Examples with AbstractDataSet org.baderlab.csplugins.enrichmentmap.model.AbstractDataSet used on opensource projects

Example 1 with AbstractDataSet

use of org.baderlab.csplugins.enrichmentmap.model.AbstractDataSet in project EnrichmentMapApp by BaderLab.

the class ControlPanelMediator method createStyleOptions.

private EMStyleOptions createStyleOptions(EnrichmentMap map, EMViewControlPanel viewPanel) {
    if (map == null || viewPanel == null)
        return null;
    Set<AbstractDataSet> dataSets = viewPanel.getDataSetSelector().getCheckedItems();
    boolean publicationReady = viewPanel.getPublicationReadyCheck().isSelected();
    boolean postAnalysis = map.hasSignatureDataSets();
    ChartData data = (ChartData) viewPanel.getChartDataCombo().getSelectedItem();
    ChartType type = getChartType(viewPanel);
    ColorScheme colorScheme = (ColorScheme) viewPanel.getChartColorsCombo().getSelectedItem();
    boolean showLabels = viewPanel.getShowChartLabelsCheck().isSelected();
    ChartOptions chartOptions = new ChartOptions(data, type, colorScheme, showLabels);
    return new EMStyleOptions(viewPanel.getNetworkView(), map, dataSets::contains, chartOptions, postAnalysis, publicationReady);
}

Example 2 with AbstractDataSet

use of org.baderlab.csplugins.enrichmentmap.model.AbstractDataSet in project EnrichmentMapApp by BaderLab.

the class DataSetSelector method update.

public void update() {
    Map<AbstractDataSet, Boolean> oldCheckedItems = new HashMap<>(checkedItems);
    items.clear();
    checkedItems.clear();
    List<AbstractDataSet> newItems = new ArrayList<>();
    newItems.addAll(map.getDataSetList());
    newItems.addAll(map.getSignatureSetList());
    if (newItems != null) {
        for (AbstractDataSet ds : newItems) {
            items.add(ds);
            boolean selected = // New items are selected by default!
            !oldCheckedItems.containsKey(ds) || oldCheckedItems.get(ds) == Boolean.TRUE;
            checkedItems.put(ds, selected);
        }
    }
    updateTable();
    updateSelectionButtons();
    updateRemoveButton();
}

Example 3 with AbstractDataSet

use of org.baderlab.csplugins.enrichmentmap.model.AbstractDataSet in project EnrichmentMapApp by BaderLab.

the class DataSetSelector method updateTable.

private void updateTable() {
    final Object[][] data = new Object[items.size()][HEARDER_NAMES.length];
    int i = 0;
    for (AbstractDataSet ds : items) {
        data[i][SELECTED_COL_IDX] = checkedItems.get(ds);
        data[i][TYPE_COL_IDX] = ds;
        data[i][NAME_COL_IDX] = ds;
        data[i][GENES_COL_IDX] = ds.getGeneSetsOfInterest().size();
        i++;
    }
    final DefaultTableModel model = new DefaultTableModel(data, HEARDER_NAMES) {

        @Override
        public boolean isCellEditable(int row, int column) {
            // TODO Allow renaming?
            return false;
        }
    };
    getTable().setModel(model);
    JCheckBox tmpField = new JCheckBox();
    makeSmall(tmpField);
    getTable().getColumnModel().getColumn(TYPE_COL_IDX).setMaxWidth(16);
    getTable().getColumnModel().getColumn(SELECTED_COL_IDX).setMaxWidth(tmpField.getPreferredSize().width);
    getTable().getColumnModel().getColumn(GENES_COL_IDX).setMaxWidth(48);
    getTable().getColumnModel().getColumn(TYPE_COL_IDX).setResizable(false);
    getTable().getColumnModel().getColumn(SELECTED_COL_IDX).setResizable(false);
}

Example 4 with AbstractDataSet

use of org.baderlab.csplugins.enrichmentmap.model.AbstractDataSet in project EnrichmentMapApp by BaderLab.

the class ControlPanelMediator method reset.

