X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=7ad5f4d0608f2dd1bab2a28df66b0ae7993a622a;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=c71a3ccc2088be6fbffcf52fc14d6fe15a8885e2;hpb=9175e97621ea51c3e98145545b3957842126c09e;p=jalview.git diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index c71a3cc..7ad5f4d 100755 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2007 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 @@ -18,11 +18,11 @@ */ package jalview.appletgui; -import jalview.datamodel.*; +import java.util.*; import java.awt.*; -import java.util.*; +import jalview.datamodel.*; /** * DOCUMENT ME! @@ -32,380 +32,426 @@ import java.util.*; */ public class FeatureRenderer { - AlignViewport av; + AlignViewport av; + Hashtable featureColours = new Hashtable(); - // A higher level for grouping features of a - // particular type - Hashtable featureGroups = null; + // 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; + // Holds web links for feature groups and feature types + // in the form label|link + Hashtable featureLinks = null; - String [] renderOrder; + // This is actually an Integer held in the hashtable, + // Retrieved using the key feature type + Object currentColour; - FontMetrics fm; - int charOffset; + String[] renderOrder; - /** - * Creates a new FeatureRenderer object. - * - * @param av DOCUMENT ME! - */ - public FeatureRenderer(AlignViewport av) - { - this.av = av; - initColours(); - } + FontMetrics fm; + int charOffset; + float transparency = 1f; - public Color findFeatureColour(Color initialCol, SequenceI seq, int i) - { - if(!av.showSequenceFeatures) - return initialCol; + TransparencySetter transparencySetter = null; - lastSequence = seq; - sequenceFeatures = lastSequence.getSequenceFeatures(); - if(sequenceFeatures==null) - return initialCol; + /** + * Creates a new FeatureRenderer object. + * + * @param av DOCUMENT ME! + */ + public FeatureRenderer(AlignViewport av) + { + this.av = av; - sfSize = sequenceFeatures.length; + if (!System.getProperty("java.version").startsWith("1.1")) + { + transparencySetter = new TransparencySetter(); + } + } + + public void transferSettings(FeatureRenderer fr) + { + renderOrder = fr.renderOrder; + featureGroups = fr.featureGroups; + featureColours = fr.featureColours; + transparency = fr.transparency; + } + + 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; + } - if(jalview.util.Comparison.isGap(lastSequence.getCharAt(i))) - return Color.white; + sfSize = sequenceFeatures.length; - currentColour = null; + if (jalview.util.Comparison.isGap(lastSequence.getCharAt(i))) + { + return Color.white; + } - drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1, -1, -1); + currentColour = null; - if(currentColour==null) - return initialCol; + drawSequence(null, lastSequence, lastSequence.findPosition(i), -1, -1); - return new Color( ((Integer)currentColour).intValue() ); + if (currentColour == null) + { + return initialCol; } - /** - * This is used by the Molecule Viewer to get the accurate colour - * of the rendered sequence - */ - boolean overview = false; + 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) + int white = Color.white.getRGB(); + public int findFeatureColour(int initialCol, int seqIndex, int column) + { + if (!av.showSequenceFeatures) { - if(!av.showSequenceFeatures) - return initialCol; + return initialCol; + } - if(seqIndex!=lastSequenceIndex) + if (seqIndex != lastSequenceIndex) + { + lastSequence = av.alignment.getSequenceAt(seqIndex); + lastSequenceIndex = seqIndex; + sequenceFeatures = lastSequence.getSequenceFeatures(); + if (sequenceFeatures == null) { - lastSequence = av.alignment.getSequenceAt(seqIndex); - lastSequenceIndex = seqIndex; - sequenceFeatures = lastSequence.getSequenceFeatures(); - if(sequenceFeatures==null) - return initialCol; - - sfSize = sequenceFeatures.length; + return initialCol; } + sfSize = sequenceFeatures.length; + } - if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column))) - return Color.white.getRGB(); + if (jalview.util.Comparison.isGap(lastSequence.getCharAt(column))) + { + return Color.white.getRGB(); + } - currentColour = null; + currentColour = null; - drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1, -1, -1); + drawSequence(null, lastSequence, lastSequence.findPosition(column), -1, -1); - if(currentColour==null) - return initialCol; + if (currentColour == null) + { + return initialCol; + } - return ((Integer)currentColour).intValue(); + 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) + { + if (seq.getSequenceFeatures() == null + || seq.getSequenceFeatures().length == 0) + { + return; } + if (transparencySetter != null && g != null) + { + transparencySetter.setTransparency(g, transparency); + } - /** - * 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 (av.featuresDisplayed == null || renderOrder == null) { - if ( seq.getSequenceFeatures() == null - || seq.getSequenceFeatures().length==0) + findAllFeatures(); + if (av.featuresDisplayed.size() < 1) + { 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) + 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) { - lastSequence = seq; - sequenceFeatures = seq.getSequenceFeatures(); - sfSize = sequenceFeatures.length; + fm = g.getFontMetrics(); } - if(!overview) + } + String type; + for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) + { + type = renderOrder[renderIndex]; + if (!av.featuresDisplayed.containsKey(type)) { - spos = lastSequence.findPosition(start); - epos = lastSequence.findPosition(end); - if(g!