// 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>>();
StructureMapping mapping, SequenceI seq,
Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
{
- SequenceFeature[] sfs = seq.getSequenceFeatures();
- if (sfs == null)
- {
- return;
- }
-
+ List<SequenceFeature> sfs = seq.getFeatures().getPositionalFeatures(
+ visibleFeatures.toArray(new String[visibleFeatures.size()]));
for (SequenceFeature sf : sfs)
{
String type = sf.getType();
*/
boolean isFromViewer = JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
.equals(sf.getFeatureGroup());
- if (isFromViewer || !visibleFeatures.contains(type))
+ if (isFromViewer)
{
continue;
}
}
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)
{