import jalview.datamodel.features.FeatureMatcherI;
import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.datamodel.ontology.OntologyI;
import jalview.gui.Help.HelpId;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
-import jalview.schemabinding.version2.Filter;
-import jalview.schemabinding.version2.JalviewUserColours;
-import jalview.schemabinding.version2.MatcherSet;
+import jalview.io.gff.SequenceOntologyFactory;
import jalview.schemes.FeatureColour;
import jalview.util.MessageManager;
import jalview.util.Platform;
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.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 javax.swing.Icon;
import javax.swing.JButton;
import javax.swing.JCheckBox;
-import javax.swing.JCheckBoxMenuItem;
import javax.swing.JColorChooser;
import javax.swing.JDialog;
import javax.swing.JInternalFrame;
import javax.swing.JSlider;
import javax.swing.JTable;
import javax.swing.ListSelectionModel;
+import javax.swing.RowFilter;
import javax.swing.SwingConstants;
import javax.swing.border.Border;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.table.AbstractTableModel;
+import javax.swing.table.JTableHeader;
import javax.swing.table.TableCellEditor;
import javax.swing.table.TableCellRenderer;
import javax.swing.table.TableColumn;
+import javax.swing.table.TableRowSorter;
+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 Font VERDANA_12 = new Font("Verdana", Font.PLAIN, 12);
+
private static final String SEQUENCE_FEATURE_COLOURS = MessageManager
.getString("label.sequence_feature_colours");
private static final int MIN_HEIGHT = 400;
- private final static String BASE_TOOLTIP = "Click to edit, right-click for menu";
+ private final static String BASE_TOOLTIP = MessageManager.getString("label.click_to_edit");
final FeatureRenderer fr;
int selectedRow = -1;
- JButton fetchDAS = new JButton();
-
- JButton saveDAS = new JButton();
-
- JButton cancelDAS = new JButton();
-
boolean resettingTable = false;
/*
*/
Map<String, float[]> typeWidth = null;
+ /*
+ * if true, 'child' feature types are not displayed
+ */
+ JCheckBox summaryView;
+
+ /*
+ * those feature types that do not have a parent feature type present
+ * (as determined by an Ontology relationship)
+ */
+ List<String> topLevelTypes;
+
/**
* Constructor
*
originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy
+ topLevelTypes = new ArrayList<>();
+
try
{
jbInit();
ex.printStackTrace();
}
+ initTable();
+
+ scrollPane.setViewportView(table);
+
+ if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder())
+ {
+ fr.findAllFeatures(true); // display everything!
+ }
+
+ discoverAllFeatureData();
+ final PropertyChangeListener change;
+ final FeatureSettings fs = this;
+ fr.addPropertyChangeListener(change = new PropertyChangeListener()
+ {
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ if (!fs.resettingTable && !fs.handlingUpdate)
+ {
+ fs.handlingUpdate = true;
+ fs.resetTable(null);
+ // new groups may be added with new sequence feature types only
+ fs.handlingUpdate = false;
+ }
+ }
+ });
+
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ if (Platform.isAMac())
+ {
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ 600, 480);
+ }
+ else
+ {
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ 600, 450);
+ }
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
+
+ frame.addInternalFrameListener(
+ new javax.swing.event.InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ fr.removePropertyChangeListener(change);
+ };
+ });
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ inConstruction = false;
+ }
+
+ /**
+ * Constructs and configures the JTable which displays columns of data for
+ * each feature type
+ */
+ protected void initTable()
+ {
table = new JTable()
{
- static final String tt = "Click to edit, right-click for menu"; // todo i18n
-
@Override
public String getToolTipText(MouseEvent e)
