- /**
- * global transparency for feature
- */
- float transparency = 1.0f;
-
- FontMetrics fm;
-
- int charOffset;
-
- Hashtable featureColours = new Hashtable();
-
- // A higher level for grouping features of a
- // particular type
- Hashtable featureGroups = new Hashtable();
-
- // This is actually an Integer held in the hashtable,
- // Retrieved using the key feature type
- Object currentColour;
-
- String[] renderOrder;
-
- PropertyChangeSupport changeSupport = new PropertyChangeSupport(this);
-
- Vector allfeatures;
-
- /**
- * Creates a new FeatureRenderer object.
- *
- * @param av
- * DOCUMENT ME!
- */
- public FeatureRenderer(AlignmentPanel ap)
- {
- this.ap = ap;
- this.av = ap.av;
- }
-
- public class FeatureRendererSettings implements Cloneable
- {
- String[] renderOrder;
-
- Hashtable featureGroups;
-
- Hashtable featureColours;
-
- float transparency;
-
- Hashtable featureOrder;
-
- public FeatureRendererSettings(String[] renderOrder,
- Hashtable featureGroups, Hashtable featureColours,
- float transparency, Hashtable featureOrder)
- {
- super();
- this.renderOrder = renderOrder;
- this.featureGroups = featureGroups;
- this.featureColours = featureColours;
- this.transparency = transparency;
- this.featureOrder = featureOrder;
- }
-
- public FeatureRendererSettings(FeatureRenderer fr)
- {
- this.renderOrder = fr.renderOrder;
- this.featureGroups = fr.featureGroups;
- this.featureColours = fr.featureColours;
- this.transparency = fr.transparency;
- this.featureOrder = fr.featureOrder;
- }
- }
-
- public FeatureRendererSettings getSettings()
- {
- return new FeatureRendererSettings(this);
- }
-
- public void transferSettings(FeatureRendererSettings fr)
- {
- this.renderOrder = fr.renderOrder;
- this.featureGroups = fr.featureGroups;
- this.featureColours = fr.featureColours;
- this.transparency = fr.transparency;
- this.featureOrder = fr.featureOrder;
- }
-
- public void transferSettings(FeatureRenderer fr)
- {
- this.renderOrder = fr.renderOrder;
- this.featureGroups = fr.featureGroups;
- this.featureColours = fr.featureColours;
- this.transparency = fr.transparency;
- this.featureOrder = fr.featureOrder;
- }
-
- BufferedImage offscreenImage;
-
- boolean offscreenRender = false;
-
- public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
- {
- return new Color(findFeatureColour(initialCol.getRGB(), seq, res));
- }
-
- /**
- * This is used by the Molecule Viewer and Overview to get the accurate
- * colourof the rendered sequence
- */
- public int findFeatureColour(int initialCol, SequenceI seq, int column)
- {
- if (!av.showSequenceFeatures)
- {
- return initialCol;
- }
-
- if (seq != lastSeq)
- {
- lastSeq = seq;
- sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
- if (sequenceFeatures != null)
- {
- sfSize = sequenceFeatures.length;
- }
- }
-
- if (sequenceFeatures != lastSeq.getDatasetSequence()
- .getSequenceFeatures())
- {
- sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
- if (sequenceFeatures != null)
- {
- sfSize = sequenceFeatures.length;
- }
- }
-
- if (sequenceFeatures == null || sfSize == 0)
- {
- return initialCol;
- }
-
- if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
- {
- return Color.white.getRGB();
- }
-
- // Only bother making an offscreen image if transparency is applied
- if (transparency != 1.0f && offscreenImage == null)
- {
- offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB);
- }
-
- currentColour = null;
-
- offscreenRender = true;
-
- if (offscreenImage != null)
- {
- offscreenImage.setRGB(0, 0, initialCol);
- drawSequence(offscreenImage.getGraphics(), lastSeq, column, column, 0);
-
- return offscreenImage.getRGB(0, 0);
- }
- else
- {
- drawSequence(null, lastSeq, lastSeq.findPosition(column), -1, -1);
-
- if (currentColour == null)
- {
- return initialCol;
- }
- else
- {
- return ((Integer) currentColour).intValue();
- }
- }
-
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g
- * DOCUMENT ME!
- * @param seq
- * DOCUMENT ME!
- * @param sg
- * DOCUMENT ME!
- * @param start
- * DOCUMENT ME!
- * @param end
- * DOCUMENT ME!
- * @param x1
- * DOCUMENT ME!
- * @param y1
- * DOCUMENT ME!
- * @param width
- * DOCUMENT ME!
- * @param height
- * DOCUMENT ME!
- */
- // String type;
- // SequenceFeature sf;
- SequenceI lastSeq;
-
- SequenceFeature[] sequenceFeatures;
-
- int sfSize, sfindex, spos, epos;
-
- /**
- * show scores as heights
- */
- protected boolean varyHeight = false;
-
- synchronized public void drawSequence(Graphics g, SequenceI seq,
- int start, int end, int y1)
- {
-
- if (seq.getDatasetSequence().getSequenceFeatures() == null
- || seq.getDatasetSequence().getSequenceFeatures().length == 0)
- {
- return;
- }
-
- if (g != null)
- {
- fm = g.getFontMetrics();
- }
-
- if (av.featuresDisplayed == null || renderOrder == null
- || newFeatureAdded)
- {
- findAllFeatures();
- if (av.featuresDisplayed.size() < 1)
- {
- return;
- }
-
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
- }
-
- if (lastSeq == null
- || seq != lastSeq
- || seq.getDatasetSequence().getSequenceFeatures() != sequenceFeatures)
- {
- lastSeq = seq;
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
- }
-
- if (transparency != 1 && g != null)
- {
- Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
- transparency));
- }
-
- if (!offscreenRender)
- {
- spos = lastSeq.findPosition(start);
- epos = lastSeq.findPosition(end);
- }
-
- 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();