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JAL-2136 merged develop into branch to fix build failure
[jalview.git]
/
src
/
jalview
/
gui
/
ChimeraViewFrame.java
diff --git
a/src/jalview/gui/ChimeraViewFrame.java
b/src/jalview/gui/ChimeraViewFrame.java
index
ec9feb7
..
37e84c7
100644
(file)
--- a/
src/jalview/gui/ChimeraViewFrame.java
+++ b/
src/jalview/gui/ChimeraViewFrame.java
@@
-484,7
+484,7
@@
public class ChimeraViewFrame extends StructureViewerBase
StructureFile pdb = null;
try
{
StructureFile pdb = null;
try
{
- String[] curfiles = jmb.getPdbFile(); // files currently in viewer
+ String[] curfiles = jmb.getStructureFiles(); // files currently in viewer
// TODO: replace with reference fetching/transfer code (validate PDBentry
// as a DBRef?)
for (int pi = 0; pi < jmb.getPdbCount(); pi++)
// TODO: replace with reference fetching/transfer code (validate PDBentry
// as a DBRef?)
for (int pi = 0; pi < jmb.getPdbCount(); pi++)
@@
-592,7
+592,8
@@
public class ChimeraViewFrame extends StructureViewerBase
}
// Explicitly map to the filename used by Chimera ;
pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos],
}
// Explicitly map to the filename used by Chimera ;
pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos],
- jmb.getChains()[pos], pe.getFile(), protocol);
+ jmb.getChains()[pos], pe.getFile(), protocol,
+ progressBar);
stashFoundChains(pdb, pe.getFile());
} catch (OutOfMemoryError oomerror)
{
stashFoundChains(pdb, pe.getFile());
} catch (OutOfMemoryError oomerror)
{
@@
-650,7
+651,7
@@
public class ChimeraViewFrame extends StructureViewerBase
/**
* Fetch PDB data and save to a local file. Returns the full path to the file,
/**
* Fetch PDB data and save to a local file. Returns the full path to the file,
- * or null if fetch fails.
+ * or null if fetch fails. TODO: refactor to common with Jmol ? duplication
*
* @param processingEntry
* @return
*
* @param processingEntry
* @return
@@
-883,4
+884,16
@@
public class ChimeraViewFrame extends StructureViewerBase
}
return reply;
}
}
return reply;
}
+
+ @Override
+ protected IProgressIndicator getIProgressIndicator()
+ {
+ return progressBar;
+ }
+
+ @Override
+ protected AAStructureBindingModel getBindingModel()
+ {
+ return jmb;
+ }
}
}