import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.schemes.GraduatedColor;
+import jalview.schemes.UserColourScheme;
+import jalview.util.QuickSort;
import jalview.viewmodel.AlignmentViewport;
import java.awt.Color;
*/
public void transferSettings(jalview.api.FeatureRenderer _fr)
{
- FeatureRenderer fr = (FeatureRenderer) _fr;
+ FeatureRendererModel fr = (FeatureRendererModel) _fr;
FeatureRendererSettings frs = new FeatureRendererSettings(fr);
this.renderOrder = frs.renderOrder;
this.featureGroups = frs.featureGroups;
ArrayList<SequenceFeature> tmp = new ArrayList<SequenceFeature>();
SequenceFeature[] features = sequence.getSequenceFeatures();
- while (features == null && sequence.getDatasetSequence() != null)
- {
- sequence = sequence.getDatasetSequence();
- features = sequence.getSequenceFeatures();
- }
-
if (features != null)
{
for (int i = 0; i < features.length; i++)
for (int i = 0; i < alignment.getHeight(); i++)
{
SequenceI asq = alignment.getSequenceAt(i);
- SequenceI dasq = asq.getDatasetSequence();
- SequenceFeature[] features = dasq != null ? dasq
- .getSequenceFeatures() : asq.getSequenceFeatures();
+ SequenceFeature[] features = asq.getSequenceFeatures();
if (features == null)
{
}
if (iSize > 1 && sort)
{
- jalview.util.QuickSort.sort(sortOrder, newf);
+ QuickSort.sortFloatObject(sortOrder, newf);
}
sortOrder = null;
System.arraycopy(newf, 0, renderOrder, opos, newf.length);
Object fc = featureColours.get(featureType);
if (fc == null)
{
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
+ UserColourScheme ucs = new UserColourScheme();
Color col = ucs.createColourFromName(featureType);
featureColours.put(featureType, fc = col);
}
{
for (int i = 0; i < typ.length; i++)
{
- if (feature_disp.isVisible(typ[i]))
+ if (!feature_disp.isVisible(typ[i]))
{
typ[i] = null;
}