanel.getChart().getYAxis().setLabel("Count");

        ChartToolsFX.addChartExportMenu(histogramPanel.getChart(), null);

        //            histogramWrapper.setVerticalLines(thresholds, ColorToolsFX.getCachedColor(240, 0, 0, 128));
        // Deal with threshold adjustment
        //            histogramWrapper.getThresholds().addListener((Observable o) -> generatePlot());
    }

    if (pValues != null) {
        // TODO: Raise earlier where p-value calculation is
        if (pValuesChanged) {
            ObservableList<XYChart.Data<Number, Number>> data = FXCollections.observableArrayList();
            for (int i = 0; i < pValueThresholds.length; i++) {
                double pValue = pValues[i];
                if (Double.isNaN(pValue))
                    continue;
                data.add(new XYChart.Data<>(pValueThresholds[i], pValue, pValueThresholdsObserved[i]));
            }

            ObservableList<XYChart.Data<Number, Number>> dataSmoothed = null;
            if (pValuesSmoothed != null) {
                dataSmoothed = FXCollections.observableArrayList();
                for (int i = 0; i < pValueThresholds.length; i++) {
                    double pValueSmoothed = pValuesSmoothed[i];
                    if (Double.isNaN(pValueSmoothed))
                        continue;
                    dataSmoothed.add(new XYChart.Data<>(pValueThresholds[i], pValueSmoothed));
                }
            }

            // Don't bother showing the smoothed data... it tends to get in the way...
            //            if (dataSmoothed != null)
            //               chartPValues.getData().setAll(new XYChart.Series<>("P-values", data), new XYChart.Series<>("Smoothed P-values", dataSmoothed));
            //            else
            chartPValues.getData().setAll(new XYChart.Series<>("P-values", data));

            // Add line to show 0.05 significance threshold
            if (pValueThresholds.length > 1) {
                Data<Number, Number> sigData1 = new Data<>(pValueThresholds[0], 0.05);
                Data<Number, Number> sigData2 = new Data<>(pValueThresholds[pValueThresholds.length - 1], 0.05);
                XYChart.Series<Number, Number> dataSignificant = new XYChart.Series<>("Signficance 0.05",
                        FXCollections.observableArrayList(sigData1, sigData2));
                chartPValues.getData().add(dataSignificant);
                sigData1.getNode().setVisible(false);
                sigData2.getNode().setVisible(false);
            }

            //               chartPValues.getData().get(0).getNode().setVisible(true);

            //               pValuesWrapper.clearThresholds();
            for (XYChart.Data<Number, Number> dataPoint : data) {
                if (!Boolean.TRUE.equals(dataPoint.getExtraValue()))
                    dataPoint.getNode().setVisible(false);
            }
            //            if (dataSmoothed != null) {
            //               for (XYChart.Data<Number, Number> dataPoint : dataSmoothed) {
            //                  dataPoint.getNode().setVisible(false);
            //               }
            //               chartPValues.getData().get(1).getNode().setOpacity(0.5);
            //            }

            //               int count = 0;               
            //               for (int i = 0; i < pValueThresholds.length; i++) {
            //                  double pValue = pValues[i];
            //                  if (Double.isNaN(pValue))
            //                     continue;
            //                  boolean observed = pValueThresholdsObserved[i];
            ////                  if (observed)
            ////                     pValuesWrapper.addThreshold(new ReadOnlyDoubleWrapper(pValueThresholds[i]), Color.rgb(0, 0, 0, 0.05));
            //                  
            //                  if (!observed) {
            ////                     StackPane pane = (StackPane)data.get(count).getNode();
            ////                     pane.setEffect(new DropShadow());
            //                     data.get(count).getNode().setVisible(false);
            //                  }
            //                  count++;
            //               }
        }

        for (int i = 0; i < threshProperties.length; i++) {
            if (i < thresholds.length)
                threshProperties[i].set(thresholds[i]);
            else
                threshProperties[i].set(Double.NaN);
        }
        boolean isInteractive = interactiveThresholds();
        histogramWrapper.setIsInteractive(isInteractive);
        pValuesWrapper.setIsInteractive(isInteractive);

        chartPValues.setVisible(true);
    }
    //         else
    //            chartPValues.setVisible(false);

    // Store values for next time
    scoreData = newScoreData;
}

From source file:qupath.lib.gui.tma.TMASummaryViewer.java

private Pane createSidePane() {
    BorderPane pane = new BorderPane();

