*/
package jalview.structures.models;
-import java.util.Locale;
-
import java.awt.Color;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.BitSet;
+import java.util.Collections;
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.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.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.MappedFeatures;
import jalview.datamodel.PDBEntry;
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
if (waiting)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Timed out waiting for structure viewer to load file "
+ notLoaded);
return false;
{
AlignmentI alignment = view.getAlignment();
HiddenColumns hiddenCols = alignment.getHiddenColumns();
-
/*
* 'matched' bit i will be set for visible alignment columns i where
* all sequences have a residue with a mapping to their PDB structure
*/
- BitSet matched = new BitSet();
final int width = alignment.getWidth();
- for (int m = 0; m < width; m++)
+ BitSet matched = new BitSet();
+ ColumnSelection cs = view.getAlignViewport().getColumnSelection();
+ // restrict to active column selection, if there is one
+ if (cs != null && cs.hasSelectedColumns()
+ && cs.getSelected().size() >= 4)
{
- if (hiddenCols == null || hiddenCols.isVisible(m))
+ for (int s : cs.getSelected())
{
- matched.set(m);
+ matched.set(s);
+ }
+ }
+ else
+ {
+ for (int m = 0; m < width; m++)
+ {
+ if (hiddenCols == null || hiddenCols.isVisible(m))
+ {
+ matched.set(m);
+ }
}
}
-
AAStructureBindingModel.SuperposeData[] structures = new AAStructureBindingModel.SuperposeData[files.length];
for (int f = 0; f < files.length; f++)
{
// todo better way to ensure synchronous than setting getReply true!!
executeCommands(commandGenerator.showBackbone(), true, null);
+ AtomSpecType backbone = structures[refStructure].isRna
+ ? AtomSpecType.PHOSPHATE
+ : AtomSpecType.ALPHA;
+ List<AtomSpecModel> models = new ArrayList<AtomSpecModel>();
+ models.add(refAtoms);
/*
* 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;
}
}
+ models.add(atomSpec);
}
}
+ List<StructureCommandI> finalView = commandGenerator
+ .centerViewOn(models);
+ if (finalView != null && finalView.size() > 0)
+ {
+ executeCommands(finalView, false, "Centered on Superposition");
+ }
}
-
return error;
}
* @param getReply
* @param msg
*/
- protected List<String> executeCommands(List<StructureCommandI> commands,
+ public List<String> executeCommands(List<StructureCommandI> commands,
boolean getReply, String msg)
{
return executeCommand(getReply, msg,
* 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
@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))
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()));
}
return f;
}
+
+ /**
+ * Use restoreSession when you want to restore a previously saved sesssion to
+ * the running viewer instance.
+ *
+ * @param absolutePath
+ */
+ public void restoreSession(String absolutePath)
+ {
+ String prefix = getViewerType().toString();
+ try {
+
+ StructureCommandI cmd = commandGenerator.restoreSession(absolutePath);
+ if (cmd != null)
+ {
+ executeCommand(cmd, false);
+ }
+ } catch (Throwable e)
+ {
+ Console.error(String.format("Error restoring %s session: %s", prefix,
+ e.toString()));
+ }
+
+ }
+
/**
* Saves the structure viewer session to the given file
*
{
return 0;
}
+
+ /**
+ * list the ligands available for display/hiding in the current view
+ * @return HETATM CODE:Molecule name
+ */
+ public Map<String, String> getHetatmNames() {
+ return Collections.EMPTY_MAP;
+ }
+ /**
+ * Generates and executes a command to show the given hetatm types as CPK
+ *
+ * @param toShow - one or more of strings from getHetatmNames
+ */
+ public void showHetatms(List<String> toShow)
+ {
+ executeCommands(commandGenerator.showHetatms(toShow), false, "Adjusting hetatm visibility");
+ }
+
}