import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsControllerI;
-import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.FeatureAttributes;
+import jalview.datamodel.features.FeatureMatcherI;
+import jalview.datamodel.features.FeatureMatcherSet;
+import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.gui.Help.HelpId;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
-import jalview.schemabinding.version2.JalviewUserColours;
import jalview.schemes.FeatureColour;
-import jalview.util.Format;
import jalview.util.MessageManager;
import jalview.util.Platform;
-import jalview.util.QuickSort;
-import jalview.util.ReverseListIterator;
-import jalview.util.matcher.Condition;
-import jalview.util.matcher.KeyedMatcher;
-import jalview.util.matcher.KeyedMatcherI;
-import jalview.util.matcher.KeyedMatcherSet;
-import jalview.util.matcher.KeyedMatcherSetI;
-import jalview.viewmodel.AlignmentViewport;
-import jalview.ws.DasSequenceFeatureFetcher;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
+import jalview.xml.binding.jalview.JalviewUserColours;
+import jalview.xml.binding.jalview.JalviewUserColours.Colour;
+import jalview.xml.binding.jalview.JalviewUserColours.Filter;
+import jalview.xml.binding.jalview.ObjectFactory;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.awt.Dimension;
-import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.Graphics;
import java.awt.GridLayout;
+import java.awt.Point;
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.awt.event.FocusAdapter;
-import java.awt.event.FocusEvent;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.awt.event.MouseAdapter;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
-import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Comparator;
+import java.util.HashMap;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
-import java.util.Vector;
import javax.help.HelpSetException;
import javax.swing.AbstractCellEditor;
import javax.swing.BorderFactory;
-import javax.swing.BoxLayout;
-import javax.swing.ButtonGroup;
import javax.swing.Icon;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JColorChooser;
-import javax.swing.JComboBox;
import javax.swing.JDialog;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JMenuItem;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
-import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
import javax.swing.JSlider;
-import javax.swing.JTabbedPane;
import javax.swing.JTable;
-import javax.swing.JTextArea;
-import javax.swing.JTextField;
import javax.swing.ListSelectionModel;
import javax.swing.SwingConstants;
-import javax.swing.SwingUtilities;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
-import javax.swing.plaf.basic.BasicArrowButton;
import javax.swing.table.AbstractTableModel;
import javax.swing.table.TableCellEditor;
import javax.swing.table.TableCellRenderer;
+import javax.swing.table.TableColumn;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamReader;
public class FeatureSettings extends JPanel
implements FeatureSettingsControllerI
{
- private static final int MIN_WIDTH = 400;
+ private static final String SEQUENCE_FEATURE_COLOURS = MessageManager
+ .getString("label.sequence_feature_colours");
- private static final int MIN_HEIGHT = 400;
+ /*
+ * column indices of fields in Feature Settings table
+ */
+ static final int TYPE_COLUMN = 0;
- private static final int MAX_TOOLTIP_LENGTH = 50;
+ static final int COLOUR_COLUMN = 1;
- DasSourceBrowser dassourceBrowser;
+ static final int FILTER_COLUMN = 2;
- DasSequenceFeatureFetcher dasFeatureFetcher;
+ static final int SHOW_COLUMN = 3;
- JPanel dasSettingsPane = new JPanel();
+ private static final int COLUMN_COUNT = 4;
+
+ private static final int MIN_WIDTH = 400;
+
+ private static final int MIN_HEIGHT = 400;
final FeatureRenderer fr;
private float originalTransparency;
- private Map<String, KeyedMatcherSetI> originalFilters;
+ private Map<String, FeatureMatcherSetI> originalFilters;
final JInternalFrame frame;
JPanel groupPanel;
JSlider transparency = new JSlider();
-
+
/*
* when true, constructor is still executing - so ignore UI events
*/
*/
Map<String, float[]> typeWidth = null;
- /*
- * fields of the feature filters tab
- */
- private JPanel filtersPane;
-
- private JPanel chooseFiltersPanel;
-
- private JComboBox<String> filteredFeatureChoice;
-
- private JRadioButton andFilters;
-
- private JRadioButton orFilters;
-
- /*
- * filters for the currently selected feature type
- */
- private List<KeyedMatcherI> filters;
-
- private JTextArea filtersAsText;
-
/**
* Constructor
*
int originalTransparencyAsPercent = (int) (originalTransparency * 100);
transparency.setMaximum(100 - originalTransparencyAsPercent);
- originalFilters = fr.getFeatureFilters();
+ originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy
try
{
@Override
public String getToolTipText(MouseEvent e)
{
- if (table.columnAtPoint(e.getPoint()) == 0)
+ String tip = null;
+ int column = table.columnAtPoint(e.getPoint());
+ switch (column)
{
- /*
- * Tooltip for feature name only
- */
- return JvSwingUtils.wrapTooltip(true, MessageManager
+ case TYPE_COLUMN:
+ tip = JvSwingUtils.wrapTooltip(true, MessageManager
.getString("label.feature_settings_click_drag"));
+ break;
+ case FILTER_COLUMN:
+ int row = table.rowAtPoint(e.getPoint());
+ FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row,
+ column);
+ tip = o.isEmpty()
+ ? MessageManager.getString("label.filters_tooltip")
+ : o.toString();
+ break;
+ default:
+ break;
}
- return null;
+ return tip;
}
};
table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
table.setFont(new Font("Verdana", Font.PLAIN, 12));
- table.setDefaultRenderer(Color.class, new ColorRenderer());
-
- table.setDefaultEditor(Color.class, new ColorEditor(this));
+ // table.setDefaultRenderer(Color.class, new ColorRenderer());
+ // table.setDefaultEditor(Color.class, new ColorEditor(this));
+ //
table.setDefaultEditor(FeatureColour.class, new ColorEditor(this));
table.setDefaultRenderer(FeatureColour.class, new ColorRenderer());
+
+ table.setDefaultEditor(FeatureMatcherSet.class, new FilterEditor(this));
+ table.setDefaultRenderer(FeatureMatcherSet.class, new FilterRenderer());
+
+ TableColumn colourColumn = new TableColumn(COLOUR_COLUMN, 75,
+ new ColorRenderer(), new ColorEditor(this));
+ table.addColumn(colourColumn);
+
+ TableColumn filterColumn = new TableColumn(FILTER_COLUMN, 75,
+ new FilterRenderer(), new FilterEditor(this));
+ table.addColumn(filterColumn);
+
table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
table.addMouseListener(new MouseAdapter()
public void mousePressed(MouseEvent evt)
{
selectedRow = table.rowAtPoint(evt.getPoint());
+ String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN);
if (evt.isPopupTrigger())
{
- popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
- table.getValueAt(selectedRow, 1), fr.getMinMax(),
- evt.getX(), evt.getY());
+ Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
+ popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(),
+ evt.getY());
}
else if (evt.getClickCount() == 2)
{
boolean toggleSelection = Platform.isControlDown(evt);
boolean extendSelection = evt.isShiftDown();
fr.ap.alignFrame.avc.markColumnsContainingFeatures(
- invertSelection, extendSelection, toggleSelection,
- (String) table.getValueAt(selectedRow, 0));
+ invertSelection, extendSelection, toggleSelection, type);
}
}
selectedRow = table.rowAtPoint(evt.getPoint());
if (evt.isPopupTrigger())
{
- popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
- table.getValueAt(selectedRow, 1), fr.getMinMax(),
- evt.getX(), evt.getY());
+ String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN);
+ Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
+ popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(),
+ evt.getY());
}
}
});
// MessageManager.getString("label.feature_settings_click_drag")));
scrollPane.setViewportView(table);
- dassourceBrowser = new DasSourceBrowser(this);
- dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
-
if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder())
{
fr.findAllFeatures(true); // display everything!