    TabPane tabPane = new TabPane();

    kmDisplay = new KaplanMeierDisplay(null, null, null, null);
    BorderPane paneKaplanMeier = new BorderPane();
    paneKaplanMeier.setCenter(kmDisplay.getView());
    paneKaplanMeier.setPadding(new Insets(10, 10, 10, 10));
    //      comboMainMeasurement.prefWidthProperty().bind(paneKaplanMeier.widthProperty());
    comboMainMeasurement.setMaxWidth(Double.MAX_VALUE);
    comboMainMeasurement.setTooltip(new Tooltip("Measurement thresholded to create survival curves etc."));

    GridPane kmTop = new GridPane();
    kmTop.add(new Label("Score"), 0, 0);
    kmTop.add(comboMainMeasurement, 1, 0);
    kmTop.add(new Label("Survival type"), 0, 1);
    kmTop.add(comboSurvival, 1, 1);// ww  w .  j a  va  2  s .c  om
    comboSurvival.setTooltip(new Tooltip("Specify overall or recurrence-free survival (if applicable)"));
    comboSurvival.setMaxWidth(Double.MAX_VALUE);
    GridPane.setHgrow(comboMainMeasurement, Priority.ALWAYS);
    GridPane.setHgrow(comboSurvival, Priority.ALWAYS);
    kmTop.setHgap(5);
    paneKaplanMeier.setTop(kmTop);
    //      kmDisplay.setOrientation(Orientation.VERTICAL);

    histogramDisplay = new HistogramDisplay(model, false);

    comboMainMeasurement.getSelectionModel().selectedItemProperty().addListener((v, o, n) -> {
        histogramDisplay.refreshCombo();
        histogramDisplay.showHistogram(n);
        updateSurvivalCurves();
    });
    comboMeasurementMethod.getSelectionModel().selectedItemProperty().addListener((v, o, n) -> {
        histogramDisplay.refreshHistogram();
        scatterPane.updateChart();
        updateSurvivalCurves();
    });
    comboSurvival.getSelectionModel().selectedItemProperty().addListener((v, o, n) -> {
        updateSurvivalCurves();
    });

    // Create a Tab for showing images
    BorderPane paneImages = new BorderPane();
    CheckBox cbShowOverlay = new CheckBox("Show overlay");
    imageAvailability.addListener((c, v, n) -> {
        if (n == ImageAvailability.OVERLAY_ONLY)
            cbShowOverlay.setSelected(true);
        else if (n == ImageAvailability.IMAGE_ONLY)
            cbShowOverlay.setSelected(false);
        cbShowOverlay.setDisable(n != ImageAvailability.BOTH);
    });
    ListView<TMAEntry> listImages = new ListView<>();
    listImages.setCellFactory(v -> new ImageListCell(cbShowOverlay.selectedProperty(), imageCache));
    listImages.widthProperty().addListener((v, o, n) -> listImages.refresh());
    listImages.setStyle("-fx-control-inner-background-alt: -fx-control-inner-background ;");
    table.getSelectionModel().getSelectedItems().addListener((Change<? extends TreeItem<TMAEntry>> e) -> {
        List<TMAEntry> entries = new ArrayList<>();
        for (TreeItem<TMAEntry> item : e.getList()) {
            if (item.getChildren().isEmpty()) {
                if (item.getValue().hasImage() || item.getValue().hasOverlay())
                    entries.add(item.getValue());
            } else {
                for (TreeItem<TMAEntry> item2 : item.getChildren()) {
                    if (item2.getValue().hasImage() || item2.getValue().hasOverlay())
                        entries.add(item2.getValue());
                }
            }
            listImages.getItems().setAll(entries);
        }
    });
    cbShowOverlay.setAlignment(Pos.CENTER);
    cbShowOverlay.setMaxWidth(Double.MAX_VALUE);
    cbShowOverlay.setPadding(new Insets(5, 5, 5, 5));
    cbShowOverlay.selectedProperty().addListener((v, o, n) -> listImages.refresh());
    paneImages.setCenter(listImages);
    paneImages.setTop(cbShowOverlay);

    // Determine visibility based upon whether there are any images to show
    //      Tab tabImages = new Tab("Images", paneImages);

