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.Vector;
+import java.util.Set;
public class FeatureSettings extends Panel implements ItemListener,
MouseListener, MouseMotionListener, ActionListener,
{
fr.findAllFeatures(true); // was default - now true to make all visible
}
+ groupPanel = new Panel();
discoverAllFeatureData();
add(lowerPanel, BorderLayout.SOUTH);
- if (groupPanel != null)
- {
- groupPanel.setLayout(new GridLayout(
- (fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote - this was
- // scaled on number of
- // visible groups. seems
- // broken
- groupPanel.validate();
+ 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);
- add(groupPanel, BorderLayout.NORTH);
- }
frame = new Frame();
frame.add(this);
final FeatureSettings me = this;
}
protected void popupSort(final MyCheckbox check,
- final Map<String, float[][]> minmax,
- int x, int y)
+ final Map<String, float[][]> minmax, int x, int y)
{
final String type = check.type;
final FeatureColourI typeCol = fr.getFeatureStyle(type);
if (fr.getAllFeatureColours() != null
&& fr.getAllFeatureColours().size() > 0)
{
- rebuildGroups();
+ // rebuildGroups();
}
resetTable(false);
}
/**
- * rebuilds the group panel
+ * Answers the visibility of the given group, and adds a checkbox for it if
+ * there is not one already
*/
- public void rebuildGroups()
+ public boolean checkGroupState(String group)
{
- boolean rdrw = false;
- if (groupPanel == null)
- {
- groupPanel = new Panel();
- }
- else
- {
- rdrw = true;
- groupPanel.removeAll();
- }
- // TODO: JAL-964 - smoothly incorporate new group entries if panel already
- // displayed and new groups present
- for (String group : fr.getFeatureGroups())
- {
- boolean vis = fr.checkGroupVisibility(group, false);
- Checkbox check = new MyCheckbox(group, vis, false);
- check.addMouseListener(this);
- check.setFont(new Font("Serif", Font.BOLD, 12));
- check.addItemListener(groupItemListener);
- // note - visibility seems to correlate with displayed. ???wtf ??
- check.setVisible(vis);
- groupPanel.add(check);
- }
- if (rdrw)
+ boolean visible = fr.checkGroupVisibility(group, true);
+
+ /*
+ * is there already a checkbox for this group?
+ */
+ for (int g = 0; g < groupPanel.getComponentCount(); g++)
{
- groupPanel.validate();
+ if (((Checkbox) groupPanel.getComponent(g)).getLabel().equals(group))
+ {
+ ((Checkbox) groupPanel.getComponent(g)).setState(visible);
+ return visible;
+ }
}
+
+ /*
+ * add a new checkbox
+ */
+ Checkbox check = new MyCheckbox(group, visible, false);
+ check.addMouseListener(this);
+ check.setFont(new Font("Serif", Font.BOLD, 12));
+ check.addItemListener(groupItemListener);
+ groupPanel.add(check);
+
+ groupPanel.validate();
+ return visible;
}
// This routine adds and removes checkboxes depending on
// Group selection states
void resetTable(boolean groupsChanged)
{
- SequenceFeature[] tmpfeatures;
- String group = null, type;
- Vector<String> visibleChecks = new Vector<String>();
+ List<String> displayableTypes = new ArrayList<String>();
+ Set<String> foundGroups = new HashSet<String>();
+
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<String>();
+ for (String group : groups)
{
- group = tmpfeatures[index].featureGroup;
-
if (group == null || fr.checkGroupVisibility(group, true))
{
- type = tmpfeatures[index].getType();
- if (!visibleChecks.contains(type))
- {
- visibleChecks.addElement(type);
- }
+ visibleGroups.add(group);
}
- index++;
}
+
+ /*
+ * 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);
}
+ /*
+ * remove any checkboxes for groups not present
+ */
+ pruneGroups(foundGroups);
+
Component[] comps;
int cSize = featurePanel.getComponentCount();
MyCheckbox check;
{
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(),
}
/**
+ * Remove from the groups panel any checkboxes for groups that are not in the
+ * foundGroups set. This enables removing a group from the display when the
+ * last feature in that group is deleted.
+ *
+ * @param foundGroups
+ */
+ protected void pruneGroups(Set<String> foundGroups)
+ {
+ for (int g = 0; g < groupPanel.getComponentCount(); g++)
+ {
+ Checkbox checkbox = (Checkbox) groupPanel.getComponent(g);
+ if (!foundGroups.contains(checkbox.getLabel()))
+ {
+ groupPanel.remove(checkbox);
+ }
+ }
+ }
+
+ /**
* update the checklist of feature types with the given type
*
* @param groupsChanged
public void adjustmentValueChanged(AdjustmentEvent evt)
{
fr.setTransparency((100 - transparency.getValue()) / 100f);
- ap.seqPanel.seqCanvas.repaint();
-
+ ap.paintAlignment(true);
}
class MyCheckbox extends Checkbox
public void paint(Graphics g)
{
Dimension d = getSize();
- if (col.isColourByLabel())
+ if (col != null)
{
- g.setColor(Color.white);
- g.fillRect(d.width / 2, 0, d.width / 2, d.height);
- /*
- * g.setColor(Color.black); Font f=g.getFont().deriveFont(9);
- * g.setFont(f);
- *
- * // g.setFont(g.getFont().deriveFont( //
- * AffineTransform.getScaleInstance( //
- * width/g.getFontMetrics().stringWidth("Label"), //
- * height/g.getFontMetrics().getHeight()))); g.drawString("Label",
- * width/2, 0);
- */
+ if (col.isColourByLabel())
+ {
+ g.setColor(Color.white);
+ g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+ /*
+ * g.setColor(Color.black); Font f=g.getFont().deriveFont(9);
+ * g.setFont(f);
+ *
+ * // g.setFont(g.getFont().deriveFont( //
+ * AffineTransform.getScaleInstance( //
+ * width/g.getFontMetrics().stringWidth("Label"), //
+ * height/g.getFontMetrics().getHeight()))); g.drawString("Label",
+ * width/2, 0);
+ */
- }
- else if (col.isGraduatedColour())
- {
- Color maxCol = col.getMaxColour();
- g.setColor(maxCol);
- g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+ }
+ else if (col.isGraduatedColour())
+ {
+ Color maxCol = col.getMaxColour();
+ g.setColor(maxCol);
+ g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+ }
}
if (hasLink)
* @param type
* @param columnsContaining
*/
- void hideFeatureColumns(final String type,
- boolean columnsContaining)
+ void hideFeatureColumns(final String type, boolean columnsContaining)
{
- if (ap.alignFrame.avc.markColumnsContainingFeatures(
- columnsContaining, false, false, type))
+ if (ap.alignFrame.avc.markColumnsContainingFeatures(columnsContaining,
+ false, false, type))
{
if (ap.alignFrame.avc.markColumnsContainingFeatures(
!columnsContaining, false, false, type))