if (!fs.resettingTable && !fs.handlingUpdate)
{
fs.handlingUpdate = true;
- fs.resetTable(null); // new groups may be added with new seuqence
- // feature types only
+ fs.resetTable(null);
+ // new groups may be added with new sequence feature types only
fs.handlingUpdate = false;
}
}
javax.swing.event.InternalFrameEvent evt)
{
fr.removePropertyChangeListener(change);
- dassourceBrowser.fs = null;
};
});
frame.setLayer(JLayeredPane.PALETTE_LAYER);
inConstruction = false;
}
- protected void popupSort(final int selectedRow, final String type,
+ protected void popupSort(final int rowSelected, final String type,
final Object typeCol, final Map<String, float[][]> minmax, int x,
int y)
{
{
if (featureColour.isSimpleColour())
{
- FeatureColourChooser fc = new FeatureColourChooser(me.fr, type);
+ FeatureTypeSettings fc = new FeatureTypeSettings(me.fr, type);
fc.addActionListener(this);
}
else
{
// bring up simple color chooser
colorChooser = new JColorChooser();
+ String title = MessageManager
+ .getString("label.select_colour");
JDialog dialog = JColorChooser.createDialog(me,
- "Select new Colour", true, // modal
+ title, true, // modal
colorChooser, this, // OK button handler
null); // no CANCEL button handler
colorChooser.setColor(featureColour.getMaxColour());
}
else
{
- if (e.getSource() instanceof FeatureColourChooser)
+ if (e.getSource() instanceof FeatureTypeSettings)
{
- FeatureColourChooser fc = (FeatureColourChooser) e.getSource();
- table.setValueAt(fc.getLastColour(), selectedRow, 1);
+ /*
+ * update after OK in feature colour dialog; the updated
+ * colour will have already been set in the FeatureRenderer
+ */
+ FeatureColourI fci = fr.getFeatureColours().get(type);
+ table.setValueAt(fci, rowSelected, 1);
table.validate();
}
else
{
// probably the color chooser!
table.setValueAt(new FeatureColour(colorChooser.getColor()),
- selectedRow, 1);
+ rowSelected, 1);
table.validate();
me.updateFeatureRenderer(
- ((FeatureTableModel) table.getModel()).getData(), false);
+ ((FeatureTableModel) table.getModel()).getData(),
+ false);
}
}
}
}
}
- populateFilterableFeatures();
-
resetTable(null);
validate();
}
}
- Object[][] data = new Object[displayableTypes.size()][3];
+ Object[][] data = new Object[displayableTypes.size()][COLUMN_COUNT];
int dataIndex = 0;
if (fr.hasRenderOrder())
continue;
}
- data[dataIndex][0] = type;
- data[dataIndex][1] = fr.getFeatureStyle(type);
- data[dataIndex][2] = new Boolean(
+ data[dataIndex][TYPE_COLUMN] = type;
+ data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type);
+ FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type);
+ data[dataIndex][FILTER_COLUMN] = featureFilter == null
+ ? new FeatureMatcherSet()
+ : featureFilter;
+ data[dataIndex][SHOW_COLUMN] = new Boolean(
af.getViewport().getFeaturesDisplayed().isVisible(type));
dataIndex++;
displayableTypes.remove(type);
while (!displayableTypes.isEmpty())
{
String type = displayableTypes.iterator().next();
- data[dataIndex][0] = type;
+ data[dataIndex][TYPE_COLUMN] = type;
- data[dataIndex][1] = fr.getFeatureStyle(type);
- if (data[dataIndex][1] == null)
+ data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type);
+ if (data[dataIndex][COLOUR_COLUMN] == null)
{
// "Colour has been updated in another view!!"
fr.clearRenderOrder();
return;
}
-
- data[dataIndex][2] = new Boolean(true);
+ FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type);
+ data[dataIndex][FILTER_COLUMN] = featureFilter == null
+ ? new FeatureMatcherSet()
+ : featureFilter;
+ data[dataIndex][SHOW_COLUMN] = new Boolean(true);
dataIndex++;
displayableTypes.remove(type);
}
if (originalData == null)
{
- originalData = new Object[data.length][3];
+ originalData = new Object[data.length][COLUMN_COUNT];
for (int i = 0; i < data.length; i++)
{
- System.arraycopy(data[i], 0, originalData[i], 0, 3);
+ System.arraycopy(data[i], 0, originalData[i], 0, COLUMN_COUNT);
}
}
else
}
/**
- * Updates 'originalData' (used for restore on Cancel) if we detect that
- * changes have been made outwith this dialog
+ * Updates 'originalData' (used for restore on Cancel) if we detect that changes
+ * have been made outwith this dialog
* <ul>
* <li>a new feature type added (and made visible)</li>
* <li>a feature colour changed (in the Amend Features dialog)</li>
.getData();
for (Object[] row : foundData)
{
- String type = (String) row[0];
+ String type = (String) row[TYPE_COLUMN];
boolean found = false;
for (Object[] current : currentData)
{
- if (type.equals(current[0]))
+ if (type.equals(current[TYPE_COLUMN]))
{
found = true;
/*
* currently dependent on object equality here;
* really need an equals method on FeatureColour
*/
- if (!row[1].equals(current[1]))
+ if (!row[COLOUR_COLUMN].equals(current[COLOUR_COLUMN]))
{
/*
* feature colour has changed externally - update originalData
*/
for (Object[] original : originalData)
{
- if (type.equals(original[0]))
+ if (type.equals(original[TYPE_COLUMN]))
{
- original[1] = row[1];
+ original[COLOUR_COLUMN] = row[COLOUR_COLUMN];
break;
}
}
/*
* new feature detected - add to original data (on top)
*/
- Object[][] newData = new Object[originalData.length + 1][3];
+ Object[][] newData = new Object[originalData.length
+ + 1][COLUMN_COUNT];
for (int i = 0; i < originalData.length; i++)
{
- System.arraycopy(originalData[i], 0, newData[i + 1], 0, 3);
+ System.arraycopy(originalData[i], 0, newData[i + 1], 0,
+ COLUMN_COUNT);
}
newData[0] = row;
originalData = newData;
/**
* Remove from the groups panel any checkboxes for groups that are not in the
- * foundGroups set. This enables removing a group from the display when the
- * last feature in that group is deleted.
+ * foundGroups set. This enables removing a group from the display when the last
+ * feature in that group is deleted.
