- continue;
- }
-
- // loop through all features in sequence to find
- // current feature to render
- for (sfindex = 0; sfindex < sfSize; sfindex++)
- {
- if (!sequenceFeatures[sfindex].type.equals(type))
- {
- continue;
- }
-
- if (featureGroups != null
- && sequenceFeatures[sfindex].featureGroup != null
- && sequenceFeatures[sfindex].featureGroup.length() != 0
- && featureGroups
- .containsKey(sequenceFeatures[sfindex].featureGroup)
- && !((Boolean) featureGroups
- .get(sequenceFeatures[sfindex].featureGroup))
- .booleanValue())
- {
- continue;
- }
-
- if (!offscreenRender
- && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex]
- .getEnd() < spos))
- {
- continue;
- }
-
- if (offscreenRender && offscreenImage == null)
- {
- if (sequenceFeatures[sfindex].begin <= start
- && sequenceFeatures[sfindex].end >= start)
- {
- currentColour = av.featuresDisplayed
- .get(sequenceFeatures[sfindex].type);
- }
- }
- else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
- {
-
- renderFeature(
- g,
- seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- new Color(((Integer) av.featuresDisplayed
- .get(sequenceFeatures[sfindex].type)).intValue()),
- start, end, y1);
- renderFeature(
- g,
- seq,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- new Color(((Integer) av.featuresDisplayed
- .get(sequenceFeatures[sfindex].type)).intValue()),
- start, end, y1);
-
- }
- else
- {
- renderFeature(g, seq, seq
- .findIndex(sequenceFeatures[sfindex].begin) - 1, seq
- .findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex].type), start, end, y1);
- }
-
- }
-
- }
-
- if (transparency != 1.0f && g != null)
- {
- Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
- 1.0f));
- }
- }
-
- char s;
-
- int i;
-
- void renderFeature(Graphics g, SequenceI seq, int fstart, int fend,
- Color featureColour, int start, int end, int y1)
- {
-
- if (((fstart <= end) && (fend >= start)))
- {
- if (fstart < start)
- { // fix for if the feature we have starts before the sequence start,
- fstart = start; // but the feature end is still valid!!