import jalview.api.SequenceRenderer;
import jalview.api.StructureSelectionManagerProvider;
import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.MappedFeatures;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
/**
*
- * A base class to hold common function for 3D structure model binding.
- * Initial version created by refactoring JMol and Chimera binding models, but
- * other structure viewers could in principle be accommodated in future.
+ * A base class to hold common function for 3D structure model binding. Initial
+ * version created by refactoring JMol and Chimera binding models, but other
+ * structure viewers could in principle be accommodated in future.
*
* @author gmcarstairs
*
public String chain = "";
+ /**
+ * is the mapped sequence not protein ?
+ */
public boolean isRna;
/*
protected boolean colourBySequence = true;
+ /**
+ * true if all sequences appear to be nucleotide
+ */
private boolean nucleotide;
private boolean finishedInit = false;
}
}
}
-
@Override
public abstract void highlightAtoms(List<AtomSpec> atoms);
structures[pdbfnum].chain = chain;
}
structures[pdbfnum].pdbId = mapping.getPdbId();
- structures[pdbfnum].isRna = theSequence.getRNA() != null;
+ structures[pdbfnum].isRna = !theSequence.isProtein();
/*
* move on to next pdb file (ignore sequences for other chains
// todo better way to ensure synchronous than setting getReply true!!
executeCommands(commandGenerator.showBackbone(), true, null);
+ AtomSpecType backbone = structures[refStructure].isRna
+ ? AtomSpecType.PHOSPHATE
+ : AtomSpecType.ALPHA;
/*
* superpose each (other) structure to the reference in turn
*/
{
AtomSpecModel atomSpec = getAtomSpec(structures[i], matched);
List<StructureCommandI> commands = commandGenerator
- .superposeStructures(refAtoms, atomSpec);
+ .superposeStructures(refAtoms, atomSpec, backbone);
List<String> replies = executeCommands(commands, true, null);
for (String reply : replies)
{
// return this error (Chimera only) to the user
- if (reply.toLowerCase(Locale.ROOT).contains("unequal numbers of atoms"))
+ if (reply.toLowerCase(Locale.ROOT)
+ .contains("unequal numbers of atoms"))
{
error += "; " + reply;
}
* executed.
* <p>
* If a reply is wanted, the execution is done synchronously (waits),
- * otherwise it is done in a separate thread (doesn't wait).
+ * otherwise it is done in a separate thread (doesn't wait). WARNING: if you
+ * are sending commands that need to execute before later calls to
+ * executeCommand (e.g. mouseovers, which clean up after previous ones) then
+ * set getReply true to ensure that commands are not executed out of order.
*
* @param getReply
* @param msg
saveSession(f);
} catch (IOException e)
{
- Cache.log.error(String.format("Error saving %s session: %s", prefix,
+ Console.error(String.format("Error saving %s session: %s", prefix,
e.toString()));
}