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

Example 11 with AbstractDataSet

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

the class ControlPanelMediator method addNetworkView.

@SuppressWarnings("unchecked")
private void addNetworkView(CyNetworkView netView) {
    invokeOnEDT(() -> {
        EnrichmentMap map = emManager.getEnrichmentMap(netView.getModel().getSUID());
        // Is the new view an EnrichmentMap one?
        if (map != null) {
            EMViewControlPanel viewPanel = getControlPanel().addEnrichmentMapView(netView);
            if (viewPanel != null) {
                // Add listeners to the new panel's fields
                viewPanel.getQValueRadio().addActionListener(evt -> {
                    viewPanel.updateFilterPanel();
                    if (!updating)
                        filterNodesAndEdges(viewPanel, map);
                });
                viewPanel.getPValueRadio().addActionListener(evt -> {
                    viewPanel.updateFilterPanel();
                    if (!updating)
                        filterNodesAndEdges(viewPanel, map);
                });
                SliderBarPanel pvSliderPanel = viewPanel.getPValueSliderPanel();
                SliderBarPanel qvSliderPanel = viewPanel.getQValueSliderPanel();
                SliderBarPanel sSliderPanel = viewPanel.getSimilaritySliderPanel();
                if (pvSliderPanel != null)
                    pvSliderPanel.addChangeListener(evt -> {
                        if (!updating)
                            filterNodesAndEdges(viewPanel, map);
                    });
                if (qvSliderPanel != null)
                    qvSliderPanel.addChangeListener(evt -> {
                        if (!updating)
                            filterNodesAndEdges(viewPanel, map);
                    });
                if (sSliderPanel != null)
                    sSliderPanel.addChangeListener(evt -> {
                        if (!updating)
                            filterNodesAndEdges(viewPanel, map);
                    });
                viewPanel.getDataSetSelector().addPropertyChangeListener("checkedData", evt -> {
                    if (!updating) {
                        viewPanel.updateChartDataCombo();
                        filterNodesAndEdges(viewPanel, map);
                        ChartData data = (ChartData) viewPanel.getChartDataCombo().getSelectedItem();
                        Set<EMDataSet> oldDataSets = filterDataSets((Collection<AbstractDataSet>) evt.getOldValue());
                        Set<EMDataSet> newDataSets = filterDataSets((Collection<AbstractDataSet>) evt.getNewValue());
                        int oldSize = oldDataSets.size();
                        int newSize = newDataSets.size();
                        boolean updateStyle = data != null && data != ChartData.NONE && oldSize != newSize;
                        updateStyle = updateStyle || oldSize == 0 && newSize > 0;
                        updateStyle = updateStyle || oldSize > 0 && newSize == 0;
                        updateStyle = updateStyle || oldSize == 1 && newSize > 1;
                        updateStyle = updateStyle || oldSize > 1 && newSize == 1;
                        if (updateStyle)
                            updateVisualStyle(map, viewPanel);
                        else
                            netView.updateView();
                    }
                });
                viewPanel.getDataSetSelector().getAddButton().addActionListener(evt -> {
                    postAnalysisPanelMediatorProvider.get().showDialog(viewPanel, netView);
                });
                viewPanel.getDataSetSelector().getRemoveButton().addActionListener(evt -> {
                    removeSignatureDataSets(map, viewPanel);
                });
                viewPanel.getChartDataCombo().addItemListener(evt -> {
                    if (!updating && evt.getStateChange() == ItemEvent.SELECTED) {
                        updating = true;
                        try {
                            viewPanel.updateChartCombos();
                        } finally {
                            updating = false;
                        }
                        updateVisualStyle(map, viewPanel, true);
                    }
                });
                viewPanel.getChartTypeCombo().addItemListener(evt -> {
                    if (!updating && evt.getStateChange() == ItemEvent.SELECTED) {
                        updating = true;
                        try {
                            viewPanel.updateChartColorsCombo();
                            viewPanel.updateChartLabelsCheck();
                        } finally {
                            updating = false;
                        }
                        updateVisualStyle(map, viewPanel, true);
                    }
                });
                viewPanel.getChartColorsCombo().addItemListener(evt -> {
                    if (!updating && evt.getStateChange() == ItemEvent.SELECTED)
                        updateVisualStyle(map, viewPanel, true);
                });
                viewPanel.getShowChartLabelsCheck().addActionListener(evt -> {
                    if (!updating)
                        updateVisualStyle(map, viewPanel, true);
                });
                viewPanel.getPublicationReadyCheck().addActionListener(evt -> {
                    if (!updating)
                        updateVisualStyle(map, viewPanel);
                });
                viewPanel.getResetStyleButton().addActionListener(evt -> {
                    updateVisualStyle(map, viewPanel);
                });
                viewPanel.getSetEdgeWidthButton().addActionListener(evt -> {
                    showEdgeWidthDialog();
                });
                viewPanel.updateChartDataCombo();
            }
        }
    });
}

Example 12 with AbstractDataSet

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

the class EMStyleBuilder method setNodeColors.

