*/
package jalview.gui;
-import jalview.api.FeatureColourI;
-import jalview.api.FeatureSettingsControllerI;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.FeatureMatcher;
-import jalview.datamodel.features.FeatureMatcherI;
-import jalview.datamodel.features.FeatureMatcherSet;
-import jalview.datamodel.features.FeatureMatcherSetI;
-import jalview.gui.Help.HelpId;
-import jalview.gui.JalviewColourChooser.ColourChooserListener;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-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.util.Locale;
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 javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamReader;
+import jalview.api.AlignViewControllerGuiI;
+import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
+import jalview.api.FeatureSettingsControllerI;
+import jalview.api.SplitContainerI;
+import jalview.api.ViewStyleI;
+import jalview.controller.FeatureSettingsControllerGuiI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcher;
+import jalview.datamodel.features.FeatureMatcherI;
+import jalview.datamodel.features.FeatureMatcherSet;
+import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.gui.Help.HelpId;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.schemes.FeatureColour;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
+import jalview.viewmodel.styles.ViewStyle;
+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;
+
public class FeatureSettings extends JPanel
- implements FeatureSettingsControllerI
+ implements FeatureSettingsControllerI, FeatureSettingsControllerGuiI
{
private static final String SEQUENCE_FEATURE_COLOURS = MessageManager
.getString("label.sequence_feature_colours");
*/
Object[][] originalData;
- float originalTransparency;
+ private float originalTransparency;
+
+ private ViewStyleI originalViewStyle;
- Map<String, FeatureMatcherSetI> originalFilters;
+ private Map<String, FeatureMatcherSetI> originalFilters;
final JInternalFrame frame;
JSlider transparency = new JSlider();
+ private JCheckBox showComplementOnTop;
+
+ private JCheckBox showComplement;
+
/*
* when true, constructor is still executing - so ignore UI events
*/
/*
* true when Feature Settings are updating from feature renderer
*/
- boolean handlingUpdate = false;
+ private boolean handlingUpdate = false;
+
+ /*
+ * a change listener to ensure the dialog is updated if
+ * FeatureRenderer discovers new features
+ */
+ private PropertyChangeListener change;
/*
* holds {featureCount, totalExtent} for each feature type
*/
Map<String, float[]> typeWidth = null;
+ private void storeOriginalSettings()
+ {
+ // save transparency for restore on Cancel
+ originalTransparency = fr.getTransparency();
+
+ updateTransparencySliderFromFR();
+
+ originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy
+ originalViewStyle = new ViewStyle(af.viewport.getViewStyle());
+ }
+
+ private void updateTransparencySliderFromFR()
+ {
+ boolean incon = inConstruction;
+ inConstruction = true;
+
+ int transparencyAsPercent = (int) (fr.getTransparency() * 100);
+ transparency.setValue(100 - transparencyAsPercent);
+ inConstruction = incon;
+ }
+
/**
* Constructor
*
this.af = alignFrame;
fr = af.getFeatureRenderer();
- // save transparency for restore on Cancel
- originalTransparency = fr.getTransparency();
- int originalTransparencyAsPercent = (int) (originalTransparency * 100);
- transparency.setMaximum(100 - originalTransparencyAsPercent);
-
- originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy
+ storeOriginalSettings();
try
{
@Override
public void mousePressed(MouseEvent evt)
{
- selectedRow = table.rowAtPoint(evt.getPoint());
+ Point pt = evt.getPoint();
+ selectedRow = table.rowAtPoint(pt);
String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN);
if (evt.isPopupTrigger())
{
Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
showPopupMenu(selectedRow, type, colour, evt.getPoint());
}
- else if (evt.getClickCount() == 2)
+ else if (evt.getClickCount() == 2
+ && table.columnAtPoint(pt) == TYPE_COLUMN)
{
boolean invertSelection = evt.isAltDown();
boolean toggleSelection = Platform.isControlDown(evt);
boolean extendSelection = evt.isShiftDown();
fr.ap.alignFrame.avc.markColumnsContainingFeatures(
invertSelection, extendSelection, toggleSelection, type);
+ fr.ap.av.sendSelection();
}
}
}
discoverAllFeatureData();