    ScrollPane scrollPane = new ScrollPane(paneKaplanMeier);
    scrollPane.setFitToWidth(true);
    scrollPane.setFitToHeight(true);
    scrollPane.setVbarPolicy(ScrollBarPolicy.AS_NEEDED);
    scrollPane.setHbarPolicy(ScrollBarPolicy.AS_NEEDED);
    Tab tabSurvival = new Tab("Survival", scrollPane);
    tabPane.getTabs().addAll(new Tab("Table", getCustomizeTablePane()),
            //            tabImages,
            new Tab("Histogram", histogramDisplay.getPane()), new Tab("Scatterplot", scatterPane.getPane()),
            tabSurvival);
    tabPane.setTabClosingPolicy(TabClosingPolicy.UNAVAILABLE);

    //      if (imageAvailability.get() != ImageAvailability.NONE)
    //         tabPane.getTabs().add(1, tabImages);
    //      
    //      imageAvailability.addListener((c, v, n) -> {
    //         if (n == ImageAvailability.NONE)
    //            tabPane.getTabs().remove(tabImages);
    //         else if (!tabPane.getTabs().contains(tabImages))
    //            tabPane.getTabs().add(1, tabImages);
    //      });

    //      tabSurvival.visibleProperty().bind(
    //            Bindings.createBooleanBinding(() -> !survivalColumns.isEmpty(), survivalColumns)
    //            );

    pane.setCenter(tabPane);

    pane.setMinWidth(350);

    return pane;
}

From source file:qupath.lib.gui.tma.TMASummaryViewer.java

private Pane getCustomizeTablePane() {
    TableView<TreeTableColumn<TMAEntry, ?>> tableColumns = new TableView<>();
    tableColumns.setPlaceholder(new Text("No columns available"));
    tableColumns.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
    tableColumns.setColumnResizePolicy(TableView.CONSTRAINED_RESIZE_POLICY);

    SortedList<TreeTableColumn<TMAEntry, ?>> sortedColumns = new SortedList<>(
            table.getColumns().filtered(p -> !p.getText().trim().isEmpty()));
    sortedColumns.setComparator((c1, c2) -> c1.getText().compareTo(c2.getText()));
    tableColumns.setItems(sortedColumns);
    sortedColumns.comparatorProperty().bind(tableColumns.comparatorProperty());
    //      sortedColumns.comparatorProperty().bind(tableColumns.comparatorProperty());

    TableColumn<TreeTableColumn<TMAEntry, ?>, String> columnName = new TableColumn<>("Column");
    columnName.setCellValueFactory(v -> v.getValue().textProperty());
    TableColumn<TreeTableColumn<TMAEntry, ?>, Boolean> columnVisible = new TableColumn<>("Visible");
    columnVisible.setCellValueFactory(v -> v.getValue().visibleProperty());
    //      columnVisible.setCellValueFactory(col -> {
    //         SimpleBooleanProperty prop = new SimpleBooleanProperty(col.getValue().isVisible());
    //         prop.addListener((v, o, n) -> col.getValue().setVisible(n));
    //         return prop;
    //      });/*from   ww  w .  j  ava  2 s  .c  o m*/
    tableColumns.setEditable(true);
    columnVisible.setCellFactory(v -> new CheckBoxTableCell<>());
    tableColumns.getColumns().add(columnName);
    tableColumns.getColumns().add(columnVisible);
    ContextMenu contextMenu = new ContextMenu();

    Action actionShowSelected = new Action("Show selected", e -> {
        for (TreeTableColumn<?, ?> col : tableColumns.getSelectionModel().getSelectedItems()) {
            if (col != null)
                col.setVisible(true);
            else {
                // Not sure why this happens...?
                logger.trace("Selected column is null!");
            }
        }
    });

    Action actionHideSelected = new Action("Hide selected", e -> {
        for (TreeTableColumn<?, ?> col : tableColumns.getSelectionModel().getSelectedItems()) {
            if (col != null)
                col.setVisible(false);
            else {
                // Not sure why this happens...?
                logger.trace("Selected column is null!");
            }
        }
    });

    contextMenu.getItems().addAll(ActionUtils.createMenuItem(actionShowSelected),
            ActionUtils.createMenuItem(actionHideSelected));
    tableColumns.setContextMenu(contextMenu);
    tableColumns.setTooltip(
            new Tooltip("Show or hide table columns - right-click to change multiple columns at once"));

