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Make sure sequence is in mouse over alignment
[jalview.git]
/
src
/
jalview
/
appletgui
/
AppletJmol.java
diff --git
a/src/jalview/appletgui/AppletJmol.java
b/src/jalview/appletgui/AppletJmol.java
index
375fe4d
..
4951516
100644
(file)
--- a/
src/jalview/appletgui/AppletJmol.java
+++ b/
src/jalview/appletgui/AppletJmol.java
@@
-30,7
+30,6
@@
import jalview.io.*;
import org.jmol.api.*;
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.api.*;
import org.jmol.adapter.smarter.SmarterJmolAdapter;
-
import org.jmol.popup.*;
import jalview.schemes.*;
import org.jmol.popup.*;
import jalview.schemes.*;
@@
-94,13
+93,13
@@
public class AppletJmol extends Frame
{
StructureSelectionManager.getStructureSelectionManager()
.setMapping(seq, pdbentry.getFile(), protocol);
{
StructureSelectionManager.getStructureSelectionManager()
.setMapping(seq, pdbentry.getFile(), protocol);
- return;
+ //PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
+ //FOR NOW, LETS JUST OPEN A NEW WINDOW
}
renderPanel = new RenderPanel();
this.add(renderPanel, BorderLayout.CENTER);
}
renderPanel = new RenderPanel();
this.add(renderPanel, BorderLayout.CENTER);
-
viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter());
viewer.setAppletContext("jalview",
viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter());
viewer.setAppletContext("jalview",
@@
-462,6
+461,14
@@
public class AppletJmol extends Frame
//End StructureListener
////////////////////////////
//End StructureListener
////////////////////////////
+ public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
+ {
+ if (!pdbfile.equals(pdbentry.getFile()))
+ return null;
+
+ return new Color(viewer.getAtomArgb(atomIndex));
+ }
+
FeatureRenderer fr;
public void colourBySequence(AlignmentPanel ap)
{
FeatureRenderer fr;
public void colourBySequence(AlignmentPanel ap)
{
@@
-495,7
+502,8
@@
public class AppletJmol extends Frame
{
for (int m = 0; m < mapping.length; m++)
{
{
for (int m = 0; m < mapping.length; m++)
{
- if (mapping[m].getSequence() == sequence[s])
+ if (mapping[m].getSequence() == sequence[s]
+ && ap.av.alignment.findIndex(sequence[s])>-1)
{
for (int r = 0; r < sequence[s].getLength(); r++)
{
{
for (int r = 0; r < sequence[s].getLength(); r++)
{