* include features at the position provided their feature type is
* displayed, and feature group is null or marked for display
*/
* include features at the position provided their feature type is
* displayed, and feature group is null or marked for display
*/
String[] oldRender = renderOrder;
renderOrder = new String[allfeatures.size()];
boolean initOrders = (featureOrder == null);
String[] oldRender = renderOrder;
renderOrder = new String[allfeatures.size()];
boolean initOrders = (featureOrder == null);
* note visible feature ordering and colours before update
*/
List<String> visibleFeatures = getDisplayedFeatureTypes();
* note visible feature ordering and colours before update
*/
List<String> visibleFeatures = getDisplayedFeatureTypes();
{
// conflict between applet and desktop - featureGroups returns the map in
// the desktop featureRenderer
{
// conflict between applet and desktop - featureGroups returns the map in
// the desktop featureRenderer
- return (featureGroups == null) ? Arrays.asList(new String[0]) : Arrays
- .asList(featureGroups.keySet().toArray(new String[0]));
+ return (featureGroups == null) ? Arrays.asList(new String[0])
+ : Arrays.asList(featureGroups.keySet().toArray(new String[0]));
for (String gp : getFeatureGroups())
{
if (checkGroupVisibility(gp, false))
for (String gp : getFeatureGroups())
{
if (checkGroupVisibility(gp, false))
SequenceFeatures.sortFeatures(features, true);
boolean simpleColour = fc == null || fc.isSimpleColour();
SequenceFeature lastFeature = null;
SequenceFeatures.sortFeatures(features, true);
boolean simpleColour = fc == null || fc.isSimpleColour();
SequenceFeature lastFeature = null;
* same extent as another (so would just redraw the same colour);
* (checking type and isContactFeature as a fail-safe here, although
* currently they are guaranteed to match in this context)
* same extent as another (so would just redraw the same colour);
* (checking type and isContactFeature as a fail-safe here, although
* currently they are guaranteed to match in this context)
{
if (lastFeature != null && sf.getBegin() == lastFeature.getBegin()
&& sf.getEnd() == lastFeature.getEnd()
{
if (lastFeature != null && sf.getBegin() == lastFeature.getBegin()
&& sf.getEnd() == lastFeature.getEnd()