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JAL-629 Test and fix --annotation --ssannotation args. Added a viewerType arg/subval...
[jalview.git]
/
src
/
jalview
/
gui
/
StructureViewer.java
diff --git
a/src/jalview/gui/StructureViewer.java
b/src/jalview/gui/StructureViewer.java
index
5effa1a
..
0c12eb2
100644
(file)
--- a/
src/jalview/gui/StructureViewer.java
+++ b/
src/jalview/gui/StructureViewer.java
@@
-119,6
+119,12
@@
public class StructureViewer
public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
SequenceI[] seqs, AlignmentPanel ap)
{
public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
SequenceI[] seqs, AlignmentPanel ap)
{
+ return viewStructures(pdbs, seqs, ap, null);
+ }
+
+ public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
+ SequenceI[] seqs, AlignmentPanel ap, ViewerType viewerType)
+ {
JalviewStructureDisplayI viewer = onlyOnePdb(pdbs, seqs, ap);
if (viewer != null)
{
JalviewStructureDisplayI viewer = onlyOnePdb(pdbs, seqs, ap);
if (viewer != null)
{
@@
-128,7
+134,8
@@
public class StructureViewer
return viewer;
}
return viewer;
}
- ViewerType viewerType = getViewerType();
+ if (viewerType == null)
+ viewerType = getViewerType();
Map<PDBEntry, SequenceI[]> seqsForPdbs = getSequencesForPdbs(pdbs,
seqs);
Map<PDBEntry, SequenceI[]> seqsForPdbs = getSequencesForPdbs(pdbs,
seqs);
@@
-299,6
+306,12
@@
public class StructureViewer
public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
SequenceI[] seqsForPdb, AlignmentPanel ap)
{
public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
SequenceI[] seqsForPdb, AlignmentPanel ap)
{
+ return viewStructures(pdb, seqsForPdb, ap, null);
+ }
+
+ public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
+ SequenceI[] seqsForPdb, AlignmentPanel ap, ViewerType viewerType)
+ {
if (sview != null)
{
sview.setAlignAddedStructures(superposeAdded);
if (sview != null)
{
sview.setAlignAddedStructures(superposeAdded);
@@
-311,7
+324,8
@@
public class StructureViewer
sview.raiseViewer();
return sview;
}
sview.raiseViewer();
return sview;
}
- ViewerType viewerType = getViewerType();
+ if (viewerType == null)
+ viewerType = getViewerType();
if (viewerType.equals(ViewerType.JMOL))
{
sview = new AppJmol(pdb, seqsForPdb, null, ap);
if (viewerType.equals(ViewerType.JMOL))
{
sview = new AppJmol(pdb, seqsForPdb, null, ap);