*/
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.schemabinding.version2.Filter;
-import jalview.schemabinding.version2.JalviewUserColours;
-import jalview.schemabinding.version2.MatcherSet;
-import jalview.schemes.FeatureColour;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
+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.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.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
+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");
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;
*/
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
*/
int selectedRow = -1;
- JButton fetchDAS = new JButton();
-
- JButton saveDAS = new JButton();
-
- JButton cancelDAS = new JButton();
-
boolean resettingTable = false;
/*
* 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
{
table = new JTable()
{
- static final String tt = "Click to edit, right-click for menu"; // todo i18n
-
@Override
public String getToolTipText(MouseEvent e)
{
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:
break;
}
+
return tip;
}
return loc;
}
};
- table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
+ JTableHeader tableHeader = table.getTableHeader();
+ tableHeader.setFont(new Font("Verdana", Font.PLAIN, 12));
+ tableHeader.setReorderingAllowed(false);
table.setFont(new Font("Verdana", Font.PLAIN, 12));
ToolTipManager.sharedInstance().registerComponent(table);
-
- // table.setDefaultRenderer(Color.class, new ColorRenderer());
- // table.setDefaultEditor(Color.class, new ColorEditor(this));
- //
- table.setDefaultEditor(FeatureColour.class, new ColorEditor(this));
+ table.setDefaultEditor(FeatureColour.class, new ColorEditor());
table.setDefaultRenderer(FeatureColour.class, new ColorRenderer());
- table.setDefaultEditor(FeatureMatcherSet.class, new FilterEditor(this));
+ table.setDefaultEditor(FeatureMatcherSet.class, new FilterEditor());
table.setDefaultRenderer(FeatureMatcherSet.class, new FilterRenderer());
-
+
TableColumn colourColumn = new TableColumn(COLOUR_COLUMN, 75,
- new ColorRenderer(), new ColorEditor(this));
+ new ColorRenderer(), new ColorEditor());
table.addColumn(colourColumn);
TableColumn filterColumn = new TableColumn(FILTER_COLUMN, 75,
- new FilterRenderer(), new FilterEditor(this));
+ new FilterRenderer(), new FilterEditor());
table.addColumn(filterColumn);
table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
@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);
- popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(),
- evt.getY());
+ 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();
}
}
{
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());
+ showPopupMenu(selectedRow, type, colour, evt.getPoint());
}
}
});
}
discoverAllFeatureData();
- final PropertyChangeListener change;
final FeatureSettings fs = this;
fr.addPropertyChangeListener(change = new PropertyChangeListener()
{
});
- frame = new JInternalFrame();
- frame.setContentPane(this);
- if (Platform.isAMac())
+ SplitContainerI splitframe = af.getSplitViewContainer();
+ if (splitframe != null)
{
- Desktop.addInternalFrame(frame,
- MessageManager.getString("label.sequence_feature_settings"),
- 600, 480);
+ frame = null; // keeps eclipse happy
+ splitframe.addFeatureSettingsUI(this);
}
else
{
- Desktop.addInternalFrame(frame,
- MessageManager.getString("label.sequence_feature_settings"),
- 600, 450);
- }
- frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
+ 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;
}
- protected void popupSort(final int rowSelected, final String type,
- final Object typeCol, final Map<String, float[][]> minmax, int x,
- int y)
+ /**
+ * Sets the state of buttons to show complement features from viewport
+ * settings
+ */
+ private void updateComplementButtons()
{
- final FeatureColourI featureColour = (FeatureColourI) typeCol;
+ 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
+ *
+ * @param rowSelected
+ * @param type
+ * @param typeCol
+ * @param pt
+ */
+ protected void showPopupMenu(final int rowSelected, final String type,
+ final Object typeCol, final Point pt)
+ {
JPopupMenu men = new JPopupMenu(MessageManager
.formatMessage("label.settings_for_param", new String[]
{ type }));
+
JMenuItem scr = new JMenuItem(
MessageManager.getString("label.sort_by_score"));
men.add(scr);
- final FeatureSettings me = this;
scr.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
- me.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)
{
- me.af.avc
- .sortAlignmentByFeatureDensity(Arrays.asList(new String[]
- { type }));
+ sortByDensity(Arrays.asList(new String[] { type }));
}
-
});
men.add(dens);
- /*
- * variable colour options include colour by label, by score,
- * by selected attribute text, or attribute value
- */
- 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)
- {
- if (featureColour.isSimpleColour())
- {
- /*
- * toggle simple colour to variable colour - show dialog
- */
- FeatureTypeSettings fc = new FeatureTypeSettings(me.fr, type);
- fc.addActionListener(this);
- }
- else
- {
- /*
- * toggle variable to simple colour - show colour chooser
- */
