*/
package jalview.appletgui;
+import java.awt.CheckboxMenuItem;
+import java.awt.Frame;
+import java.awt.Menu;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.SortedMap;
+import java.util.TreeMap;
+import java.util.Vector;
+
import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentAnnotationUtils;
import jalview.analysis.AlignmentUtils;
import jalview.util.MessageManager;
import jalview.util.UrlLink;
-import java.awt.CheckboxMenuItem;
-import java.awt.Frame;
-import java.awt.Menu;
-import java.awt.MenuItem;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.SortedMap;
-import java.util.TreeMap;
-import java.util.Vector;
-
public class APopupMenu extends java.awt.PopupMenu
implements ActionListener, ItemListener
{
void addFeatureLinks(final SequenceI seq, List<String> links)
{
Menu linkMenu = new Menu(MessageManager.getString("action.link"));
- Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+ Map<String, List<String>> linkset = new LinkedHashMap<>();
for (String link : links)
{
* Temporary store to hold distinct calcId / type pairs for the tooltip.
* Using TreeMap means calcIds are shown in alphabetical order.
*/
- SortedMap<String, String> tipEntries = new TreeMap<String, String>();
- final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
+ SortedMap<String, String> tipEntries = new TreeMap<>();
+ final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
AlignmentI al = this.ap.av.getAlignment();
AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
candidates, al);
}
int gSize = sg.getSize();
- List<SequenceI> seqs = new ArrayList<SequenceI>();
- List<SequenceFeature> features = new ArrayList<SequenceFeature>();
+ List<SequenceI> seqs = new ArrayList<>();
+ List<SequenceFeature> features = new ArrayList<>();
for (int i = 0; i < gSize; i++)
{
if (start <= end)
{
seqs.add(sg.getSequenceAt(i));
- features.add(new SequenceFeature(null, null, null, start, end,
+ features.add(new SequenceFeature(null, null, start, end,
"Jalview"));
}
}
{
ap.alignFrame.sequenceFeatures.setState(true);
ap.av.setShowSequenceFeatures(true);
- ap.highlightSearchResults(null);
+ ap.av.setSearchResults(null); // clear highlighting
+ ap.repaint(); // draw new/amended features
}
}
}
contents.append(MessageManager
.formatMessage("label.annotation_for_displayid", new Object[]
{ seq.getDisplayId(true) }));
- new SequenceAnnotationReport(null).createSequenceAnnotationReport(
- contents, seq, true, true,
- (ap.seqPanel.seqCanvas.fr != null)
- ? ap.seqPanel.seqCanvas.fr.getMinMax()
- : null);
+ new SequenceAnnotationReport(false).createSequenceAnnotationReport(
+ contents, seq, true, true, ap.seqPanel.seqCanvas.fr);
contents.append("</p>");
}
Frame frame = new Frame();
{
seq.setName(dialog.getName());
seq.setDescription(dialog.getDescription());
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
}
}
else
{
- new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null, ap,
+ new mc_view.AppletPDBViewer(entry, new SequenceI[] { seq }, null, ap,
DataSourceType.URL);
}
BLOSUM62Colour.setName(JalviewColourScheme.Blosum62.toString());
BLOSUM62Colour.addItemListener(this);
PIDColour.setLabel(
- MessageManager.getString("label.colourScheme_%_identity"));
+ MessageManager.getString("label.colourScheme_%identity"));
PIDColour.setName(JalviewColourScheme.PID.toString());
PIDColour.addItemListener(this);
zappoColour
.setName(JalviewColourScheme.Hydrophobic.toString());
hydrophobicityColour.addItemListener(this);
helixColour.setLabel(MessageManager
- .getString("label.colourScheme_helix_propensity"));
+ .getString("label.colourScheme_helixpropensity"));
helixColour.setName(JalviewColourScheme.Helix.toString());
helixColour.addItemListener(this);
strandColour.setLabel(MessageManager
- .getString("label.colourScheme_strand_propensity"));
+ .getString("label.colourScheme_strandpropensity"));
strandColour.setName(JalviewColourScheme.Strand.toString());
strandColour.addItemListener(this);
turnColour.setLabel(
- MessageManager.getString("label.colourScheme_turn_propensity"));
+ MessageManager.getString("label.colourScheme_turnpropensity"));
turnColour.setName(JalviewColourScheme.Turn.toString());
turnColour.addItemListener(this);
buriedColour.setLabel(
- MessageManager.getString("label.colourScheme_buried_index"));
+ MessageManager.getString("label.colourScheme_buriedindex"));
buriedColour.setName(JalviewColourScheme.Buried.toString());
buriedColour.addItemListener(this);
nucleotideColour.setLabel(
void refresh()
{
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
protected void clustalColour_actionPerformed()
SequenceGroup sg = ap.av.getSelectionGroup();
ap.av.getAlignment().deleteGroup(sg);
ap.av.setSelectionGroup(null);
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
void createGroupMenuItem_actionPerformed()
* the insertion order, which is the order of the annotations on the
* alignment.
*/
- Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
- Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
+ Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
+ Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
AlignmentAnnotationUtils.asList(annotations), forSequences);