*
* @param foundGroups
*/
}
}
+ /**
+ * Offers a file chooser dialog, and then loads the feature colours and
+ * filters from file in XML format and unmarshals to Jalview feature settings
+ */
void load()
{
JalviewFileChooser chooser = new JalviewFileChooser("fc",
- "Sequence Feature Colours");
+ SEQUENCE_FEATURE_COLOURS);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.load_feature_colours"));
if (value == JalviewFileChooser.APPROVE_OPTION)
{
File file = chooser.getSelectedFile();
+ load(file);
+ }
+ }
- try
- {
- InputStreamReader in = new InputStreamReader(
- new FileInputStream(file), "UTF-8");
+ /**
+ * Loads feature colours and filters from XML stored in the given file
+ *
+ * @param file
+ */
+ void load(File file)
+ {
+ try
+ {
+ InputStreamReader in = new InputStreamReader(
+ new FileInputStream(file), "UTF-8");
- JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
+ JAXBContext jc = JAXBContext
+ .newInstance("jalview.xml.binding.jalview");
+ javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+ XMLStreamReader streamReader = XMLInputFactory.newInstance()
+ .createXMLStreamReader(in);
+ JAXBElement<JalviewUserColours> jbe = um.unmarshal(streamReader,
+ JalviewUserColours.class);
+ JalviewUserColours jucs = jbe.getValue();
- for (int i = jucs.getColourCount() - 1; i >= 0; i--)
- {
- String name;
- jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
- if (newcol.hasMax())
- {
- Color mincol = null, maxcol = null;
- try
- {
- mincol = new Color(Integer.parseInt(newcol.getMinRGB(), 16));
- maxcol = new Color(Integer.parseInt(newcol.getRGB(), 16));
+ // JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
- } catch (Exception e)
- {
- Cache.log.warn("Couldn't parse out graduated feature color.",
- e);
- }
- FeatureColourI gcol = new FeatureColour(mincol, maxcol,
- newcol.getMin(), newcol.getMax());
- if (newcol.hasAutoScale())
- {
- gcol.setAutoScaled(newcol.getAutoScale());
- }
- if (newcol.hasColourByLabel())
- {
- gcol.setColourByLabel(newcol.getColourByLabel());
- }
- if (newcol.hasThreshold())
- {
- gcol.setThreshold(newcol.getThreshold());
- }
- if (newcol.getThreshType().length() > 0)
- {
- String ttyp = newcol.getThreshType();
- if (ttyp.equalsIgnoreCase("ABOVE"))
- {
- gcol.setAboveThreshold(true);
- }
- if (ttyp.equalsIgnoreCase("BELOW"))
- {
- gcol.setBelowThreshold(true);
- }
- }
- fr.setColour(name = newcol.getName(), gcol);
- }
- else
- {
- Color color = new Color(
- Integer.parseInt(jucs.getColour(i).getRGB(), 16));
- fr.setColour(name = jucs.getColour(i).getName(),
- new FeatureColour(color));
- }
- fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount());
- }
- if (table != null)
+ /*
+ * load feature colours
+ */
+ for (int i = jucs.getColour().size() - 1; i >= 0; i--)
+ {
+ Colour newcol = jucs.getColour().get(i);
+ FeatureColourI colour = jalview.project.Jalview2XML
+ .parseColour(newcol);
+ fr.setColour(newcol.getName(), colour);
+ fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size());
+ }
+
+ /*
+ * load feature filters; loaded filters will replace any that are
+ * currently defined, other defined filters are left unchanged
+ */
+ for (int i = 0; i < jucs.getFilter().size(); i++)
+ {
+ Filter filterModel = jucs.getFilter().get(i);
+ String featureType = filterModel.getFeatureType();
+ FeatureMatcherSetI filter = jalview.project.Jalview2XML
+ .parseFilter(featureType, filterModel.getMatcherSet());
+ if (!filter.isEmpty())
{
- resetTable(null);
- Object[][] data = ((FeatureTableModel) table.getModel())
- .getData();
- ensureOrder(data);
- updateFeatureRenderer(data, false);
- table.repaint();
+ fr.setFeatureFilter(featureType, filter);
}
- } catch (Exception ex)
+ }
+
+ /*
+ * update feature settings table
+ */
+ if (table != null)
{
- System.out.println("Error loading User Colour File\n" + ex);
+ resetTable(null);
+ Object[][] data = ((FeatureTableModel) table.getModel())
+ .getData();
+ ensureOrder(data);
+ updateFeatureRenderer(data, false);
+ table.repaint();
}
+ } catch (Exception ex)
+ {
+ System.out.println("Error loading User Colour File\n" + ex);
}
}
+ /**
+ * Offers a file chooser dialog, and then saves the current feature colours
+ * and any filters to the selected file in XML format
+ */
void save()
{
JalviewFileChooser chooser = new JalviewFileChooser("fc",
- "Sequence Feature Colours");
+ SEQUENCE_FEATURE_COLOURS);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.save_feature_colours"));
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- String choice = chooser.getSelectedFile().getPath();
- jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
- ucs.setSchemeName("Sequence Features");
- try
- {
- PrintWriter out = new PrintWriter(new OutputStreamWriter(
- new FileOutputStream(choice), "UTF-8"));
+ save(chooser.getSelectedFile());
+ }
+ }
+
+ /**
+ * Saves feature colours and filters to the given file
+ *
+ * @param file
+ */
+ void save(File file)
+ {
+ JalviewUserColours ucs = new JalviewUserColours();
+ ucs.setSchemeName("Sequence Features");
+ try
+ {
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(
+ new FileOutputStream(file), "UTF-8"));
- Set<String> fr_colours = fr.getAllFeatureColours();
- Iterator<String> e = fr_colours.iterator();
- float[] sortOrder = new float[fr_colours.size()];
- String[] sortTypes = new String[fr_colours.size()];
- int i = 0;
- while (e.hasNext())
+ /*
+ * sort feature types by colour order, from 0 (highest)
+ * to 1 (lowest)
+ */
+ Set<String> fr_colours = fr.getAllFeatureColours();
+ String[] sortedTypes = fr_colours
+ .toArray(new String[fr_colours.size()]);
+ Arrays.sort(sortedTypes, new Comparator<String>()
+ {
+ @Override
+ public int compare(String type1, String type2)
{
- sortTypes[i] = e.next();
- sortOrder[i] = fr.getOrder(sortTypes[i]);
- i++;
+ return Float.compare(fr.getOrder(type1), fr.getOrder(type2));
}
- QuickSort.sort(sortOrder, sortTypes);
- sortOrder = null;
- for (i = 0; i < sortTypes.length; i++)
+ });
+
+ /*
+ * save feature colours
+ */
+ for (String featureType : sortedTypes)
+ {
+ FeatureColourI fcol = fr.getFeatureStyle(featureType);
+ Colour col = jalview.project.Jalview2XML.marshalColour(featureType,
+ fcol);
+ ucs.getColour().add(col);
+ }
+
+ /*
+ * save any feature filters
+ */
+ for (String featureType : sortedTypes)
+ {
+ FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
+ if (filter != null && !filter.isEmpty())
{
- jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
- col.setName(sortTypes[i]);
- FeatureColourI fcol = fr.getFeatureStyle(sortTypes[i]);
- if (fcol.isSimpleColour())
- {
- col.setRGB(Format.getHexString(fcol.getColour()));
- }
- else
- {
- col.setRGB(Format.getHexString(fcol.getMaxColour()));
- col.setMin(fcol.getMin());
- col.setMax(fcol.getMax());
- col.setMinRGB(
- jalview.util.Format.getHexString(fcol.getMinColour()));
- col.setAutoScale(fcol.isAutoScaled());
- col.setThreshold(fcol.getThreshold());
- col.setColourByLabel(fcol.isColourByLabel());
- col.setThreshType(fcol.isAboveThreshold() ? "ABOVE"
- : (fcol.isBelowThreshold() ? "BELOW" : "NONE"));
- }
- ucs.addColour(col);
+ Iterator<FeatureMatcherI> iterator = filter.getMatchers().iterator();
+ FeatureMatcherI firstMatcher = iterator.next();
+ jalview.xml.binding.jalview.FeatureMatcherSet ms = jalview.project.Jalview2XML
+ .marshalFilter(firstMatcher, iterator,
+ filter.isAnded());
+ Filter filterModel = new Filter();
+ filterModel.setFeatureType(featureType);
+ filterModel.setMatcherSet(ms);
+ ucs.getFilter().add(filterModel);
}
- ucs.marshal(out);
- out.close();
- } catch (Exception ex)
- {
- ex.printStackTrace();
}
+ JAXBContext jaxbContext = JAXBContext
+ .newInstance(JalviewUserColours.class);
+ Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
+ jaxbMarshaller.marshal(
+ new ObjectFactory().createJalviewUserColours(ucs), out);
+
+ // jaxbMarshaller.marshal(object, pout);
+ // marshaller.marshal(object);
+ out.flush();
+
+ // ucs.marshal(out);
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
}
}
public void invertSelection()
{
- for (int i = 0; i < table.getRowCount(); i++)
+ Object[][] data = ((FeatureTableModel) table.getModel()).getData();
+ for (int i = 0; i < data.length; i++)
{
- Boolean value = (Boolean) table.getValueAt(i, 2);
-
- table.setValueAt(new Boolean(!value.booleanValue()), i, 2);
+ data[i][SHOW_COLUMN] = !(Boolean) data[i][SHOW_COLUMN];
}
+ updateFeatureRenderer(data, true);
+ table.repaint();
}
public void orderByAvWidth()
float[] width = new float[data.length];
float[] awidth;
float max = 0;
- int num = 0;
+
for (int i = 0; i < data.length; i++)
{
- awidth = typeWidth.get(data[i][0]);
+ awidth = typeWidth.get(data[i][TYPE_COLUMN]);
if (awidth[0] > 0)
{
width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better
// weight - but have to make per
// sequence, too (awidth[2])
// if (width[i]==1) // hack to distinguish single width sequences.
