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refactor to allow distinct StructureSelectionManager instances for
[jalview.git]
/
src
/
jalview
/
gui
/
AppJmol.java
diff --git
a/src/jalview/gui/AppJmol.java
b/src/jalview/gui/AppJmol.java
index
62f4d13
..
fdf00c0
100644
(file)
--- a/
src/jalview/gui/AppJmol.java
+++ b/
src/jalview/gui/AppJmol.java
@@
-116,7
+116,7
@@
public class AppJmol extends GStructureViewer implements Runnable,
}
// / TODO: check if protocol is needed to be set, and if chains are
// autodiscovered.
}
// / TODO: check if protocol is needed to be set, and if chains are
// autodiscovered.
- jmb = new AppJmolBinding(this, pdbentrys, seqs, null, null);
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
jmb.setLoadingFromArchive(true);
addAlignmentPanel(ap);
jmb.setLoadingFromArchive(true);
addAlignmentPanel(ap);
@@
-233,8
+233,7
@@
public class AppJmol extends GStructureViewer implements Runnable,
progressBar = ap.alignFrame;
// ////////////////////////////////
// Is the pdb file already loaded?
progressBar = ap.alignFrame;
// ////////////////////////////////
// Is the pdb file already loaded?
- String alreadyMapped = StructureSelectionManager
- .getStructureSelectionManager().alreadyMappedToFile(
+ String alreadyMapped = jmb.ssm.alreadyMappedToFile(
pdbentry.getId());
if (alreadyMapped != null)
pdbentry.getId());
if (alreadyMapped != null)
@@
-247,8
+246,7
@@
public class AppJmol extends GStructureViewer implements Runnable,
if (option == JOptionPane.YES_OPTION)
{
if (option == JOptionPane.YES_OPTION)
{
- StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, chains, alreadyMapped,
+ jmb.ssm.setMapping(seq, chains, alreadyMapped,
AppletFormatAdapter.FILE);
if (ap.seqPanel.seqCanvas.fr != null)
{
AppletFormatAdapter.FILE);
if (ap.seqPanel.seqCanvas.fr != null)
{
@@
-309,7
+307,7
@@
public class AppJmol extends GStructureViewer implements Runnable,
}
// /////////////////////////////////
}
// /////////////////////////////////
- jmb = new AppJmolBinding(this, new PDBEntry[]
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), new PDBEntry[]
{ pdbentry }, new SequenceI[][]
{ seq }, null, null);
addAlignmentPanel(ap);
{ pdbentry }, new SequenceI[][]
{ seq }, null, null);
addAlignmentPanel(ap);
@@
-868,8
+866,7
@@
public class AppJmol extends GStructureViewer implements Runnable,
{
for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)
{
{
for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)
{
- cap.appendText(StructureSelectionManager
- .getStructureSelectionManager().printMapping(
+ cap.appendText(jmb.printMapping(
jmb.pdbentry[pdbe].getFile()));
cap.appendText("\n");
}
jmb.pdbentry[pdbe].getFile()));
cap.appendText("\n");
}