*/
package jalview.gui;
+import jalview.api.AlignViewportI;
import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsControllerI;
import jalview.datamodel.AlignmentI;
import jalview.gui.Help.HelpId;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
-import jalview.schemabinding.version2.Filter;
-import jalview.schemabinding.version2.JalviewUserColours;
-import jalview.schemabinding.version2.MatcherSet;
import jalview.schemes.FeatureColour;
import jalview.util.MessageManager;
import jalview.util.Platform;
-import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
-import jalview.ws.DasSequenceFeatureFetcher;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.xml.binding.jalview.JalviewUserColours;
+import jalview.xml.binding.jalview.JalviewUserColours.Colour;
+import jalview.xml.binding.jalview.JalviewUserColours.Filter;
+import jalview.xml.binding.jalview.ObjectFactory;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.awt.Dimension;
+import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.Graphics;
import java.awt.GridLayout;
import java.util.List;
import java.util.Map;
import java.util.Set;
-import java.util.Vector;
import javax.help.HelpSetException;
import javax.swing.AbstractCellEditor;
import javax.swing.Icon;
import javax.swing.JButton;
import javax.swing.JCheckBox;
-import javax.swing.JCheckBoxMenuItem;
import javax.swing.JColorChooser;
import javax.swing.JDialog;
import javax.swing.JInternalFrame;
import javax.swing.JTable;
import javax.swing.ListSelectionModel;
import javax.swing.SwingConstants;
-import javax.swing.SwingUtilities;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.table.AbstractTableModel;
import javax.swing.table.TableCellEditor;
import javax.swing.table.TableCellRenderer;
import javax.swing.table.TableColumn;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamReader;
public class FeatureSettings extends JPanel
implements FeatureSettingsControllerI
private static final int MIN_HEIGHT = 400;
- DasSourceBrowser dassourceBrowser;
-
- DasSequenceFeatureFetcher dasFeatureFetcher;
-
- JPanel dasSettingsPane = new JPanel();
-
final FeatureRenderer fr;
public final AlignFrame af;
JSlider transparency = new JSlider();
+ JCheckBox showComplement;
+
+ JCheckBox showComplementOnTop;
+
/*
* when true, constructor is still executing - so ignore UI events
*/
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:
// MessageManager.getString("label.feature_settings_click_drag")));
scrollPane.setViewportView(table);
- dassourceBrowser = new DasSourceBrowser(this);
- dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
-
if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder())
{
fr.findAllFeatures(true); // display everything!
javax.swing.event.InternalFrameEvent evt)
{
fr.removePropertyChangeListener(change);
- dassourceBrowser.fs = null;
};
});
frame.setLayer(JLayeredPane.PALETTE_LAYER);
});
men.add(dens);
- /*
- * variable colour options include colour by label, by score,
- * by selected attribute text, or attribute value
- */
- final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem(
- MessageManager.getString("label.variable_colour"));
- mxcol.setSelected(!featureColour.isSimpleColour());
- men.add(mxcol);
- mxcol.addActionListener(new ActionListener()
- {
- JColorChooser colorChooser;
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- if (e.getSource() == mxcol)
- {
- if (featureColour.isSimpleColour())
- {
- FeatureTypeSettings fc = new FeatureTypeSettings(me.fr, type);
- fc.addActionListener(this);
- }
- else
- {
- // bring up simple color chooser
- colorChooser = new JColorChooser();
- String title = MessageManager
- .getString("label.select_colour");
- JDialog dialog = JColorChooser.createDialog(me,
- title, true, // modal
- colorChooser, this, // OK button handler
- null); // no CANCEL button handler
- colorChooser.setColor(featureColour.getMaxColour());
- dialog.setVisible(true);
- }
- }
- else
- {
- if (e.getSource() instanceof FeatureTypeSettings)
- {
- /*
- * update after OK in feature colour dialog; the updated
- * colour will have already been set in the FeatureRenderer
- */
- FeatureColourI fci = fr.getFeatureColours().get(type);
- table.setValueAt(fci, rowSelected, 1);
- table.validate();
- }
- else
- {
- // probably the color chooser!
