@SuppressWarnings("serial")
public class AnnotationColourChooser extends AnnotationRowFilter
{
- private static final int ONETHOUSAND = 1000;
-
private ColourSchemeI oldcs;
private JButton defColours;
JPanel maxColour = new JPanel();
private JCheckBox thresholdIsMin = new JCheckBox();
+ private JCheckBox transparency = new JCheckBox();
protected static final int MIN_WIDTH = 500;
"error.implementation_error_dont_know_about_threshold_setting"));
}
thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
- thresholdValue.setText("" + acg.getAnnotationThreshold());
+ thresholdValue.setText(String.valueOf(acg.getAnnotationThreshold()));
}
jbInit();
}
});
+ transparency.setBackground(Color.white);
+ transparency.setFont(JvSwingUtils.getLabelFont());
+ transparency
+ .setText(MessageManager.getString("Use Transparency"));
+ transparency.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ transparency_actionPerformed();
+ }
+ });
this.setLayout(new BorderLayout());
JPanel jPanel1 = new JPanel();
JPanel jPanel2 = new JPanel();
jPanel2.add(annotations, "grow, wrap");
jPanel2.add(seqAssociated);
jPanel2.add(useOriginalColours);
+ jPanel2.add(transparency);
JPanel colpanel = new JPanel(new FlowLayout());
colpanel.setBackground(Color.white);
colpanel.add(minColour);
this.validate();
}
+ protected void transparency_actionPerformed()
+ {
+ updateView();
+ }
protected void resetColours_actionPerformed()
{
setDefaultMinMax();
updateView();
}
};
- JalviewColourChooser.showColourChooser(Desktop.getDesktop(), ttl,
+ JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(), ttl,
colourPanel.getBackground(), listener);
}
{
updateView();
}
- getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+ getCurrentAnnotation().threshold.value = getSliderValue();
propagateSeqAssociatedThreshold(updateAllAnnotation,
getCurrentAnnotation());
ap.paintAlignment(false, false);
thresholdValue.setEnabled(true);
thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
+ final AlignmentAnnotation currentAnnotation = getCurrentAnnotation();
if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
{
slider.setEnabled(false);
thresholdIsMin.setEnabled(false);
}
else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
- && getCurrentAnnotation().threshold == null)
+ && currentAnnotation.threshold == null)
{
- getCurrentAnnotation().setThreshold(new GraphLine(
- (getCurrentAnnotation().graphMax
- - getCurrentAnnotation().graphMin) / 2f,
+ currentAnnotation.setThreshold(new GraphLine(
+ (currentAnnotation.graphMax - currentAnnotation.graphMin)
+ / 2f,
"Threshold", Color.black));
}
if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
{
adjusting = true;
- float range = getCurrentAnnotation().graphMax * ONETHOUSAND
- - getCurrentAnnotation().graphMin * ONETHOUSAND;
-
- slider.setMinimum(
- (int) (getCurrentAnnotation().graphMin * ONETHOUSAND));
- slider.setMaximum(
- (int) (getCurrentAnnotation().graphMax * ONETHOUSAND));
- slider.setValue(
- (int) (getCurrentAnnotation().threshold.value * ONETHOUSAND));
- thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
- slider.setMajorTickSpacing((int) (range / 10f));
+ setSliderModel(currentAnnotation.graphMin, currentAnnotation.graphMax,
+ currentAnnotation.threshold.value);
slider.setEnabled(true);
+
+ setThresholdValueText();
thresholdValue.setEnabled(true);
adjusting = false;
}
- colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
+ colorAlignmentContaining(currentAnnotation, selectedThresholdItem);
ap.alignmentChanged();
}
acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
+ acg.setPositionToTransparency(transparency.isSelected());
+
this.ap.alignFrame.changeColour(acg);
if (av.getAlignment().getGroups() != null)
{
continue;
}
- sg.setColourScheme(
- acg.getInstance(av, sg));
+ sg.setColourScheme(acg.getInstance(av, sg));
}
}
}