{
String tip = null;
int column = table.columnAtPoint(e.getPoint());
int row = table.rowAtPoint(e.getPoint());
-
switch (column)
{
case TYPE_COLUMN:
- tip = JvSwingUtils.wrapTooltip(true, MessageManager
+ /*
+ * drag to reorder not enabled in Summary View
+ */
+ tip = summaryView.isSelected()
+ ? MessageManager.getString(
+ "label.feature_settings_select_columns")
+ : JvSwingUtils.wrapTooltip(true, MessageManager
.getString("label.feature_settings_click_drag"));
break;
case COLOUR_COLUMN:
FeatureColourI colour = (FeatureColourI) table.getValueAt(row,
column);
- tip = getColorTooltip(colour);
+ tip = getColorTooltip(colour, true);
break;
case FILTER_COLUMN:
FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row,
column);
tip = o.isEmpty()
- ? MessageManager.getString("label.filters_tooltip")
+ ? MessageManager
+ .getString("label.configure_feature_tooltip")
: o.toString();
break;
default:
}
return tip;
}
+
+ /**
+ * Position the tooltip near the bottom edge of, and half way across, the
+ * current cell
+ */
+ @Override
+ public Point getToolTipLocation(MouseEvent e)
+ {
+ Point point = e.getPoint();
+ int column = table.columnAtPoint(point);
+ int row = table.rowAtPoint(point);
+ Rectangle r = getCellRect(row, column, false);
+ Point loc = new Point(r.x + r.width / 2, r.y + r.height - 3);
+ return loc;
+ }
};
- 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));
- //
+ JTableHeader tableHeader = table.getTableHeader();
+ tableHeader.setFont(VERDANA_12);
+ tableHeader.setReorderingAllowed(false);
+ table.setFont(VERDANA_12);
+
table.setDefaultEditor(FeatureColour.class, new ColorEditor(this));
table.setDefaultRenderer(FeatureColour.class, new ColorRenderer());
String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN);
if (evt.isPopupTrigger())
{
- Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
- popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(),
- evt.getY());
+ popupMenu(selectedRow, type, evt.getX(), evt.getY());
}
else if (evt.getClickCount() == 2)
{
boolean invertSelection = evt.isAltDown();
boolean toggleSelection = Platform.isControlDown(evt);
boolean extendSelection = evt.isShiftDown();
+ String[] terms = getTermsInScope(type);
fr.ap.alignFrame.avc.markColumnsContainingFeatures(
- invertSelection, extendSelection, toggleSelection, type);
+ invertSelection, extendSelection, toggleSelection, terms);
}
}
if (evt.isPopupTrigger())
{
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());
+ popupMenu(selectedRow, type, evt.getX(), evt.getY());
}
}
});
public void mouseDragged(MouseEvent evt)
{
int newRow = table.rowAtPoint(evt.getPoint());
- if (newRow != selectedRow && selectedRow != -1 && newRow != -1)
- {
- /*
- * reposition 'selectedRow' to 'newRow' (the dragged to location)
- * this could be more than one row away for a very fast drag action
- * so just swap it with adjacent rows until we get it there
- */
- Object[][] data = ((FeatureTableModel) table.getModel())
- .getData();
- int direction = newRow < selectedRow ? -1 : 1;
- for (int i = selectedRow; i != newRow; i += direction)
- {
- Object[] temp = data[i];
- data[i] = data[i + direction];
- data[i + direction] = temp;
- }
- updateFeatureRenderer(data);
- table.repaint();
- selectedRow = newRow;
- }
+ dragRow(newRow);
}
});
- // table.setToolTipText(JvSwingUtils.wrapTooltip(true,
- // MessageManager.getString("label.feature_settings_click_drag")));
- scrollPane.setViewportView(table);
+ }
- if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder())
+ /**
+ * Answers an array consisting of the given type, and also (if 'Summary View'
+ * is selected), any feature types which are child terms of it in the Sequence
+ * Ontology
+ *
+ * @param type
+ * @return
+ */
+ protected String[] getTermsInScope(String type)
+ {
+ if (!summaryView.isSelected())
{
- fr.findAllFeatures(true); // display everything!
