*/
package jalview.structures.models;
-import java.util.Locale;
-
import java.awt.Color;
import java.io.File;
import java.io.IOException;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import javax.swing.SwingUtilities;
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;
}
@Override
public void updateColours(Object source)
{
+ if (getViewer() == null)
+ {
+ // can happen if a viewer was not instantiated or cleaned up and is still
+ // registered - mostly during tests
+ return;
+ }
AlignmentViewPanel ap = (AlignmentViewPanel) source;
// ignore events from panels not used to colour this view
if (!getViewer().isUsedForColourBy(ap))