import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.renderer.seqfeatures.FeatureColourFinder;
FeatureRenderer fr = viewPanel.getFeatureRenderer();
FeatureColourFinder finder = new FeatureColourFinder(fr);
AlignViewportI viewport = viewPanel.getAlignViewport();
- ColumnSelection cs = viewport.getColumnSelection();
+ HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
AlignmentI al = viewport.getAlignment();
Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<Object, AtomSpecModel>();
Color lastColour = null;
// final colour range
if (lastColour != null)
{
- addColourRange(colourMap, lastColour, pdbfnum, startPos, lastPos,
- lastChain);
+ addColourRange(colourMap, lastColour, pdbfnum, startPos,
+ lastPos, lastChain);
}
// break;
}
* @return
*/
public static StructureMappingcommandSet getSetAttributeCommandsForFeatures(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] seqs, AlignmentViewPanel viewPanel)
+ StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
+ AlignmentViewPanel viewPanel)
{
Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
ssm, files, seqs, viewPanel);
* @return
*/
protected static Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] seqs, AlignmentViewPanel viewPanel)
+ StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
+ AlignmentViewPanel viewPanel)
{
Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<String, Map<Object, AtomSpecModel>>();
}
for (int[] range : mappedRanges)
{
- addColourRange(featureValues, value, modelNumber, range[0], range[1],
- mapping.getChain());
+ addColourRange(featureValues, value, modelNumber, range[0],
+ range[1], mapping.getChain());
}
}
}
* to an underscore.
*
* @param featureType
- * @return <pre>
- * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
- * </pre>
+ * @return
+ *
+ * <pre>
+ * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
+ * </pre>
*/
protected static String makeAttributeName(String featureType)
{