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still trying to prevent null painting
[jalview.git]
/
src
/
jalview
/
appletgui
/
AppletJmol.java
diff --git
a/src/jalview/appletgui/AppletJmol.java
b/src/jalview/appletgui/AppletJmol.java
index
375fe4d
..
14e6704
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.*;
@@
-68,6
+67,7
@@
public class AppletJmol extends Frame
TextField inputLine;
TextArea history;
SequenceI[] sequence;
TextField inputLine;
TextArea history;
SequenceI[] sequence;
+ String [] chains;
StructureSelectionManager ssm;
RenderPanel renderPanel;
AlignmentPanel ap;
StructureSelectionManager ssm;
RenderPanel renderPanel;
AlignmentPanel ap;
@@
-79,11
+79,13
@@
public class AppletJmol extends Frame
public AppletJmol(PDBEntry pdbentry,
SequenceI[] seq,
public AppletJmol(PDBEntry pdbentry,
SequenceI[] seq,
+ String[] chains,
AlignmentPanel ap,
String protocol)
{
this.ap = ap;
this.sequence = seq;
AlignmentPanel ap,
String protocol)
{
this.ap = ap;
this.sequence = seq;
+ this.chains = chains;
this.pdbentry = pdbentry;
String alreadyMapped = StructureSelectionManager
this.pdbentry = pdbentry;
String alreadyMapped = StructureSelectionManager
@@
-93,14
+95,14
@@
public class AppletJmol extends Frame
if (alreadyMapped != null)
{
StructureSelectionManager.getStructureSelectionManager()
if (alreadyMapped != null)
{
StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, pdbentry.getFile(), protocol);
- return;
+ .setMapping(seq, chains, pdbentry.getFile(), protocol);
+ //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",
@@
-167,9
+169,7
@@
public class AppletJmol extends Frame
viewer.openFile(pdbentry.getFile());
}
viewer.openFile(pdbentry.getFile());
}
- this.setBounds(400, 400, 400, 400);
-
- this.setVisible(true);
+ jalview.bin.JalviewLite.addFrame(this, "Jmol", 400,400);
}
public void loadInline(String string)
}
public void loadInline(String string)
@@
-441,14
+441,15
@@
public class AppletJmol extends Frame
resetLastRes.append(":" + chain);
}
resetLastRes.append(":" + chain);
}
- eval.append(";color gold;wireframe 100");
+ eval.append(";wireframe 100");//;color gold
Color col = new Color(viewer.getAtomArgb(atomIndex));
Color col = new Color(viewer.getAtomArgb(atomIndex));
- resetLastRes.append(";color["
- + col.getRed() + ","
- + col.getGreen() + ","
- + col.getBlue() + "];wireframe 0");
+ resetLastRes.append(";wireframe 0;"//color["
+ // + col.getRed() + ","
+ // + col.getGreen() + ","
+ // + col.getBlue() + "]"
+ );
viewer.evalStringQuiet(eval.toString());
viewer.evalStringQuiet(eval.toString());
@@
-462,7
+463,16
@@
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;
FeatureRenderer fr;
+ String lastCommand;
public void colourBySequence(AlignmentPanel ap)
{
if(!colourBySequence)
public void colourBySequence(AlignmentPanel ap)
{
if(!colourBySequence)
@@
-474,7
+484,7
@@
public class AppletJmol extends Frame
if (mapping.length < 1)
return;
if (mapping.length < 1)
return;
- SequenceRenderer sr = ap.seqPanel.seqCanvas.getSequenceRenderer();
+ SequenceRenderer sr = new SequenceRenderer(ap.av);
boolean showFeatures = false;
if (ap.av.showSequenceFeatures)
boolean showFeatures = false;
if (ap.av.showSequenceFeatures)
@@
-495,7
+505,8
@@
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++)
{
@@
-540,7
+551,10
@@
public class AppletJmol extends Frame
}
}
}
}
- viewer.evalStringQuiet(command.toString());
+ if (lastCommand == null || !lastCommand.equals(command.toString()))
+ viewer.evalStringQuiet(command.toString());
+
+ lastCommand = command.toString();
}
StringBuffer condenseCommand(String command, int pos)
}
StringBuffer condenseCommand(String command, int pos)
@@
-608,14
+622,14
@@
public class AppletJmol extends Frame
MCview.PDBfile pdb;
if (loadedInline)
{
MCview.PDBfile pdb;
if (loadedInline)
{
- pdb = ssm.setMapping(sequence,
+ pdb = ssm.setMapping(sequence,chains,
pdbentry.getFile(),
AppletFormatAdapter.PASTE);
pdbentry.setFile("INLINE"+pdb.id);
}
else
{
pdbentry.getFile(),
AppletFormatAdapter.PASTE);
pdbentry.setFile("INLINE"+pdb.id);
}
else
{
- pdb = ssm.setMapping(sequence,
+ pdb = ssm.setMapping(sequence,chains,
pdbentry.getFile(),
AppletFormatAdapter.URL);
}
pdbentry.getFile(),
AppletFormatAdapter.URL);
}