public void reset(ViewParams params) {
    long netViewID = params.getNetworkViewID();
    invokeOnEDT(() -> {
        EMViewControlPanel viewPanel = getControlPanel().getViewControlPanel(netViewID);
        if (viewPanel == null)
            return;
        EnrichmentMap map = emManager.getEnrichmentMap(viewPanel.getNetworkView().getModel().getSUID());
        if (map == null)
            return;
        try {
            // Update Filters
            if (params.getPValue() != null && viewPanel.getPValueSliderPanel() != null)
                viewPanel.getPValueSliderPanel().setValue(params.getPValue());
            if (params.getQValue() != null && viewPanel.getQValueSliderPanel() != null)
                viewPanel.getQValueSliderPanel().setValue(params.getQValue());
            if (params.getSimilarityCoefficient() != null && viewPanel.getSimilaritySliderPanel() != null)
                viewPanel.getSimilaritySliderPanel().setValue(params.getSimilarityCoefficient());
            if (params.getNodeCutoffParam() == CutoffParam.P_VALUE)
                viewPanel.getPValueRadio().doClick();
            else if (params.getNodeCutoffParam() == CutoffParam.Q_VALUE)
                viewPanel.getQValueRadio().doClick();
            Set<String> filteredOutDataSetNames = params.getFilteredOutDataSets();
            if (filteredOutDataSetNames != null && !filteredOutDataSetNames.isEmpty()) {
                Set<AbstractDataSet> allDataSets = viewPanel.getAllDataSets();
                Set<AbstractDataSet> filteredDataSets = allDataSets.stream().filter(ds -> !filteredOutDataSetNames.contains(ds.getName())).collect(Collectors.toSet());
                viewPanel.getDataSetSelector().setCheckedItems(filteredDataSets);
            }
            // Update Style options
            ChartOptions chartOptions = params.getChartOptions();
            viewPanel.getChartDataCombo().setSelectedItem(chartOptions != null ? chartOptions.getData() : null);
            viewPanel.getChartTypeCombo().setSelectedItem(chartOptions != null ? chartOptions.getType() : null);
            viewPanel.getChartColorsCombo().setSelectedItem(chartOptions != null ? chartOptions.getColorScheme() : null);
            viewPanel.getShowChartLabelsCheck().setSelected(chartOptions != null && chartOptions.isShowLabels());
            viewPanel.getPublicationReadyCheck().setSelected(params.isPublicationReady());
            viewPanel.updateChartDataCombo();
            updateVisualStyle(map, viewPanel);
            filterNodesAndEdges(viewPanel, map);
        } finally {
            updating = false;
        }
    });
}

Example 5 with AbstractDataSet

use of org.baderlab.csplugins.enrichmentmap.model.AbstractDataSet in project EnrichmentMapApp by BaderLab.

the class ControlPanelMediator method getAllViewParams.

public Map<Long, ViewParams> getAllViewParams() {
    Map<Long, ViewParams> map = new HashMap<>();
    getControlPanel().getAllControlPanels().forEach((suid, panel) -> {
        CutoffParam cuttofParam = panel.getPValueRadio().isSelected() ? CutoffParam.P_VALUE : CutoffParam.Q_VALUE;
        Double pVal = panel.getPValueSliderPanel() != null ? panel.getPValueSliderPanel().getValue() : null;
        Double qVal = panel.getQValueSliderPanel() != null ? panel.getQValueSliderPanel().getValue() : null;
        Double sCoeff = panel.getSimilaritySliderPanel() != null ? panel.getSimilaritySliderPanel().getValue() : null;
        Set<AbstractDataSet> uncheckedDataSets = panel.getUncheckedDataSets();
        Set<String> filteredDataSets = uncheckedDataSets.stream().map(AbstractDataSet::getName).collect(Collectors.toSet());
        EMStyleOptions options = createStyleOptions(panel.getNetworkView());
        boolean pubReady = panel.getPublicationReadyCheck().isSelected();
        ViewParams params = new ViewParams(suid, cuttofParam, pVal, qVal, sCoeff, filteredDataSets, options.getChartOptions(), pubReady);
        map.put(suid, params);
    });
    return map;
}