- num++;
}
else
{
// awidth = (float[]) typeWidth.get(data[i][0]);
if (width[i] == 0)
{
- width[i] = fr.getOrder(data[i][0].toString());
+ width[i] = fr.getOrder(data[i][TYPE_COLUMN].toString());
if (width[i] < 0)
{
- width[i] = fr.setOrder(data[i][0].toString(), i / data.length);
+ width[i] = fr.setOrder(data[i][TYPE_COLUMN].toString(),
+ i / data.length);
}
}
else
{
width[i] /= max; // normalize
- fr.setOrder(data[i][0].toString(), width[i]); // store for later
+ fr.setOrder(data[i][TYPE_COLUMN].toString(), width[i]); // store for later
}
if (i > 0)
{
}
/**
- * Update the priority order of features; only repaint if this changed the
- * order of visible features
+ * Update the priority order of features; only repaint if this changed the order
+ * of visible features
*
* @param data
* @param visibleNew
*/
private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
{
- if (fr.setFeaturePriority(data, visibleNew))
+ FeatureSettingsBean[] rowData = getTableAsBeans(data);
+
+ if (fr.setFeaturePriority(rowData, visibleNew))
{
af.alignPanel.paintAlignment(true, true);
}
}
+ /**
+ * Converts table data into an array of data beans
+ */
+ private FeatureSettingsBean[] getTableAsBeans(Object[][] data)
+ {
+ FeatureSettingsBean[] rowData = new FeatureSettingsBean[data.length];
+ for (int i = 0; i < data.length; i++)
+ {
+ String type = (String) data[i][TYPE_COLUMN];
+ FeatureColourI colour = (FeatureColourI) data[i][COLOUR_COLUMN];
+ FeatureMatcherSetI theFilter = (FeatureMatcherSetI) data[i][FILTER_COLUMN];
+ Boolean isShown = (Boolean) data[i][SHOW_COLUMN];
+ rowData[i] = new FeatureSettingsBean(type, colour, theFilter,
+ isShown);
+ }
+ return rowData;
+ }
+
private void jbInit() throws Exception
{
this.setLayout(new BorderLayout());
JPanel settingsPane = new JPanel();
settingsPane.setLayout(new BorderLayout());
- filtersPane = new JPanel();
-
- dasSettingsPane.setLayout(new BorderLayout());
-
JPanel bigPanel = new JPanel();
bigPanel.setLayout(new BorderLayout());
JButton loadColours = new JButton(
MessageManager.getString("label.load_colours"));
loadColours.setFont(JvSwingUtils.getLabelFont());
+ loadColours.setToolTipText(
+ MessageManager.getString("label.load_colours_tooltip"));
loadColours.addActionListener(new ActionListener()
{
@Override
JButton saveColours = new JButton(
MessageManager.getString("label.save_colours"));
saveColours.setFont(JvSwingUtils.getLabelFont());
+ saveColours.setToolTipText(
+ MessageManager.getString("label.save_colours_tooltip"));
saveColours.addActionListener(new ActionListener()
{
@Override
if (!inConstruction)
{
fr.setTransparency((100 - transparency.getValue()) / 100f);
- af.alignPanel.paintAlignment(true,true);
+ af.alignPanel.paintAlignment(true, true);
}
}
});
transparency.setMaximum(70);
transparency.setToolTipText(
MessageManager.getString("label.transparency_tip"));
- fetchDAS.setText(MessageManager.getString("label.fetch_das_features"));
- fetchDAS.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- fetchDAS_actionPerformed(e);
- }
- });
- saveDAS.setText(MessageManager.getString("action.save_as_default"));
- saveDAS.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- saveDAS_actionPerformed(e);
- }
- });
-
- JPanel dasButtonPanel = new JPanel();
- dasButtonPanel.setBorder(BorderFactory.createEtchedBorder());
- dasSettingsPane.setBorder(null);
- cancelDAS.setEnabled(false);
- cancelDAS.setText(MessageManager.getString("action.cancel_fetch"));
- cancelDAS.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- cancelDAS_actionPerformed(e);
- }
- });
-
- JTabbedPane tabbedPane = new JTabbedPane();
- this.add(tabbedPane, BorderLayout.CENTER);
- tabbedPane.addTab(MessageManager.getString("label.feature_settings"),
- settingsPane);
- tabbedPane.addTab(MessageManager.getString("label.filters"),
- filtersPane);
- // tabbedPane.addTab(MessageManager.getString("label.das_settings"),
- // dasSettingsPane);
JPanel transPanel = new JPanel(new GridLayout(1, 2));
bigPanel.add(transPanel, BorderLayout.SOUTH);
buttonPanel.add(loadColours);
buttonPanel.add(saveColours);
bigPanel.add(scrollPane, BorderLayout.CENTER);
- dasSettingsPane.add(dasButtonPanel, BorderLayout.SOUTH);
- dasButtonPanel.add(fetchDAS);
- dasButtonPanel.add(cancelDAS);
- dasButtonPanel.add(saveDAS);
settingsPane.add(bigPanel, BorderLayout.CENTER);
settingsPane.add(buttonPanel, BorderLayout.SOUTH);
-
- initFiltersTab();
+ this.add(settingsPane);
}
- /**
- * Populates initial layout of the feature attribute filters panel
- */
- protected void initFiltersTab()
+ // ///////////////////////////////////////////////////////////////////////
+ // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
+ // ///////////////////////////////////////////////////////////////////////
+ class FeatureTableModel extends AbstractTableModel
{
- filters = new ArrayList<>();
+ private String[] columnNames = {
+ MessageManager.getString("label.feature_type"),
+ MessageManager.getString("action.colour"),
+ MessageManager.getString("label.filter"),
+ MessageManager.getString("label.show") };
- /*
- * choose feature type
- */
- JPanel chooseTypePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
- chooseTypePanel.setBackground(Color.white);
- chooseTypePanel.setBorder(BorderFactory
- .createTitledBorder(MessageManager
- .getString("label.feature_type")));
- filteredFeatureChoice = new JComboBox<>();
- filteredFeatureChoice.addItemListener(new ItemListener()
+ private Object[][] data;
+
+ FeatureTableModel(Object[][] data)
{
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- refreshFiltersDisplay();
- }
- });
- chooseTypePanel.add(new JLabel(MessageManager
- .getString("label.feature_to_filter")));
- chooseTypePanel.add(filteredFeatureChoice);
- populateFilterableFeatures();
+ this.data = data;
+ }
- /*
- * the panel with the filters for the selected feature type
- */
- JPanel filtersPanel = new JPanel();
- filtersPanel.setLayout(new BoxLayout(filtersPanel, BoxLayout.Y_AXIS));
- filtersPanel.setBackground(Color.white);
- filtersPanel.setBorder(BorderFactory
- .createTitledBorder(MessageManager.getString("label.filters")));
+ public Object[][] getData()
+ {
+ return data;
+ }
- /*
- * add AND or OR radio buttons
- */
- JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
- andOrPanel.setBackground(Color.white);
- andFilters = new JRadioButton("And");
- orFilters = new JRadioButton("Or");
- ActionListener actionListener = new ActionListener()
+ public void setData(Object[][] data)
{
- @Override
- public void actionPerformed(ActionEvent e)
- {
- filtersChanged();
- }
- };
- andFilters.addActionListener(actionListener);
- orFilters.addActionListener(actionListener);
- ButtonGroup andOr = new ButtonGroup();
- andOr.add(andFilters);
- andOr.add(orFilters);
- andFilters.setSelected(true);
- andOrPanel.add(new JLabel(MessageManager
- .getString("label.join_conditions")));
- andOrPanel.add(andFilters);
- andOrPanel.add(orFilters);
- filtersPanel.add(andOrPanel);
+ this.data = data;
+ }
- /*
- * panel with filters - populated by refreshFiltersDisplay
- */
- chooseFiltersPanel = new JPanel();
- chooseFiltersPanel.setLayout(new BoxLayout(chooseFiltersPanel,
- BoxLayout.Y_AXIS));
- filtersPanel.add(chooseFiltersPanel);
+ @Override
+ public int getColumnCount()
+ {
+ return columnNames.length;
+ }
- /*
- * a read-only text view of the current filters
- */
- JPanel showFiltersPanel = new JPanel(new BorderLayout(5, 5));
- showFiltersPanel.setBackground(Color.white);
- showFiltersPanel.setBorder(BorderFactory
- .createTitledBorder(MessageManager
- .getString("label.match_condition")));
- filtersAsText = new JTextArea();
- filtersAsText.setLineWrap(true);
- filtersAsText.setWrapStyleWord(true);
- showFiltersPanel.add(filtersAsText);
-
- filtersPane.setLayout(new BorderLayout());
- filtersPane.add(chooseTypePanel, BorderLayout.NORTH);
- filtersPane.add(filtersPanel, BorderLayout.CENTER);
- filtersPane.add(showFiltersPanel, BorderLayout.SOUTH);
+ public Object[] getRow(int row)
+ {
+ return data[row];
+ }
- /*
- * update display for initial feature type selection
- */
- refreshFiltersDisplay();
- }
+ @Override
+ public int getRowCount()
+ {
+ return data.length;
+ }
- /**
- * Adds entries to the 'choose feature to filter' drop-down choice. Only
- * feature types which have known attributes (so can be filtered) are
- * included, so recall this method to update the list (check for newly added
- * attributes).