- final PropertyChangeListener change;
final FeatureSettings fs = this;
fr.addPropertyChangeListener(change = new PropertyChangeListener()
{
});
- frame = new JInternalFrame();
- frame.setContentPane(this);
- Desktop.addInternalFrame(frame,
- MessageManager.getString("label.sequence_feature_settings"),
- 600, Platform.isAMacAndNotJS() ? 480 : 450);
- frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
+ SplitContainerI splitframe = af.getSplitViewContainer();
+ if (splitframe != null)
+ {
+ frame = null; // keeps eclipse happy
+ splitframe.addFeatureSettingsUI(this);
+ }
+ else
+ {
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ Rectangle bounds = af.getFeatureSettingsGeometry();
+ String title;
+ if (af.getAlignPanels().size() > 1 || Desktop.getAlignmentPanels(
+ af.alignPanel.av.getSequenceSetId()).length > 1)
+ {
+ title = MessageManager.formatMessage(
+ "label.sequence_feature_settings_for_view",
+ af.alignPanel.getViewName());
+ }
+ else
+ {
+ title = MessageManager.getString("label.sequence_feature_settings");
+ }
+ if (bounds == null)
+ {
+ if (Platform.isAMacAndNotJS())
+ {
+ Desktop.addInternalFrame(frame, title, 600, 480);
+ }
+ else
+ {
+ Desktop.addInternalFrame(frame, title, 600, 450);
+ }
+ }
+ else
+ {
+ Desktop.addInternalFrame(frame, title, false, bounds.width,
+ bounds.height);
+ frame.setBounds(bounds);
+ frame.setVisible(true);
+ }
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
- frame.addInternalFrameListener(
- new javax.swing.event.InternalFrameAdapter()
- {
- @Override
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
+ frame.addInternalFrameListener(
+ new javax.swing.event.InternalFrameAdapter()
{
- fr.removePropertyChangeListener(change);
- };
- });
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ @Override
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ featureSettings_isClosed();
+ };
+ });
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ }
inConstruction = false;
}
/**
+ * Sets the state of buttons to show complement features from viewport
+ * settings
+ */
+ private void updateComplementButtons()
+ {
+ showComplement.setSelected(af.getViewport().isShowComplementFeatures());
+ showComplementOnTop
+ .setSelected(af.getViewport().isShowComplementFeaturesOnTop());
+ }
+
+ @Override
+ public AlignViewControllerGuiI getAlignframe()
+ {
+ return af;
+ }
+
+ @Override
+ public void featureSettings_isClosed()
+ {
+ fr.removePropertyChangeListener(change);
+ change = null;
+ }
+
+ /**
* Constructs and shows a popup menu of possible actions on the selected row
* and feature type
*
JPopupMenu men = new JPopupMenu(MessageManager
.formatMessage("label.settings_for_param", new String[]
{ type }));
- final FeatureColourI featureColour = (FeatureColourI) typeCol;
-
- /*
- * menu option to select (or deselect) variable colour
- */
- final JCheckBoxMenuItem variableColourCB = new JCheckBoxMenuItem(
- MessageManager.getString("label.variable_colour"));
- variableColourCB.setSelected(!featureColour.isSimpleColour());
- men.add(variableColourCB);
-
- /*
- * checkbox action listener doubles up as listener to OK
- * from the variable colour / filters dialog
- */
- variableColourCB.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- if (e.getSource() == variableColourCB)
- {
- men.setVisible(true); // BH 2018 for JavaScript because this is a
- // checkbox
- men.setVisible(false); // BH 2018 for JavaScript because this is a
- // checkbox
- if (featureColour.isSimpleColour())
- {
- /*
- * toggle simple colour to variable colour - show dialog
- */
- FeatureTypeSettings fc = new FeatureTypeSettings(fr, type);
- fc.addActionListener(this);
- }
- else
- {
- /*
- * toggle variable to simple colour - show colour chooser
- */
- String title = MessageManager
- .formatMessage("label.select_colour_for", type);
- ColourChooserListener listener = new ColourChooserListener()
- {
- @Override
- public void colourSelected(Color c)
- {
- table.setValueAt(new FeatureColour(c), rowSelected,
- COLOUR_COLUMN);
- table.validate();
- updateFeatureRenderer(
- ((FeatureTableModel) table.getModel()).getData(),
- false);
- }
- };
- JalviewColourChooser.showColourChooser(FeatureSettings.this,
- title, featureColour.getMaxColour(), listener);
- }
- }
- 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, COLOUR_COLUMN);
- // BH 2018 setting a table value does not invalidate it.
