*/
package jalview.gui;
-import jalview.bin.Cache;
-import jalview.datamodel.SequenceGroup;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.ColourSchemeI;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.util.Hashtable;
+import java.util.Vector;
import javax.swing.BorderFactory;
import javax.swing.JButton;
-import javax.swing.JColorChooser;
+import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JInternalFrame;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.SequenceGroup;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
import net.miginfocom.swing.MigLayout;
@SuppressWarnings("serial")
public class AnnotationColourChooser extends AnnotationRowFilter
{
+ private ColourSchemeI oldcs;
- ColourSchemeI oldcs;
+ private JButton defColours;
- Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
-
- /**
- * enabled if the user is dragging the slider - try to keep updates to a
- * minimun
- */
+ private Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
- JComboBox<String> annotations;
+ private JCheckBox useOriginalColours = new JCheckBox();
- JButton defColours = new JButton();
+ JPanel minColour = new JPanel();
- JPanel jPanel1 = new JPanel();
+ JPanel maxColour = new JPanel();
- JPanel jPanel2 = new JPanel();
+ private JCheckBox thresholdIsMin = new JCheckBox();
- BorderLayout borderLayout1 = new BorderLayout();
+ protected static final int MIN_WIDTH = 500;
- private JComboBox<String> threshold = new JComboBox<String>();
+ protected static final int MIN_HEIGHT = 240;
public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
{
+ this(av,ap,null);
+ }
+ public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap,AnnotationColourGradient initSettings)
+ {
super(av, ap);
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)
}
}
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
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();
setDefaultMinMax();
adjusting = true;
- if (oldcs instanceof AnnotationColourGradient)
+ if (oldcs instanceof AnnotationColourGradient && initSettings==null)
{
- AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- currentColours.setSelected(acg.isPredefinedColours()
- || acg.getBaseColour() != null);
+ // init from oldcs
+ initialiseFrom((AnnotationColourGradient) oldcs);
+ } else {
+ // use initial colour gradient - if any..
+ initialiseFrom(initSettings);
+ }
+
+ jbInit();
+ adjusting = false;
+
+ updateView();
+ frame.invalidate();
+ frame.pack();
+ }
+ private void initialiseFrom(AnnotationColourGradient acg)
+ {
+ if (acg!=null)
+ {
+ useOriginalColours.setSelected(
+ acg.isPredefinedColours() || acg.getBaseColour() != null);
if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
{
minColour.setBackground(acg.getMinColour());
seqAssociated.setSelected(acg.isSeqAssociated());
}
- annotations = new JComboBox<String>(
- getAnnotationItems(seqAssociated.isSelected()));
+ Vector<String> annotItems = getAnnotationItems(
+ seqAssociated.isSelected());
+ annotations = new JComboBox<>(annotItems);
populateThresholdComboBox(threshold);
- if (oldcs instanceof AnnotationColourGradient)
+ if (acg!=null)
{
- AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- annotations.setSelectedItem(acg.getAnnotation());
+ String label = getAnnotationMenuLabel(acg.getAnnotation());
+ // TODO: workaround below shouldn't be necessary - there's a bug in getAnnotationMenuLabel!
+ if (acg.isSeqAssociated())
+ {
+ label = acg.getAnnotation().label;
+ }
+ annotations.setSelectedItem(label);
switch (acg.getAboveThreshold())
{
case AnnotationColourGradient.NO_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.thresholdIsMinMax);
- thresholdValue.setText("" + acg.getAnnotationThreshold());
- }
-
- try
- {
- jbInit();
- } catch (Exception ex)
- {
+ thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
+ thresholdValue.setText(String.valueOf(acg.getAnnotationThreshold()));
}
- adjusting = false;
-
- updateView();
- frame.invalidate();
- frame.pack();
}
- public AnnotationColourChooser()
+ @Override
+ protected void jbInit()
{
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
+ super.jbInit();
- private void jbInit() throws Exception
- {
minColour.setFont(JvSwingUtils.getLabelFont());
minColour.setBorder(BorderFactory.createEtchedBorder());
minColour.setPreferredSize(new Dimension(40, 20));
{
if (minColour.isEnabled())
{
- minColour_actionPerformed();
+ showColourChooser(minColour, "label.select_colour_minimum_value");
}
}
});
{
if (maxColour.isEnabled())
{
- maxColour_actionPerformed();
+ showColourChooser(maxColour, "label.select_colour_maximum_value");
}
}
});
- ok.setOpaque(false);
- ok.setText(MessageManager.getString("action.ok"));
- ok.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- ok_actionPerformed();
- }
- });
- cancel.setOpaque(false);
- cancel.setText(MessageManager.getString("action.cancel"));
- cancel.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- cancel_actionPerformed();
- }
- });
+
+ defColours = new JButton();
defColours.setOpaque(false);
defColours.setText(MessageManager.getString("action.set_defaults"));
defColours.setToolTipText(MessageManager
}
});
- annotations.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- annotations_actionPerformed();
- }
- });
- getThreshold().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)
{
- threshold_actionPerformed();
- }
- });
- thresholdValue.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- thresholdValue_actionPerformed();
- }
- });
- slider.setPaintLabels(false);
- slider.setPaintTicks(true);
- slider.setBackground(Color.white);
- slider.setEnabled(false);
- slider.setOpaque(false);
- slider.setPreferredSize(new Dimension(100, 32));
- thresholdValue.setEnabled(false);
- thresholdValue.setColumns(7);
- currentColours.setFont(JvSwingUtils.getLabelFont());
- currentColours.setOpaque(false);
