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[jalview.git]
/
src
/
jalview
/
ext
/
jmol
/
JalviewJmolBinding.java
diff --git
a/src/jalview/ext/jmol/JalviewJmolBinding.java
b/src/jalview/ext/jmol/JalviewJmolBinding.java
index
c7496df
..
729780c
100644
(file)
--- a/
src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/
src/jalview/ext/jmol/JalviewJmolBinding.java
@@
-63,11
+63,6
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
implements JmolStatusListener, JmolSelectionListener,
ComponentListener
{
implements JmolStatusListener, JmolSelectionListener,
ComponentListener
{
- /*
- * state flag used to check if the Jmol viewer's paint method can be called
- */
- private boolean finishedInit = false;
-
boolean allChainsSelected = false;
/*
boolean allChainsSelected = false;
/*
@@
-259,8
+254,17
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
public void superposeStructures(AlignmentI[] _alignment,
int[] _refStructure, ColumnSelection[] _hiddenCols)
{
public void superposeStructures(AlignmentI[] _alignment,
int[] _refStructure, ColumnSelection[] _hiddenCols)
{
+ while (viewer.isScriptExecuting())
+ {
+ try
+ {
+ Thread.sleep(10);
+ } catch (InterruptedException i)
+ {
+ }
+ ;
+ }
String[] files = getPdbFile();
String[] files = getPdbFile();
-
if (!waitForFileLoad(files))
{
return;
if (!waitForFileLoad(files))
{
return;
@@
-272,7
+276,7
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
String nSeconds = " ";
if (files.length > 10)
{
String nSeconds = " ";
if (files.length > 10)
{
- nSeconds = " 0.00001 ";
+ nSeconds = " 0.005 ";
}
else
{
}
else
{
@@
-281,7
+285,7
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
}
// see JAL-1345 - should really automatically turn off the animation for
// large numbers of structures, but Jmol doesn't seem to allow that.
}
// see JAL-1345 - should really automatically turn off the animation for
// large numbers of structures, but Jmol doesn't seem to allow that.
- nSeconds = " ";
+ // nSeconds = " ";
// union of all aligned positions are collected together.
for (int a = 0; a < _alignment.length; a++)
{
// union of all aligned positions are collected together.
for (int a = 0; a < _alignment.length; a++)
{
@@
-667,6
+671,7
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
// applet path with docroot - discard as format won't match pdbfile
mset[0] = m;
}
// applet path with docroot - discard as format won't match pdbfile
mset[0] = m;
}
+ _modelFileNameMap[0] = 0; // filename index for first model is always 0.
}
int j = 1;
for (int i = 1; i < mset.length; i++)
}
int j = 1;
for (int i = 1; i < mset.length; i++)
@@
-942,7
+947,7
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
String mdlString = "";
if ((p = strInfo.indexOf(":")) > -1)
{
String mdlString = "";
if ((p = strInfo.indexOf(":")) > -1)
{
- picked += strInfo.substring(p + 1, strInfo.indexOf("."));
+ picked += strInfo.substring(p, strInfo.indexOf("."));
}
if ((p = strInfo.indexOf("/")) > -1)
}
if ((p = strInfo.indexOf("/")) > -1)
@@
-1216,7
+1221,7
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
// }
if (!isLoadingFromArchive())
{
// }
if (!isLoadingFromArchive())
{
- viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
+ viewer.evalStringQuiet("model *; select backbone;restrict;cartoon;wireframe off;spacefill off");
}
// register ourselves as a listener and notify the gui that it needs to
// update itself.
}
// register ourselves as a listener and notify the gui that it needs to
// update itself.
@@
-1401,16
+1406,6
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
return null;
}
return null;
}
- public boolean isFinishedInit()
- {
- return finishedInit;
- }
-
- public void setFinishedInit(boolean finishedInit)
- {
- this.finishedInit = finishedInit;
- }
-
/**
*
*/
/**
*
*/