- // System.out.println("FeatureSettings is valied" +
- // table.validate();
- }
- }
- }
- });
-
- men.addSeparator();
JMenuItem scr = new JMenuItem(
MessageManager.getString("label.sort_by_score"));
men.add(scr);
scr.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
- af.avc.sortAlignmentByFeatureScore(Arrays.asList(new String[]
- { type }));
+ sortByScore(Arrays.asList(new String[] { type }));
}
});
JMenuItem dens = new JMenuItem(
MessageManager.getString("label.sort_by_density"));
dens.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
- af.avc.sortAlignmentByFeatureDensity(Arrays.asList(new String[]
- { type }));
+ sortByDensity(Arrays.asList(new String[] { type }));
}
});
men.add(dens);
{
fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
false, type);
+ fr.ap.av.sendSelection();
}
});
JMenuItem clearCols = new JMenuItem(MessageManager
{
fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
false, type);
+ fr.ap.av.sendSelection();
}
});
JMenuItem hideCols = new JMenuItem(
public void actionPerformed(ActionEvent arg0)
{
fr.ap.alignFrame.hideFeatureColumns(type, true);
+ fr.ap.av.sendSelection();
}
});
JMenuItem hideOtherCols = new JMenuItem(
public void actionPerformed(ActionEvent arg0)
{
fr.ap.alignFrame.hideFeatureColumns(type, false);
+ fr.ap.av.sendSelection();
}
});
men.add(selCols);
men.show(table, pt.x, pt.y);
}
+ /**
+ * Sort the sequences in the alignment by the number of features for the given
+ * feature types (or all features if null)
+ *
+ * @param featureTypes
+ */
+ protected void sortByDensity(List<String> featureTypes)
+ {
+ af.avc.sortAlignmentByFeatureDensity(featureTypes);
+ }
+
+ /**
+ * Sort the sequences in the alignment by average score for the given feature
+ * types (or all features if null)
+ *
+ * @param featureTypes
+ */
+ protected void sortByScore(List<String> featureTypes)
+ {
+ af.avc.sortAlignmentByFeatureScore(featureTypes);
+ }
+
+ /**
+ * Returns true if at least one feature type is visible. Else shows a warning
+ * dialog and returns false.
+ *
+ * @param title
+ * @return
+ */
+ private boolean canSortBy(String title)
+ {
+ if (fr.getDisplayedFeatureTypes().isEmpty())
+ {
+ JvOptionPane.showMessageDialog(this,
+ MessageManager.getString("label.no_features_to_sort_by"),
+ title, JvOptionPane.OK_OPTION);
+ return false;
+ }
+ return true;
+ }
+
@Override
synchronized public void discoverAllFeatureData()
{
{
fr.setGroupVisibility(check.getText(), check.isSelected());
resetTable(new String[] { grp });
- af.alignPanel.paintAlignment(true, true);
+ refreshDisplay();
}
});
groupPanel.add(check);
table.repaint();
}
+ /**
+ * close ourselves but leave any existing UI handlers (e.g a CDS/Protein
+ * tabbed feature settings dialog) intact
+ */
+ public void closeOldSettings()
+ {
+ closeDialog(false);
+ }
+
+ /**
+ * close the feature settings dialog (and any containing frame)
+ */
public void close()
{
+ closeDialog(true);
+ }
+
+ private void closeDialog(boolean closeContainingFrame)
+ {
try
{
- frame.setClosed(true);
+ if (frame != null)
+ {
+ af.setFeatureSettingsGeometry(frame.getBounds());
+ frame.setClosed(true);
+ }
+ else
+ {
+ SplitContainerI sc = af.getSplitViewContainer();
+ sc.closeFeatureSettings(this, closeContainingFrame);
+ af.featureSettings = null;
+ }
} catch (Exception exe)
{
}
if (fr.setFeaturePriority(rowData, visibleNew))
{
- af.alignPanel.paintAlignment(true, true);
+ refreshDisplay();
}
}
{
this.setLayout(new BorderLayout());
+ final boolean hasComplement = af.getViewport()
+ .getCodingComplement() != null;
+
JPanel settingsPane = new JPanel();
settingsPane.setLayout(new BorderLayout());
}
});
- JButton sortByScore = new JButton(
- MessageManager.getString("label.seq_sort_by_score"));
+ final String byScoreLabel = MessageManager
+ .getString("label.seq_sort_by_score");
+ JButton sortByScore = new JButton(byScoreLabel);
sortByScore.setFont(JvSwingUtils.getLabelFont());
sortByScore.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- af.avc.sortAlignmentByFeatureScore(null);
+ if (canSortBy(byScoreLabel))
+ {
+ sortByScore(null);
+ }
}
});
- JButton sortByDens = new JButton(
- MessageManager.getString("label.sequence_sort_by_density"));
+ final String byDensityLabel = MessageManager
+ .getString("label.sequence_sort_by_density");
+ JButton sortByDens = new JButton(byDensityLabel);
sortByDens.setFont(JvSwingUtils.getLabelFont());
sortByDens.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- af.avc.sortAlignmentByFeatureDensity(null);
+ if (canSortBy(byDensityLabel))
+ {
+ sortByDensity(null);
+ }
}
});
}
}
});
-
- JButton cancel = new JButton(MessageManager.getString("action.cancel"));
+ // Cancel for a SplitFrame should just revert changes to the currently
+ // displayed
+ // settings. May want to do this for either or both - so need a splitview
+ // feature settings cancel/OK.
