- sfSize = sequenceFeatures.length;
- String type;
- for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
- {
- type = renderOrder[renderIndex];
-
- if (type == null || !av.featuresDisplayed.containsKey(type))
- {
- 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)
- {
- // this is passed out to the overview and other sequence renderers
- // (e.g. molecule viewer) to get displayed colour for rendered
- // sequence
- currentColour = new Integer(
- getColour(sequenceFeatures[sfindex]).getRGB());
- // used to be retreived from av.featuresDisplayed
- // 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,
- getColour(sequenceFeatures[sfindex])
- // 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,
- getColour(sequenceFeatures[sfindex])
- // new Color(((Integer) av.featuresDisplayed
- // .get(sequenceFeatures[sfindex].type)).intValue())
- , start, end, y1);
-
- }
- else if (showFeature(sequenceFeatures[sfindex]))
- {
- if (av.showSeqFeaturesHeight
- && sequenceFeatures[sfindex].score != Float.NaN)
- {
- renderScoreFeature(g, seq, seq
- .findIndex(sequenceFeatures[sfindex].begin) - 1, seq
- .findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex]), start, end, y1,
- normaliseScore(sequenceFeatures[sfindex]));
- }
- else
- {
- renderFeature(g, seq, seq
- .findIndex(sequenceFeatures[sfindex].begin) - 1, seq
- .findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex]), start, end, y1);
- }
- }
-
- }
-
- }
-
- if (transparency != 1.0f && g != null)
- {
- Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
- 1.0f));
- }
- }
-
- Hashtable minmax = new Hashtable();