/* * Jalview - A Sequence Alignment Editor and Viewer * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ package jalview.appletgui; import jalview.datamodel.*; import java.awt.*; import java.util.*; /** * DOCUMENT ME! * * @author $author$ * @version $Revision$ */ public class FeatureRenderer { AlignViewport av; SequenceGroup currentSequenceGroup = null; SequenceGroup[] allGroups = null; Graphics graphics; // The following vector holds the features which are // to be added, in the correct order or rendering Vector featuresDisplayed; // A higher level for grouping features of a // paritcular type Hashtable featureGroups = null; Color currentColour = null; boolean drawText = true; FontMetrics fm; int charOffset; /** * Creates a new FeatureRenderer object. * * @param av DOCUMENT ME! */ public FeatureRenderer(AlignViewport av) { this.av = av; initColours(); } //boolean highlightTransparent = true; /** * 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! */ public void drawSequence(Graphics g, SequenceI seq, int start, int end, int x1, int y1, int width, int height) { fm = g.getFontMetrics(); if(seq.getSequenceFeatures()==null) return; Enumeration e = null, e2; String type; if(featuresDisplayed!=null) e = featuresDisplayed.elements(); else e = seq.getSequenceFeatures().elements(); while (e.hasMoreElements()) { SequenceFeature sf=null; if(featuresDisplayed!=null) { e2 = seq.getSequenceFeatures().elements(); type = e.nextElement().toString(); while(e2.hasMoreElements()) { sf = (SequenceFeature) e2.nextElement(); if(sf.getType().equals(type)) break; else sf = null; } } else { sf = (SequenceFeature) e.nextElement(); type = sf.getType(); } if(sf==null) continue; if(featureGroups!=null && sf.getFeatureGroup()!=null && featureGroups.containsKey(sf.getFeatureGroup()) && !((Boolean)featureGroups.get(sf.getFeatureGroup())).booleanValue()) { continue; } if (sf.getBegin() > seq.getEnd()) { continue; } if (type.equals("disulfide bond")) { renderFeature(g, seq, seq.findIndex(sf.getBegin()) - 1, seq.findIndex(sf.getBegin()) - 1, type, start, end, x1, y1, width, height); renderFeature(g, seq, seq.findIndex(sf.getEnd()) - 1, seq.findIndex(sf.getEnd()) - 1, type, start, end, x1, y1, width, height); } else renderFeature(g, seq, seq.findIndex(sf.getBegin()) - 1, seq.findIndex(sf.getEnd()) - 1, type, start, end, x1, y1, width, height); } } void renderFeature(Graphics g, SequenceI seq, int fstart, int fend, String type, int start, int end, int x1, int y1, int width, int height) { 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; } for (int i = fstart; i <= fend; i++) { char s = seq.getSequence().charAt(i); if (jalview.util.Comparison.isGap(s)) { continue; } currentColour = getColour(type); g.setColor(currentColour); g.fillRect( (i - start) * width, y1, width, height); if (drawText) { g.setColor(Color.white); charOffset = (width - fm.charWidth(s)) / 2; g.drawString(String.valueOf(s), charOffset + x1 + (width * (i - start)), (y1 + height) - height / 5); } } } } Image offscreen; Frame nullframe; public Color findFeatureColour(Color initialCol, SequenceI seq, int i) { currentColour = initialCol; if(offscreen == null) { nullframe = new Frame(); nullframe.addNotify(); offscreen = nullframe.createImage(1, 1); } drawSequence(offscreen.getGraphics(), seq, i, i, 0, 0, 1, 1); return currentColour; } public Color getColour(String featureType) { return (Color)featureColours.get(featureType); } public void setColour(String featureType, Color col) { featureColours.put(featureType, col); } public void addNewFeature(String name, Color col) { setColour(name, col); if (featuresDisplayed == null) featuresDisplayed = new Vector(); featuresDisplayed.insertElementAt(name, 0); } /* public void setTransparency(float value) { transparency = value; } public float getTransparency() { return transparency; }*/ public void setFeaturePriority(Object [][] data) { // The feature table will display high priority // features at the top, but theses are the ones // we need to render last, so invert the data if(featuresDisplayed!=null) featuresDisplayed.removeAllElements(); else featuresDisplayed = new Vector(); for(int i=data.length-1; i>-1; i--) { String type = data[i][0].toString(); setColour(type, (Color)data[i][1]); if( ((Boolean)data[i][2]).booleanValue() ) featuresDisplayed.addElement(type); } } Hashtable featureColours = new Hashtable(); void initColours() { featureColours.put("active site", new Color(255, 75, 0)); featureColours.put("binding site", new Color(245, 85, 0)); featureColours.put("calcium-binding region", new Color(235, 95, 0)); featureColours.put("chain", new Color(225, 105, 0)); featureColours.put("coiled-coil region", new Color(215, 115, 0)); featureColours.put("compositionally biased region", new Color(205, 125, 0)); featureColours.put("cross-link", new Color(195, 135, 0)); featureColours.put("disulfide bond", new Color(185, 145, 0)); featureColours.put("DNA-binding region", new Color(175, 155, 0)); featureColours.put("domain", new Color(165, 165, 0)); featureColours.put("glycosylation site", new Color(155, 175, 0)); featureColours.put("helix", new Color(145, 185, 0)); featureColours.put("initiator methionine", new Color(135, 195, 5)); featureColours.put("lipid moiety-binding region", new Color(125, 205, 15)); featureColours.put("metal ion-binding site", new Color(115, 215, 25)); featureColours.put("modified residue", new Color(105, 225, 35)); featureColours.put("mutagenesis site", new Color(95, 235, 45)); featureColours.put("non-consecutive residues", new Color(85, 245, 55)); featureColours.put("non-terminal residue", new Color(75, 255, 65)); featureColours.put("nucleotide phosphate-binding region", new Color(65, 245, 75)); featureColours.put("peptide", new Color(55, 235, 85)); featureColours.put("propeptide", new Color(45, 225, 95)); featureColours.put("region of interest", new Color(35, 215, 105)); featureColours.put("repeat", new Color(25, 205, 115)); featureColours.put("selenocysteine", new Color(15, 195, 125)); featureColours.put("sequence conflict", new Color(5, 185, 135)); featureColours.put("sequence variant", new Color(0, 175, 145)); featureColours.put("short sequence motif", new Color(0, 165, 155)); featureColours.put("signal peptide", new Color(0, 155, 165)); featureColours.put("site", new Color(0, 145, 175)); featureColours.put("splice variant", new Color(0, 135, 185)); featureColours.put("strand", new Color(0, 125, 195)); featureColours.put("topological domain", new Color(0, 115, 205)); featureColours.put("transit peptide", new Color(0, 105, 215)); featureColours.put("transmembrane region", new Color(0, 95, 225)); featureColours.put("turn", new Color(0, 85, 235)); featureColours.put("unsure residue", new Color(0, 75, 245)); featureColours.put("zinc finger region", new Color(0, 65, 255)); } }