*/
package jalview.gui;
-import jalview.analysis.Conservation;
-import jalview.analysis.TreeModel;
-import jalview.api.AlignViewportI;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.SequenceNode;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.UserColourScheme;
-import jalview.structure.SelectionSource;
-import jalview.util.Format;
-import jalview.util.MappingUtils;
-import jalview.util.MessageManager;
-
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.print.Printable;
import java.awt.print.PrinterException;
import java.awt.print.PrinterJob;
-import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
import java.util.Vector;
-import javax.swing.JColorChooser;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
import javax.swing.ToolTipManager;
+import jalview.analysis.Conservation;
+import jalview.analysis.TreeModel;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.schemes.ColourSchemeI;
+import jalview.structure.SelectionSource;
+import jalview.util.Format;
+import jalview.util.MessageManager;
+
/**
* DOCUMENT ME!
*
TreePanel tp;
- AlignViewport av;
+ private AlignViewport av;
- AlignmentPanel ap;
+ private AlignmentPanel ap;
Font font;
int offy;
- float threshold;
+ private float threshold;
String longestName;
int labelLength = -1;
- Hashtable nameHash = new Hashtable();
+ Map<Object, Rectangle> nameHash = new Hashtable<>();
- Hashtable nodeHash = new Hashtable();
+ Map<SequenceNode, Rectangle> nodeHash = new Hashtable<>();
SequenceNode highlightNode;
{
this.tp = tp;
this.av = ap.av;
- this.ap = ap;
+ this.setAssociatedPanel(ap);
font = av.getFont();
scrollPane = scroller;
addMouseListener(this);
*/
public Object findElement(int x, int y)
{
- Enumeration keys = nameHash.keys();
-
- while (keys.hasMoreElements())
+ for (Entry<Object, Rectangle> entry : nameHash.entrySet())
{
- Object ob = keys.nextElement();
- Rectangle rect = (Rectangle) nameHash.get(ob);
+ Rectangle rect = entry.getValue();
if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y)
&& (y <= (rect.y + rect.height)))
{
- return ob;
+ return entry.getKey();
}
}
- keys = nodeHash.keys();
-
- while (keys.hasMoreElements())
+ for (Entry<SequenceNode, Rectangle> entry : nodeHash.entrySet())
{
- Object ob = keys.nextElement();
- Rectangle rect = (Rectangle) nodeHash.get(ob);
+ Rectangle rect = entry.getValue();
if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y)
&& (y <= (rect.y + rect.height)))
{
- return ob;
+ return entry.getKey();
}
}
if ((node.left() == null) && (node.right() == null))
{
double height = node.height;
- double dist = node.dist;
-
- int xstart = (int) ((height - dist) * wscale) + offx;
+ // double dist = node.dist;
+ // int xstart = (int) ((height - dist) * wscale) + offx;
int xend = (int) (height * wscale) + offx;
int ypos = (int) (node.ycount * chunk) + offy;
return;
}
- if ((node.left() == null) && (node.right() == null)) // TODO: internal node
+ node.color = c;
+ if (node.element() instanceof SequenceI)
{
- node.color = c;
-
- if (node.element() instanceof SequenceI)
+ final SequenceI seq = (SequenceI) node.element();
+ AlignmentPanel[] aps = getAssociatedPanels();
+ if (aps != null)
{
- AlignmentPanel[] aps = getAssociatedPanels();
- if (aps != null)
+ for (int a = 0; a < aps.length; a++)
{
- for (int a = 0; a < aps.length; a++)
- {
- final SequenceI seq = (SequenceI) node.element();
- aps[a].av.setSequenceColour(seq, c);
- }
+ aps[a].av.setSequenceColour(seq, c);
}
}
}
- else
- {
- node.color = c;
- setColor((SequenceNode) node.left(), c);
- setColor((SequenceNode) node.right(), c);
- }
+ setColor((SequenceNode) node.left(), c);
+ setColor((SequenceNode) node.right(), c);
}
/**
{
fm = g.getFontMetrics(font);
- if (nameHash.size() == 0)
+ int nameCount = nameHash.size();
+ if (nameCount == 0)
{
repaint();
}
if (fitToWindow || (!fitToWindow && (scrollPane
- .getHeight() > ((fm.getHeight() * nameHash.size()) + offy))))
+ .getHeight() > ((fm.getHeight() * nameCount) + offy))))
{
draw(g, scrollPane.getWidth(), scrollPane.getHeight());
setPreferredSize(null);
else
{
setPreferredSize(new Dimension(scrollPane.getWidth(),
- fm.getHeight() * nameHash.size()));
- draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());
+ fm.getHeight() * nameCount));
+ draw(g, scrollPane.getWidth(), fm.getHeight() * nameCount);
}
scrollPane.revalidate();
*/
void chooseSubtreeColour()
{
- Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_subtree_colour"),
- highlightNode.color);
- if (col != null)
+ String ttl = MessageManager.getString("label.select_subtree_colour");
+ ColourChooserListener listener = new ColourChooserListener()
{
- setColor(highlightNode, col);
- PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
- repaint();
- }
+ @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);
+
+ /*
+ * clear partition (don't show vertical line) if
+ * it is to the right of all nodes
+ */
+ if (groups.isEmpty())
+ {
+ threshold = 0f;
+ }
}
- 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(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())
- {
- 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);
- }
+ SequenceGroup sg = new SequenceGroup(_sg);
+ AlignViewport viewport = aps[a].av;
- aps[a].av.getAlignment().addGroup(new SequenceGroup(sg));
- // TODO can we push all of the below into AlignViewportI?
- final AlignViewportI codingComplement = aps[a].av
- .getCodingComplement();
- if (codingComplement != null)
+ // Propagate group colours in each view
+ if (viewport.getGlobalColourScheme() != null)
{
- SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av,
- codingComplement);
- if (mappedGroup.getSequences().size() > 0)
+ cs = viewport.getGlobalColourScheme().getInstance(viewport, sg);
+ sg.setColourScheme(cs);
+ sg.getGroupColourScheme().setThreshold(
+ viewport.getResidueShading().getThreshold(),
+ viewport.isIgnoreGapsConsensus());
+
+ if (viewport.getResidueShading().conservationApplied())
{
- codingComplement.getAlignment().addGroup(mappedGroup);
- for (SequenceI seq : mappedGroup.getSequences())
- {
- codingComplement.setSequenceColour(seq, col.brighter());
- }
+ 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
+ viewport.setUpdateStructures(true);
+ // propagate structure view update and sequence group to complement view
+ viewport.addSequenceGroup(sg);
}
}
- // notify the panel(s) to redo any group specific stuff.
+ // notify the panel(s) to redo any group specific stuff
+ // also updates structure views if necessary
for (int a = 0; a < aps.length; a++)
{
aps[a].updateAnnotation();
- // TODO: JAL-868 - need to ensure view colour change message is broadcast
- // to any Jmols listening in
final AlignViewportI codingComplement = aps[a].av
.getCodingComplement();
if (codingComplement != null)
}
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