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

Example 6 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 7 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;
}

Example 8 with AbstractDataSet

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

the class DataSetSelector method getSelectedItems.

public Set<AbstractDataSet> getSelectedItems() {
    Set<AbstractDataSet> set = new HashSet<>();
    int[] selectedRows = getTable().getSelectedRows();
    for (int r : selectedRows) {
        AbstractDataSet ds = (AbstractDataSet) table.getModel().getValueAt(r, NAME_COL_IDX);
        set.add(ds);
    }
    return set;
}

Example 9 with AbstractDataSet

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

the class DataSetSelector method updateRemoveButton.

private void updateRemoveButton() {
    boolean onlySignatureSelected = true;
    int[] selectedRows = getTable().getSelectedRows();
    if (selectedRows.length > 0) {
        for (int r : selectedRows) {
            AbstractDataSet ds = (AbstractDataSet) table.getModel().getValueAt(r, NAME_COL_IDX);
            if (ds instanceof EMSignatureDataSet == false) {
                onlySignatureSelected = false;
                break;
            }
        }
    } else {
        onlySignatureSelected = false;
    }
    getRemoveButton().setEnabled(onlySignatureSelected);
}

Example 10 with AbstractDataSet

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

the class DataSetSelector method setCheckedItems.

public void setCheckedItems(Set<AbstractDataSet> newValue) {
    final Set<AbstractDataSet> oldValue = getCheckedItems();
    checkedItems.clear();
    final int rowCount = getTable().getRowCount();
    for (int i = 0; i < rowCount; i++) {
        AbstractDataSet ds = (AbstractDataSet) getTable().getValueAt(i, NAME_COL_IDX);
        boolean checked = newValue != null && newValue.contains(ds);
        getTable().setValueAt(checked, i, SELECTED_COL_IDX);
        checkedItems.put(ds, checked);
    }
    getTable().repaint();
    updateSelectionButtons();
    firePropertyChange("checkedData", oldValue, getCheckedItems());
}