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Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git...
[jalview.git]
/
src
/
jalview
/
appletgui
/
AppletJmol.java
diff --git
a/src/jalview/appletgui/AppletJmol.java
b/src/jalview/appletgui/AppletJmol.java
index
49219b9
..
7fda3c4
100644
(file)
--- a/
src/jalview/appletgui/AppletJmol.java
+++ b/
src/jalview/appletgui/AppletJmol.java
@@
-134,7
+134,7
@@
public class AppletJmol extends EmbmenuFrame implements
AlignmentPanel ap;
AlignmentPanel ap;
- List<AlignmentPanel> _aps = new ArrayList<AlignmentPanel>(); // remove? never
+ List<AlignmentPanel> _aps = new ArrayList<>(); // remove? never
// added to
String fileLoadingError;
// added to
String fileLoadingError;
@@
-213,7
+213,7
@@
public class AppletJmol extends EmbmenuFrame implements
{
reader = StructureSelectionManager
.getStructureSelectionManager(ap.av.applet)
{
reader = StructureSelectionManager
.getStructureSelectionManager(ap.av.applet)
- .setMapping(seq, chains, pdbentry.getFile(), protocol);
+ .setMapping(seq, chains, pdbentry.getFile(), protocol, null);
// PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
// FOR NOW, LETS JUST OPEN A NEW WINDOW
}
// PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
// FOR NOW, LETS JUST OPEN A NEW WINDOW
}
@@
-335,7
+335,7
@@
public class AppletJmol extends EmbmenuFrame implements
}
FileParse fp = new FileParse(pdbentry.getFile(), protocol);
fp.mark();
}
FileParse fp = new FileParse(pdbentry.getFile(), protocol);
fp.mark();
- // reader = new MCview.PDBfile(fp);
+ // reader = new mc_view.PDBfile(fp);
// could set ID, etc.
// if (!reader.isValid())
// {
// could set ID, etc.
// if (!reader.isValid())
// {
@@
-394,7
+394,7
@@
public class AppletJmol extends EmbmenuFrame implements
void centerViewer()
{
void centerViewer()
{
- Vector<String> toshow = new Vector<String>();
+ Vector<String> toshow = new Vector<>();
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof CheckboxMenuItem)