import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.ext.rbvi.chimera.AtomSpecModel;
import jalview.gui.IProgressIndicator;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.AtomSpec;
-import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MessageManager;
}
Thread colourby = null;
+
/**
* Sends a set of colour commands to the structure viewer
*
- * @param colourBySequenceCommands
+ * @param commands
*/
@Override
- protected void colourBySequence(
- final StructureMappingcommandSet[] colourBySequenceCommands)
+ protected void colourBySequence(final String[] commands)
{
if (colourby != null)
{
@Override
public void run()
{
- for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
+ for (String cmd : commands)
{
- for (String cbyseq : cpdbbyseq.commands)
- {
- executeWhenReady(cbyseq);
- }
+ executeWhenReady(cmd);
}
}
});
/**
* @param files
- * @param sr
* @param viewPanel
* @return
*/
@Override
- protected StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
+ protected String[] getColourBySequenceCommands(
+ String[] files, AlignmentViewPanel viewPanel)
{
- return JmolCommands.getColourBySequenceCommand(getSsm(), files,
- getSequence(), sr, viewPanel);
+ Map<Object, AtomSpecModel> map = buildColoursMap(viewPanel);
+
+ return JmolCommands.getColourBySequenceCommand(map);
}
/**
@Override
public void showStructures(AlignViewportI av, boolean refocus)
{
- // TODO show Jmol structure optionally restricted to visible alignment
- // and/or selected chains
+ StringBuilder cmd = new StringBuilder(128);
+
+ if (isShowAlignmentOnly())
+ {
+ cmd.append("hide *;");
+
+ AtomSpecModel model = getShownResidues(av);
+ String atomSpec = JmolCommands.getAtomSpec(model);
+
+ cmd.append("display ").append(atomSpec);
+ }
+ else
+ {
+ cmd.append("display *");
+ }
+ cmd.append("; cartoon");
+ if (refocus)
+ {
+ cmd.append("; zoom 100");
+ }
+ evalStateCommand(cmd.toString());
+ }
+
+ /**
+ * Answers a Jmol syntax style structure model specification. Model number 0, 1,
+ * 2... is formatted as "1.1", "2.1", "3.1" etc.
+ */
+ @Override
+ public String getModelSpec(int model)
+ {
+ return String.valueOf(model + 1) + ".1";
}
}