private void setNodeColors(VisualStyle vs, EMStyleOptions options) {
    String prefix = options.getAttributePrefix();
    List<AbstractDataSet> dataSets = options.getDataSets().stream().filter(// Ignore Signature Data Sets in charts
    ds -> ds instanceof EMDataSet).collect(Collectors.toList());
    if (dataSets.size() == 1) {
        // Only 1 Data Set? Use node colour instead of charts...
        EMDataSet ds = (EMDataSet) dataSets.iterator().next();
        // Create boundary conditions
        BoundaryRangeValues<Paint> bv3a = new BoundaryRangeValues<>(Colors.MAX_PHENOTYPE_2, Colors.MAX_PHENOTYPE_2, Colors.MAX_PHENOTYPE_2);
        BoundaryRangeValues<Paint> bv3b = new BoundaryRangeValues<>(Colors.LIGHTER_PHENOTYPE_2, Colors.LIGHTER_PHENOTYPE_2, Colors.MAX_PHENOTYPE_2);
        BoundaryRangeValues<Paint> bv3c = new BoundaryRangeValues<>(Colors.LIGHTEST_PHENOTYPE_2, Colors.LIGHTEST_PHENOTYPE_2, Colors.LIGHTER_PHENOTYPE_2);
        BoundaryRangeValues<Paint> bv3d = new BoundaryRangeValues<>(Colors.LIGHTEST_PHENOTYPE_2, Colors.OVER_COLOR, Colors.OVER_COLOR);
        BoundaryRangeValues<Paint> bv3e = new BoundaryRangeValues<>(Colors.OVER_COLOR, Colors.OVER_COLOR, Colors.OVER_COLOR);
        BoundaryRangeValues<Paint> bv3f = new BoundaryRangeValues<>(Colors.OVER_COLOR, Colors.OVER_COLOR, Colors.LIGHTEST_PHENOTYPE_1);
        BoundaryRangeValues<Paint> bv3g = new BoundaryRangeValues<>(Colors.LIGHTEST_PHENOTYPE_1, Colors.LIGHTEST_PHENOTYPE_1, Colors.LIGHTER_PHENOTYPE_1);
        BoundaryRangeValues<Paint> bv3h = new BoundaryRangeValues<>(Colors.LIGHTER_PHENOTYPE_1, Colors.LIGHTER_PHENOTYPE_1, Colors.MAX_PHENOTYPE_1);
        BoundaryRangeValues<Paint> bv3i = new BoundaryRangeValues<>(Colors.MAX_PHENOTYPE_1, Colors.MAX_PHENOTYPE_1, Colors.MAX_PHENOTYPE_1);
        // Continuous Mapping - set node colour based on the sign of the ES score of the dataset
        ContinuousMapping<Double, Paint> cm = (ContinuousMapping<Double, Paint>) cmFactory.createVisualMappingFunction(Columns.NODE_COLOURING.with(prefix, ds.getName()), Double.class, BasicVisualLexicon.NODE_FILL_COLOR);
        // Silence events fired by this mapping to prevent unnecessary style and view updates
        eventHelper.silenceEventSource(cm);
        try {
            // Set the attribute point values associated with the boundary values
            cm.addPoint(-1.0, bv3a);
            cm.addPoint(-0.995, bv3b);
            cm.addPoint(-0.95, bv3c);
            cm.addPoint(-0.9, bv3d);
            cm.addPoint(0.0, bv3e);
            cm.addPoint(0.9, bv3f);
            cm.addPoint(0.95, bv3g);
            cm.addPoint(0.995, bv3h);
            cm.addPoint(1.0, bv3i);
        } finally {
            eventHelper.unsilenceEventSource(cm);
        }
        vs.addVisualMappingFunction(cm);
        // Then we need to use bypass to colour the hub nodes (signature genesets)
        List<EMSignatureDataSet> signatureDataSets = options.getEnrichmentMap().getSignatureSetList();
        CyNetworkView netView = options.getNetworkView();
        CyNetwork net = netView.getModel();
        for (EMSignatureDataSet sds : signatureDataSets) {
            for (Long suid : sds.getNodeSuids()) {
                CyNode node = net.getNode(suid);
                if (node != null) {
                    View<CyNode> nv = netView.getNodeView(node);
                    if (nv != null)
                        nv.setLockedValue(NODE_FILL_COLOR, Colors.SIG_NODE_COLOR);
                }
            }
        }
    } else {
        // 2 or more Data Sets? Use simple node colours and charts...
        // Add mapping function for node fill color
        DiscreteMapping<String, Paint> dm = (DiscreteMapping<String, Paint>) dmFactory.createVisualMappingFunction(Columns.NODE_GS_TYPE.with(prefix, null), String.class, NODE_FILL_COLOR);
        // Silence events fired by this mapping to prevent unnecessary style and view updates
        eventHelper.silenceEventSource(dm);
        try {
            dm.putMapValue(Columns.NODE_GS_TYPE_ENRICHMENT, Colors.DEF_NODE_COLOR);
            dm.putMapValue(Columns.NODE_GS_TYPE_SIGNATURE, Colors.SIG_NODE_COLOR);
        } finally {
            eventHelper.unsilenceEventSource(dm);
        }
        vs.addVisualMappingFunction(dm);
    }
}