+ return new String[] { type };
}
- discoverAllFeatureData();
- final PropertyChangeListener change;
- final FeatureSettings fs = this;
- fr.addPropertyChangeListener(change = new PropertyChangeListener()
- {
- @Override
- public void propertyChange(PropertyChangeEvent evt)
- {
- if (!fs.resettingTable && !fs.handlingUpdate)
- {
- fs.handlingUpdate = true;
- fs.resetTable(null);
- // new groups may be added with new sequence feature types only
- fs.handlingUpdate = false;
- }
- }
+ List<String> terms = new ArrayList<>();
+ terms.add(type);
- });
+ OntologyI so = SequenceOntologyFactory.getInstance();
- frame = new JInternalFrame();
- frame.setContentPane(this);
- if (Platform.isAMac())
- {
- Desktop.addInternalFrame(frame,
- MessageManager.getString("label.sequence_feature_settings"),
- 600, 480);
- }
- else
+ Object[][] data = ((FeatureTableModel) table.getModel()).getData();
+ for (Object[] row : data)
{
- Desktop.addInternalFrame(frame,
- MessageManager.getString("label.sequence_feature_settings"),
- 600, 450);
+ String type2 = (String) row[TYPE_COLUMN];
+ if (!type2.equals(type) && so.isA(type2, type))
+ {
+ terms.add(type2);
+ }
}
- frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
-
- frame.addInternalFrameListener(
- new javax.swing.event.InternalFrameAdapter()
- {
- @Override
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- {
- fr.removePropertyChangeListener(change);
- };
- });
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
- inConstruction = false;
+ return terms.toArray(new String[terms.size()]);
}
- protected void popupSort(final int rowSelected, final String type,
- final Object typeCol, final Map<String, float[][]> minmax, int x,
+ protected void popupMenu(final int rowSelected, final String type, int x,
int y)
{
- final FeatureColourI featureColour = (FeatureColourI) typeCol;
-
JPopupMenu men = new JPopupMenu(MessageManager
.formatMessage("label.settings_for_param", new String[]
{ type }));
final FeatureSettings me = this;
scr.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
- me.af.avc
- .sortAlignmentByFeatureScore(Arrays.asList(new String[]
- { type }));
+ String[] types = getTermsInScope(type);
+ me.af.avc.sortAlignmentByFeatureScore(Arrays.asList(types));
}
-
});
JMenuItem dens = new JMenuItem(
MessageManager.getString("label.sort_by_density"));
dens.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
- me.af.avc
- .sortAlignmentByFeatureDensity(Arrays.asList(new String[]
- { type }));
+ String[] types = getTermsInScope(type);
+ me.af.avc.sortAlignmentByFeatureDensity(Arrays.asList(types));
}
-
});
men.add(dens);
- /*
- * variable colour options include colour by label, by score,
- * by selected attribute text, or attribute value
- */
- final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem(
- MessageManager.getString("label.variable_colour"));
- mxcol.setSelected(!featureColour.isSimpleColour());
- men.add(mxcol);
- mxcol.addActionListener(new ActionListener()
- {
- JColorChooser colorChooser;
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- if (e.getSource() == mxcol)
- {
- if (featureColour.isSimpleColour())
- {
- 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,
- title, true, // modal
- colorChooser, this, // OK button handler
- null); // no CANCEL button handler
- colorChooser.setColor(featureColour.getMaxColour());
- dialog.setVisible(true);
- }
- }
- else
- {
- if (e.getSource() instanceof FeatureTypeSettings)
- {
- /*
- * 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()),
- rowSelected, 1);
- table.validate();
- me.updateFeatureRenderer(
- ((FeatureTableModel) table.getModel()).getData(),
