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.io.gff.SequenceOntologyFactory;
import jalview.schemes.FeatureColour;
import jalview.util.MessageManager;
import jalview.util.Platform;
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.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.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;
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");
*/
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()
{
@Override
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:
default:
break;
}
-
return tip;
}
return loc;
}
};
+
JTableHeader tableHeader = table.getTableHeader();
- tableHeader.setFont(new Font("Verdana", Font.PLAIN, 12));
+ tableHeader.setFont(VERDANA_12);
tableHeader.setReorderingAllowed(false);
- table.setFont(new Font("Verdana", Font.PLAIN, 12));
+ 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);
@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);
data[dataIndex][FILTER_COLUMN] = featureFilter == null
? new FeatureMatcherSet()
: featureFilter;
- data[dataIndex][SHOW_COLUMN] = new Boolean(
+ data[dataIndex][SHOW_COLUMN] = Boolean.valueOf(
af.getViewport().getFeaturesDisplayed().isVisible(type));
dataIndex++;
displayableTypes.remove(type);
data[dataIndex][FILTER_COLUMN] = featureFilter == null
? new FeatureMatcherSet()
: featureFilter;
- data[dataIndex][SHOW_COLUMN] = new Boolean(true);
+ data[dataIndex][SHOW_COLUMN] = Boolean.valueOf(true);
dataIndex++;
displayableTypes.remove(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(
}
});
+ summaryView = new JCheckBox(
+ MessageManager.getString("label.summary_view"));
+ summaryView
+ .setToolTipText(
+ MessageManager.getString("label.group_by_so"));
+ 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
}
/**
- * 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);
}
{
// bring up graduated chooser.
chooser = new FeatureTypeSettings(me.fr, type);
- /**
- * @j2sNative
- */
- {
- chooser.setRequestFocusEnabled(true);
- chooser.requestFocus();
- }
+ chooser.setRequestFocusEnabled(true);
+ chooser.requestFocus();
chooser.addActionListener(this);
// Make the renderer reappear.
fireEditingStopped();
* (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);
}
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(
import jalview.datamodel.features.FeatureMatcherI;
import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
import jalview.schemes.FeatureColour;
import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import java.awt.event.MouseEvent;
import java.text.DecimalFormat;
import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
import javax.swing.BorderFactory;
import javax.swing.BoxLayout;
import javax.swing.JRadioButton;
import javax.swing.JSlider;
import javax.swing.JTextField;
- import javax.swing.SwingConstants;
+ import javax.swing.border.EmptyBorder;
import javax.swing.border.LineBorder;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
- import javax.swing.plaf.basic.BasicArrowButton;
/**
* A dialog where the user can configure colour scheme, and any filters, for one
/*
* the colour and filters to reset to on Cancel
+ * (including feature sub-types if modified)
*/
- private final FeatureColourI originalColour;
+ private Map<String, FeatureColourI> originalColours;
- private final FeatureMatcherSetI originalFilter;
+ private Map<String, FeatureMatcherSetI> originalFilters;
/*
* set flag to true when setting values programmatically,
private JPanel chooseFiltersPanel;
+ /*
+ * the root Sequence Ontology terms (if any) that is a parent of
+ * the current feature type
+ */
+ private String rootSOTerm;
+
+ /*
+ * a map whose keys are Sequence Ontology terms - selected from the
+ * current term and its parents in the SO - whose subterms include
+ * additional feature types; the map entry is the list of additional
+ * feature types that match the key or have it as a parent term; in
+ * other words, distinct 'aggregations' that include the current feature type
+ */
+ private final Map<String, List<String>> relatedSoTerms;
+
+ /*
+ * if true, filter or colour settings are also applied to
+ * any sub-types of parentTerm in the Sequence Ontology
+ */
+ private boolean applyFiltersToSubtypes;
+
+ private boolean applyColourToSubtypes;
+
+ private String parentSOTerm;
+
/**
* Constructor
*
this.fr = frender;
this.featureType = theType;
ap = fr.ap;
- originalFilter = fr.getFeatureFilter(theType);
- originalColour = fr.getFeatureColours().get(theType);
-
+
+ SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ relatedSoTerms = so.findSequenceOntologyGroupings(
+ this.featureType, fr.getRenderOrder());
+
+ /*
+ * save original colours and filters for this feature type,
+ * and any related types, to restore on Cancel
+ */
+ originalFilters = new HashMap<>();
+ originalFilters.put(theType, fr.getFeatureFilter(theType));
+ originalColours = new HashMap<>();
+ originalColours.put(theType, fr.getFeatureColours().get(theType));
+ for (List<String> related : relatedSoTerms.values())
+ {
+ for (String type : related)
+ {
+ originalFilters.put(type, fr.getFeatureFilter(type));
+ originalColours.put(type, fr.getFeatureColours().get(type));
+ }
+ }
+
adjusting = true;
-
+
try
{
initialise();
ex.printStackTrace();
return;
}
-
+
updateColoursTab();
-
+
updateFiltersTab();
-
+
adjusting = false;
-
+
colourChanged(false);
-
+
String title = MessageManager
.formatMessage("label.display_settings_for", new String[]
{ theType });
}
/**
+ * Answers a (possibly empty) map of any Sequence Ontology terms (the current
+ * feature type and its parents) which incorporate additional known feature
+ * types (the map entry).