- */
- protected void populateFilterableFeatures()
- {
- /*
- * suppress action handler while updating the list
- */
- ItemListener listener = filteredFeatureChoice.getItemListeners()[0];
- filteredFeatureChoice.removeItemListener(listener);
+ @Override
+ public String getColumnName(int col)
+ {
+ return columnNames[col];
+ }
- filteredFeatureChoice.removeAllItems();
- ReverseListIterator<String> types = new ReverseListIterator<>(
- fr.getRenderOrder());
+ @Override
+ public Object getValueAt(int row, int col)
+ {
+ return data[row][col];
+ }
- boolean found = false;
- while (types.hasNext())
+ /**
+ * Answers the class of the object in column c of the first row of the table
+ */
+ @Override
+ public Class<?> getColumnClass(int c)
{
- String type = types.next();
- if (FeatureAttributes.getInstance().hasAttributes(type))
- {
- filteredFeatureChoice.addItem(type);
- found = true;
- }
+ Object v = getValueAt(0, c);
+ return v == null ? null : v.getClass();
}
- if (!found)
+
+ @Override
+ public boolean isCellEditable(int row, int col)
{
- filteredFeatureChoice // todo i18n
- .addItem("No filterable feature attributes known");
+ return col == 0 ? false : true;
}
- filteredFeatureChoice.addItemListener(listener);
+ @Override
+ public void setValueAt(Object value, int row, int col)
+ {
+ data[row][col] = value;
+ fireTableCellUpdated(row, col);
+ updateFeatureRenderer(data);
+ }
}
- /**
- * Refreshes the display to show any filters currently configured for the
- * selected feature type (editable, with 'remove' option), plus one extra row
- * for adding a condition. This should be called on change of selected feature
- * type, or after a filter has been removed, added or amended.
- */
- protected void refreshFiltersDisplay()
+ class ColorRenderer extends JLabel implements TableCellRenderer
{
- /*
- * clear the panel and list of filter conditions
- */
- chooseFiltersPanel.removeAll();
- filters.clear();
+ javax.swing.border.Border unselectedBorder = null;
- /*
- * look up attributes known for feature type
- */
- String selectedType = (String) filteredFeatureChoice.getSelectedItem();
- List<String> attNames = FeatureAttributes.getInstance().getAttributes(
- selectedType);
+ javax.swing.border.Border selectedBorder = null;
- /*
- * if this feature type has filters set, load them first
- */
- KeyedMatcherSetI featureFilters = fr.getFeatureFilter(selectedType);
- filtersAsText.setText("");
- if (featureFilters != null)
- {
- filtersAsText.setText(featureFilters.toString());
- if (!featureFilters.isAnded())
- {
- orFilters.setSelected(true);
- }
- featureFilters.getMatchers().forEach(matcher -> filters.add(matcher));
- }
-
- /*
- * and an empty filter for the user to populate (add)
- */
- KeyedMatcherI noFilter = new KeyedMatcher("", Condition.values()[0], "");
- filters.add(noFilter);
-
- /*
- * render the conditions in rows, each in its own JPanel
- */
- int filterIndex = 0;
- for (KeyedMatcherI filter : filters)
- {
- String key = filter.getKey();
- Condition condition = filter.getMatcher()
- .getCondition();
- String pattern = filter.getMatcher().getPattern();
- JPanel row = addFilter(key, attNames, condition, pattern, filterIndex);
- chooseFiltersPanel.add(row);
- filterIndex++;
- }
-
- filtersPane.validate();
- filtersPane.repaint();
- }
-
- /**
- * A helper method that constructs a panel with one filter condition:
- * <ul>
- * <li>a drop-down list of attribute names to choose from</li>
- * <li>a drop-down list of conditions to choose from</li>
- * <li>a text field for input of a match pattern</li>
- * <li>optionally, a 'remove' button</li>
- * </ul>
- * If attribute, condition or pattern are not null, they are set as defaults
- * for the input fields. The 'remove' button is added unless the pattern is
- * null or empty (incomplete filter condition).
- *
- * @param attribute
- * @param attNames
- * @param cond
- * @param pattern
- * @param filterIndex
- * @return
- */
- protected JPanel addFilter(String attribute, List<String> attNames,
- Condition cond, String pattern, int filterIndex)
- {
- JPanel filterRow = new JPanel(new FlowLayout(FlowLayout.LEFT));
- filterRow.setBackground(Color.white);
-
- /*
- * inputs for attribute, condition, pattern
- */
- /*
- * drop-down choice of attribute, with description as a tooltip
- * if we can obtain it
- */
- String featureType = (String) filteredFeatureChoice.getSelectedItem();
- final JComboBox<String> attCombo = populateAttributesDropdown(
- featureType, attNames);
- JComboBox<Condition> condCombo = new JComboBox<>();
- JTextField patternField = new JTextField(8);
-
- /*
- * action handlers that validate and (if valid) apply changes
- */
- ActionListener actionListener = new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- if (attCombo.getSelectedItem() != null)
- {
- if (validateFilter(patternField, condCombo))
- {
- updateFilter(attCombo, condCombo, patternField, filterIndex);
- filtersChanged();
- }
- }
- }
- };
- ItemListener itemListener = new ItemListener()
- {
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- actionListener.actionPerformed(null);
- }
- };
-
- if ("".equals(attribute))
- {
- attCombo.setSelectedItem(null);
- }
- else
- {
- attCombo.setSelectedItem(attribute);
- }
- attCombo.addItemListener(itemListener);
-
- filterRow.add(attCombo);
+ final String baseTT = "Click to edit, right/apple click for menu.";
- /*
- * drop-down choice of test condition
- */
- for (Condition c : Condition.values())
- {
- condCombo.addItem(c);
- }
- if (cond != null)
+ public ColorRenderer()
{
- condCombo.setSelectedItem(cond);
+ setOpaque(true); // MUST do this for background to show up.