- String title = MessageManager.getString("label.select_colour");
- ColourChooserListener listener = new ColourChooserListener()
- {
- @Override
- public void colourSelected(Color c)
- {
- table.setValueAt(new FeatureColour(c), rowSelected,
- COLOUR_COLUMN);
- table.validate();
- me.updateFeatureRenderer(
- ((FeatureTableModel) table.getModel()).getData(),
- false);
- }
- };
- JalviewColourChooser.showColourChooser(me, 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);
- table.validate();
- }
- }
- }
-
- });
-
JMenuItem selCols = new JMenuItem(
MessageManager.getString("label.select_columns_containing"));
selCols.addActionListener(new ActionListener()
{
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.add(clearCols);
men.add(hideCols);
men.add(hideOtherCols);
- men.show(table, x, y);
+ 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
{
fr.setGroupVisibility(check.getText(), check.isSelected());
resetTable(new String[] { grp });
- af.alignPanel.paintAlignment(true, true);
+ refreshDisplay();
}
});
groupPanel.add(check);
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);
}
}
/**
- * 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>
/**
* 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
*/
*/
void load()
{
- // TODO: JAL-3048 relies on Castor XML parsing: not needed for JS-jalview core
- // functionalty
-
JalviewFileChooser chooser = new JalviewFileChooser("fc",
SEQUENCE_FEATURE_COLOURS);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.load_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.load"));
-
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ chooser.setResponseHandler(0, new Runnable()
{
- File file = chooser.getSelectedFile();
- load(file);
- }
+ @Override
+ public void run()
+ {
+ File file = chooser.getSelectedFile();
+ load(file);
+ }
+ });
+ chooser.showOpenDialog(this);
}
/**
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);
if (table != null)
{
resetTable(null);
- Object[][] data = ((FeatureTableModel) table.getModel())
- .getData();
+ Object[][] data = ((FeatureTableModel) table.getModel()).getData();
ensureOrder(data);
updateFeatureRenderer(data, false);
table.repaint();
*/
void save()
{
- // TODO: JAL-3048 not needed for Jalview-JS - save colours
JalviewFileChooser chooser = new JalviewFileChooser("fc",
SEQUENCE_FEATURE_COLOURS);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.save_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.save"));
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ int option = chooser.showSaveDialog(this);
+ if (option == JalviewFileChooser.APPROVE_OPTION)
{
- save(chooser.getSelectedFile());
+ File file = chooser.getSelectedFile();
+ save(file);
}
}
ucs.setSchemeName("Sequence Features");
try
{
- PrintWriter out = new PrintWriter(new OutputStreamWriter(
- new FileOutputStream(file), "UTF-8"));
+ PrintWriter out = new PrintWriter(
+ new OutputStreamWriter(new FileOutputStream(file), "UTF-8"));
/*
* sort feature types by colour order, from 0 (highest)
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);
}
/*
FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
if (filter != null && !filter.isEmpty())
{
- Iterator<FeatureMatcherI> iterator = filter.getMatchers().iterator();
+ Iterator<FeatureMatcherI> iterator = filter.getMatchers()
+ .iterator();
FeatureMatcherI firstMatcher = iterator.next();
- MatcherSet ms = Jalview2XML.marshalFilter(firstMatcher, iterator,
- filter.isAnded());
+ 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)
{
else
{
width[i] /= max; // normalize
- fr.setOrder(data[i][TYPE_COLUMN].toString(), width[i]); // store for later
+ fr.setOrder(data[i][TYPE_COLUMN].toString(), width[i]); // store for
+ // later
}
if (i > 0)
{
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)
{
}
}
/**
- * 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
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);
- }
- });
-
- JButton help = new JButton(MessageManager.getString("action.help"));
- help.setFont(JvSwingUtils.getLabelFont());
- help.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- try
- {
- Help.showHelpWindow(HelpId.SequenceFeatureSettings);
- } catch (HelpSetException e1)
+ if (canSortBy(byDensityLabel))
{
- e1.printStackTrace();
+ sortByDensity(null);
}
}
});
+
+ JButton help = new JButton(MessageManager.getString("action.help"));
help.setFont(JvSwingUtils.getLabelFont());
- help.setText(MessageManager.getString("action.help"));
help.addActionListener(new ActionListener()
{
@Override
}
}
});
-
- 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
{
boolean thr = false;
StringBuilder tx = new StringBuilder();
-
+
if (gcol.isColourByAttribute())
{
tx.append(FeatureMatcher
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;
+ }
}
@Override
renderGraduatedColor(comp, gcol, w, h);
}
+ @SuppressWarnings("serial")
class ColorEditor extends AbstractCellEditor
implements TableCellEditor, ActionListener
{
- FeatureSettings me;
-
FeatureColourI currentColor;
FeatureTypeSettings chooser;
int rowSelected = 0;
- public ColorEditor(FeatureSettings fs)
+ public ColorEditor()
{
- this.me = fs;
// Set up the editor (from the table's point of view),
// which is a button.
