X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=c71a3ccc2088be6fbffcf52fc14d6fe15a8885e2;hb=9175e97621ea51c3e98145545b3957842126c09e;hp=f6fe0be236d530c49500f40e23fe3ff6b6f6162d;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index f6fe0be..c71a3cc 100755 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -1,98 +1,411 @@ /* -* 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 -*/ - + * 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; + + + // 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 Color findFeatureColour(Color initialCol, SequenceI seq, int i) + { + 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; + } + - SequenceGroup currentSequenceGroup = null; - SequenceGroup [] allGroups = null; - Color resBoxColour; - Graphics graphics; + if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column))) + return Color.white.getRGB(); - public FeatureRenderer(AlignViewport av) - { - this.av = av; - } + currentColour = null; + drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1, -1, -1); + + if(currentColour==null) + return initialCol; + + return ((Integer)currentColour).intValue(); + } - 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() ) + + /** + * 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) { - SequenceFeature sf = (SequenceFeature)e.nextElement(); - if(sf.getStart()>seq.getEnd()) - continue; + if ( seq.getSequenceFeatures() == null + || seq.getSequenceFeatures().length==0) + return; + - int fstart = seq.findIndex(sf.getStart())-1; - int fend = seq.findIndex(sf.getEnd())-1; + if (av.featuresDisplayed == null || renderOrder==null) + { + findAllFeatures(); + if(av.featuresDisplayed.size()<1) + return; - if( (fstart<=end && fend>=start) ) + sequenceFeatures = seq.getSequenceFeatures(); + sfSize = sequenceFeatures.length; + } + if(lastSequence==null || seq!=lastSequence) { - if(fstart<0) // fix for if the feature we have starts before the sequence start, - fstart = 0;// but the feature end is still valid!! + 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); } - else + } + } + + + 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) { - for (int i = fstart; i <= fend; i++) + fend = end; + } + + for (i = fstart; i <= fend; i++) { - char s = seq.getSequence().charAt(i); - if( jalview.util.Comparison.isGap(s) ) + s = seq.getSequence().charAt(i); + + if (jalview.util.Comparison.isGap(s)) + { continue; + } - g.setColor(Color.blue); - g.fillRect( (i-start) * width, y1, width, height); + g.setColor(featureColour); - g.setColor(Color.white); + g.fillRect( (i - start) * width, y1, width, height); - FontMetrics fm = g.getFontMetrics(); - int charOffset = (width - fm.charWidth(s)) / 2; - int pady = height / 5; + g.setColor(Color.white); + charOffset = (width - fm.charWidth(s)) / 2; g.drawString(String.valueOf(s), - charOffset + x1 + width * (i-start), - y1 + height - pady); + 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)); } - } } + + +