*/
package jalview.gui;
+import jalview.analysis.Conservation;
import jalview.datamodel.SequenceGroup;
import jalview.jbgui.GSliderPanel;
-import jalview.schemes.CollectionColourSchemeI;
+import jalview.renderer.ResidueShaderI;
import jalview.util.MessageManager;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.beans.PropertyVetoException;
+import java.util.List;
import javax.swing.JInternalFrame;
import javax.swing.JLayeredPane;
*/
public class SliderPanel extends GSliderPanel
{
+ private static final String BACKGROUND = "Background";
+
static JInternalFrame conservationSlider;
static JInternalFrame PIDSlider;
boolean forConservation = true;
- CollectionColourSchemeI cs;
+ ResidueShaderI cs;
+
+ /**
+ * Returns the currently displayed slider panel (or null if none).
+ *
+ * @return
+ */
+ public static SliderPanel getSliderPanel()
+ {
+ if (conservationSlider != null && conservationSlider.isVisible())
+ {
+ return (SliderPanel) conservationSlider.getContentPane();
+ }
+ if (PIDSlider != null && PIDSlider.isVisible())
+ {
+ return (SliderPanel) PIDSlider.getContentPane();
+ }
+ return null;
+ }
/**
* Creates a new SliderPanel object.
* DOCUMENT ME!
*/
public SliderPanel(final AlignmentPanel ap, int value,
- boolean forConserve, CollectionColourSchemeI scheme)
+ boolean forConserve, ResidueShaderI scheme)
{
this.ap = ap;
this.cs = scheme;
if (forConservation)
{
- label.setText(MessageManager
- .getString("label.enter_value_increase_conservation_visibility"));
+ label.setText(MessageManager.getString(
+ "label.enter_value_increase_conservation_visibility"));
slider.setMinimum(0);
slider.setMaximum(100);
}
else
{
- label.setText(MessageManager
- .getString("label.enter_percentage_identity_above_which_colour_residues"));
+ label.setText(MessageManager.getString(
+ "label.enter_percentage_identity_above_which_colour_residues"));
slider.setMinimum(0);
slider.setMaximum(100);
}
@Override
public void mouseReleased(MouseEvent evt)
{
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
});
}
/**
- * DOCUMENT ME!
+ * Method to 'set focus' of the Conservation slider panel
*
* @param ap
- * DOCUMENT ME!
- * @param ccs
- * DOCUMENT ME!
+ * the panel to repaint on change of slider
+ * @param rs
+ * the colour scheme to update on change of slider
* @param source
- * DOCUMENT ME!
+ * a text description for the panel's title
*
- * @return DOCUMENT ME!
+ * @return
*/
public static int setConservationSlider(AlignmentPanel ap,
- CollectionColourSchemeI ccs, String source)
+ ResidueShaderI rs, String source)
{
- SliderPanel sp = null;
+ SliderPanel sliderPanel = null;
if (conservationSlider == null)
{
- sp = new SliderPanel(ap, ccs.getConservationInc(), true, ccs);
+ sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true, rs);
conservationSlider = new JInternalFrame();
- conservationSlider.setContentPane(sp);
+ conservationSlider.setContentPane(sliderPanel);
conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
}
else
{
- sp = (SliderPanel) conservationSlider.getContentPane();
- sp.valueField.setText(String.valueOf(ccs.getConservationInc()));
- sp.cs = ccs;
+ sliderPanel = (SliderPanel) conservationSlider.getContentPane();
+ sliderPanel.valueField
+ .setText(String.valueOf(rs.getConservationInc()));
+ sliderPanel.cs = rs;
+ sliderPanel.ap = ap;
+ sliderPanel.slider.setValue(rs.getConservationInc());
}
- conservationSlider
- .setTitle(MessageManager.formatMessage(
- "label.conservation_colour_increment",
- new String[] { source }));
+ conservationSlider.setTitle(MessageManager.formatMessage(
+ "label.conservation_colour_increment", new String[]
+ { source == null ? BACKGROUND : source }));
- if (ap.av.getAlignment().getGroups() != null)
+ List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
+ if (groups != null && !groups.isEmpty())
{
- sp.setAllGroupsCheckEnabled(true);
+ sliderPanel.setAllGroupsCheckEnabled(true);
}
else
{
- sp.setAllGroupsCheckEnabled(false);
+ sliderPanel.setAllGroupsCheckEnabled(false);
}
- return sp.getValue();
+ return sliderPanel.getValue();
}
/**
{
Desktop.addInternalFrame(conservationSlider,
conservationSlider.getTitle(), 420, 90, false);
- conservationSlider
- .addInternalFrameListener(new InternalFrameAdapter()
- {
- @Override
- public void internalFrameClosed(InternalFrameEvent e)
- {
- conservationSlider = null;
- }
- });
+ conservationSlider.addInternalFrameListener(new InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(InternalFrameEvent e)
+ {
+ conservationSlider = null;
+ }
+ });
conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
}
}
/**
- * DOCUMENT ME!