+ setHorizontalTextPosition(SwingConstants.CENTER);
+ setVerticalTextPosition(SwingConstants.CENTER);
}
- condCombo.addItemListener(itemListener);
- filterRow.add(condCombo);
- /*
- * pattern to match against
- */
- patternField.setText(pattern);
- patternField.addActionListener(actionListener);
- patternField.addFocusListener(new FocusAdapter()
+ @Override
+ public Component getTableCellRendererComponent(JTable tbl, Object color,
+ boolean isSelected, boolean hasFocus, int row, int column)
{
- @Override
- public void focusLost(FocusEvent e)
+ FeatureColourI cellColour = (FeatureColourI) color;
+ setOpaque(true);
+ setToolTipText(baseTT);
+ setBackground(tbl.getBackground());
+ if (!cellColour.isSimpleColour())
{
- actionListener.actionPerformed(null);
+ Rectangle cr = tbl.getCellRect(row, column, false);
+ FeatureSettings.renderGraduatedColor(this, cellColour,
+ (int) cr.getWidth(), (int) cr.getHeight());
}
- });
- filterRow.add(patternField);
-
- /*
- * add remove button if filter is populated (non-empty pattern)
- */
- if (pattern != null && pattern.trim().length() > 0)
- {
- // todo: gif for - button
- JButton removeCondition = new BasicArrowButton(SwingConstants.WEST);
- removeCondition.setToolTipText(MessageManager
- .getString("label.delete_row"));
- removeCondition.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- filters.remove(filterIndex);
- filtersChanged();
- }
- });
- filterRow.add(removeCondition);
- }
-
- return filterRow;
- }
-
- /**
- * A helper method to build the drop-down choice of attributes for a feature.
- * Where metadata is available with a description for an attribute, that is
- * added as a tooltip.
- *
- * @param featureType
- * @param attNames
- */
- protected JComboBox<String> populateAttributesDropdown(
- String featureType, List<String> attNames)
- {
- List<String> tooltips = new ArrayList<>();
- FeatureAttributes fa = FeatureAttributes.getInstance();
- for (String attName : attNames)
- {
- String desc = fa.getDescription(featureType, attName);
- if (desc != null && desc.length() > MAX_TOOLTIP_LENGTH)
+ else
{
- desc = desc.substring(0, MAX_TOOLTIP_LENGTH) + "...";
+ this.setText("");
+ this.setIcon(null);
+ setBackground(cellColour.getColour());
}
- tooltips.add(desc == null ? "" : desc);
- }
-
- JComboBox<String> attCombo = JvSwingUtils.buildComboWithTooltips(
- attNames, tooltips);
- if (attNames.isEmpty())
- {
- attCombo.setToolTipText(MessageManager
- .getString("label.no_attributes"));
- }
- return attCombo;
- }
-
- /**
- * Action on any change to feature filtering, namely
- * <ul>
- * <li>change of selected attribute</li>
- * <li>change of selected condition</li>
- * <li>change of match pattern</li>
- * <li>removal of a condition</li>
- * </ul>
- * The action should be to
- * <ul>
- * <li>parse and validate the filters</li>
- * <li>if valid, update the filter text box</li>
- * <li>and apply the filters to the viewport</li>
- * </ul>
- */
- protected void filtersChanged()
- {
- /*
- * update the filter conditions for the feature type
- */
- String featureType = (String) filteredFeatureChoice.getSelectedItem();
- boolean anded = andFilters.isSelected();
- KeyedMatcherSetI combined = new KeyedMatcherSet();
-
- for (KeyedMatcherI filter : filters)
- {
- String pattern = filter.getMatcher().getPattern();
- if (pattern.trim().length() > 0)
+ if (isSelected)
{
- if (anded)
- {
- combined.and(filter);
- }
- else
+ if (selectedBorder == null)
{
- combined.or(filter);
+ selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
+ tbl.getSelectionBackground());
}
+ setBorder(selectedBorder);
}
- }
-
- /*
- * save the filter conditions in the FeatureRenderer
- * (note this might now be an empty filter with no conditions)
- */
- fr.setFeatureFilter(featureType, combined);
-
- filtersAsText.setText(combined.toString());
-
- refreshFiltersDisplay();
-
- af.alignPanel.paintAlignment(true, true);
- }
-
- /**
- * Constructs a filter condition from the given input fields, and replaces the
- * condition at filterIndex with the new one
- *
- * @param attCombo
- * @param condCombo
- * @param valueField
- * @param filterIndex
- */
- protected void updateFilter(JComboBox<String> attCombo,
- JComboBox<Condition> condCombo, JTextField valueField,
- int filterIndex)
- {
- String attName = (String) attCombo.getSelectedItem();
- Condition cond = (Condition) condCombo.getSelectedItem();
- String pattern = valueField.getText();
- KeyedMatcherI km = new KeyedMatcher(attName, cond, pattern);
-
- filters.set(filterIndex, km);
- }
-
- public void fetchDAS_actionPerformed(ActionEvent e)
- {
- fetchDAS.setEnabled(false);
- cancelDAS.setEnabled(true);
- dassourceBrowser.setGuiEnabled(false);
- Vector<jalviewSourceI> selectedSources = dassourceBrowser
- .getSelectedSources();
- doDasFeatureFetch(selectedSources, true, true);
- }
-
- /**
- * get the features from selectedSources for all or the current selection
- *
- * @param selectedSources
- * @param checkDbRefs
- * @param promptFetchDbRefs
- */
- private void doDasFeatureFetch(List<jalviewSourceI> selectedSources,
- boolean checkDbRefs, boolean promptFetchDbRefs)
- {
- SequenceI[] dataset, seqs;
- int iSize;
- AlignmentViewport vp = af.getViewport();
- if (vp.getSelectionGroup() != null
- && vp.getSelectionGroup().getSize() > 0)
- {
- iSize = vp.getSelectionGroup().getSize();
- dataset = new SequenceI[iSize];
- seqs = vp.getSelectionGroup().getSequencesInOrder(vp.getAlignment());
- }
- else
- {
- iSize = vp.getAlignment().getHeight();
- seqs = vp.getAlignment().getSequencesArray();
- }
-
- dataset = new SequenceI[iSize];
- for (int i = 0; i < iSize; i++)
- {
- dataset[i] = seqs[i].getDatasetSequence();
- }
-
- cancelDAS.setEnabled(true);
- dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset,
- this, selectedSources, checkDbRefs, promptFetchDbRefs);
- af.getViewport().setShowSequenceFeatures(true);
- af.showSeqFeatures.setSelected(true);
- }
-
- /**
- * blocking call to initialise the das source browser
- */
- public void initDasSources()
- {
- dassourceBrowser.initDasSources();
- }
-
- /**
- * examine the current list of das sources and return any matching the given
- * nicknames in sources
- *
- * @param sources
- * Vector of Strings to resolve to DAS source nicknames.
- * @return sources that are present in source list.
- */
- public List<jalviewSourceI> resolveSourceNicknames(Vector<String> sources)
- {
- return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
- }
-
- /**
- * get currently selected das sources. ensure you have called initDasSources
- * before calling this.
- *
- * @return vector of selected das source nicknames
- */
- public Vector<jalviewSourceI> getSelectedSources()
- {
- return dassourceBrowser.getSelectedSources();
- }
-
- /**
- * properly initialise DAS fetcher and then initiate a new thread to fetch
- * features from the named sources (rather than any turned on by default)
- *
- * @param sources
- * @param block
- * if true then runs in same thread, otherwise passes to the Swing
- * executor
- */
- public void fetchDasFeatures(Vector<String> sources, boolean block)
- {
- initDasSources();
- List<jalviewSourceI> resolved = dassourceBrowser.sourceRegistry
- .resolveSourceNicknames(sources);
- if (resolved.size() == 0)
- {
- resolved = dassourceBrowser.getSelectedSources();
- }
- if (resolved.size() > 0)
- {
- final List<jalviewSourceI> dassources = resolved;
- fetchDAS.setEnabled(false);
- // cancelDAS.setEnabled(true); doDasFetch does this.