// This button brings up the color chooser dialog,
/*
* simple colour chooser
*/
- String ttl = MessageManager.getString("label.select_colour");
- ColourChooserListener listener = new ColourChooserListener() {
+ String ttl = MessageManager
+ .formatMessage("label.select_colour_for", type);
+ ColourChooserListener listener = new ColourChooserListener()
+ {
@Override
public void colourSelected(Color c)
{
currentColor = new FeatureColour(c);
- me.table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN);
+ table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN);
+ fireEditingStopped();
+ }
+
+ @Override
+ public void cancel()
+ {
+ fireEditingStopped();
}
};
- JalviewColourChooser.showColourChooser(button, ttl, currentColor.getColour(), listener);
+ JalviewColourChooser.showColourChooser(button, ttl,
+ currentColor.getColour(), listener);
}
else
{
/*
* variable colour and filters dialog
*/
- chooser = new FeatureTypeSettings(me.fr, type);
+ chooser = new FeatureTypeSettings(fr, type);
+ if (!Platform.isJS())
/**
- * @j2sNative
+ * Java only
+ *
+ * @j2sIgnore
*/
{
chooser.setRequestFocusEnabled(true);
chooser.requestFocus();
}
chooser.addActionListener(this);
- // Make the renderer reappear.
fireEditingStopped();
}
}
* update table data without triggering updateFeatureRenderer
*/
currentColor = fr.getFeatureColours().get(type);
- FeatureMatcherSetI currentFilter = me.fr.getFeatureFilter(type);
+ FeatureMatcherSetI currentFilter = fr.getFeatureFilter(type);
if (currentFilter == null)
{
currentFilter = new FeatureMatcherSet();
.getData()[rowSelected];
data[COLOUR_COLUMN] = currentColor;
data[FILTER_COLUMN] = currentFilter;
-
fireEditingStopped();
- me.table.validate();
+ // SwingJS needs an explicit repaint() here,
+ // rather than relying upon no validation having
+ // occurred since the stopEditing call was made.
+ // Its laying out has not been stopped by the modal frame
+ table.validate();
+ table.repaint();
}
}
+ /**
+ * Override allows access to this method from anonymous inner classes
+ */
+ @Override
+ protected void fireEditingStopped()
+ {
+ super.fireEditingStopped();
+ }
+
// Implement the one CellEditor method that AbstractCellEditor doesn't.
@Override
public Object getCellEditorValue()
// Implement the one method defined by TableCellEditor.
@Override
- public Component getTableCellEditorComponent(JTable theTable, Object value,
- boolean isSelected, int row, int column)
+ 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();
+ type = table.getValueAt(row, TYPE_COLUMN).toString();
button.setOpaque(true);
- button.setBackground(me.getBackground());
+ button.setBackground(FeatureSettings.this.getBackground());
if (!currentColor.isSimpleColour())
{
JLabel btn = new JLabel();
/**
* 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.
+ * 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.
*/
+ @SuppressWarnings("serial")
class FilterEditor extends AbstractCellEditor
implements TableCellEditor, ActionListener
{
- FeatureSettings me;
FeatureMatcherSetI currentFilter;
int rowSelected = 0;
- public FilterEditor(FeatureSettings me)
+ public FilterEditor()
{
- this.me = me;
button = new JButton();
button.setActionCommand(EDIT);
button.addActionListener(this);
{
if (button == e.getSource())
{
- FeatureTypeSettings chooser = new FeatureTypeSettings(me.fr, type);
+ FeatureTypeSettings chooser = new FeatureTypeSettings(fr, type);
chooser.addActionListener(this);
chooser.setRequestFocusEnabled(true);
chooser.requestFocus();
* update table data without triggering updateFeatureRenderer
*/
FeatureColourI currentColor = fr.getFeatureColours().get(type);
- currentFilter = me.fr.getFeatureFilter(type);
+ currentFilter = 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();
+ // SwingJS needs an explicit repaint() here,
+ // rather than relying upon no validation having
+ // occurred since the stopEditing call was made.
+ // Its laying out has not been stopped by the modal frame
+ table.validate();
+ table.repaint();
}
}
}
@Override
- public Component getTableCellEditorComponent(JTable theTable, Object value,
- boolean isSelected, int row, int column)
+ 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();
+ type = table.getValueAt(row, TYPE_COLUMN).toString();
button.setOpaque(true);
- button.setBackground(me.getBackground());
+ button.setBackground(FeatureSettings.this.getBackground());
button.setText(currentFilter.toString());
button.setIcon(null);
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
g.fillRect(s1, 0, e1 - s1, height);
}
g.setColor(gcol.getMaxColour());
- g.fillRect(0, e1, width - e1, height);
+ // g.fillRect(0, e1, width - e1, height); // BH 2018
+ g.fillRect(e1, 0, width - e1, height);
}
}
}
git://source.jalview.org / jalview.git / blobdiff