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use new utility class for platform info
[jalview.git]
/
src
/
jalview
/
gui
/
AppJmol.java
diff --git
a/src/jalview/gui/AppJmol.java
b/src/jalview/gui/AppJmol.java
index
4a091b2
..
5f1a70b
100644
(file)
--- a/
src/jalview/gui/AppJmol.java
+++ b/
src/jalview/gui/AppJmol.java
@@
-33,6
+33,7
@@
import jalview.structure.*;
import jalview.datamodel.PDBEntry;
import jalview.io.*;
import jalview.schemes.*;
import jalview.datamodel.PDBEntry;
import jalview.io.*;
import jalview.schemes.*;
+import jalview.ws.EBIFetchClient;
import org.jmol.api.*;
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.api.*;
import org.jmol.adapter.smarter.SmarterJmolAdapter;
@@
-413,6
+414,7
@@
public synchronized void addSequence(SequenceI [] seq)
public void seqColour_actionPerformed(ActionEvent actionEvent)
{
public void seqColour_actionPerformed(ActionEvent actionEvent)
{
+ lastCommand = null;
colourBySequence = seqColour.isSelected();
colourBySequence(ap.alignFrame.alignPanel);
}
colourBySequence = seqColour.isSelected();
colourBySequence(ap.alignFrame.alignPanel);
}
@@
-588,17
+590,13
@@
public synchronized void addSequence(SequenceI [] seq)
resetLastRes.append(":" + chain);
}
resetLastRes.append(":" + chain);
}
- eval.append(";color gold;wireframe 100");
+ eval.append(";wireframe 100;"+eval.toString()+".CA;");
- Color col = new Color(viewer.getAtomArgb(atomIndex));
+ resetLastRes.append(";wireframe 0;"+resetLastRes.toString()+".CA;spacefill 0;");
- resetLastRes.append(";color["
- + col.getRed() + ","
- + col.getGreen() + ","
- + col.getBlue() + "];wireframe 0");
+ eval.append("spacefill 200;select none");
viewer.evalStringQuiet(eval.toString());
viewer.evalStringQuiet(eval.toString());
-
}
public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
}
public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
@@
-655,11
+653,7
@@
public synchronized void addSequence(SequenceI [] seq)
{
for (int m = 0; m < mapping.length; m++)
{
{
for (int m = 0; m < mapping.length; m++)
{
- System.out.println(mapping[m].getSequence().getName()+" "+sequence[s].getName()+" "
- +((mapping[m].getSequence() == sequence[s])
- +" "+(ap.av.alignment.findIndex(sequence[s]))));
-
- 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++)
&& ap.av.alignment.findIndex(sequence[s])>-1)
{
for (int r = 0; r < sequence[s].getLength(); r++)
@@
-851,7
+845,8
@@
public synchronized void addSequence(SequenceI [] seq)
if (chainId != null)
picked+=(":"+chainId.substring(1, chainId.length()));
if (chainId != null)
picked+=(":"+chainId.substring(1, chainId.length()));
- picked+=".C";
+ picked+=".CA";
+
if (!atomsPicked.contains(picked))
{
if (!atomsPicked.contains(picked))
{