+ JButton cancel = new JButton(MessageManager
+ .getString(hasComplement ? "action.revert" : "action.cancel"));
+ cancel.setToolTipText(MessageManager.getString(hasComplement
+ ? "action.undo_changes_to_feature_settings"
+ : "action.undo_changes_to_feature_settings_and_close_the_dialog"));
cancel.setFont(JvSwingUtils.getLabelFont());
+ // TODO: disable cancel (and apply!) until current settings are different
cancel.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- fr.setTransparency(originalTransparency);
- fr.setFeatureFilters(originalFilters);
- updateFeatureRenderer(originalData);
- close();
+ revert();
+ refreshDisplay();
+ if (!hasComplement)
+ {
+ close();
+ }
}
});
-
- JButton ok = new JButton(MessageManager.getString("action.ok"));
+ // Cancel for the whole dialog should cancel both CDS and Protein.
+ // OK for an individual feature settings just applies changes, but dialog
+ // remains open
+ JButton ok = new JButton(MessageManager
+ .getString(hasComplement ? "action.apply" : "action.ok"));
ok.setFont(JvSwingUtils.getLabelFont());
ok.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- close();
+ if (!hasComplement)
+ {
+ close();
+ }
+ else
+ {
+ storeOriginalSettings();
+ }
}
});
if (!inConstruction)
{
fr.setTransparency((100 - transparency.getValue()) / 100f);
- af.alignPanel.paintAlignment(true, true);
+ refreshDisplay();
}
}
});
transparency.setToolTipText(
MessageManager.getString("label.transparency_tip"));
- JPanel transPanel = new JPanel(new GridLayout(1, 2));
- bigPanel.add(transPanel, BorderLayout.SOUTH);
+ boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
+ String text = MessageManager
+ .formatMessage("label.show_linked_features",
+ nucleotide
+ ? MessageManager.getString("label.protein")
+ .toLowerCase(Locale.ROOT)
+ : "CDS");
+ showComplement = new JCheckBox(text);
+ showComplement.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ af.getViewport()
+ .setShowComplementFeatures(showComplement.isSelected());
+ refreshDisplay();
+ }
+ });
+
+ showComplementOnTop = new JCheckBox(
+ MessageManager.getString("label.on_top"));
+ showComplementOnTop.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ af.getViewport().setShowComplementFeaturesOnTop(
+ showComplementOnTop.isSelected());
+ refreshDisplay();
+ }
+ });
+
+ updateComplementButtons();
+
+ 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);
- transPanel.add(transparency);
- transPanel.add(transbuttons);
+
+ JPanel transPanelLeft = new JPanel(
+ new GridLayout(hasComplement ? 4 : 2, 1));
+ transPanelLeft.add(new JLabel(" Colour transparency" + ":"));
+ transPanelLeft.add(transparency);
+ if (hasComplement)
+ {
+ JPanel cp = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ cp.add(showComplement);
+ cp.add(showComplementOnTop);
+ transPanelLeft.add(cp);
+ }
+ lowerPanel.add(transPanelLeft);
+ lowerPanel.add(transbuttons);
JPanel buttonPanel = new JPanel();
buttonPanel.add(ok);
}
/**
+ * Repaints alignment, structure and overview (if shown). If there is a
+ * complementary view which is showing this view's features, then also
+ * repaints that.
+ */
+ void refreshDisplay()
+ {
+ af.alignPanel.paintAlignment(true, true);
+ AlignViewportI complement = af.getViewport().getCodingComplement();
+ if (complement != null && complement.isShowComplementFeatures())
+ {
+ AlignFrame af2 = Desktop.getAlignFrameFor(complement);
+ af2.alignPanel.paintAlignment(true, true);
+ }
+ }
+
+ /**
* 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;
+ }
}
@Override
return button;
}
}
+
+ public boolean isOpen()
+ {
+ if (af.getSplitViewContainer() != null)
+ {
+ return af.getSplitViewContainer().isFeatureSettingsOpen();
+ }
+ return frame != null && !frame.isClosed();
+ }
+
+ @Override
+ public void revert()
+ {
+ fr.setTransparency(originalTransparency);
+ fr.setFeatureFilters(originalFilters);
+ updateFeatureRenderer(originalData);
+ af.getViewport().setViewStyle(originalViewStyle);
+ updateTransparencySliderFromFR();
+ updateComplementButtons();
+ refreshDisplay();
+ }
}
class FeatureIcon implements Icon
git://source.jalview.org / jalview.git / blobdiff