Examples with CyTable org.cytoscape.model.CyTable used on opensource projects

Example 66 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class GradientEditor method setValue.

@Override
@SuppressWarnings({ "unchecked", "rawtypes" })
public void setValue(final Object value) {
    if (value instanceof ContinuousMapping == false)
        throw new IllegalArgumentException("Value should be ContinuousMapping: this is " + value);
    final CyApplicationManager appMgr = servicesUtil.get(CyApplicationManager.class);
    final CyNetwork currentNetwork = appMgr.getCurrentNetwork();
    if (currentNetwork == null)
        return;
    ContinuousMapping<?, ?> mTest = (ContinuousMapping<?, ?>) value;
    // TODO: error chekcing
    mapping = (ContinuousMapping<Double, Color>) value;
    Class<? extends CyIdentifiable> type = (Class<? extends CyIdentifiable>) mapping.getVisualProperty().getTargetDataType();
    final CyNetworkTableManager netTblMgr = servicesUtil.get(CyNetworkTableManager.class);
    final CyTable attr = netTblMgr.getTable(appMgr.getCurrentNetwork(), type, CyNetwork.DEFAULT_ATTRS);
    final VisualMappingManager vmMgr = servicesUtil.get(VisualMappingManager.class);
    editorPanel = new GradientEditorPanel(vmMgr.getCurrentVisualStyle(), mapping, attr, editorManager.getValueEditor(Paint.class), servicesUtil);
}

Example 67 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class CellEditorEventHandler method copyMappingValues.

@SuppressWarnings({ "unchecked", "rawtypes" })
private void copyMappingValues(final VisualMappingFunction<?, ?> source, final VisualMappingFunction<?, ?> target) {
    if (source instanceof ContinuousMapping && target instanceof ContinuousMapping) {
        final CyNetwork curNet = servicesUtil.get(CyApplicationManager.class).getCurrentNetwork();
        if (curNet != null) {
            final ContinuousMapping cm1 = (ContinuousMapping<?, ?>) source;
            final ContinuousMapping cm2 = (ContinuousMapping<?, ?>) target;
            final List<ContinuousMappingPoint<?, ?>> points1 = cm1.getAllPoints();
            if (points1 == null || points1.isEmpty())
                return;
            // Check if source point values are valid
            for (final ContinuousMappingPoint<?, ?> p : points1) {
                final Object v = p.getValue();
                if (!(v instanceof Number) || Double.isInfinite(((Number) v).doubleValue()) || Double.isNaN(((Number) v).doubleValue()))
                    // Do not copy!
                    return;
            }
            final VisualProperty<?> vp = source.getVisualProperty();
            final CyTable dataTable = curNet.getTable(vp.getTargetDataType(), CyNetwork.DEFAULT_ATTRS);
            final CyColumn col = dataTable.getColumn(target.getMappingColumnName());
            if (col == null)
                return;
            // Make sure the source points are sorted by their values
            final TreeSet<ContinuousMappingPoint<?, ?>> srcPoints = new TreeSet<ContinuousMappingPoint<?, ?>>(new Comparator<ContinuousMappingPoint<?, ?>>() {

                @Override
                public int compare(final ContinuousMappingPoint<?, ?> o1, final ContinuousMappingPoint<?, ?> o2) {
                    final double v1 = ((Number) o1.getValue()).doubleValue();
                    final double v2 = ((Number) o2.getValue()).doubleValue();
                    return Double.compare(v1, v2);
                }
            });
            srcPoints.addAll(points1);
            // Make sure the target mapping has no points, so delete any existing one
            int tgtPointsSize = cm2.getPointCount();
            for (int i = 0; i < tgtPointsSize; i++) cm2.removePoint(i);
            // Convert the source points and copy them to the target mapping
            int srcPointsSize = srcPoints.size();
            for (int i = 0; i < srcPointsSize; i++) {
                final ContinuousMappingPoint<?, ?> mp = cm1.getPoint(i);
                final double srcVal = ((Number) cm1.getPoint(i).getValue()).doubleValue();
                cm2.addPoint(srcVal, mp.getRange());
            }
        }
    } else if (source instanceof DiscreteMapping && target instanceof DiscreteMapping) {
    // TODO The problem here is that the new mapping entries haven't been created yet
    // final DiscreteMapping dm1 = (DiscreteMapping<?, ?>) source;
    // final DiscreteMapping dm2 = (DiscreteMapping<?, ?>) target;
    // final Map map1 = dm1.getAll();
    // final Map map2 = dm2.getAll();
    // System.out.println("MAP 1: " + map1.size());
    // System.out.println("MAP 2: " + map2.size());
    // 
    // if (map1 == null || map1.isEmpty() || map2 == null || map2.isEmpty())
    // return;
    // 
    // final Iterator<?> tgtKeyIter = map2.keySet().iterator();
    // 
    // for (final Object srcVal : map1.values()) {
    // if (tgtKeyIter.hasNext()) {
    // final Object tgtKey = tgtKeyIter.next();
    // dm2.putMapValue(tgtKey, srcVal);
    // } else {
    // break;
    // }
    // }
    }
}