+ * <p>
+ * For example if {@code stop_gained} and {@code stop_lost} are known feature
+ * types, then SO term {@ nonsynonymous_variant} is the first common parent of
+ * both terms
+ *
+ * @param featureType
+ * the current feature type being configured
+ * @param featureTypes
+ * all known feature types on the alignment
+ * @return
+ */
+ protected static Map<String, List<String>> findSequenceOntologyGroupings(
+ String featureType, List<String> featureTypes)
+ {
+ List<String> sortedTypes = new ArrayList<>(featureTypes);
+ Collections.sort(sortedTypes);
+
+ Map<String, List<String>> parents = new HashMap<>();
+
+ /*
+ * method:
+ * walk up featureType and all of its parents
+ * find other feature types which are subsumed by each term
+ * add each distinct aggregation of included feature types to the map
+ */
+ List<String> candidates = new ArrayList<>();
+ SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ candidates.add(featureType);
+ while (!candidates.isEmpty())
+ {
+ String term = candidates.remove(0);
+ List<String> includedFeatures = new ArrayList<>();
+ for (String type : sortedTypes)
+ {
+ if (!type.equals(featureType) && so.isA(type, term))
+ {
+ includedFeatures.add(type);
+ }
+ }
+ if (!includedFeatures.isEmpty()
+ && !parents.containsValue(includedFeatures))
+ {
+ parents.put(term, includedFeatures);
+ }
+ candidates.addAll(so.getParents(term));
+ }
+
+ return parents;
+ }
+
+ /**
* Configures the widgets on the Colours tab according to the current feature
* colour scheme
*/
* if not set, default max colour to last plain colour,
* and make min colour a pale version of max colour
*/
+ FeatureColourI originalColour = originalColours.get(featureType);
Color max = originalColour.getMaxColour();
if (max == null)
{
MessageManager.getString("action.colour"), true);
/*
+ * option to apply colour to other selected types as well
+ */
+ if (!relatedSoTerms.isEmpty())
+ {
+ applyColourToSubtypes = false;
+ colourByPanel.add(initSubtypesPanel(false));
+ }
+
+ /*
* simple colour radio button and colour picker
*/
JPanel simpleColourPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
singleColour.setFont(JvSwingUtils.getLabelFont());
singleColour.setBorder(BorderFactory.createLineBorder(Color.black));
singleColour.setPreferredSize(new Dimension(40, 20));
- // if (originalColour.isGraduatedColour())
- // {
- // singleColour.setBackground(originalColour.getMaxColour());
- // singleColour.setForeground(originalColour.getMaxColour());
- // }
- // else
- // {
- singleColour.setBackground(originalColour.getColour());
- singleColour.setForeground(originalColour.getColour());
- // }
+ FeatureColourI originalColour = originalColours.get(featureType);
+ singleColour.setBackground(originalColour.getColour());
+ singleColour.setForeground(originalColour.getColour());
+
singleColour.addMouseListener(new MouseAdapter()
{
@Override
return colourByPanel;
}
+ /**
+ * Constructs and returns a panel with the option to apply any changes also to
+ * sub-types of SO terms at or above the feature type
+ *
+ * @return
+ */
+ protected JPanel initSubtypesPanel(final boolean forFilters)
+ {
+ JPanel toSubtypes = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ toSubtypes.setBackground(Color.WHITE);
+
+ /*
+ * checkbox 'apply to sub-types of...'
