package jalview.renderer.seqfeatures; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import java.awt.AlphaComposite; import java.awt.Color; import java.awt.FontMetrics; import java.awt.Graphics; import java.awt.Graphics2D; import java.awt.image.BufferedImage; public class FeatureRenderer extends jalview.viewmodel.seqfeatures.FeatureRendererModel { FontMetrics fm; int charOffset; boolean offscreenRender = false; protected SequenceI lastSeq; char s; int i; int av_charHeight, av_charWidth; boolean av_validCharWidth, av_isShowSeqFeatureHeight; protected void updateAvConfig() { av_charHeight = av.getCharHeight(); av_charWidth = av.getCharWidth(); av_validCharWidth = av.isValidCharWidth(); av_isShowSeqFeatureHeight = av.isShowSequenceFeaturesHeight(); } void renderFeature(Graphics g, SequenceI seq, int fstart, int fend, Color featureColour, int start, int end, int y1) { updateAvConfig(); 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); } } } void renderScoreFeature(Graphics g, SequenceI seq, int fstart, int fend, Color featureColour, int start, int end, int y1, byte[] bs) { updateAvConfig(); 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; int ystrt = 0, yend = av_charHeight; if (bs[0] != 0) { // signed - zero is always middle of residue line. if (bs[1] < 128) { yend = av_charHeight * (128 - bs[1]) / 512; ystrt = av_charHeight - yend / 2; } else { ystrt = av_charHeight / 2; yend = av_charHeight * (bs[1] - 128) / 512; } } else { yend = av_charHeight * bs[1] / 255; ystrt = av_charHeight - yend; } for (i = fstart; i <= fend; i++) { s = seq.getCharAt(i); if (jalview.util.Comparison.isGap(s)) { continue; } g.setColor(featureColour); int x = (i - start) * av_charWidth; g.drawRect(x, y1, av_charWidth, av_charHeight); g.fillRect(x, y1 + ystrt, av_charWidth, yend); if (offscreenRender || !av_validCharWidth) { continue; } g.setColor(Color.black); charOffset = (av_charWidth - fm.charWidth(s)) / 2; g.drawString(String.valueOf(s), charOffset + (av_charWidth * (i - start)), pady); } } } BufferedImage offscreenImage; 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 synchronized int findFeatureColour(int initialCol, final SequenceI seq, int column) { if (!av.isShowSequenceFeatures()) { return initialCol; } SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures(); if (seq != lastSeq) { lastSeq = seq; lastSequenceFeatures = sequenceFeatures; if (lastSequenceFeatures != null) { sfSize = lastSequenceFeatures.length; } } else { if (lastSequenceFeatures != sequenceFeatures) { lastSequenceFeatures = sequenceFeatures; if (lastSequenceFeatures != null) { sfSize = lastSequenceFeatures.length; } } } if (lastSequenceFeatures == 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; // TODO: non-threadsafe - each rendering thread needs its own instance of // the feature renderer - or this should be synchronized. 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(); } } } private volatile SequenceFeature[] lastSequenceFeatures; int sfSize; int sfindex; int spos; int epos; public synchronized void drawSequence(Graphics g, final SequenceI seq, int start, int end, int y1) { SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures(); if (sequenceFeatures == null || sequenceFeatures.length == 0) { return; } if (g != null) { fm = g.getFontMetrics(); } updateFeatures(); if (lastSeq == null || seq != lastSeq || sequenceFeatures != lastSequenceFeatures) { lastSeq = seq; lastSequenceFeatures = sequenceFeatures; } 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 = lastSequenceFeatures.length; String type; for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) { type = renderOrder[renderIndex]; if (type == null || !showFeatureOfType(type)) { continue; } // loop through all features in sequence to find // current feature to render for (sfindex = 0; sfindex < sfSize; sfindex++) { final SequenceFeature sequenceFeature = lastSequenceFeatures[sfindex]; if (!sequenceFeature.type.equals(type)) { continue; } if (featureGroups != null && sequenceFeature.featureGroup != null && sequenceFeature.featureGroup.length() != 0 && featureGroups.containsKey(sequenceFeature.featureGroup) && !featureGroups.get(sequenceFeature.featureGroup) .booleanValue()) { continue; } if (!offscreenRender && (sequenceFeature.getBegin() > epos || sequenceFeature .getEnd() < spos)) { continue; } if (offscreenRender && offscreenImage == null) { if (sequenceFeature.begin <= start && sequenceFeature.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(sequenceFeature).getRGB()); // used to be retreived from av.featuresDisplayed // currentColour = av.featuresDisplayed // .get(sequenceFeatures[sfindex].type); } } else if (sequenceFeature.type.equals("disulfide bond")) { renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1, seq.findIndex(sequenceFeature.begin) - 1, getColour(sequenceFeature) // new Color(((Integer) av.featuresDisplayed // .get(sequenceFeatures[sfindex].type)).intValue()) , start, end, y1); renderFeature(g, seq, seq.findIndex(sequenceFeature.end) - 1, seq.findIndex(sequenceFeature.end) - 1, getColour(sequenceFeature) // new Color(((Integer) av.featuresDisplayed // .get(sequenceFeatures[sfindex].type)).intValue()) , start, end, y1); } else if (showFeature(sequenceFeature)) { if (av_isShowSeqFeatureHeight && sequenceFeature.score != Float.NaN) { renderScoreFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1, seq.findIndex(sequenceFeature.end) - 1, getColour(sequenceFeature), start, end, y1, normaliseScore(sequenceFeature)); } else { renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1, seq.findIndex(sequenceFeature.end) - 1, getColour(sequenceFeature), start, end, y1); } } } } if (transparency != 1.0f && g != null && transparencyAvailable) { Graphics2D g2 = (Graphics2D) g; g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 1.0f)); } } boolean transparencyAvailable = true; protected void setTransparencyAvailable(boolean isTransparencyAvailable) { transparencyAvailable = isTransparencyAvailable; } @Override public boolean isTransparencyAvailable() { return transparencyAvailable; } /** * Called when alignment in associated view has new/modified features to * discover and display. * */ public void featuresAdded() { lastSeq = null; findAllFeatures(); } }