- Runnable fetcher = new Runnable()
+ else
{
-
- @Override
- public void run()
+ if (unselectedBorder == null)
{
- doDasFeatureFetch(dassources, true, false);
-
+ unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
+ tbl.getBackground());
}
- };
- if (block)
- {
- fetcher.run();
- }
- else
- {
- SwingUtilities.invokeLater(fetcher);
- }
- }
- }
-
- public void saveDAS_actionPerformed(ActionEvent e)
- {
- dassourceBrowser
- .saveProperties(jalview.bin.Cache.applicationProperties);
- }
-
- public void complete()
- {
- fetchDAS.setEnabled(true);
- cancelDAS.setEnabled(false);
- dassourceBrowser.setGuiEnabled(true);
-
- }
-
- public void cancelDAS_actionPerformed(ActionEvent e)
- {
- if (dasFeatureFetcher != null)
- {
- dasFeatureFetcher.cancel();
- }
- complete();
- }
-
- public void noDasSourceActive()
- {
- complete();
- JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.getString("label.no_das_sources_selected_warn"),
- MessageManager.getString("label.no_das_sources_selected_title"),
- JvOptionPane.DEFAULT_OPTION, JvOptionPane.INFORMATION_MESSAGE);
- }
-
- /**
- * Answers true unless a numeric condition has been selected with a
- * non-numeric value. Sets the value field to RED with a tooltip if in error.
- * <p>
- * If the pattern entered is empty, this method returns false, but does not
- * mark the field as invalid. This supports selecting an attribute for a new
- * condition before a match pattern has been entered.
- *
- * @param value
- * @param condCombo
- */
- protected boolean validateFilter(JTextField value,
- JComboBox<Condition> condCombo)
- {
- if (value == null || condCombo == null)
- {
- return true; // fields not populated
- }
-
- Condition cond = (Condition) condCombo.getSelectedItem();
- value.setBackground(Color.white);
- value.setToolTipText("");
- String v1 = value.getText().trim();
- if (v1.length() == 0)
- {
- return false;
- }
-
- if (cond.isNumeric())
- {
- try
- {
- Float.valueOf(v1);
- } catch (NumberFormatException e)
- {
- value.setBackground(Color.red);
- value.setToolTipText(MessageManager
- .getString("label.numeric_required"));
- return false;
+ setBorder(unselectedBorder);
}
- }
-
- return true;
- }
- // ///////////////////////////////////////////////////////////////////////
- // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
- // ///////////////////////////////////////////////////////////////////////
- class FeatureTableModel extends AbstractTableModel
- {
- FeatureTableModel(Object[][] data)
- {
- this.data = data;
- }
-
- private String[] columnNames = {
- MessageManager.getString("label.feature_type"),
- MessageManager.getString("action.colour"),
- MessageManager.getString("label.display") };
-
- private Object[][] data;
-
- public Object[][] getData()
- {
- return data;
- }
-
- public void setData(Object[][] data)
- {
- this.data = data;
- }
-
- @Override
- public int getColumnCount()
- {
- return columnNames.length;
- }
-
- public Object[] getRow(int row)
- {
- return data[row];
- }
-
- @Override
- public int getRowCount()
- {
- return data.length;
- }
-
- @Override
- public String getColumnName(int col)
- {
- return columnNames[col];
- }
-
- @Override
- public Object getValueAt(int row, int col)
- {
- return data[row][col];
- }
-
- @Override
- public Class getColumnClass(int c)
- {
- return getValueAt(0, c).getClass();
- }
-
- @Override
- public boolean isCellEditable(int row, int col)
- {
- return col == 0 ? false : true;
- }
-
- @Override
- public void setValueAt(Object value, int row, int col)
- {
- data[row][col] = value;
- fireTableCellUpdated(row, col);
- updateFeatureRenderer(data);
+ return this;
}
-
}
- class ColorRenderer extends JLabel implements TableCellRenderer
+ class FilterRenderer extends JLabel implements TableCellRenderer
{
javax.swing.border.Border unselectedBorder = null;
javax.swing.border.Border selectedBorder = null;
- final String baseTT = "Click to edit, right/apple click for menu.";
-
- public ColorRenderer()
+ public FilterRenderer()
{
setOpaque(true); // MUST do this for background to show up.
setHorizontalTextPosition(SwingConstants.CENTER);
}
@Override
- public Component getTableCellRendererComponent(JTable tbl, Object color,
- boolean isSelected, boolean hasFocus, int row, int column)
+ public Component getTableCellRendererComponent(JTable tbl,
+ Object filter, boolean isSelected, boolean hasFocus, int row,
+ int column)
{
- FeatureColourI cellColour = (FeatureColourI) color;
+ FeatureMatcherSetI theFilter = (FeatureMatcherSetI) filter;
setOpaque(true);
- setToolTipText(baseTT);
+ String asText = theFilter.toString();
setBackground(tbl.getBackground());
- if (!cellColour.isSimpleColour())
- {
- Rectangle cr = tbl.getCellRect(row, column, false);
- FeatureSettings.renderGraduatedColor(this, cellColour,
- (int) cr.getWidth(), (int) cr.getHeight());
- }
- else
- {
- this.setText("");
- this.setIcon(null);
- setBackground(cellColour.getColour());
- }
+ this.setText(asText);
+ this.setIcon(null);
+
if (isSelected)
{
if (selectedBorder == null)
if (gcol.isColourByAttribute())
{
- tx.append(gcol.getAttributeName());
+ tx.append(String.join(":", gcol.getAttributeName()));
}
else if (!gcol.isColourByLabel())
{
}
else
{
- comp.setToolTipText(tt.append(" ").append(comp.getToolTipText())
- .toString());
+ comp.setToolTipText(
+ tt.append(" ").append(comp.getToolTipText()).toString());
+ }
+ }
+ }
+
+ class ColorEditor extends AbstractCellEditor
+ implements TableCellEditor, ActionListener
+ {
+ FeatureSettings me;
+
+ FeatureColourI currentColor;
+
+ FeatureTypeSettings chooser;
+
+ String type;
+
+ JButton button;
+
+ JColorChooser colorChooser;
+
+ JDialog dialog;
+
+ protected static final String EDIT = "edit";
+
+ int rowSelected = 0;
+
+ public ColorEditor(FeatureSettings me)
+ {
+ this.me = me;
+ // Set up the editor (from the table's point of view),
+ // which is a button.
+ // This button brings up the color chooser dialog,
+ // which is the editor from the user's point of view.
+ button = new JButton();
+ button.setActionCommand(EDIT);
+ button.addActionListener(this);
+ button.setBorderPainted(false);
+ // Set up the dialog that the button brings up.
+ colorChooser = new JColorChooser();
+ dialog = JColorChooser.createDialog(button,
+ MessageManager.getString("label.select_colour"), true, // modal
+ colorChooser, this, // OK button handler
+ null); // no CANCEL button handler
+ }
+
+ /**
+ * Handles events from the editor button and from the dialog's OK button.
+ */
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // todo test e.getSource() instead here
+ if (EDIT.equals(e.getActionCommand()))
+ {
+ // The user has clicked the cell, so
+ // bring up the dialog.
+ if (currentColor.isSimpleColour())
+ {
+ // bring up simple color chooser
+ button.setBackground(currentColor.getColour());
+ colorChooser.setColor(currentColor.getColour());
+ dialog.setVisible(true);
+ }
+ else
+ {
+ // bring up graduated chooser.
+ chooser = new FeatureTypeSettings(me.fr, type);
+ chooser.setRequestFocusEnabled(true);
+ chooser.requestFocus();
+ chooser.addActionListener(this);
+ chooser.showTab(true);
+ }
+ // Make the renderer reappear.