+ */
+ JCheckBox applyToSubtypesCB = new JCheckBox(MessageManager
+ .formatMessage("label.apply_to_subtypes", rootSOTerm));
+ toSubtypes.add(applyToSubtypesCB);
+ toSubtypes
+ .setToolTipText(MessageManager.getString("label.group_by_so"));
+
+ /*
+ * combobox to choose 'parent' of sub-types
+ */
+ List<String> soTerms = new ArrayList<>();
+ for (String term : relatedSoTerms.keySet())
+ {
+ soTerms.add(term);
+ }
+ // sort from most restrictive to most inclusive
+ Collections.sort(soTerms, new Comparator<String>()
+ {
+ @Override
+ public int compare(String o1, String o2)
+ {
+ return Integer.compare(relatedSoTerms.get(o1).size(),
+ relatedSoTerms.get(o2).size());
+ }
+ });
+ List<String> tooltips = new ArrayList<>();
+ for (String term : soTerms)
+ {
+ tooltips.add(getSOTermsTooltip(relatedSoTerms.get(term)));
+ }
+ JComboBox<String> parentType = JvSwingUtils
+ .buildComboWithTooltips(soTerms, tooltips);
+ toSubtypes.add(parentType);
+
+ /*
+ * on toggle of checkbox, or change of parent SO term,
+ * reset and then reapply filters to the selected scope
+ */
+ final ActionListener action = new ActionListener()
+ {
+ /*
+ * reset and reapply settings on toggle of checkbox
+ */
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ parentSOTerm = (String) parentType.getSelectedItem();
+ if (forFilters)
+ {
+ applyFiltersToSubtypes = applyToSubtypesCB.isSelected();
+ restoreOriginalFilters();
+ filtersChanged();
+ }
+ else
+ {
+ applyColourToSubtypes = applyToSubtypesCB.isSelected();
+ restoreOriginalColours();
+ colourChanged(true);
+ }
+ }
+ };
+ applyToSubtypesCB.addActionListener(action);
+ parentType.addActionListener(action);
+
+ return toSubtypes;
+ }
+
private void showColourChooser(JPanel colourPanel, String key)
{
Color col = JColorChooser.showDialog(this,
FeatureColourI acg = makeColourFromInputs();
/*
- * save the colour, and repaint stuff
+ * save the colour, and set on subtypes if selected
*/
fr.setColour(featureType, acg);
+ if (applyColourToSubtypes)
+ {
+ for (String child : relatedSoTerms.get(parentSOTerm))
+ {
+ fr.setColour(child, acg);
+ }
+ }
+ refreshFeatureSettings();
ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
updateColoursTab();
@Override
protected void raiseClosed()
{
+ refreshFeatureSettings();
+ }
+
+ protected void refreshFeatureSettings()
+ {
if (this.featureSettings != null)
{
- featureSettings.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
+ featureSettings.actionPerformed(new ActionEvent(this, 0, "REFRESH"));
}
}
/**
* Action on Cancel is to restore colour scheme and filters as they were when
- * the dialog was opened
+ * the dialog was opened (including any feature sub-types that may have been
+ * changed)
*/
@Override
public void cancelPressed()
{
- fr.setColour(featureType, originalColour);
- fr.setFeatureFilter(featureType, originalFilter);
+ restoreOriginalColours();
+ restoreOriginalFilters();
ap.paintAlignment(true, true);
}
/**
+ * Restores filters for all feature types to their values when the dialog was
+ * opened
+ */
+ protected void restoreOriginalFilters()
+ {
+ for (Entry<String, FeatureMatcherSetI> entry : originalFilters
+ .entrySet())
+ {
+ fr.setFeatureFilter(entry.getKey(), entry.getValue());
+ }
+ }
+
+ /**
+ * Restores colours for all feature types to their values when the dialog was
+ * opened
+ */
+ protected void restoreOriginalColours()
+ {
+ for (Entry<String, FeatureColourI> entry : originalColours.entrySet())