- table.setValueAt(new FeatureColour(colorChooser.getColor()),
- rowSelected, 1);
- table.validate();
- me.updateFeatureRenderer(
- ((FeatureTableModel) table.getModel()).getData(),
- false);
- }
- }
- }
-
- });
-
JMenuItem selCols = new JMenuItem(
MessageManager.getString("label.select_columns_containing"));
selCols.addActionListener(new ActionListener()
{
fr.setGroupVisibility(check.getText(), check.isSelected());
resetTable(new String[] { grp });
- af.alignPanel.paintAlignment(true, true);
+ refreshDisplay();
}
});
groupPanel.add(check);
InputStreamReader in = new InputStreamReader(
new FileInputStream(file), "UTF-8");
- JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
+ JAXBContext jc = JAXBContext
+ .newInstance("jalview.xml.binding.jalview");
+ javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+ XMLStreamReader streamReader = XMLInputFactory.newInstance()
+ .createXMLStreamReader(in);
+ JAXBElement<JalviewUserColours> jbe = um.unmarshal(streamReader,
+ JalviewUserColours.class);
+ JalviewUserColours jucs = jbe.getValue();
+
+ // JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
/*
* load feature colours
*/
- for (int i = jucs.getColourCount() - 1; i >= 0; i--)
+ for (int i = jucs.getColour().size() - 1; i >= 0; i--)
{
- jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
- FeatureColourI colour = Jalview2XML.unmarshalColour(newcol);
+ Colour newcol = jucs.getColour().get(i);
+ FeatureColourI colour = jalview.project.Jalview2XML
+ .parseColour(newcol);
fr.setColour(newcol.getName(), colour);
- fr.setOrder(newcol.getName(), i / (float) jucs.getColourCount());
+ fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size());
}
/*
* load feature filters; loaded filters will replace any that are
* currently defined, other defined filters are left unchanged
*/
- for (int i = 0; i < jucs.getFilterCount(); i++)
+ for (int i = 0; i < jucs.getFilter().size(); i++)
{
- jalview.schemabinding.version2.Filter filterModel = jucs
- .getFilter(i);
+ Filter filterModel = jucs.getFilter().get(i);
String featureType = filterModel.getFeatureType();
- FeatureMatcherSetI filter = Jalview2XML.unmarshalFilter(featureType,
- filterModel.getMatcherSet());
+ FeatureMatcherSetI filter = jalview.project.Jalview2XML
+ .parseFilter(featureType, filterModel.getMatcherSet());
if (!filter.isEmpty())
{
fr.setFeatureFilter(featureType, filter);
for (String featureType : sortedTypes)
{
FeatureColourI fcol = fr.getFeatureStyle(featureType);
- jalview.schemabinding.version2.Colour col = Jalview2XML.marshalColour(
- featureType, fcol);
- ucs.addColour(col);
+ Colour col = jalview.project.Jalview2XML.marshalColour(featureType,
+ fcol);
+ ucs.getColour().add(col);
}
/*
{
Iterator<FeatureMatcherI> iterator = filter.getMatchers().iterator();
FeatureMatcherI firstMatcher = iterator.next();
- MatcherSet ms = Jalview2XML.marshalFilter(firstMatcher, iterator,
+ jalview.xml.binding.jalview.FeatureMatcherSet ms = jalview.project.Jalview2XML
+ .marshalFilter(firstMatcher, iterator,
filter.isAnded());
Filter filterModel = new Filter();
filterModel.setFeatureType(featureType);
filterModel.setMatcherSet(ms);
- ucs.addFilter(filterModel);
+ ucs.getFilter().add(filterModel);
}
}
+ JAXBContext jaxbContext = JAXBContext
+ .newInstance(JalviewUserColours.class);
+ Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
+ jaxbMarshaller.marshal(
+ new ObjectFactory().createJalviewUserColours(ucs), out);
- ucs.marshal(out);
+ // jaxbMarshaller.marshal(object, pout);
+ // marshaller.marshal(object);
+ out.flush();
+
+ // ucs.marshal(out);
out.close();
} catch (Exception ex)
{
public void invertSelection()
{
- for (int i = 0; i < table.getRowCount(); i++)
