import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
import java.awt.BorderLayout;
import java.awt.Button;
import java.util.Map;
import java.util.Set;
-public class FeatureSettings extends Panel implements ItemListener,
- MouseListener, MouseMotionListener, ActionListener,
- AdjustmentListener, FeatureSettingsControllerI
+public class FeatureSettings extends Panel
+ implements ItemListener, MouseListener, MouseMotionListener,
+ ActionListener, AdjustmentListener, FeatureSettingsControllerI
{
+ private static final int TYPE_COLUMN = 0;
+
+ private static final int COLOUR_COLUMN = 1;
+
+ private static final int SHOW_COLUMN = 2;
+
FeatureRenderer fr;
AlignmentPanel ap;
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)
{
- List<String> displayableTypes = new ArrayList<String>();
- Set<String> foundGroups = new HashSet<String>();
+ List<String> displayableTypes = new ArrayList<>();
+ Set<String> foundGroups = new HashSet<>();
AlignmentI alignment = av.getAlignment();
* and keep track of which groups are visible
*/
Set<String> groups = seq.getFeatures().getFeatureGroups(true);
- Set<String> visibleGroups = new HashSet<String>();
+ Set<String> visibleGroups = new HashSet<>();
for (String group : groups)
{
- if (group == null || fr.checkGroupVisibility(group, true))
+ // if (group == null || fr.checkGroupVisibility(group, true))
+ if (group == null || checkGroupState(group))
{
visibleGroups.add(group);
}
}
+ foundGroups.addAll(groups);
/*
* get distinct feature types for visible groups
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;
- Object[][] tmp = new Object[cSize][3];
+ /*
+ * temporary! leave column[2] empty - used for Filter in
+ * gui.FeatureSettings
+ */
+ int columnCount = 4;
+ Object[][] tmp = new Object[cSize][columnCount];
int tmpSize = 0;
for (int i = 0; i < cSize; i++)
{
MyCheckbox check = (MyCheckbox) comps[i];
- tmp[tmpSize][0] = check.type;
- tmp[tmpSize][1] = fr.getFeatureStyle(check.type);
- tmp[tmpSize][2] = new Boolean(check.getState());
+ tmp[tmpSize][TYPE_COLUMN /* 0 */] = check.type;
+ tmp[tmpSize][COLOUR_COLUMN /* 1 */] = fr.getFeatureStyle(check.type);
+ tmp[tmpSize][SHOW_COLUMN /* 3 */] = new Boolean(check.getState());
tmpSize++;
}
- Object[][] data = new Object[tmpSize][3];
+ Object[][] data = new Object[tmpSize][columnCount];
System.arraycopy(tmp, 0, data, 0, tmpSize);
- fr.setFeaturePriority(data);
+ fr.setFeaturePriority(getTableAsBeans(data));
- ap.paintAlignment(true);
+ ap.paintAlignment(updateOverview, updateOverview);
}
+ /**
+ * Converts table data into an array of data beans
+ */
+ private FeatureSettingsBean[] getTableAsBeans(Object[][] data)
+ {
+ FeatureSettingsBean[] rowData = new FeatureSettingsBean[data.length];
+ for (int i = 0; i < data.length; i++)
+ {
+ String type = (String) data[i][TYPE_COLUMN];
+ FeatureColourI colour = (FeatureColourI) data[i][COLOUR_COLUMN];
+ Boolean isShown = (Boolean) data[i][SHOW_COLUMN];
+ // feature filter set to null as not (yet) offered in applet
+ rowData[i] = new FeatureSettingsBean(type, colour, null, isShown);
+ }
+ return rowData;
+ }
MyCheckbox selectedCheck;
boolean dragging = false;
}
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