- currentColours.setText(MessageManager
- .getString("label.use_original_colours"));
- currentColours.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()
{
}
});
- this.setLayout(borderLayout1);
+ this.setLayout(new BorderLayout());
+ JPanel jPanel1 = new JPanel();
+ JPanel jPanel2 = new JPanel();
jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
jPanel1.setBackground(Color.white);
jPanel2.setBackground(Color.white);
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()
+ protected void showColourChooser(JPanel colourPanel, String titleKey)
{
- Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_colour_minimum_value"),
- minColour.getBackground());
- if (col != null)
+ String ttl = MessageManager.getString(titleKey);
+ ColourChooserListener listener = new ColourChooserListener()
{
- minColour.setBackground(col);
- }
- minColour.repaint();
- updateView();
- }
-
- public void maxColour_actionPerformed()
- {
- Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_colour_maximum_value"),
- maxColour.getBackground());
- if (col != null)
- {
- maxColour.setBackground(col);
- }
- maxColour.repaint();
- updateView();
+ @Override
+ public void colourSelected(Color c)
+ {
+ colourPanel.setBackground(c);
+ colourPanel.repaint();
+ updateView();
+ }
+ };
+ JalviewColourChooser.showColourChooser(Desktop.getDesktop(), ttl,
+ colourPanel.getBackground(), listener);
}
@Override
public void reset()
{
- av.setGlobalColourScheme(oldcs);
+ this.ap.alignFrame.changeColour(oldcs);
if (av.getAlignment().getGroups() != null)
{
{
if (slider.isEnabled())
{
- if (currentColours.isSelected()
- && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+ if (useOriginalColours.isSelected() && !(av
+ .getGlobalColourScheme() instanceof AnnotationColourGradient))
{
updateView();
}
- getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+ getCurrentAnnotation().threshold.value = getSliderValue();
propagateSeqAssociatedThreshold(updateAllAnnotation,
getCurrentAnnotation());
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
}
- public JComboBox<String> getThreshold()
- {
- return threshold;
- }
-
- public void setThreshold(JComboBox<String> threshold)
- {
- this.threshold = threshold;
- }
-
- 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()]]);
+ int selIndex = annotations
+ .getSelectedIndex();
+ int annIndex = annmap[selIndex];
+ setCurrentAnnotation(
+ av.getAlignment().getAlignmentAnnotation()[annIndex]);
- int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
- .getSelectedIndex());
+ int selectedThresholdItem = getSelectedThresholdItem(
+ getThreshold().getSelectedIndex());
slider.setEnabled(true);
thresholdValue.setEnabled(true);
- thresholdIsMin.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 jalview.datamodel.GraphLine(
- (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
- "Threshold", Color.black));
+ currentAnnotation.setThreshold(new GraphLine(
+ (currentAnnotation.graphMax - currentAnnotation.graphMin)
+ / 2f,
+ "Threshold", Color.black));
}
if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
{
adjusting = true;
- float range = getCurrentAnnotation().graphMax * 1000
- - getCurrentAnnotation().graphMin * 1000;
-
- slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
- slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
- slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
- 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;
}
- colorAlignmContaining(getCurrentAnnotation(), selectedThresholdItem);
+ colorAlignmentContaining(currentAnnotation, selectedThresholdItem);
ap.alignmentChanged();
- // ensure all associated views (overviews, structures, etc) are notified of
- // updated colours.
- ap.paintAlignment(true);
}
+ protected void colorAlignmentContaining(AlignmentAnnotation currentAnn,
+ int selectedThresholdOption)
+ {
+
+ AnnotationColourGradient acg = null;
+ if (useOriginalColours.isSelected())
+ {
+ acg = new AnnotationColourGradient(currentAnn,
+ av.getGlobalColourScheme(), selectedThresholdOption);
+ }
+ else
+ {
+ acg = new AnnotationColourGradient(currentAnn,
+ minColour.getBackground(), maxColour.getBackground(),
+ selectedThresholdOption);
+ }
+ acg.setSeqAssociated(seqAssociated.isSelected());
+
+ if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
+ {
+ acg.setPredefinedColours(true);
+ }
+
+ acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
+
+ this.ap.alignFrame.changeColour(acg);
+
+ if (av.getAlignment().getGroups() != null)
+ {
+
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ {
+ if (sg.cs == null)
+ {
+ continue;
+ }
+ sg.setColourScheme(acg.getInstance(av, sg));
+ }
+ }
+ }
+
+ @Override
+ protected void sliderDragReleased()
+ {
+ super.sliderDragReleased();
+ ap.paintAlignment(true, true);
+ }
+
+ /**
+ * construct and display a colourchooser for a given annotation row
+ *
+ * @param av
+ * @param ap
+ * @param alignmentAnnotation
+ * @param perseq - when true, enable per-sequence if alignment annotation is per sequence
+ */
+ public static void displayFor(AlignViewport av, AlignmentPanel ap,
+ AlignmentAnnotation alignmentAnnotation, boolean perSeq)
+ {
+ ColourSchemeI global = av.getGlobalColourScheme();
+ AnnotationColourGradient newCS = new AnnotationColourGradient(alignmentAnnotation, global, alignmentAnnotation.threshold!=null ? AnnotationColourGradient.ABOVE_THRESHOLD:AnnotationColourGradient.NO_THRESHOLD);
+ if (alignmentAnnotation.sequenceRef!=null)
+ {
+ newCS.setSeqAssociated(perSeq);
+ }
+ for (int i=0;i<alignmentAnnotation.annotations.length;i++)
+ {
+ Annotation ann = alignmentAnnotation.annotations[i];
+ if (ann!=null && ann.colour!=null && !ann.colour.equals(Color.white))
+ {
+ newCS.setPredefinedColours(true);
+ break;
+ }
+ }
+ AnnotationColourChooser achooser = new AnnotationColourChooser(av,ap,newCS);
+ }
}
git://source.jalview.org / jalview.git / blobdiff