import java.awt.event.ActionListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
-import java.util.Hashtable;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Map.Entry;
import java.util.Vector;
import javax.swing.BorderFactory;
private JButton defColours;
- private Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
+ private Map<SequenceGroup, ColourSchemeI> oldgroupColours;
- private JCheckBox currentColours = new JCheckBox();
+ private Map<AlignmentAnnotation, GraphLine> oldGraphLines;
+
+ private Map<GraphLine, Float> oldThresholds;
+
+ private JCheckBox useOriginalColours = new JCheckBox();
private JPanel minColour = new JPanel();
private JCheckBox thresholdIsMin = new JCheckBox();
+ protected static final int MIN_WIDTH = 500;
+
+ protected static final int MIN_HEIGHT = 240;
+
+ /**
+ * Constructor
+ *
+ * @param av
+ * @param ap
+ */
public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
{
super(av, ap);
- oldcs = av.getGlobalColourScheme();
- if (av.getAlignment().getGroups() != null)
- {
- oldgroupColours = new Hashtable<SequenceGroup, ColourSchemeI>();
- for (SequenceGroup sg : ap.av.getAlignment().getGroups())
- {
- if (sg.cs != null)
- {
- oldgroupColours.put(sg, sg.cs);
- }
- }
- }
+
+ saveInitialState();
+
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
Desktop.addInternalFrame(frame,
MessageManager.getString("label.colour_by_annotation"), 520,
215);
-
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
addSliderChangeListener();
addSliderMouseListeners();
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- currentColours.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());
frame.pack();
}
+ /**
+ * Saves the global and group colour schemes as they are when the dialog is
+ * opened, so they can be restored on Cancel. Note we also save the threshold
+ * value for each annotation, in case this gets modified.
+ */
+ void saveInitialState()
+ {
+ oldcs = av.getGlobalColourScheme();
+ if (av.getAlignment().getGroups() != null)
+ {
+ oldgroupColours = new HashMap<>();
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ {
+ if (sg.getColourScheme() != null)
+ {
+ oldgroupColours.put(sg, sg.getColourScheme());
+ }
+ }
+ }
+
+ /*
+ * save any existing annotation threshold settings; note we make a copy
+ * of each in case the current threshold value gets amended
+ */
+ oldGraphLines = new HashMap<>();
+ oldThresholds = new HashMap<>();
+ AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+ if (anns != null)
+ {
+ for (AlignmentAnnotation ann : anns)
+ {
+ GraphLine thresh = ann.getThreshold();
+ oldGraphLines.put(ann, thresh);
+ if (thresh != null)
+ {
+ oldThresholds.put(thresh, thresh.value);
+ }
+ }
+ }
+ }
+
@Override
protected void jbInit()
{
}
});
- currentColours.setFont(JvSwingUtils.getLabelFont());
- currentColours.setOpaque(false);
- currentColours.setText(MessageManager
- .getString("label.use_original_colours"));
- currentColours.addActionListener(new ActionListener()
+ useOriginalColours.setFont(JvSwingUtils.getLabelFont());
+ useOriginalColours.setOpaque(false);
+ useOriginalColours.setText(
+ MessageManager.getString("label.use_original_colours"));
+ useOriginalColours.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- currentColours_actionPerformed();
+ originalColours_actionPerformed();
}
});
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()
{
jPanel1.add(cancel);
jPanel2.add(annotations, "grow, wrap");
jPanel2.add(seqAssociated);
- jPanel2.add(currentColours);
+ jPanel2.add(useOriginalColours);
JPanel colpanel = new JPanel(new FlowLayout());
colpanel.setBackground(Color.white);
colpanel.add(minColour);
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()
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- sg.cs = oldgroupColours.get(sg);
+ sg.setColourScheme(oldgroupColours.get(sg));
+ }
+ }
+ for (Entry<AlignmentAnnotation, GraphLine> entry : oldGraphLines
+ .entrySet())
+ {
+ GraphLine graphLine = entry.getValue();
+ entry.getKey().setThreshold(graphLine);
+ if (graphLine != null)
+ {
+ graphLine.value = oldThresholds.get(graphLine).floatValue();
}
}
}
{
if (slider.isEnabled())
{
- if (currentColours.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);
}
}
- public void currentColours_actionPerformed()
+ public void originalColours_actionPerformed()
{
- if (currentColours.isSelected())
+ boolean selected = useOriginalColours.isSelected();
+ if (selected)
{
reset();
}
- maxColour.setEnabled(!currentColours.isSelected());
- minColour.setEnabled(!currentColours.isSelected());
+ maxColour.setEnabled(!selected);
+ minColour.setEnabled(!selected);
+ thresholdIsMin.setEnabled(!selected);
updateView();
}
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);
- thresholdIsMin.setEnabled(true);
+ thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
{
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 (currentColours.isSelected())
+ if (useOriginalColours.isSelected())
{
acg = new AnnotationColourGradient(currentAnn,
av.getGlobalColourScheme(), selectedThresholdOption);
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 (currentColours.isSelected())
- {
- sg.cs = new AnnotationColourGradient(currentAnn, sg.cs,
- selectedThresholdOption);
- ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
- .isSelected());
- }
- else
- {
- sg.cs = new AnnotationColourGradient(currentAnn,
- minColour.getBackground(), maxColour.getBackground(),
- selectedThresholdOption);
- ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
- .isSelected());
- }
+ sg.setColourScheme(
+ acg.getInstance(sg, ap.av.getHiddenRepSequences()));
}
}
- return false;
+ }
+
+ @Override
+ protected void sliderDragReleased()
+ {
+ super.sliderDragReleased();
+ ap.paintAlignment(true, true);
}
}
git://source.jalview.org / jalview.git / blobdiff