+ Object[][] data = ((FeatureTableModel) table.getModel()).getData();
+ for (int i = 0; i < data.length; i++)
{
- Boolean value = (Boolean) table.getValueAt(i, SHOW_COLUMN);
-
- table.setValueAt(new Boolean(!value.booleanValue()), i, SHOW_COLUMN);
+ data[i][SHOW_COLUMN] = !(Boolean) data[i][SHOW_COLUMN];
}
+ updateFeatureRenderer(data, true);
+ table.repaint();
}
public void orderByAvWidth()
if (fr.setFeaturePriority(rowData, visibleNew))
{
- af.alignPanel.paintAlignment(true, true);
+ refreshDisplay();
}
}
JPanel settingsPane = new JPanel();
settingsPane.setLayout(new BorderLayout());
- dasSettingsPane.setLayout(new BorderLayout());
-
JPanel bigPanel = new JPanel();
bigPanel.setLayout(new BorderLayout());
if (!inConstruction)
{
fr.setTransparency((100 - transparency.getValue()) / 100f);
- af.alignPanel.paintAlignment(true, true);
+ refreshDisplay();
}
}
});
transparency.setMaximum(70);
transparency.setToolTipText(
MessageManager.getString("label.transparency_tip"));
- fetchDAS.setText(MessageManager.getString("label.fetch_das_features"));
- fetchDAS.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- fetchDAS_actionPerformed(e);
- }
- });
- saveDAS.setText(MessageManager.getString("action.save_as_default"));
- saveDAS.addActionListener(new ActionListener()
+
+ boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
+ showComplement = new JCheckBox(
+ "Show " + (nucleotide ? "protein" : "CDS") + " features");
+ showComplement.setSelected(af.getViewport().isShowComplementFeatures());
+ showComplement.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- saveDAS_actionPerformed(e);
+ af.getViewport()
+ .setShowComplementFeatures(showComplement.isSelected());
+ refreshDisplay();
}
});
- JPanel dasButtonPanel = new JPanel();
- dasButtonPanel.setBorder(BorderFactory.createEtchedBorder());
- dasSettingsPane.setBorder(null);
- cancelDAS.setEnabled(false);
- cancelDAS.setText(MessageManager.getString("action.cancel_fetch"));
- cancelDAS.addActionListener(new ActionListener()
+ showComplementOnTop = new JCheckBox("on top");
+ showComplementOnTop
+ .setSelected(af.getViewport().isShowComplementFeaturesOnTop());
+ showComplementOnTop.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- cancelDAS_actionPerformed(e);
+ af.getViewport().setShowComplementFeaturesOnTop(
+ showComplementOnTop.isSelected());
+ refreshDisplay();
}
});
- 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);
- transPanel.add(transparency);
- transPanel.add(transbuttons);
+
+ boolean hasComplement = af.getViewport().getCodingComplement() != null;
+ JPanel transPanelLeft = new JPanel(
+ new GridLayout(hasComplement ? 3 : 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);
buttonPanel.add(loadColours);
buttonPanel.add(saveColours);
bigPanel.add(scrollPane, BorderLayout.CENTER);
- dasSettingsPane.add(dasButtonPanel, BorderLayout.SOUTH);
- dasButtonPanel.add(fetchDAS);
- dasButtonPanel.add(cancelDAS);
- dasButtonPanel.add(saveDAS);
settingsPane.add(bigPanel, BorderLayout.CENTER);
settingsPane.add(buttonPanel, BorderLayout.SOUTH);
this.add(settingsPane);
}
- public void fetchDAS_actionPerformed(ActionEvent e)
- {
- fetchDAS.setEnabled(false);
- cancelDAS.setEnabled(true);
- dassourceBrowser.setGuiEnabled(false);
- Vector<jalviewSourceI> selectedSources = dassourceBrowser
- .getSelectedSources();
- doDasFeatureFetch(selectedSources, true, true);
- }
-
/**
- * get the features from selectedSources for all or the current selection
- *
- * @param selectedSources
- * @param checkDbRefs
- * @param promptFetchDbRefs
+ * Repaints alignment, structure and overview (if shown). If there is a
+ * complementary view which is showing this view's features, then also
+ * repaints that.
