- 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
- 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();
-
- /**
- * normalise a score against the max/min bounds for the feature type.
- *
- * @param sequenceFeature
- * @return byte[] { signed, normalised signed (-127 to 127) or unsigned
- * (0-255) value.
- */
- private final byte[] normaliseScore(SequenceFeature sequenceFeature)
- {
- float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0];
- final byte[] r = new byte[]
- { 0, (byte) 255 };
- if (mm != null)
- {
- if (r[0] != 0 || mm[0] < 0.0)
- {
- r[0] = 1;
- r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1]));
- }
- else
- {
- r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1]));
- }
- }
- return r;
- }
-
- 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!!
- }
-
- if (fend >= end)
- {
- fend = end;
- }
- int pady = (y1 + av.charHeight) - av.charHeight / 5;
- for (i = fstart; i <= fend; i++)
- {
- s = seq.getCharAt(i);
-
- if (jalview.util.Comparison.isGap(s))
- {
- continue;
- }
-
- g.setColor(featureColour);
-
- g.fillRect((i - start) * av.charWidth, y1, av.charWidth,
- av.charHeight);
-
- if (offscreenRender || !av.validCharWidth)
- {
- continue;
- }
-
- g.setColor(Color.white);
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- g.drawString(String.valueOf(s), charOffset
- + (av.charWidth * (i - start)), pady);
-