    BorderPane paneColumns = new BorderPane(tableColumns);
    paneColumns.setBottom(PanelToolsFX.createColumnGridControls(ActionUtils.createButton(actionShowSelected),
            ActionUtils.createButton(actionHideSelected)));

    VBox paneRows = new VBox();

    // Create a box to filter on some metadata text
    ComboBox<String> comboMetadata = new ComboBox<>();
    comboMetadata.setItems(metadataNames);
    comboMetadata.getSelectionModel().getSelectedItem();
    comboMetadata.setPromptText("Select column");
    TextField tfFilter = new TextField();
    CheckBox cbExact = new CheckBox("Exact");
    // Set listeners
    cbExact.selectedProperty().addListener(
            (v, o, n) -> setMetadataTextPredicate(comboMetadata.getSelectionModel().getSelectedItem(),
                    tfFilter.getText(), cbExact.isSelected(), !cbExact.isSelected()));
    tfFilter.textProperty().addListener(
            (v, o, n) -> setMetadataTextPredicate(comboMetadata.getSelectionModel().getSelectedItem(),
                    tfFilter.getText(), cbExact.isSelected(), !cbExact.isSelected()));
    comboMetadata.getSelectionModel().selectedItemProperty().addListener(
            (v, o, n) -> setMetadataTextPredicate(comboMetadata.getSelectionModel().getSelectedItem(),
                    tfFilter.getText(), cbExact.isSelected(), !cbExact.isSelected()));

    GridPane paneMetadata = new GridPane();
    paneMetadata.add(comboMetadata, 0, 0);
    paneMetadata.add(tfFilter, 1, 0);
    paneMetadata.add(cbExact, 2, 0);
    paneMetadata.setPadding(new Insets(10, 10, 10, 10));
    paneMetadata.setVgap(2);
    paneMetadata.setHgap(5);
    comboMetadata.setMaxWidth(Double.MAX_VALUE);
    GridPane.setHgrow(tfFilter, Priority.ALWAYS);
    GridPane.setFillWidth(comboMetadata, Boolean.TRUE);
    GridPane.setFillWidth(tfFilter, Boolean.TRUE);

    TitledPane tpMetadata = new TitledPane("Metadata filter", paneMetadata);
    tpMetadata.setExpanded(false);
    //      tpMetadata.setCollapsible(false);
    Tooltip tooltipMetadata = new Tooltip(
            "Enter text to filter entries according to a selected metadata column");
    Tooltip.install(paneMetadata, tooltipMetadata);
    tpMetadata.setTooltip(tooltipMetadata);
    paneRows.getChildren().add(tpMetadata);

    // Add measurement predicate
    TextField tfCommand = new TextField();
    tfCommand.setTooltip(new Tooltip("Predicate used to filter entries for inclusion"));

    TextFields.bindAutoCompletion(tfCommand, e -> {
        int ind = tfCommand.getText().lastIndexOf("\"");
        if (ind < 0)
            return Collections.emptyList();
        String part = tfCommand.getText().substring(ind + 1);
        return measurementNames.stream().filter(n -> n.startsWith(part)).map(n -> "\"" + n + "\" ")
                .collect(Collectors.toList());
    });

    String instructions = "Enter a predicate to filter entries.\n"
            + "Only entries passing the test will be included in any results.\n"
            + "Examples of predicates include:\n" + "    \"Num Tumor\" > 200\n"
            + "    \"Num Tumor\" > 100 && \"Num Stroma\" < 1000";
    //      labelInstructions.setTooltip(new Tooltip("Note: measurement names must be in \"inverted commands\" and\n" + 
    //            "&& indicates 'and', while || indicates 'or'."));

    BorderPane paneMeasurementFilter = new BorderPane(tfCommand);
    Label label = new Label("Predicate: ");
    label.setAlignment(Pos.CENTER);
    label.setMaxHeight(Double.MAX_VALUE);
    paneMeasurementFilter.setLeft(label);