Example 68 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class MappingFunctionFactoryProxy method getMappingFactories.

public Set<VisualMappingFunctionFactory> getMappingFactories() {
    final SortedSet<VisualMappingFunctionFactory> set = new TreeSet<VisualMappingFunctionFactory>(new Comparator<VisualMappingFunctionFactory>() {

        @Override
        public int compare(final VisualMappingFunctionFactory f1, final VisualMappingFunctionFactory f2) {
            // Locale-specific sorting
            final Collator collator = Collator.getInstance(Locale.getDefault());
            collator.setStrength(Collator.PRIMARY);
            return collator.compare(f1.toString(), f2.toString());
        }
    });
    final MappingFunctionFactoryManager mappingFactoryMgr = servicesUtil.get(MappingFunctionFactoryManager.class);
    set.addAll(mappingFactoryMgr.getFactories());
    if (currentColumnName != null && currentTargetDataType != null) {
        // Remove the factories that don't make sense for the current column type
        final CyApplicationManager appMgr = servicesUtil.get(CyApplicationManager.class);
        final CyNetwork net = appMgr.getCurrentNetwork();
        if (net != null) {
            final CyTable table = net.getTable(currentTargetDataType, CyNetwork.DEFAULT_ATTRS);
            final CyColumn column = table.getColumn(currentColumnName);
            if (column != null && !Number.class.isAssignableFrom(column.getType()))
                set.remove(mappingFactoryMgr.getFactory(ContinuousMapping.class));
        }
    }
    return set;
}

Example 69 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class AttributeSetProxy method handleEvent.

@Override
public void handleEvent(final NetworkAddedEvent e) {
    final CyNetwork network = e.getNetwork();
    final Map<Class<? extends CyIdentifiable>, Set<CyTable>> object2tableMap = new HashMap<Class<? extends CyIdentifiable>, Set<CyTable>>();
    final Map<Class<? extends CyIdentifiable>, AttributeSet> attrSetMap = new HashMap<Class<? extends CyIdentifiable>, AttributeSet>();
    final CyNetworkTableManager netTblMgr = servicesUtil.get(CyNetworkTableManager.class);
    for (final Class<? extends CyIdentifiable> objectType : graphObjects) {
        final Map<String, CyTable> tableMap = netTblMgr.getTables(network, objectType);
        final Collection<CyTable> tables = tableMap.values();
        object2tableMap.put(objectType, new HashSet<CyTable>(tables));
        final AttributeSet attrSet = new AttributeSet(objectType);
        for (CyTable table : tables) {
            final Collection<CyColumn> columns = table.getColumns();
            for (final CyColumn column : columns) {
                final Class<?> type = column.getType();
                attrSet.getAttrMap().put(column.getName(), type);
            }
        }
        attrSetMap.put(objectType, attrSet);
    }
    attrSets.put(network, attrSetMap);
    tableSets.put(network, object2tableMap);
}

Example 70 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class AttributeSetProxy method handleEvent.

@Override
public void handleEvent(final ColumnNameChangedEvent e) {
    final CyTable table = e.getSource();
    for (CyNetwork network : tableSets.keySet()) {
        Map<Class<? extends CyIdentifiable>, Set<CyTable>> tMap = tableSets.get(network);
        for (final Class<? extends CyIdentifiable> objectType : graphObjects) {
            final Set<CyTable> targetTables = tMap.get(objectType);
            if (targetTables.contains(table)) {
                attrSets.get(network).get(objectType).getAttrMap().remove(e.getOldColumnName());
                attrSets.get(network).get(objectType).getAttrMap().put(e.getNewColumnName(), table.getColumn(e.getNewColumnName()).getType());
                return;
            }
        }
    }
}