- false);
- }
- }
- }
-
- });
-
JMenuItem selCols = new JMenuItem(
MessageManager.getString("label.select_columns_containing"));
selCols.addActionListener(new ActionListener()
@Override
public void actionPerformed(ActionEvent arg0)
{
+ String[] types = getTermsInScope(type);
fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
- false, type);
+ false, types);
}
});
JMenuItem clearCols = new JMenuItem(MessageManager
@Override
public void actionPerformed(ActionEvent arg0)
{
+ String[] types = getTermsInScope(type);
fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
- false, type);
+ false, types);
}
});
JMenuItem hideCols = new JMenuItem(
@Override
public void actionPerformed(ActionEvent arg0)
{
- fr.ap.alignFrame.hideFeatureColumns(type, true);
+ String[] types = getTermsInScope(type);
+ fr.ap.alignFrame.hideFeatureColumns(true, types);
}
});
JMenuItem hideOtherCols = new JMenuItem(
@Override
public void actionPerformed(ActionEvent arg0)
{
- fr.ap.alignFrame.hideFeatureColumns(type, false);
+ String[] types = getTermsInScope(type);
+ fr.ap.alignFrame.hideFeatureColumns(false, types);
}
});
men.add(selCols);
*/
Set<String> types = seq.getFeatures().getFeatureTypesForGroups(true,
visibleGroups.toArray(new String[visibleGroups.size()]));
+
for (String type : types)
{
displayableTypes.add(type);
}
}
+ /*
+ * enable 'Summary View' if some types are sub-types of others
+ */
+ Set<String> parents = SequenceOntologyFactory.getInstance()
+ .getParentTerms(displayableTypes);
+ summaryView.setEnabled(parents.size() < displayableTypes.size());
+
Object[][] data = new Object[displayableTypes.size()][COLUMN_COUNT];
int dataIndex = 0;
{
continue;
}
-
data[dataIndex][TYPE_COLUMN] = type;
data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type);
FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type);
updateOriginalData(data);
}
- table.setModel(new FeatureTableModel(data));
+ /*
+ * recreate the table model
+ */
+ FeatureTableModel dataModel = new FeatureTableModel(data);
+ table.setModel(dataModel);
+
+ /*
+ * we want to be able to filter out rows for sub-types, but not to sort
+ * rows, so have to add a RowFilter to a disabled TableRowSorter (!)
+ */
+ final TableRowSorter<FeatureTableModel> sorter = new TableRowSorter<>(
+ dataModel);
+ for (int i = 0; i < table.getColumnCount(); i++)
+ {
+ sorter.setSortable(i, false);
+ }
+
+ /*
+ * filter rows to only top-level Ontology types if requested
+ */
+ sorter.setRowFilter(new RowFilter<FeatureTableModel, Integer>()
+ {
+ @Override
+ public boolean include(
+ Entry<? extends FeatureTableModel, ? extends Integer> entry)
+ {
+ if (!summaryView.isSelected())
+ {
+ return true;
+ }
+ int row = entry.getIdentifier(); // this is model, not view, row number
+ String featureType = (String) entry.getModel().getData()[row][TYPE_COLUMN];
+ return parents.contains(featureType);
+ }
+ });
+ table.setRowSorter(sorter);
+
table.getColumnModel().getColumn(0).setPreferredWidth(200);
groupPanel.setLayout(
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();
+
+ // JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
/*
* load feature colours
*/
- for (int i = jucs.getColourCount() - 1; i >= 0; i--)
+ for (int i = jucs.getColour().size() - 1; i >= 0; i--)
{
- jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
- FeatureColourI colour = Jalview2XML.unmarshalColour(newcol);
+ 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.getColourCount());
+ 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.getFilterCount(); i++)
+ for (int i = 0; i < jucs.getFilter().size(); i++)
{
