/* * 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; // A higher level for grouping features of a // particular type Hashtable featureGroups = null; // This is actually an Integer held in the hashtable, // Retrieved using the key feature type Object currentColour; String [] renderOrder; FontMetrics fm; int charOffset; /** * Creates a new FeatureRenderer object. * * @param av DOCUMENT ME! */ public FeatureRenderer(AlignViewport av) { this.av = av; initColours(); } public void transferSettings(FeatureRenderer fr) { renderOrder = fr.renderOrder; featureGroups = fr.featureGroups; featureColours = fr.featureColours; } public Color findFeatureColour(Color initialCol, SequenceI seq, int i) { overview = true; if(!av.showSequenceFeatures) return initialCol; lastSequence = seq; sequenceFeatures = lastSequence.getSequenceFeatures(); if(sequenceFeatures==null) return initialCol; sfSize = sequenceFeatures.length; if(jalview.util.Comparison.isGap(lastSequence.getCharAt(i))) return Color.white; currentColour = null; drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1, -1, -1); if(currentColour==null) return initialCol; return new Color( ((Integer)currentColour).intValue() ); } /** * This is used by the Molecule Viewer to get the accurate colour * of the rendered sequence */ boolean overview = false; int white = Color.white.getRGB(); public int findFeatureColour(int initialCol, int seqIndex, int column) { if(!av.showSequenceFeatures) return initialCol; if(seqIndex!=lastSequenceIndex) { lastSequence = av.alignment.getSequenceAt(seqIndex); lastSequenceIndex = seqIndex; sequenceFeatures = lastSequence.getSequenceFeatures(); if(sequenceFeatures==null) return initialCol; sfSize = sequenceFeatures.length; } if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column))) return Color.white.getRGB(); currentColour = null; drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1, -1, -1); if(currentColour==null) return initialCol; 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; int lastSequenceIndex=-1; SequenceI lastSequence; SequenceFeature [] sequenceFeatures; int sfSize, sfindex, spos, epos; public void drawSequence(Graphics g, SequenceI seq, int start, int end, int y1, int width, int height) { if ( seq.getSequenceFeatures() == null || seq.getSequenceFeatures().length==0) return; if (av.featuresDisplayed == null || renderOrder==null) { findAllFeatures(); if(av.featuresDisplayed.size()<1) return; sequenceFeatures = seq.getSequenceFeatures(); sfSize = sequenceFeatures.length; } if(lastSequence==null || seq!=lastSequence) { lastSequence = seq; sequenceFeatures = seq.getSequenceFeatures(); sfSize = sequenceFeatures.length; } if(!overview) { spos = lastSequence.findPosition(start); epos = lastSequence.findPosition(end); if(g!=null) fm = g.getFontMetrics(); } String type; for(int renderIndex=0; renderIndex epos || sequenceFeatures[sfindex].getEnd() < spos)) continue; if (overview) { 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, width, height); 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, width, height); } else renderFeature(g, seq, seq.findIndex(sequenceFeatures[sfindex].begin) - 1, seq.findIndex(sequenceFeatures[sfindex].end) - 1, getColour(sequenceFeatures[sfindex].type), start, end, y1, width, height); } } } char s; int i; void renderFeature(Graphics g, SequenceI seq, int fstart, int fend, Color featureColour, int start, int end, 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 (i = fstart; i <= fend; i++) { s = seq.getSequence().charAt(i); if (jalview.util.Comparison.isGap(s)) { continue; } g.setColor(featureColour); g.fillRect( (i - start) * width, y1, width, height); g.setColor(Color.white); charOffset = (width - fm.charWidth(s)) / 2; g.drawString(String.valueOf(s), charOffset + (width * (i - start)), (y1 + height) - height / 5); //pady = height / 5; } } } void findAllFeatures() { av.featuresDisplayed = new Hashtable(); Vector allfeatures = new Vector(); for (int i = 0; i < av.alignment.getHeight(); i++) { SequenceFeature [] features = av.alignment.getSequenceAt(i).getSequenceFeatures(); if (features == null) continue; int index = 0; while (index < features.length) { if (!av.featuresDisplayed.containsKey(features[index].getType())) { av.featuresDisplayed.put(features[index].getType(), new Integer( getColour(features[index].getType()).getRGB()) ); allfeatures.addElement(features[index].getType()); } index++; } } renderOrder = new String[allfeatures.size()]; Enumeration en = allfeatures.elements(); int i = allfeatures.size()-1; while(en.hasMoreElements()) { renderOrder[i] = en.nextElement().toString(); i--; } } public Color getColour(String featureType) { return (Color)featureColours.get(featureType); } public void addNewFeature(String name, Color col) { setColour(name, col); if(av.featuresDisplayed==null) av.featuresDisplayed = new Hashtable(); av.featuresDisplayed.put(name, "NOGROUP"); } public void setColour(String featureType, Color col) { featureColours.put(featureType, col); } 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(av.featuresDisplayed!=null) av.featuresDisplayed.clear(); renderOrder = new String[data.length]; if (data.length > 0) for (int i = 0; i < data.length; i++) { String type = data[i][0].toString(); setColour(type, (Color) data[i][1]); if ( ( (Boolean) data[i][2]).booleanValue()) { av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB())); } renderOrder[data.length - i - 1] = 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)); } }