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JAL-2321 use configured values for structure derived annotation
[jalview.git]
/
src
/
jalview
/
structure
/
StructureSelectionManager.java
diff --git
a/src/jalview/structure/StructureSelectionManager.java
b/src/jalview/structure/StructureSelectionManager.java
index
cdb4e0a
..
cd986c0
100644
(file)
--- a/
src/jalview/structure/StructureSelectionManager.java
+++ b/
src/jalview/structure/StructureSelectionManager.java
@@
-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())
{
@@
-606,7
+616,10
@@
public class StructureSelectionManager
}
if (forStructureView)
{
}
if (forStructureView)
{
- mappings.addAll(seqToStrucMapping);
+ for (StructureMapping sm : seqToStrucMapping)
+ {
+ addStructureMapping(sm); // not addAll!
+ }
}
if (progress != null)
{
}
if (progress != null)
{
@@
-658,7
+671,10
@@
public class StructureSelectionManager
public void addStructureMapping(StructureMapping sm)
{
public void addStructureMapping(StructureMapping sm)
{
- mappings.add(sm);
+ if (!mappings.contains(sm))
+ {
+ mappings.add(sm);
+ }
}
/**
}
/**