*/
package jalview.gui;
+import java.util.Locale;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Hashtable;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+import java.util.SortedMap;
+import java.util.TreeMap;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JScrollPane;
+
import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentAnnotationUtils;
import jalview.analysis.AlignmentUtils;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.MappedFeatures;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.ResidueCount;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.io.CountReader;
import jalview.io.FileFormatI;
import jalview.io.FileFormats;
import jalview.io.FormatAdapter;
import jalview.util.UrlLink;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.BitSet;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Hashtable;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Objects;
-import java.util.SortedMap;
-import java.util.TreeMap;
-import java.util.Vector;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JInternalFrame;
-import javax.swing.JLabel;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JPanel;
-import javax.swing.JPopupMenu;
-import javax.swing.JRadioButtonMenuItem;
-import javax.swing.JScrollPane;
+import java.io.IOException;
+import java.net.MalformedURLException;
/**
* The popup menu that is displayed on right-click on a sequence id, or in the
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.web_browser_not_found_unix"),
MessageManager.getString("label.web_browser_not_found"),
JvOptionPane.WARNING_MESSAGE);
}
}
+ if (seq.hasHMMProfile())
+ {
+ menuItem = new JMenuItem(MessageManager
+ .getString("action.add_background_frequencies"));
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ ResidueCount counts = CountReader.getBackgroundFrequencies(ap,
+ seq);
+ if (counts != null)
+ {
+ seq.getHMM().setBackgroundFrequencies(counts);
+ ap.alignFrame.buildColourMenu();
+ }
+ } catch (MalformedURLException e1)
+ {
+ e1.printStackTrace();
+ } catch (IOException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
+ });
+ add(menuItem);
+ }
+
menuItem = new JMenuItem(
MessageManager.getString("action.hide_sequences"));
menuItem.addActionListener(new ActionListener()
buildGroupURLMenu(sg, groupLinks);
}
// Add a 'show all structures' for the current selection
- Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
+ Hashtable<String, PDBEntry> pdbe = new Hashtable<>();
+ Hashtable<String, PDBEntry> reppdb = new Hashtable<>();
SequenceI sqass = null;
for (SequenceI sq : alignPanel.av.getSequenceSelection())
}
/**
- * Add a link to show feature details for each sequence feature
+ * Add a menu item to show feature details for each sequence feature. Any
+ * linked 'virtual' features (CDS/protein) are also optionally found and
+ * included.
*
* @param features
- * @param column
* @param seq
+ * @param column
*/
protected void addFeatureDetails(List<SequenceFeature> features,
- SequenceI seq, int column)
+ final SequenceI seq, final int column)
{
/*
* add features in CDS/protein complement at the corresponding
String name = seq.getName();
for (final SequenceFeature sf : features)
{
- addFeatureDetailsMenuItem(details, name, sf);
+ addFeatureDetailsMenuItem(details, name, sf, null);
}
if (mf != null)
{
- name = mf.fromSeq == seq ? mf.mapping.getTo().getName()
- : mf.fromSeq.getName();
for (final SequenceFeature sf : mf.features)
{
- addFeatureDetailsMenuItem(details, name, sf);
+ addFeatureDetailsMenuItem(details, name, sf, mf);
}
}
}
/**
- * A helper method to add one menu item whose action is to show details for one
- * feature. The menu text includes feature description, but this may be
+ * A helper method to add one menu item whose action is to show details for
+ * one feature. The menu text includes feature description, but this may be
* truncated.
*
* @param details
* @param seqName
* @param sf
+ * @param mf
*/
void addFeatureDetailsMenuItem(JMenu details, final String seqName,
- final SequenceFeature sf)
+ final SequenceFeature sf, MappedFeatures mf)
{
int start = sf.getBegin();
int end = sf.getEnd();
+ if (mf != null)
+ {
+ /*
+ * show local rather than linked feature coordinates
+ */
+ int[] beginRange = mf.getMappedPositions(start, start);
+ start = beginRange[0];
+ int[] endRange = mf.getMappedPositions(end, end);
+ end = endRange[endRange.length - 1];
+ }
StringBuilder desc = new StringBuilder();
desc.append(sf.getType()).append(" ").append(String.valueOf(start));
if (start != end)
{
- desc.append("-").append(String.valueOf(end));
+ desc.append(sf.isContactFeature() ? ":" : "-");
+ desc.append(String.valueOf(end));
}
String description = sf.getDescription();
if (description != null)
@Override
public void actionPerformed(ActionEvent e)
{
- showFeatureDetails(seqName, sf);
+ showFeatureDetails(sf, seqName, mf);
}
});
details.add(item);
}
/**
- * Opens a panel showing a text report of feature dteails
- *
- * @param seqName
+ * Opens a panel showing a text report of feature details
*
* @param sf
+ * @param seqName
+ * @param mf
*/
- protected void showFeatureDetails(String seqName, SequenceFeature sf)
+ protected void showFeatureDetails(SequenceFeature sf, String seqName,
+ MappedFeatures mf)
{
JInternalFrame details;
if (Platform.isJS())
// TODO JAL-3026 set style of table correctly for feature details
JLabel reprt = new JLabel(MessageManager
.formatMessage("label.html_content", new Object[]
- { sf.getDetailsReport(seqName) }));
+ { sf.getDetailsReport(seqName, mf) }));
reprt.setBackground(Color.WHITE);
reprt.setOpaque(true);
panel.add(reprt, BorderLayout.CENTER);
*/
{
CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
- // it appears Java's CSS does not support border-collaps :-(
+ // it appears Java's CSS does not support border-collapse :-(
cap.addStylesheetRule("table { border-collapse: collapse;}");
cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
- cap.setText(sf.getDetailsReport(seqName));
+ cap.setText(sf.getDetailsReport(seqName, mf));
details = cap;
}
Desktop.addInternalFrame(details,
for (int d = 0; d < nd; d++)
{
DBRefEntry e = dbr.get(d);
- String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
+ String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(Locale.ROOT);
Object[] sarray = commonDbrefs.get(src);
if (sarray == null)
{
boolean usingNames = false;
// Now see which parts of the group apply for this URL
String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
- Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
+ Object[] idset = commonDbrefs.get(ltarget.toUpperCase(Locale.ROOT));
String[] seqstr, ids; // input to makeUrl
if (idset != null)
{
menuItem.setEnabled(true);
for (String calcId : tipEntries.keySet())
{
- tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
+ tooltip.append("<br>" + calcId + "/" + tipEntries.get(calcId));
}
String tooltipText = JvSwingUtils.wrapTooltip(true,
tooltip.toString());
"label.create_sequence_details_report_annotation_for",
new Object[]
{ seq.getDisplayId(true) }) + "</h2></p><p>");
- new SequenceAnnotationReport(null).createSequenceAnnotationReport(
+ new SequenceAnnotationReport(false).createSequenceAnnotationReport(
contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
contents.append("</p>");
}
ap.paintAlignment(false, false);
}
sequence.setDescription(dialog.getDescription());
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
+ ap.av.notifyAlignment();
}
});
}
refresh();
}
};
- JalviewColourChooser.showColourChooser(Desktop.getDesktop(),
+ JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(),
title, Color.BLUE, listener);
}
startEnd, caseChange);
ap.alignFrame.addHistoryItem(caseCommand);
+ ap.av.notifyAlignment();
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
}
}
sg.getStartRes(), sg.getEndRes() + 1,
ap.av.getAlignment());
ap.alignFrame.addHistoryItem(editCommand);
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
+ ap.av.notifyAlignment();
}
});
}
git://source.jalview.org / jalview.git / blobdiff