- jalview.schemabinding.version2.Filter filterModel = jucs
- .getFilter(i);
+ Filter filterModel = jucs.getFilter().get(i);
String featureType = filterModel.getFeatureType();
- FeatureMatcherSetI filter = Jalview2XML.unmarshalFilter(featureType,
- filterModel.getMatcherSet());
+ FeatureMatcherSetI filter = jalview.project.Jalview2XML
+ .parseFilter(featureType, filterModel.getMatcherSet());
if (!filter.isEmpty())
{
fr.setFeatureFilter(featureType, filter);
for (String featureType : sortedTypes)
{
FeatureColourI fcol = fr.getFeatureStyle(featureType);
- jalview.schemabinding.version2.Colour col = Jalview2XML.marshalColour(
- featureType, fcol);
- ucs.addColour(col);
+ Colour col = jalview.project.Jalview2XML.marshalColour(featureType,
+ fcol);
+ ucs.getColour().add(col);
}
/*
{
Iterator<FeatureMatcherI> iterator = filter.getMatchers().iterator();
FeatureMatcherI firstMatcher = iterator.next();
- MatcherSet ms = Jalview2XML.marshalFilter(firstMatcher, iterator,
+ 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.addFilter(filterModel);
+ ucs.getFilter().add(filterModel);
}
}
+ 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);
+ // ucs.marshal(out);
out.close();
} catch (Exception ex)
{
}
}
});
- help.setFont(JvSwingUtils.getLabelFont());
- help.setText(MessageManager.getString("action.help"));
- help.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- try
- {
- Help.showHelpWindow(HelpId.SequenceFeatureSettings);
- } catch (HelpSetException e1)
- {
- e1.printStackTrace();
- }
- }
- });
JButton cancel = new JButton(MessageManager.getString("action.cancel"));
cancel.setFont(JvSwingUtils.getLabelFont());
}
});
+ summaryView = new JCheckBox(
+ MessageManager.getString("label.summary_view"));
+ summaryView
+ .setToolTipText(
+ MessageManager.getString("label.summary_view_tip"));
+ summaryView.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ resetTable(null);
+ }
+ });
+
transparency.setMaximum(70);
transparency.setToolTipText(
MessageManager.getString("label.transparency_tip"));
- JPanel transPanel = new JPanel(new GridLayout(1, 2));
- bigPanel.add(transPanel, BorderLayout.SOUTH);
+ JPanel lowerPanel = new JPanel(new GridLayout(1, 2));
+ bigPanel.add(lowerPanel, BorderLayout.SOUTH);
JPanel transbuttons = new JPanel(new GridLayout(5, 1));
transbuttons.add(optimizeOrder);
transbuttons.add(sortByScore);
transbuttons.add(sortByDens);
transbuttons.add(help);
+ JPanel transPanel = new JPanel(new GridLayout(3, 1));
+ transPanel.add(summaryView);
+ transPanel.add(new JLabel(" Colour transparency" + ":"));
transPanel.add(transparency);
- transPanel.add(transbuttons);
+ lowerPanel.add(transPanel);
+ lowerPanel.add(transbuttons);
JPanel buttonPanel = new JPanel();
buttonPanel.add(ok);
}
/**
+ * Reorders features by 'dragging' selectedRow to 'newRow'
+ *
+ * @param newRow
+ */
+ protected void dragRow(int newRow)
+ {
+ if (summaryView.isSelected())
+ {
+ // no drag while in summary view
+ return;
+ }
+
+ if (newRow != selectedRow && selectedRow != -1 && newRow != -1)
+ {
+ /*
+ * reposition 'selectedRow' to 'newRow' (the dragged to location)
+ * this could be more than one row away for a very fast drag action
+ * so just swap it with adjacent rows until we get it there
+ */
+ Object[][] data = ((FeatureTableModel) table.getModel())
+ .getData();
+ int direction = newRow < selectedRow ? -1 : 1;
+ for (int i = selectedRow; i != newRow; i += direction)
+ {
+ Object[] temp = data[i];
+ data[i] = data[i + direction];
+ data[i + direction] = temp;
+ }
+ updateFeatureRenderer(data);
+ table.repaint();
+ selectedRow = newRow;
+ }
+ }
+
+ protected void refreshTable()
+ {
