import jalview.schemes.HydrophobicColourScheme;
import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.PIDColourScheme;
-import jalview.schemes.ResidueProperties;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TaylorColourScheme;
import jalview.schemes.TurnColourScheme;
public class APopupMenu extends java.awt.PopupMenu implements
ActionListener, ItemListener
{
- private static final String ALL_ANNOTATIONS = "All";
-
Menu groupMenu = new Menu();
MenuItem editGroupName = new MenuItem();
// collect matching db-refs
DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
- seq.getDBRef(), new String[] { target });
+ seq.getDBRefs(), new String[] { target });
// collect id string too
String id = seq.getName();
String descr = seq.getDescription();
MenuItem item = new MenuItem(label);
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ap.alignFrame.showURL(url, target);
linkMenu.add(item);
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == abovePIDColour)
}
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
Object source = evt.getSource();
void addPDB()
{
- if (seq.getAllPDBEntries() != null)
+ Vector<PDBEntry> pdbs = seq.getAllPDBEntries();
+ if (pdbs != null&& !pdbs.isEmpty())
{
- PDBEntry entry = seq.getAllPDBEntries().firstElement();
+ PDBEntry entry = pdbs.firstElement();
if (ap.av.applet.jmolAvailable)
{
"label.represent_group_with", new Object[] { "" }));
revealAll.setLabel(MessageManager.getString("action.reveal_all"));
revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
- menu1.setLabel(MessageManager.getString("label.group") + ":");
+ menu1.setLabel(MessageManager.getString("label.group:"));
add(groupMenu);
this.add(seqMenu);
this.add(hideSeqs);
if (conservationMenuItem.getState())
{
- sg.cs.setConservation(Conservation.calculateConservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(ap.av
- .getHiddenRepSequences()), 0, ap.av.getAlignment()
- .getWidth(), false, ap.av.getConsPercGaps(), false));
+ sg.cs.setConservation(Conservation.calculateConservation("Group", 3,
+ sg.getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
+ .getAlignment().getWidth(), false, ap.av
+ .getConsPercGaps(), false));
SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
SliderPanel.showConservationSlider();
}
void hideSequences(boolean representGroup)
{
- SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg == null || sg.getSize() < 1)
- {
- ap.av.hideSequence(new SequenceI[] { seq });
- return;
- }
-
- ap.av.setSelectionGroup(null);
-
- if (representGroup)
- {
- ap.av.hideRepSequences(seq, sg);
-
- return;
- }
-
- int gsize = sg.getSize();
- SequenceI[] hseqs;
-
- hseqs = new SequenceI[gsize];
-
- int index = 0;
- for (int i = 0; i < gsize; i++)
- {
- hseqs[index++] = sg.getSequenceAt(i);
- }
-
- ap.av.hideSequence(hseqs);
- ap.av.sendSelection();
+ ap.av.hideSequences(seq, representGroup);
}
/**
showMenu.removeAll();
hideMenu.removeAll();
- final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
+ final List<String> all = Arrays.asList(new String[] { MessageManager
+ .getString("label.all") });
addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
false);