+ * Method to 'set focus' of the PID slider panel
*
* @param ap
- * DOCUMENT ME!
- * @param ccs
- * DOCUMENT ME!
+ * the panel to repaint on change of slider
+ * @param rs
+ * the colour scheme to update on change of slider
* @param source
- * DOCUMENT ME!
+ * a text description for the panel's title
*
- * @return DOCUMENT ME!
+ * @return
*/
- public static int setPIDSliderSource(AlignmentPanel ap,
- CollectionColourSchemeI ccs, String source)
+ public static int setPIDSliderSource(AlignmentPanel ap, ResidueShaderI rs,
+ String source)
{
- SliderPanel pid = null;
+ int threshold = rs.getThreshold();
- int threshold = ccs.getThreshold();
+ SliderPanel sliderPanel = null;
if (PIDSlider == null)
{
- pid = new SliderPanel(ap, threshold, false, ccs);
+ sliderPanel = new SliderPanel(ap, threshold, false, rs);
PIDSlider = new JInternalFrame();
- PIDSlider.setContentPane(pid);
+ PIDSlider.setContentPane(sliderPanel);
PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
}
else
{
- pid = (SliderPanel) PIDSlider.getContentPane();
- pid.cs = ccs;
- pid.valueField.setText(String.valueOf(ccs.getThreshold()));
+ sliderPanel = (SliderPanel) PIDSlider.getContentPane();
+ sliderPanel.cs = rs;
+ sliderPanel.ap = ap;
+ sliderPanel.valueField.setText(String.valueOf(rs.getThreshold()));
+ sliderPanel.slider.setValue(rs.getThreshold());
}
- PIDSlider
- .setTitle(MessageManager.formatMessage(
- "label.percentage_identity_threshold",
- new String[] { source }));
+ PIDSlider.setTitle(MessageManager.formatMessage(
+ "label.percentage_identity_threshold", new String[]
+ { source == null ? BACKGROUND : source }));
if (ap.av.getAlignment().getGroups() != null)
{
- pid.setAllGroupsCheckEnabled(true);
+ sliderPanel.setAllGroupsCheckEnabled(true);
}
else
{
- pid.setAllGroupsCheckEnabled(false);
+ sliderPanel.setAllGroupsCheckEnabled(false);
}
- return pid.getValue();
+ return sliderPanel.getValue();
}
/**
* DOCUMENT ME!
+ *
+ * @return
*/
- public static void showPIDSlider()
+ public static JInternalFrame showPIDSlider()
{
hideConservationSlider();
});
PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
}
+ return PIDSlider;
}
/**
{
ap.av.setThreshold(percent);
}
- updateColourScheme(percent, cs);
+ updateColourScheme(percent, cs, null);
if (allGroupsCheck.isSelected())
{
- for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
+ for (SequenceGroup sg : groups)
{
- updateColourScheme(percent, sg.getGroupColourScheme());
+ updateColourScheme(percent, sg.getGroupColourScheme(), sg);
}
}
*
* @param percent
* @param scheme
+ * @param sg
*/
- protected void updateColourScheme(int percent, CollectionColourSchemeI scheme)
+ protected void updateColourScheme(int percent, ResidueShaderI scheme,
+ SequenceGroup sg)
{
if (scheme == null)
{
}
if (forConservation)
{
+ if (!scheme.conservationApplied() && sg != null)
+ {
+ /*
+ * first time the colour scheme has had Conservation shading applied
+ * - compute conservation
+ */
+ Conservation c = new Conservation("Group", sg.getSequences(null),
+ sg.getStartRes(), sg.getEndRes());
+ c.calculate();
+ c.verdict(false, ap.av.getConsPercGaps());
+ sg.cs.setConservation(c);
+
+ }
+ scheme.setConservationApplied(true);
scheme.setConservationInc(percent);
}
else
public void setAllGroupsCheckEnabled(boolean b)
{
allGroupsCheck.setEnabled(b);
+ allGroupsCheck.setSelected(ap.av.getColourAppliesToAllGroups());
}
/**
static int getValue(JInternalFrame slider)
{
- return slider == null ? 0 : ((SliderPanel) slider.getContentPane())
- .getValue();
+ return slider == null ? 0
+ : ((SliderPanel) slider.getContentPane()).getValue();
}
public static int getPIDValue()
return getValue(PIDSlider);
}
+ /**
+ * Answers true if the SliderPanel is for Conservation, false if it is for PID
+ * threshold
+ *
+ * @return
+ */
+ public boolean isForConservation()
+ {
+ return forConservation;
+ }
+
+ /**
+ * Answers the title for the slider panel; this may include 'Background' if
+ * for the alignment, or the group id if for a group
+ *
+ * @return
+ */
+ public String getTitle()
+ {
+ String title = null;
+ if (isForConservation())
+ {
+ if (conservationSlider != null)
+ {
+ title = conservationSlider.getTitle();
+ }
+ }
+ else if (PIDSlider != null)
+ {
+ title = PIDSlider.getTitle();
+ }
+ return title;
+ }
}