*/
- private void doDasFeatureFetch(List<jalviewSourceI> selectedSources,
- boolean checkDbRefs, boolean promptFetchDbRefs)
+ void refreshDisplay()
{
- SequenceI[] dataset, seqs;
- int iSize;
- AlignmentViewport vp = af.getViewport();
- if (vp.getSelectionGroup() != null
- && vp.getSelectionGroup().getSize() > 0)
+ af.alignPanel.paintAlignment(true, true);
+ AlignViewportI complement = af.getViewport().getCodingComplement();
+ if (complement != null && complement.isShowComplementFeatures())
{
- iSize = vp.getSelectionGroup().getSize();
- dataset = new SequenceI[iSize];
- seqs = vp.getSelectionGroup().getSequencesInOrder(vp.getAlignment());
+ AlignFrame af2 = Desktop.getAlignFrameFor(complement);
+ af2.alignPanel.paintAlignment(true, true);
}
- else
- {
- iSize = vp.getAlignment().getHeight();
- seqs = vp.getAlignment().getSequencesArray();
- }
-
- dataset = new SequenceI[iSize];
- for (int i = 0; i < iSize; i++)
- {
- dataset[i] = seqs[i].getDatasetSequence();
- }
-
- cancelDAS.setEnabled(true);
- dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset,
- this, selectedSources, checkDbRefs, promptFetchDbRefs);
- af.getViewport().setShowSequenceFeatures(true);
- af.showSeqFeatures.setSelected(true);
- }
-
- /**
- * blocking call to initialise the das source browser
- */
- public void initDasSources()
- {
- dassourceBrowser.initDasSources();
- }
-
- /**
- * examine the current list of das sources and return any matching the given
- * nicknames in sources
- *
- * @param sources
- * Vector of Strings to resolve to DAS source nicknames.
- * @return sources that are present in source list.
- */
- public List<jalviewSourceI> resolveSourceNicknames(Vector<String> sources)
- {
- return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
- }
-
- /**
- * get currently selected das sources. ensure you have called initDasSources
- * before calling this.
- *
- * @return vector of selected das source nicknames
- */
- public Vector<jalviewSourceI> getSelectedSources()
- {
- return dassourceBrowser.getSelectedSources();
- }
-
- /**
- * properly initialise DAS fetcher and then initiate a new thread to fetch
- * features from the named sources (rather than any turned on by default)
- *
- * @param sources
- * @param block
- * if true then runs in same thread, otherwise passes to the Swing
- * executor
- */
- public void fetchDasFeatures(Vector<String> sources, boolean block)
- {
- initDasSources();
- List<jalviewSourceI> resolved = dassourceBrowser.sourceRegistry
- .resolveSourceNicknames(sources);
- if (resolved.size() == 0)
- {
- resolved = dassourceBrowser.getSelectedSources();
- }
- if (resolved.size() > 0)
- {
- final List<jalviewSourceI> dassources = resolved;
- fetchDAS.setEnabled(false);
- // cancelDAS.setEnabled(true); doDasFetch does this.
- Runnable fetcher = new Runnable()
- {
-
- @Override
- public void run()
- {
- doDasFeatureFetch(dassources, true, false);
-
- }
- };
- if (block)
- {
- fetcher.run();
- }
- else
- {
- SwingUtilities.invokeLater(fetcher);
- }
- }
- }
-
- public void saveDAS_actionPerformed(ActionEvent e)
- {
- dassourceBrowser
- .saveProperties(jalview.bin.Cache.applicationProperties);
- }
-
- public void complete()
- {
- fetchDAS.setEnabled(true);
- cancelDAS.setEnabled(false);
- dassourceBrowser.setGuiEnabled(true);
-
- }
-
- public void cancelDAS_actionPerformed(ActionEvent e)
- {
- if (dasFeatureFetcher != null)
- {
- dasFeatureFetcher.cancel();
- }
- complete();
- }
-
- public void noDasSourceActive()
- {
- complete();
- JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.getString("label.no_das_sources_selected_warn"),
- MessageManager.getString("label.no_das_sources_selected_title"),
- JvOptionPane.DEFAULT_OPTION, JvOptionPane.INFORMATION_MESSAGE);
}
// ///////////////////////////////////////////////////////////////////////
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
{
// bring up graduated chooser.
chooser = new FeatureTypeSettings(me.fr, type);
- chooser.setRequestFocusEnabled(true);
- chooser.requestFocus();
+ /**
+ * @j2sNative
+ */
+ {
+ chooser.setRequestFocusEnabled(true);
+ chooser.requestFocus();
+ }
chooser.addActionListener(this);
- chooser.showTab(true);
+ // Make the renderer reappear.
+ fireEditingStopped();
}
- // Make the renderer reappear.
- fireEditingStopped();
-
}
else
{
chooser.getWidth(), chooser.getHeight());
chooser.validate();
}
- chooser.showTab(false);
fireEditingStopped();
}
else if (e.getSource() instanceof Component)
git://source.jalview.org / jalview.git / blobdiff