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JAL-3906 use indicate to highlight current mousedOver residue in Jalview in a Pymol...
[jalview.git]
/
src
/
jalview
/
gui
/
PymolBindingModel.java
diff --git
a/src/jalview/gui/PymolBindingModel.java
b/src/jalview/gui/PymolBindingModel.java
index
ec3be0a
..
6aba7b6
100644
(file)
--- a/
src/jalview/gui/PymolBindingModel.java
+++ b/
src/jalview/gui/PymolBindingModel.java
@@
-6,7
+6,7
@@
import java.util.List;
import java.util.Map;
import jalview.api.AlignmentViewPanel;
import java.util.Map;
import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.pymol.PymolCommands;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.pymol.PymolCommands;
@@
-70,15
+70,14
@@
public class PymolBindingModel extends AAStructureBindingModel
public void highlightAtoms(List<AtomSpec> atoms)
{
/*
public void highlightAtoms(List<AtomSpec> atoms)
{
/*
- * https://pymolwiki.org/index.php/Label#examples
+ * https://pymolwiki.org/index.php/indicate#examples
*/
StringBuilder sb = new StringBuilder();
for (AtomSpec atom : atoms)
{
// todo promote to StructureCommandsI.showLabel()
*/
StringBuilder sb = new StringBuilder();
for (AtomSpec atom : atoms)
{
// todo promote to StructureCommandsI.showLabel()
- // todo handle CA|P correctly
String modelId = getModelIdForFile(atom.getPdbFile());
String modelId = getModelIdForFile(atom.getPdbFile());
- sb.append(String.format(" %s//%s/%d/CA", modelId,
+ sb.append(String.format(" %s//%s/%d/*", modelId,
atom.getChain(),
atom.getPdbResNum()));
}
atom.getChain(),
atom.getPdbResNum()));
}
@@
-87,18
+86,9
@@
public class PymolBindingModel extends AAStructureBindingModel
{
return;
}
{
return;
}
- StructureCommandI command = new StructureCommand("label", labelSpec, LABEL_FORMAT);
+ StructureCommandI command = new StructureCommand("indicate", labelSpec);
executeCommand(command, false);
executeCommand(command, false);
- /*
- * and remove the label(s) previously shown
- */
- if (lastLabelSpec != null)
- {
- command = new StructureCommand("label", lastLabelSpec, "");
- executeCommand(command, false);
- }
-
lastLabelSpec = labelSpec;
}
lastLabelSpec = labelSpec;
}
@@
-156,7
+146,7
@@
public class PymolBindingModel extends AAStructureBindingModel
}
else
{
}
else
{
- Cache.error("Failed to launch PyMOL!");
+ Console.error("Failed to launch PyMOL!");
}
return pymol != null;
}
}
return pymol != null;
}
@@
-184,7
+174,7
@@
public class PymolBindingModel extends AAStructureBindingModel
// pdbId.replace('-', 0)
} catch (Exception x)
{
// pdbId.replace('-', 0)
} catch (Exception x)
{
- Cache.error("Unxpected encoding exception for '"+pdbId+"'",x);
+ Console.error("Unxpected encoding exception for '"+pdbId+"'",x);
}
cmd.addParameter(pdbId);
}
cmd.addParameter(pdbId);