*/
package jalview.ext.rbvi.chimera;
-import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
if (getSsm() != null)
{
getSsm().addStructureViewerListener(this);
- // ssm.addSelectionListener(this);
- FeatureRenderer fr = getFeatureRenderer(null);
- if (fr != null)
- {
- fr.featuresAdded();
- }
- refreshGUI();
}
return true;
} catch (Exception q)
/**
* @param files
* @param sr
- * @param fr
- * @param viewport
+ * @param viewPanel
* @return
*/
@Override
protected StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, FeatureRenderer fr,
- AlignViewportI viewport)
+ String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
{
return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
- getSequence(), sr, fr, viewport);
+ getSequence(), sr, viewPanel);
}
/**
{
// TODO refactor as required to pull up to an interface
AlignmentI alignment = avp.getAlignment();
- FeatureRenderer fr = getFeatureRenderer(avp);
-
- /*
- * fr is null if feature display is turned off
- */
- if (fr == null)
- {
- return 0;
- }
String[] files = getStructureFiles();
if (files == null)
StructureMappingcommandSet commandSet = ChimeraCommands
.getSetAttributeCommandsForFeatures(getSsm(), files,
- getSequence(), fr, alignment);
+ getSequence(), avp);
String[] commands = commandSet.commands;
if (commands.length > 10)
{