import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsControllerI;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.event.MouseMotionListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
+import java.util.ArrayList;
import java.util.Arrays;
-import java.util.Enumeration;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
-import java.util.Vector;
-public class FeatureSettings extends Panel implements ItemListener,
- MouseListener, MouseMotionListener, ActionListener,
- AdjustmentListener, FeatureSettingsControllerI
+public class FeatureSettings extends Panel
+ implements ItemListener, MouseListener, MouseMotionListener,
+ ActionListener, AdjustmentListener, FeatureSettingsControllerI
{
FeatureRenderer fr;
add(lowerPanel, BorderLayout.SOUTH);
- groupPanel.setLayout(new GridLayout(
- (fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote - this was
- // scaled on number of
- // visible groups. seems
- // broken
+ groupPanel.setLayout(
+ new GridLayout((fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote
+ // - this
+ // was
+ // scaled
+ // on
+ // number
+ // of
+ // visible
+ // groups.
+ // seems
+ // broken
groupPanel.validate();
add(groupPanel, BorderLayout.NORTH);
public void paint(Graphics g)
{
g.setColor(Color.black);
- g.drawString(MessageManager
- .getString("label.no_features_added_to_this_alignment"), 10, 20);
- g.drawString(MessageManager
- .getString("label.features_can_be_added_from_searches_1"), 10,
- 40);
- g.drawString(MessageManager
- .getString("label.features_can_be_added_from_searches_2"), 10,
- 60);
+ g.drawString(MessageManager.getString(
+ "label.no_features_added_to_this_alignment"), 10, 20);
+ g.drawString(MessageManager.getString(
+ "label.features_can_be_added_from_searches_1"), 10, 40);
+ g.drawString(MessageManager.getString(
+ "label.features_can_be_added_from_searches_2"), 10, 60);
}
protected void popupSort(final MyCheckbox check,
{
final String type = check.type;
final FeatureColourI typeCol = fr.getFeatureStyle(type);
- PopupMenu men = new PopupMenu(MessageManager.formatMessage(
- "label.settings_for_type", new String[] { type }));
+ PopupMenu men = new PopupMenu(MessageManager
+ .formatMessage("label.settings_for_type", new String[]
+ { type }));
java.awt.MenuItem scr = new MenuItem(
MessageManager.getString("label.sort_by_score"));
men.add(scr);
@Override
public void actionPerformed(ActionEvent e)
{
- me.ap.alignFrame.avc.sortAlignmentByFeatureScore(Arrays
- .asList(new String[] { type }));
+ me.ap.alignFrame.avc
+ .sortAlignmentByFeatureScore(Arrays.asList(new String[]
+ { type }));
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(Arrays
- .asList(new String[] { type }));
+ me.ap.alignFrame.avc
+ .sortAlignmentByFeatureDensity(Arrays.asList(new String[]
+ { type }));
}
});
});
men.add(selectContaining);
- MenuItem selectNotContaining = new MenuItem(
- MessageManager.getString("label.select_columns_not_containing"));
+ MenuItem selectNotContaining = new MenuItem(MessageManager
+ .getString("label.select_columns_not_containing"));
selectNotContaining.addActionListener(new ActionListener()
{
@Override
// Group selection states
void resetTable(boolean groupsChanged)
{
- SequenceFeature[] tmpfeatures;
- String group = null, type;
- Vector<String> visibleChecks = new Vector<String>();
- Set<String> foundGroups = new HashSet<String>();
+ List<String> displayableTypes = new ArrayList<>();
+ Set<String> foundGroups = new HashSet<>();
+
AlignmentI alignment = av.getAlignment();
for (int i = 0; i < alignment.getHeight(); i++)
{
- if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
- {
- continue;
- }
+ SequenceI seq = alignment.getSequenceAt(i);
- tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
- int index = 0;
- while (index < tmpfeatures.length)
+ /*
+ * get the sequence's groups for positional features
+ * and keep track of which groups are visible
+ */
+ Set<String> groups = seq.getFeatures().getFeatureGroups(true);
+ Set<String> visibleGroups = new HashSet<>();
+ for (String group : groups)
{
- group = tmpfeatures[index].featureGroup;
- foundGroups.add(group);
-
+ // if (group == null || fr.checkGroupVisibility(group, true))
if (group == null || checkGroupState(group))
{
- type = tmpfeatures[index].getType();
- if (!visibleChecks.contains(type))
- {
- visibleChecks.addElement(type);
- }
+ visibleGroups.add(group);
}
- index++;
}
+ foundGroups.addAll(groups);
+
+ /*
+ * get distinct feature types for visible groups
+ * record distinct visible types
+ */
+ Set<String> types = seq.getFeatures().getFeatureTypesForGroups(true,
+ visibleGroups.toArray(new String[visibleGroups.size()]));
+ displayableTypes.addAll(types);
}
/*
{
comps = featurePanel.getComponents();
check = (MyCheckbox) comps[i];
- if (!visibleChecks.contains(check.type))
+ if (!displayableTypes.contains(check.type))
{
featurePanel.remove(i);
cSize--;
{
String item = rol.get(ro);
- if (!visibleChecks.contains(item))
+ if (!displayableTypes.contains(item))
{
continue;
}
- visibleChecks.removeElement(item);
+ displayableTypes.remove(item);
addCheck(false, item);
}
}
- // now add checkboxes which should be visible,
- // if they have not already been added
- Enumeration<String> en = visibleChecks.elements();
-
- while (en.hasMoreElements())
+ /*
+ * now add checkboxes which should be visible,
+ * if they have not already been added
+ */
+ for (String type : displayableTypes)
{
- addCheck(groupsChanged, en.nextElement().toString());
+ addCheck(groupsChanged, type);
}
- featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(),
- 1, 10, 5));
+ featurePanel.setLayout(
+ new GridLayout(featurePanel.getComponentCount(), 1, 10, 5));
featurePanel.validate();
if (scrollPane != null)
Checkbox check = (Checkbox) featurePanel.getComponent(i);
check.setState(!check.getState());
}
- selectionChanged();
+ selectionChanged(true);
}
private ItemListener groupItemListener = new ItemListener()
@Override
public void itemStateChanged(ItemEvent evt)
{
- selectionChanged();
+ selectionChanged(true);
}
- void selectionChanged()
+ void selectionChanged(boolean updateOverview)
{
Component[] comps = featurePanel.getComponents();
int cSize = comps.length;
fr.setFeaturePriority(data);
- ap.paintAlignment(true);
+ ap.paintAlignment(updateOverview, updateOverview);
}
MyCheckbox selectedCheck;
}
else
{
- comp = featurePanel.getComponentAt(evt.getX(), evt.getY()
- + evt.getComponent().getLocation().y);
+ comp = featurePanel.getComponentAt(evt.getX(),
+ evt.getY() + evt.getComponent().getLocation().y);
}
if (comp != null && comp instanceof Checkbox)
{
featurePanel.removeAll();
resetTable(false);
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
@Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
fr.setTransparency((100 - transparency.getValue()) / 100f);
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
class MyCheckbox extends Checkbox
git://source.jalview.org / jalview.git / blobdiff