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Merge branch 'develop' into Jalview-JS/develop
[jalview.git]
/
src
/
jalview
/
structure
/
StructureSelectionManager.java
diff --git
a/src/jalview/structure/StructureSelectionManager.java
b/src/jalview/structure/StructureSelectionManager.java
index
d68f346
..
6261e74
100644
(file)
--- a/
src/jalview/structure/StructureSelectionManager.java
+++ b/
src/jalview/structure/StructureSelectionManager.java
@@
-56,9
+56,9
@@
import java.util.List;
import java.util.Map;
import java.util.Vector;
import java.util.Map;
import java.util.Vector;
-import MCview.Atom;
-import MCview.PDBChain;
-import MCview.PDBfile;
+import mc_view.Atom;
+import mc_view.PDBChain;
+import mc_view.PDBfile;
public class StructureSelectionManager
{
public class StructureSelectionManager
{
@@
-398,8
+398,11
@@
public class StructureSelectionManager
{
// FIXME if sourceType is not null, we've lost data here
sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
{
// FIXME if sourceType is not null, we've lost data here
sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
- pdb = new JmolParser(pdbFile, sourceType);
-
+ pdb = new JmolParser(false, pdbFile, sourceType);
+ pdb.addSettings(parseSecStr && processSecondaryStructure,
+ parseSecStr && addTempFacAnnot,
+ parseSecStr && secStructServices);
+ pdb.doParse();
if (pdb.getId() != null && pdb.getId().trim().length() > 0
&& DataSourceType.FILE == sourceType)
{
if (pdb.getId() != null && pdb.getId().trim().length() > 0
&& DataSourceType.FILE == sourceType)
{
@@
-573,6
+576,13
@@
public class StructureSelectionManager
{
System.err.println(e.getMessage());
}
{
System.err.println(e.getMessage());
}
+ catch (Exception e)
+ {
+ System.err
+ .println(
+ "Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair");
+ System.err.println(e.getMessage());
+ }
}
if (!foundSiftsMappings.isEmpty())
{
}
if (!foundSiftsMappings.isEmpty())
{