git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge remote-tracking branch 'origin/releases/Release_2_10_2b1_Branch'
[jalview.git]
/
src
/
jalview
/
appletgui
/
ExtJmol.java
diff --git
a/src/jalview/appletgui/ExtJmol.java
b/src/jalview/appletgui/ExtJmol.java
index
5ffbaa4
..
3966536
100644
(file)
--- a/
src/jalview/appletgui/ExtJmol.java
+++ b/
src/jalview/appletgui/ExtJmol.java
@@
-26,6
+26,7
@@
import jalview.api.SequenceRenderer;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.io.DataSourceType;
import java.awt.Container;
import java.util.ArrayList;
import java.awt.Container;
import java.util.ArrayList;
@@
-48,9
+49,8
@@
public class ExtJmol extends JalviewJmolBinding
private AlignmentPanel ap;
private AlignmentPanel ap;
- protected ExtJmol(jalview.appletgui.AlignFrame alframe,
- PDBEntry[] pdbentry, SequenceI[][] seq,
- String protocol)
+ protected ExtJmol(AlignFrame alframe, PDBEntry[] pdbentry,
+ SequenceI[][] seq, DataSourceType protocol)
{
super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
protocol);
{
super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
protocol);
@@
-81,10
+81,10
@@
public class ExtJmol extends JalviewJmolBinding
@Override
public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
@Override
public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
- AlignmentPanel ap = (AlignmentPanel) alignment;
- if (ap.av.isShowSequenceFeatures())
+ AlignmentPanel alignPanel = (AlignmentPanel) alignment;
+ if (alignPanel.av.isShowSequenceFeatures())
{
{
- return ap.getFeatureRenderer();
+ return alignPanel.getFeatureRenderer();
}
else
{
}
else
{
@@
-172,8
+172,8
@@
public class ExtJmol extends JalviewJmolBinding
{
// This never gets called because we haven't overriden the associated Jmol's
// console
{
// This never gets called because we haven't overriden the associated Jmol's
// console
- System.err
- .println("WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="
+ System.err.println(
+ "WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="
+ show);
}
+ show);
}