X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=4a97e43b4e00355f59b4bcde416b159a98d7d377;hb=0705a85fe0a3d391e5aba360340a0c342c898366;hp=a8412f0d1137f541de1c67dee9dbfc5fe08bdf4f;hpb=ec955aa655d8320258b91eb079bc57f688cd0a07;p=jalview.git diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index a8412f0..4a97e43 100755 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -1,79 +1,272 @@ +/* + * 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; + AlignViewport av; + SequenceGroup currentSequenceGroup = null; + SequenceGroup[] allGroups = null; + Color resBoxColour; + Graphics graphics; + float transparency = .4f; - SequenceGroup currentSequenceGroup = null; - SequenceGroup [] allGroups = null; - Color resBoxColour; - Graphics graphics; + // The following vector holds the features which are + // to be added, in the correct order or rendering + Vector featuresDisplayed; - public FeatureRenderer(AlignViewport av) - { - this.av = av; - } + /** + * Creates a new FeatureRenderer object. + * + * @param av DOCUMENT ME! + */ + public FeatureRenderer(AlignViewport av) + { + this.av = av; + initColours(); + String version = System.getProperty("java.version"); + if (version.indexOf("1.1") == 0) + highlightTransparent = false; + } - public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height) - { - Vector features = seq.getSequenceFeatures(); - Enumeration e = features.elements(); - while( e.hasMoreElements() ) +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, SequenceGroup[] sg, + int start, int end, int x1, int y1, int width, int height) { - SequenceFeature sf = (SequenceFeature)e.nextElement(); - if(sf.getStart()>seq.getEnd()) - continue; - int fstart = seq.findIndex(sf.getStart())-1; - int fend = seq.findIndex(sf.getEnd())-1; + if(seq.getSequenceFeatures()==null) + return; - if( (fstart<=end && fend>=start) ) - { - if(fstart<0) // fix for if the feature we have starts before the sequence start, - fstart = 0;// but the feature end is still valid!! + Enumeration e = null, e2; + String type; + if(featuresDisplayed!=null) + e = featuresDisplayed.elements(); + else + e = seq.getSequenceFeatures().elements(); - if(fstart==fend) + if(highlightTransparent) { - g.setColor(Color.red); - g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4); - g.setColor(Color.white); + // MyGraphics.SetTransparency(g, transparency); + } - char s = seq.getSequence().charAt(fstart); - FontMetrics fm = g.getFontMetrics(); - int charOffset = (width - fm.charWidth(s))/2; - int pady = height/5; - g.drawString(String.valueOf(s), charOffset + x1 + width * (fstart - start), y1 + height - pady); - } - else + while (e.hasMoreElements()) { - for (int i = fstart; i <= fend; i++) - { - char s = seq.getSequence().charAt(i); - if( jalview.util.Comparison.isGap(s) ) + 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; - g.setColor(Color.blue); - g.fillRect( (i-start) * width, y1, width, height); - g.setColor(Color.white); + if (sf.getBegin() > seq.getEnd()) + { + continue; + } - FontMetrics fm = g.getFontMetrics(); - int charOffset = (width - fm.charWidth(s)) / 2; - int pady = height / 5; - g.drawString(String.valueOf(s), - charOffset + x1 + width * (i-start), - y1 + height - pady); + int fstart = seq.findIndex(sf.getBegin()) - 1; + int fend = seq.findIndex(sf.getEnd()) - 1; + + 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; + } + + if (fstart == fend) + { + g.setColor(getColour(type)); + g.fillRoundRect((fstart - start) * width, y1, width, + height, 4, 4); + g.setColor(Color.white); + + char s = seq.getSequence().charAt(fstart); + FontMetrics fm = g.getFontMetrics(); + int charOffset = (width - fm.charWidth(s)) / 2; + int pady = height / 5; + g.drawString(String.valueOf(s), + charOffset + x1 + (width * (fstart - start)), + (y1 + height) - pady); + } + else + { + for (int i = fstart; i <= fend; i++) + { + char s = seq.getSequence().charAt(i); + + if (jalview.util.Comparison.isGap(s)) + { + continue; + } + + g.setColor(getColour(type)); + g.fillRect((i - start) * width, y1, width, height); + + g.setColor(Color.white); + + FontMetrics fm = g.getFontMetrics(); + int charOffset = (width - fm.charWidth(s)) / 2; + int pady = height / 5; + g.drawString(String.valueOf(s), + charOffset + x1 + (width * (i - start)), + (y1 + height) - pady); + } + } + } } - } + + if (highlightTransparent) + { + // MyGraphics.SetTransparency(g, 1.0f); + } + } + + public Color getColour(String featureType) + { + return (Color)featureColours.get(featureType); + } + + public void setColour(String featureType, Color col) + { + featureColours.put(featureType, col); + } + + 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 + 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)); } - } } + + +