+ Object[][] data = ((FeatureTableModel) table.getModel()).getData();
+ for (Object[] row : data)
+ {
+ String type = (String) row[TYPE_COLUMN];
+ FeatureColourI colour = fr.getFeatureColours().get(type);
+ FeatureMatcherSetI filter = fr.getFeatureFilter(type);
+ if (filter == null)
+ {
+ filter = new FeatureMatcherSet();
+ }
+ row[COLOUR_COLUMN] = colour;
+ row[FILTER_COLUMN] = filter;
+ }
+ repaint();
+ }
+
+ /*
* Answers a suitable tooltip to show on the colour cell of the table
*
* @param fcol
+ * @param withHint
+ * if true include 'click to edit' and similar text
* @return
*/
- public static String getColorTooltip(FeatureColourI fcol)
+ public static String getColorTooltip(FeatureColourI fcol,
+ boolean withHint)
{
if (fcol == null)
{
}
if (fcol.isSimpleColour())
{
- return BASE_TOOLTIP;
+ return withHint ? BASE_TOOLTIP : null;
}
String description = fcol.getDescription();
description = description.replaceAll("<", "<");
description = description.replaceAll(">", ">");
StringBuilder tt = new StringBuilder(description);
- tt.append("<br>").append(BASE_TOOLTIP).append("</br>");
+ if (withHint)
+ {
+ tt.append("<br>").append(BASE_TOOLTIP).append("</br>");
+ }
return JvSwingUtils.wrapTooltip(true, tt.toString());
}
private String[] columnNames = {
MessageManager.getString("label.feature_type"),
MessageManager.getString("action.colour"),
- MessageManager.getString("label.filter"),
+ MessageManager.getString("label.configuration"),
MessageManager.getString("label.show") };
private Object[][] data;
}
/**
- * Answers the class of the object in column c of the first row of the table
+ * Answers the class of column c of the table
*/
@Override
public Class<?> getColumnClass(int c)
{
- Object v = getValueAt(0, c);
- return v == null ? null : v.getClass();
+ switch (c)
+ {
+ case TYPE_COLUMN:
+ return String.class;
+ case COLOUR_COLUMN:
+ return FeatureColour.class;
+ case FILTER_COLUMN:
+ return FeatureMatcherSet.class;
+ default:
+ return Boolean.class;
+ }
}
+ /**
+ * Answers true for all columns except Feature Type
+ */
@Override
public boolean isCellEditable(int row, int col)
{
- return col == 0 ? false : true;
+ return col != TYPE_COLUMN;
}
+ /**
+ * Sets the value in the model for a given row and column. If Visibility
+ * (Show/Hide) is being set, and the table is in Summary View, then it is
+ * set also on any sub-types of the row's feature type.
+ */
@Override
public void setValueAt(Object value, int row, int col)
{
data[row][col] = value;
fireTableCellUpdated(row, col);
+ if (summaryView.isSelected() && col == SHOW_COLUMN)
+ {
+ setSubtypesVisibility(row, (Boolean) value);
+ }
updateFeatureRenderer(data);
}
+ /**
+ * Sets the visibility of any feature types which are sub-types of the type
+ * in the given row of the table
+ *
+ * @param row
+ * @param value
+ */
+ protected void setSubtypesVisibility(int row, Boolean value)
+ {
+ String type = (String) data[row][TYPE_COLUMN];
+ OntologyI so = SequenceOntologyFactory.getInstance();
+
+ for (int r = 0; r < data.length; r++)
+ {
+ if (r != row)
+ {
+ String type2 = (String) data[r][TYPE_COLUMN];
+ if (so.isA(type2, type))
+ {
+ data[r][SHOW_COLUMN] = value;
+ fireTableCellUpdated(r, SHOW_COLUMN);
+ }
+ }
+ }
+ }
}
class ColorRenderer extends JLabel implements TableCellRenderer
String type;
- JButton button;
+ JButton colourButton;
JColorChooser colorChooser;
// 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);
+ colourButton = new JButton();
+ colourButton.setActionCommand(EDIT);
+ colourButton.addActionListener(this);
+ colourButton.setBorderPainted(false);
// Set up the dialog that the button brings up.