=null) - fm = g.getFontMetrics(); + continue; } - String type; - for(int renderIndex=0; renderIndex epos - || sequenceFeatures[sfindex].getEnd() < spos)) - continue; + if (!overview && (sequenceFeatures[sfindex].getBegin() > epos + || sequenceFeatures[sfindex].getEnd() < spos)) + { + continue; + } - if (overview) + if (overview) + { + if (sequenceFeatures[sfindex].begin <= start && + sequenceFeatures[sfindex].end >= start) { - if (sequenceFeatures[sfindex].begin <= start && - sequenceFeatures[sfindex].end >= start) - { - currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex]. - type); - } - + 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 if (sequenceFeatures[sfindex].type.equals("disulfide bond")) + { - } - 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); + 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); + 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); } + else + { + renderFeature(g, seq, + seq.findIndex(sequenceFeatures[sfindex].begin) - 1, + seq.findIndex(sequenceFeatures[sfindex].end) - 1, + getColour(sequenceFeatures[sfindex].type), + start, end, y1); + } + } } + if (transparencySetter != null && g != null) + { + transparencySetter.setTransparency(g, 1.0f); + } + } - 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) + char s; + int i; + void renderFeature(Graphics g, SequenceI seq, + int fstart, int fend, Color featureColour, int start, + int end, int y1) + { + + 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 (((fstart <= end) && (fend >= start))) + if (fend >= end) { - if (fstart < start) - { // fix for if the feature we have starts before the sequence start, - fstart = start; // but the feature end is still valid!! - } + fend = end; + } + + for (i = fstart; i <= fend; i++) + { + s = seq.getCharAt(i); - if (fend >= end) + if (jalview.util.Comparison.isGap(s)) { - fend = end; + continue; } - for (i = fstart; i <= fend; i++) - { - s = seq.getSequence().charAt(i); - - if (jalview.util.Comparison.isGap(s)) - { - continue; - } + g.setColor(featureColour); - g.setColor(featureColour); + g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight); - g.fillRect( (i - start) * width, y1, width, height); + if (!av.validCharWidth) + { + continue; + } - 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; + g.setColor(Color.white); + charOffset = (av.charWidth - fm.charWidth(s)) / 2; + g.drawString(String.valueOf(s), + charOffset + (av.charWidth * (i - start)), + (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5; - } } } + } + + void findAllFeatures() + { + jalview.schemes.UserColourScheme ucs = new + jalview.schemes.UserColourScheme(); - void findAllFeatures() + av.featuresDisplayed = new Hashtable(); + Vector allfeatures = new Vector(); + for (int i = 0; i < av.alignment.getHeight(); i++) { - av.featuresDisplayed = new Hashtable(); - Vector allfeatures = new Vector(); - for (int i = 0; i < av.alignment.getHeight(); i++) - { - SequenceFeature [] features = av.alignment.getSequenceAt(i).getSequenceFeatures(); + SequenceFeature[] features = av.alignment.getSequenceAt(i). + getSequenceFeatures(); - if (features == null) - continue; + if (features == null) + { + continue; + } - int index = 0; - while (index < features.length) + int index = 0; + while (index < features.length) + { + if (!av.featuresDisplayed.containsKey(features[index].getType())) { - if (!av.featuresDisplayed.containsKey(features[index].getType())) + if (getColour(features[index].getType()) == null) { - av.featuresDisplayed.put(features[index].getType(), - new Integer( getColour(features[index].getType()).getRGB()) ); - allfeatures.addElement(features[index].getType()); + featureColours.put(features[index].getType(), + ucs.createColourFromName(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--; + av.featuresDisplayed.put(features[index].getType(), + new Integer(getColour(features[index]. + getType()).getRGB())); + allfeatures.addElement(features[index].getType()); + } + index++; } } - public Color getColour(String featureType) + renderOrder = new String[allfeatures.size()]; + Enumeration en = allfeatures.elements(); + int i = allfeatures.size() - 1; + while (en.hasMoreElements()) { - return (Color)featureColours.get(featureType); + renderOrder[i] = en.nextElement().toString(); + i--; } + } - public void addNewFeature(String name, Color col) - { - - setColour(name, col); - if(av.featuresDisplayed==null) - av.featuresDisplayed = new Hashtable(); + public Color getColour(String featureType) + { + return (Color) featureColours.get(featureType); + } + public void addNewFeature(String name, Color col) + { - av.featuresDisplayed.put(name, "NOGROUP"); - } - - public void setColour(String featureType, Color col) + setColour(name, col); + if (av.featuresDisplayed == null) { - featureColours.put(featureType, col); + av.featuresDisplayed = new Hashtable(); } - 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(); + av.featuresDisplayed.put(name, "NOGROUP"); + } - renderOrder = new String[data.length]; + public void setColour(String featureType, Color col) + { + featureColours.put(featureType, col); + } - 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() + 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) { - 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)); + 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; + } + } + } +} +class TransparencySetter +{ + void setTransparency(Graphics g, float value) + { + /* Graphics2D g2 = (Graphics2D) g; + g2.setComposite( + AlphaComposite.getInstance( + AlphaComposite.SRC_OVER, value));*/ + } +}