oldcs = av.getGlobalColourScheme();
if (av.getAlignment().getGroups() != null)
{
- oldgroupColours = new Hashtable<SequenceGroup, ColourSchemeI>();
+ oldgroupColours = new Hashtable<>();
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
if (sg.getColourScheme() != null)
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- useOriginalColours.setSelected(acg.isPredefinedColours()
- || acg.getBaseColour() != null);
+ useOriginalColours.setSelected(
+ acg.isPredefinedColours() || acg.getBaseColour() != null);
if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
{
minColour.setBackground(acg.getMinColour());
seqAssociated.setSelected(acg.isSeqAssociated());
}
- Vector<String> annotItems = getAnnotationItems(seqAssociated
- .isSelected());
- annotations = new JComboBox<String>(annotItems);
+ Vector<String> annotItems = getAnnotationItems(
+ seqAssociated.isSelected());
+ annotations = new JComboBox<>(annotItems);
populateThresholdComboBox(threshold);
getThreshold().setSelectedIndex(2);
break;
default:
- throw new Error(
- MessageManager
- .getString("error.implementation_error_dont_know_about_threshold_setting"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_dont_know_about_threshold_setting"));
}
thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
thresholdValue.setText("" + acg.getAnnotationThreshold());
useOriginalColours.setFont(JvSwingUtils.getLabelFont());
useOriginalColours.setOpaque(false);
- useOriginalColours.setText(MessageManager
- .getString("label.use_original_colours"));
+ useOriginalColours.setText(
+ MessageManager.getString("label.use_original_colours"));
useOriginalColours.addActionListener(new ActionListener()
{
@Override
});
thresholdIsMin.setBackground(Color.white);
thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
- thresholdIsMin.setText(MessageManager
- .getString("label.threshold_minmax"));
+ thresholdIsMin
+ .setText(MessageManager.getString("label.threshold_minmax"));
thresholdIsMin.addActionListener(new ActionListener()
{
@Override
});
seqAssociated.setBackground(Color.white);
seqAssociated.setFont(JvSwingUtils.getLabelFont());
- seqAssociated.setText(MessageManager
- .getString("label.per_sequence_only"));
+ seqAssociated
+ .setText(MessageManager.getString("label.per_sequence_only"));
seqAssociated.addActionListener(new ActionListener()
{
private void setDefaultMinMax()
{
- minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
- Color.orange));
- maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
- Color.red));
+ minColour.setBackground(
+ Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
+ maxColour.setBackground(
+ Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
}
public void minColour_actionPerformed()
{
if (slider.isEnabled())
{
- if (useOriginalColours.isSelected()
- && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+ if (useOriginalColours.isSelected() && !(av
+ .getGlobalColourScheme() instanceof AnnotationColourGradient))
{
updateView();
}
getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
propagateSeqAssociatedThreshold(updateAllAnnotation,
getCurrentAnnotation());
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
}
return;
}
- setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[annotations
- .getSelectedIndex()]]);
+ setCurrentAnnotation(
+ av.getAlignment().getAlignmentAnnotation()[annmap[annotations
+ .getSelectedIndex()]]);
- int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
- .getSelectedIndex());
+ int selectedThresholdItem = getSelectedThresholdItem(
+ getThreshold().getSelectedIndex());
slider.setEnabled(true);
thresholdValue.setEnabled(true);
else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
&& getCurrentAnnotation().threshold == null)
{
- getCurrentAnnotation()
- .setThreshold(
- new GraphLine(
- (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
- "Threshold", Color.black));
+ getCurrentAnnotation().setThreshold(new GraphLine(
+ (getCurrentAnnotation().graphMax
+ - getCurrentAnnotation().graphMin) / 2f,
+ "Threshold", Color.black));
}
if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
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));
+ 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));
slider.setEnabled(true);
colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
ap.alignmentChanged();
- // ensure all associated views (overviews, structures, etc) are notified of
- // updated colours.
- ap.paintAlignment(true);
}
- protected boolean colorAlignmentContaining(AlignmentAnnotation currentAnn, int selectedThresholdOption)
+ protected void colorAlignmentContaining(AlignmentAnnotation currentAnn,
+ int selectedThresholdOption)
{
-
+
AnnotationColourGradient acg = null;
if (useOriginalColours.isSelected())
{
selectedThresholdOption);
}
acg.setSeqAssociated(seqAssociated.isSelected());
-
+
if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
{
acg.setPredefinedColours(true);
}
-
+
acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
-
+
av.setGlobalColourScheme(acg);
-
+
if (av.getAlignment().getGroups() != null)
{
-
+
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
if (sg.cs == null)
{
continue;
}
-
- if (useOriginalColours.isSelected())
- {
- sg.setColourScheme(new AnnotationColourGradient(currentAnn, sg
- .getColourScheme(), selectedThresholdOption));
- ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
- .isSelected());
- }
- else
- {
- sg.setColourScheme(new AnnotationColourGradient(currentAnn,
- minColour.getBackground(), maxColour.getBackground(),
- selectedThresholdOption));
- ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
- .isSelected());
- }
+ sg.setColourScheme(
+ acg.getInstance(sg, ap.av.getHiddenRepSequences()));
}
}
- return false;
}
}