colorChooser = new JColorChooser();
- dialog = JColorChooser.createDialog(button,
+ dialog = JColorChooser.createDialog(colourButton,
MessageManager.getString("label.select_colour"), true, // modal
colorChooser, this, // OK button handler
null); // no CANCEL button handler
if (currentColor.isSimpleColour())
{
// bring up simple color chooser
- button.setBackground(currentColor.getColour());
+ colourButton.setBackground(currentColor.getColour());
colorChooser.setColor(currentColor.getColour());
dialog.setVisible(true);
}
chooser.setRequestFocusEnabled(true);
chooser.requestFocus();
chooser.addActionListener(this);
- chooser.showTab(true);
+ // Make the renderer reappear.
+ fireEditingStopped();
}
- // Make the renderer reappear.
- fireEditingStopped();
-
}
else
{
* (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;
+ refreshTable();
}
fireEditingStopped();
me.table.validate();
currentColor = (FeatureColourI) value;
this.rowSelected = row;
type = me.table.getValueAt(row, TYPE_COLUMN).toString();
- button.setOpaque(true);
- button.setBackground(me.getBackground());
+ colourButton.setOpaque(true);
+ colourButton.setBackground(me.getBackground());
if (!currentColor.isSimpleColour())
{
JLabel btn = new JLabel();
- btn.setSize(button.getSize());
+ btn.setSize(colourButton.getSize());
FeatureSettings.renderGraduatedColor(btn, currentColor);
- button.setBackground(btn.getBackground());
- button.setIcon(btn.getIcon());
- button.setText(btn.getText());
+ colourButton.setBackground(btn.getBackground());
+ colourButton.setIcon(btn.getIcon());
+ colourButton.setText(btn.getText());
}
else
{
- button.setText("");
- button.setIcon(null);
- button.setBackground(currentColor.getColour());
+ colourButton.setText("");
+ colourButton.setIcon(null);
+ colourButton.setBackground(currentColor.getColour());
}
- return button;
+ return colourButton;
}
}
String type;
- JButton button;
+ JButton filterButton;
protected static final String EDIT = "edit";
public FilterEditor(FeatureSettings me)
{
this.me = me;
- button = new JButton();
- button.setActionCommand(EDIT);
- button.addActionListener(this);
- button.setBorderPainted(false);
+ filterButton = new JButton();
+ filterButton.setActionCommand(EDIT);
+ filterButton.addActionListener(this);
+ filterButton.setBorderPainted(false);
}
/**
@Override
public void actionPerformed(ActionEvent e)
{
- if (button == e.getSource())
+ if (filterButton == e.getSource())
{
FeatureTypeSettings chooser = new FeatureTypeSettings(me.fr, type);
chooser.addActionListener(this);
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;
+ refreshTable();
fireEditingStopped();
me.table.validate();
}
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.setIcon(null);
- return button;
+ filterButton.setOpaque(true);
+ filterButton.setBackground(me.getBackground());
+ filterButton.setText(currentFilter.toString());
+ filterButton.setToolTipText(currentFilter.toString());
+ filterButton.setIcon(null);
+ return filterButton;
}
}
}
class FeatureIcon implements Icon
{
+ private static final Font VERDANA_9 = new Font("Verdana", Font.PLAIN, 9);
+
FeatureColourI gcol;
Color backg;
// need an icon here.
g.setColor(gcol.getMaxColour());
- g.setFont(new Font("Verdana", Font.PLAIN, 9));
+ g.setFont(VERDANA_9);
// g.setFont(g.getFont().deriveFont(
// AffineTransform.getScaleInstance(