import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.UserColourScheme;
import jalview.structure.SelectionSource;
import jalview.util.Format;
import jalview.util.MessageManager;
import java.util.List;
import java.util.Vector;
-import javax.swing.JColorChooser;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
TreePanel tp;
- AlignViewport av;
+ private AlignViewport av;
- AlignmentPanel ap;
+ private AlignmentPanel ap;
Font font;
int offy;
- float threshold;
+ private float threshold;
String longestName;
{
this.tp = tp;
this.av = ap.av;
- this.ap = ap;
+ this.setAssociatedPanel(ap);
font = av.getFont();
scrollPane = scroller;
addMouseListener(this);
node.color = c;
if (node.element() instanceof SequenceI)
{
+ final SequenceI seq = (SequenceI) node.element();
AlignmentPanel[] aps = getAssociatedPanels();
if (aps != null)
{
for (int a = 0; a < aps.length; a++)
{
- final SequenceI seq = (SequenceI) node.element();
aps[a].av.setSequenceColour(seq, c);
}
}
}
- if ((node.left() != null) || (node.right() != null)) // TODO: internal node
- {
- setColor((SequenceNode) node.left(), c);
- setColor((SequenceNode) node.right(), c);
- }
+ setColor((SequenceNode) node.left(), c);
+ setColor((SequenceNode) node.right(), c);
}
/**
*/
if (e.isPopupTrigger())
{
- chooseSubtreeColour();
+ if (highlightNode != null) {
+ chooseSubtreeColour();
+ }
e.consume(); // prevent mouseClicked happening
}
}
*/
void chooseSubtreeColour()
{
- Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_subtree_colour"),
- highlightNode.color);
- if (col != null)
- {
- setColor(highlightNode, col);
- PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
- repaint();
- }
+ String ttl = MessageManager.getString("label.select_subtree_colour");
+ ColourChooserListener listener = new ColourChooserListener() {
+ @Override
+ public void colourSelected(Color c)
+ {
+ setColor(highlightNode, c);
+ PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+ repaint();
+ }
+ };
+ JalviewColourChooser.showColourChooser(this, ttl, highlightNode.color, listener);
}
@Override
if (ob instanceof SequenceI)
{
treeSelectionChanged((Sequence) ob);
- PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+ PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId());
repaint();
av.sendSelection();
return;
.deleteAllGroups();
aps[a].av.getCodingComplement().clearSequenceColours();
}
+ aps[a].av.setUpdateStructures(true);
}
colourGroups(groups);
}
}
- PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+ PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId());
repaint();
}
}
ColourSchemeI cs = null;
- SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true,
+ SequenceGroup _sg = new SequenceGroup(sequences, null, cs, true, true,
false, 0, av.getAlignment().getWidth() - 1);
- if (av.getGlobalColourScheme() != null)
- {
- if (av.getGlobalColourScheme() instanceof UserColourScheme)
- {
- cs = new UserColourScheme(
- ((UserColourScheme) av.getGlobalColourScheme())
- .getColours());
-
- }
- else
- {
- cs = ColourSchemeProperty.getColourScheme(av, sg,
- ColourSchemeProperty
- .getColourName(av.getGlobalColourScheme()));
- }
- // cs is null if shading is an annotationColourGradient
- // if (cs != null)
- // {
- // cs.setThreshold(av.getViewportColourScheme().getThreshold(),
- // av.isIgnoreGapsConsensus());
- // }
- }
- sg.setColourScheme(cs);
- sg.getGroupColourScheme().setThreshold(
- av.getResidueShading().getThreshold(),
- av.isIgnoreGapsConsensus());
- // sg.recalcConservation();
- sg.setName("JTreeGroup:" + sg.hashCode());
- sg.setIdColour(col);
+ _sg.setName("JTreeGroup:" + _sg.hashCode());
+ _sg.setIdColour(col);
for (int a = 0; a < aps.length; a++)
{
- if (aps[a].av.getGlobalColourScheme() != null
- && aps[a].av.getResidueShading().conservationApplied())
+ SequenceGroup sg = new SequenceGroup(_sg);
+ AlignViewport viewport = aps[a].av;
+
+ // Propagate group colours in each view
+ if (viewport.getGlobalColourScheme() != null)
{
- Conservation c = new Conservation("Group", sg.getSequences(null),
- sg.getStartRes(), sg.getEndRes());
- c.calculate();
- c.verdict(false, aps[a].av.getConsPercGaps());
- sg.cs.setConservation(c);
+ cs = viewport.getGlobalColourScheme().getInstance(viewport, sg);
+ sg.setColourScheme(cs);
+ sg.getGroupColourScheme().setThreshold(
+ viewport.getResidueShading().getThreshold(),
+ viewport.isIgnoreGapsConsensus());
+
+ if (viewport.getResidueShading().conservationApplied())
+ {
+ Conservation c = new Conservation("Group",
+ sg.getSequences(null), sg.getStartRes(),
+ sg.getEndRes());
+ c.calculate();
+ c.verdict(false, viewport.getConsPercGaps());
+ sg.cs.setConservation(c);
+ }
}
// indicate that associated structure views will need an update
- aps[a].av.setUpdateStructures(true);
+ viewport.setUpdateStructures(true);
// propagate structure view update and sequence group to complement view
- aps[a].av.addSequenceGroup(new SequenceGroup(sg));
+ viewport.addSequenceGroup(sg);
}
}
}
else
{
- return new AlignmentPanel[] { ap };
+ return new AlignmentPanel[] { getAssociatedPanel() };
}
}
+
+ public AlignmentPanel getAssociatedPanel()
+ {
+ return ap;
+ }
+
+ public void setAssociatedPanel(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ }
+
+ public AlignViewport getViewport()
+ {
+ return av;
+ }
+
+ public void setViewport(AlignViewport av)
+ {
+ this.av = av;
+ }
+
+ public float getThreshold()
+ {
+ return threshold;
+ }
+
+ public void setThreshold(float threshold)
+ {
+ this.threshold = threshold;
+ }
+
+ public boolean isApplyToAllViews()
+ {
+ return this.applyToAllViews;
+ }
+
+ public void setApplyToAllViews(boolean applyToAllViews)
+ {
+ this.applyToAllViews = applyToAllViews;
+ }
}
git://source.jalview.org / jalview.git / blobdiff