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
JAL-3811 document SHOW_JWS2_SERVICES user preference and provide new menu option...
[jalview.git]
/
src
/
jalview
/
gui
/
StructureViewer.java
diff --git
a/src/jalview/gui/StructureViewer.java
b/src/jalview/gui/StructureViewer.java
index
b7767fa
..
0c8354b
100644
(file)
--- a/
src/jalview/gui/StructureViewer.java
+++ b/
src/jalview/gui/StructureViewer.java
@@
-49,6
+49,11
@@
public class StructureViewer
StructureSelectionManager ssm;
StructureSelectionManager ssm;
+ /**
+ * decide if new structures are aligned to existing ones
+ */
+ private boolean superposeAdded = true;
+
public enum ViewerType
{
JMOL, CHIMERA
public enum ViewerType
{
JMOL, CHIMERA
@@
-127,6
+132,7
@@
public class StructureViewer
new SequenceI[seqsForPdbs.size()][]);
if (sview != null)
{
new SequenceI[seqsForPdbs.size()][]);
if (sview != null)
{
+ sview.setAlignAddedStructures(superposeAdded);
new Thread(new Runnable()
{
@Override
new Thread(new Runnable()
{
@Override
@@
-152,11
+158,12
@@
public class StructureViewer
if (viewerType.equals(ViewerType.JMOL))
{
if (viewerType.equals(ViewerType.JMOL))
{
- sview = new AppJmol(ap, pdbsForFile, theSeqs);
+ sview = new AppJmol(ap, superposeAdded, pdbsForFile, theSeqs);
}
else if (viewerType.equals(ViewerType.CHIMERA))
{
}
else if (viewerType.equals(ViewerType.CHIMERA))
{
- sview = new ChimeraViewFrame(pdbsForFile, theSeqs, ap);
+ sview = new ChimeraViewFrame(pdbsForFile, superposeAdded, theSeqs,
+ ap);
}
else
{
}
else
{
@@
-279,11
+286,14
@@
public class StructureViewer
{
if (sview != null)
{
{
if (sview != null)
{
- if (!sview.addAlreadyLoadedFile(seqsForPdb, null, ap, pdb.getId()))
+ sview.setAlignAddedStructures(superposeAdded);
+ String pdbId = pdb.getId();
+ if (!sview.addAlreadyLoadedFile(seqsForPdb, null, ap, pdbId))
{
{
- sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdb.getId());
+ sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdbId);
}
sview.updateTitleAndMenus();
}
sview.updateTitleAndMenus();
+ sview.raiseViewer();
return sview;
}
ViewerType viewerType = getViewerType();
return sview;
}
ViewerType viewerType = getViewerType();
@@
-373,4
+383,9
@@
public class StructureViewer
return sview != null && sview.isVisible();
}
return sview != null && sview.isVisible();
}
+ public void setSuperpose(boolean alignAddedStructures)
+ {
+ superposeAdded = alignAddedStructures;
+ }
+
}
}