+ {
+ fr.setColour(entry.getKey(), entry.getValue());
+ }
+ }
+
+ /**
* Action on text entry of a threshold value
*/
protected void thresholdValue_actionPerformed()
*/
adjusting = true;
float f = Float.parseFloat(thresholdValue.getText());
- f = Float.max(f, this.min);
+ f = Float.max(f, this.min);
f = Float.min(f, this.max);
thresholdValue.setText(String.valueOf(f));
slider.setValue((int) (f * scaleFactor));
{
filters = new ArrayList<>();
+ JPanel outerPanel = new JPanel();
+ outerPanel.setLayout(new BoxLayout(outerPanel, BoxLayout.Y_AXIS));
+ outerPanel.setBackground(Color.white);
+
+ /*
+ * option to apply colour to other selected types as well
+ */
+ if (!relatedSoTerms.isEmpty())
+ {
+ applyFiltersToSubtypes = false;
+ outerPanel.add(initSubtypesPanel(true));
+ }
+
JPanel filtersPanel = new JPanel();
filtersPanel.setLayout(new BoxLayout(filtersPanel, BoxLayout.Y_AXIS));
filtersPanel.setBackground(Color.white);
JvSwingUtils.createTitledBorder(filtersPanel,
MessageManager.getString("label.filters"), true);
+ outerPanel.add(filtersPanel);
JPanel andOrPanel = initialiseAndOrPanel();
filtersPanel.add(andOrPanel);
chooseFiltersPanel.setBackground(Color.white);
filtersPanel.add(chooseFiltersPanel);
- return filtersPanel;
+ return outerPanel;
}
/**
*/
private JPanel initialiseAndOrPanel()
{
- JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ JPanel andOrPanel = new JPanel(new BorderLayout());
andOrPanel.setBackground(Color.white);
+
andFilters = new JRadioButton(MessageManager.getString("label.and"));
orFilters = new JRadioButton(MessageManager.getString("label.or"));
ActionListener actionListener = new ActionListener()
new JLabel(MessageManager.getString("label.join_conditions")));
andOrPanel.add(andFilters);
andOrPanel.add(orFilters);
+
return andOrPanel;
}
/**
+ * Builds a tooltip for the 'Apply also to...' combobox with a list of known
+ * feature types (excluding the current type) which are sub-types of the
+ * selected Sequence Ontology term
+ *
+ * @param
+ * @return
+ */
+ protected String getSOTermsTooltip(List<String> list)
+ {
+ StringBuilder sb = new StringBuilder(20 * relatedSoTerms.size());
+ sb.append(MessageManager.getString("label.apply_also_to"));
+ for (String child : list)
+ {
+ sb.append("<br>").append(child);
+ }
+ String tooltip = JvSwingUtils.wrapTooltip(true, sb.toString());
+ return tooltip;
+ }
+
+ /**
* 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 after a filter has been
if (!patternField.isEnabled()
|| (pattern != null && pattern.trim().length() > 0))
{
- // todo: gif for button drawing '-' or 'x'
- JButton removeCondition = new BasicArrowButton(SwingConstants.WEST);
- removeCondition
- .setToolTipText(MessageManager.getString("label.delete_row"));
+ JButton removeCondition = new JButton("\u2717"); // Dingbats cursive x
+ removeCondition.setToolTipText(
+ MessageManager.getString("label.delete_condition"));
+ removeCondition.setBorder(new EmptyBorder(0, 0, 0, 0));
removeCondition.addActionListener(new ActionListener()
{
@Override
* (note this might now be an empty filter with no conditions)
*/
fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
+ if (applyFiltersToSubtypes)
+ {
+ for (String child : relatedSoTerms.get(parentSOTerm))
+ {
+ fr.setFeatureFilter(child, combined.isEmpty() ? null : combined);
+ }
+ }
+
+ refreshFeatureSettings();
ap.paintAlignment(true, true);
updateFiltersTab();
git://source.jalview.org / jalview.git / commitdiff