    Button btnApply = new Button("Apply");
    btnApply.setOnAction(e -> {
        TablePredicate predicateNew = new TablePredicate(tfCommand.getText());
        if (predicateNew.isValid()) {
            predicateMeasurements.set(predicateNew);
        } else {
            DisplayHelpers.showErrorMessage("Invalid predicate",
                    "Current predicate '" + tfCommand.getText() + "' is invalid!");
        }
        e.consume();
    });
    TitledPane tpMeasurementFilter = new TitledPane("Measurement filter", paneMeasurementFilter);
    tpMeasurementFilter.setExpanded(false);
    Tooltip tooltipInstructions = new Tooltip(instructions);
    tpMeasurementFilter.setTooltip(tooltipInstructions);
    Tooltip.install(paneMeasurementFilter, tooltipInstructions);
    paneMeasurementFilter.setRight(btnApply);

    paneRows.getChildren().add(tpMeasurementFilter);

    logger.info("Predicate set to: {}", predicateMeasurements.get());

    VBox pane = new VBox();
    //      TitledPane tpColumns = new TitledPane("Select column", paneColumns);
    //      tpColumns.setMaxHeight(Double.MAX_VALUE);
    //      tpColumns.setCollapsible(false);
    pane.getChildren().addAll(paneColumns, new Separator(), paneRows);
    VBox.setVgrow(paneColumns, Priority.ALWAYS);

    return pane;
}

From source file:acmi.l2.clientmod.l2smr.Controller.java

private void onException(String text, Throwable ex) {
    ex.printStackTrace();//w  ww  .j  av  a  2  s. co  m

    Platform.runLater(() -> {
        if (SHOW_STACKTRACE) {
            Alert alert = new Alert(Alert.AlertType.ERROR);
            alert.setTitle("Error");
            alert.setHeaderText(null);
            alert.setContentText(text);

            StringWriter sw = new StringWriter();
            PrintWriter pw = new PrintWriter(sw);
            ex.printStackTrace(pw);
            String exceptionText = sw.toString();

            Label label = new Label("Exception stacktrace:");

            TextArea textArea = new TextArea(exceptionText);
            textArea.setEditable(false);
            textArea.setWrapText(true);

            textArea.setMaxWidth(Double.MAX_VALUE);
            textArea.setMaxHeight(Double.MAX_VALUE);
            GridPane.setVgrow(textArea, Priority.ALWAYS);
            GridPane.setHgrow(textArea, Priority.ALWAYS);

            GridPane expContent = new GridPane();
            expContent.setMaxWidth(Double.MAX_VALUE);
            expContent.add(label, 0, 0);
            expContent.add(textArea, 0, 1);

            alert.getDialogPane().setExpandableContent(expContent);

            alert.showAndWait();
        } else {
            //noinspection ThrowableResultOfMethodCallIgnored
            Throwable t = getTop(ex);

            Alert alert = new Alert(Alert.AlertType.ERROR);
            alert.setTitle(t.getClass().getSimpleName());
            alert.setHeaderText(text);
            alert.setContentText(t.getMessage());

            alert.showAndWait();
        }
    });
}

From source file:UI.MainStageController.java

/**
 * creates the file not found alert box//  w w  w.j a  v a  2s  .c om
 */
private void fileNotFoundAlertBox() {
    fileNotFoundAlert = new Alert(Alert.AlertType.ERROR);
    fileNotFoundAlert.setTitle("File not found");
    fileNotFoundAlert.setHeaderText("File not found");
    fileNotFoundAlert.setContentText("Could not find the file you were looking for");

    //style the alert
    DialogPane dialogPane = fileNotFoundAlert.getDialogPane();
    dialogPane.getStylesheets().add("/UI/alertStyle.css");

    Exception fileNotFoundException = new FileNotFoundException("Could not find your selected file");

    //create expandable exception
    StringWriter sw = new StringWriter();
    PrintWriter pw = new PrintWriter(sw);
    fileNotFoundException.printStackTrace(pw);
    String exceptionText = sw.toString();

    Label label = new Label("The exception stacktrace was: ");

    TextArea textArea = new TextArea(exceptionText);
    textArea.setEditable(false);
    textArea.setWrapText(true);

    textArea.setMaxWidth(Double.MAX_VALUE);
    textArea.setMaxHeight(Double.MAX_VALUE);
    GridPane.setVgrow(textArea, Priority.ALWAYS);
    GridPane.setHgrow(textArea, Priority.ALWAYS);

    GridPane expContent = new GridPane();
    expContent.setMaxWidth(Double.MAX_VALUE);
    expContent.add(label, 0, 0);
    expContent.add(textArea, 0, 1);

    // Set expandable Exception into the dialog pane.
    fileNotFoundAlert.getDialogPane().setExpandableContent(expContent);
    fileNotFoundAlert.showAndWait();
}