+ fireEditingStopped();
+
+ }
+ else
+ {
+ if (currentColor.isSimpleColour())
+ {
+ /*
+ * read off colour picked in colour chooser after OK pressed
+ */
+ currentColor = new FeatureColour(colorChooser.getColor());
+ me.table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN);
+ }
+ else
+ {
+ /*
+ * after OK in variable colour dialog, any changes to colour
+ * (or filters!) are already set in FeatureRenderer, so just
+ * update table data without triggering updateFeatureRenderer
+ */
+ currentColor = fr.getFeatureColours().get(type);
+ FeatureMatcherSetI currentFilter = me.fr.getFeatureFilter(type);
+ if (currentFilter == null)
+ {
+ currentFilter = new FeatureMatcherSet();
+ }
+ Object[] data = ((FeatureTableModel) table.getModel())
+ .getData()[rowSelected];
+ data[COLOUR_COLUMN] = currentColor;
+ data[FILTER_COLUMN] = currentFilter;
+ }
+ fireEditingStopped();
+ me.table.validate();
+ }
+ }
+
+ // Implement the one CellEditor method that AbstractCellEditor doesn't.
+ @Override
+ public Object getCellEditorValue()
+ {
+ return currentColor;
+ }
+
+ // Implement the one method defined by TableCellEditor.
+ @Override
+ public Component getTableCellEditorComponent(JTable theTable, Object value,
+ boolean isSelected, int row, int column)
+ {
+ currentColor = (FeatureColourI) value;
+ this.rowSelected = row;
+ type = me.table.getValueAt(row, TYPE_COLUMN).toString();
+ button.setOpaque(true);
+ button.setBackground(me.getBackground());
+ if (!currentColor.isSimpleColour())
+ {
+ JLabel btn = new JLabel();
+ btn.setSize(button.getSize());
+ FeatureSettings.renderGraduatedColor(btn, currentColor);
+ button.setBackground(btn.getBackground());
+ button.setIcon(btn.getIcon());
+ button.setText(btn.getText());
+ }
+ else
+ {
+ button.setText("");
+ button.setIcon(null);
+ button.setBackground(currentColor.getColour());
+ }
+ return button;
+ }
+ }
+
+ /**
+ * The cell editor for the Filter column. It displays the text of any filters
+ * for the feature type in that row (in full as a tooltip, possible abbreviated
+ * as display text). On click in the cell, opens the Feature Display Settings
+ * dialog at the Filters tab.
+ */
+ class FilterEditor extends AbstractCellEditor
+ implements TableCellEditor, ActionListener
+ {
+ FeatureSettings me;
+
+ FeatureMatcherSetI currentFilter;
+
+ Point lastLocation;
+
+ String type;
+
+ JButton button;
+
+ protected static final String EDIT = "edit";
+
+ int rowSelected = 0;
+
+ public FilterEditor(FeatureSettings me)
+ {
+ this.me = me;
+ button = new JButton();
+ button.setActionCommand(EDIT);
+ button.addActionListener(this);
+ button.setBorderPainted(false);
+ }
+
+ /**
+ * Handles events from the editor button
+ */
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (button == e.getSource())
+ {
+ FeatureTypeSettings chooser = new FeatureTypeSettings(me.fr, type);
+ chooser.addActionListener(this);
+ chooser.setRequestFocusEnabled(true);
+ chooser.requestFocus();
+ if (lastLocation != null)
+ {
+ // todo open at its last position on screen
+ chooser.setBounds(lastLocation.x, lastLocation.y,
+ chooser.getWidth(), chooser.getHeight());
+ chooser.validate();
+ }
+ chooser.showTab(false);
+ fireEditingStopped();
+ }
+ else if (e.getSource() instanceof Component)
+ {
+
+ /*
+ * after OK in variable colour dialog, any changes to filter
+ * (or colours!) are already set in FeatureRenderer, so just
+ * update table data without triggering updateFeatureRenderer
+ */
+ FeatureColourI currentColor = fr.getFeatureColours().get(type);
+ currentFilter = me.fr.getFeatureFilter(type);
+ if (currentFilter == null)
+ {
+ currentFilter = new FeatureMatcherSet();
+ }
+ Object[] data = ((FeatureTableModel) table.getModel())
+ .getData()[rowSelected];
+ data[COLOUR_COLUMN] = currentColor;
+ data[FILTER_COLUMN] = currentFilter;
+ fireEditingStopped();
+ me.table.validate();
}
}
+
+ @Override
+ public Object getCellEditorValue()
+ {
+ return currentFilter;
+ }
+
+ @Override
+ public Component getTableCellEditorComponent(JTable theTable, Object value,
+ boolean isSelected, int row, int column)
+ {
+ currentFilter = (FeatureMatcherSetI) value;
+ this.rowSelected = row;
+ type = me.table.getValueAt(row, TYPE_COLUMN).toString();
+ button.setOpaque(true);
+ button.setBackground(me.getBackground());
+ button.setText(currentFilter.toString());
+ button.setToolTipText(currentFilter.toString());
+ button.setIcon(null);
+ return button;
+ }
}
}
}
}
}
-
-class ColorEditor extends AbstractCellEditor
- implements TableCellEditor, ActionListener
-{
- FeatureSettings me;
-
- FeatureColourI currentColor;
-
- FeatureColourChooser chooser;
-
- String type;
-
- JButton button;
-
- JColorChooser colorChooser;
-
- JDialog dialog;
-
- protected static final String EDIT = "edit";
-
- int selectedRow = 0;
-
- public ColorEditor(FeatureSettings me)
- {
- this.me = me;
- // Set up the editor (from the table's point of view),
- // which is a button.
- // This button brings up the color chooser dialog,
- // which is the editor from the user's point of view.
- button = new JButton();
- button.setActionCommand(EDIT);
- button.addActionListener(this);
- button.setBorderPainted(false);
- // Set up the dialog that the button brings up.
- colorChooser = new JColorChooser();
- dialog = JColorChooser.createDialog(button,
- MessageManager.getString("label.select_new_colour"), true, // modal
- colorChooser, this, // OK button handler
- null); // no CANCEL button handler
- }
-
- /**
- * Handles events from the editor button and from the dialog's OK button.
- */
- @Override
- public void actionPerformed(ActionEvent e)
- {
-
- if (EDIT.equals(e.getActionCommand()))
- {
- // The user has clicked the cell, so
- // bring up the dialog.
- if (currentColor.isSimpleColour())
- {
- // bring up simple color chooser
- button.setBackground(currentColor.getColour());
- colorChooser.setColor(currentColor.getColour());
- dialog.setVisible(true);
- }
- else
- {
- // bring up graduated chooser.
- chooser = new FeatureColourChooser(me.fr, type);
- chooser.setRequestFocusEnabled(true);
- chooser.requestFocus();
- chooser.addActionListener(this);
- }
- // Make the renderer reappear.
- fireEditingStopped();
-
- }
- else
- { // User pressed dialog's "OK" button.
- if (currentColor.isSimpleColour())
- {
- currentColor = new FeatureColour(colorChooser.getColor());
- }
- else
- {
- currentColor = chooser.getLastColour();
- }
- me.table.setValueAt(getCellEditorValue(), selectedRow, 1);
- fireEditingStopped();
- me.table.validate();
- }
- }
-
- // Implement the one CellEditor method that AbstractCellEditor doesn't.
- @Override
- public Object getCellEditorValue()
- {
- return currentColor;
- }
-
- // Implement the one method defined by TableCellEditor.
- @Override
- public Component getTableCellEditorComponent(JTable table, Object value,
- boolean isSelected, int row, int column)
- {
- currentColor = (FeatureColourI) value;
- this.selectedRow = row;
- type = me.table.getValueAt(row, 0).toString();
- button.setOpaque(true);
- button.setBackground(me.getBackground());
- if (!currentColor.isSimpleColour())
- {
- JLabel btn = new JLabel();
- btn.setSize(button.getSize());
- FeatureSettings.renderGraduatedColor(btn, currentColor);
- button.setBackground(btn.getBackground());
- button.setIcon(btn.getIcon());
- button.setText(btn.getText());
- }
- else
- {
- button.setText("");
- button.setIcon(null);
- button.setBackground(currentColor.getColour());
- }
- return button;
- }
-}
git://source.jalview.org / jalview.git / blobdiff