X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=a2d6bdebbe9d8cf8265a53a78fb4ab98d95b266f;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=6fbdee858b359fdd7321ef94a7b8efd49734baf7;hpb=0f71bfca98457c30f1051f142c31b6aaa3e23ead;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index 6fbdee8..a2d6bde 100755 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -1,473 +1,474 @@ -/* - * 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.gui; - -import jalview.datamodel.*; - -import java.awt.*; - -import java.util.*; - -import java.awt.image.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class FeatureRenderer -{ - AlignViewport av; - Color resBoxColour; - float transparency = 1.0f; - FontMetrics fm; - int charOffset; - - // 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; - - - /** - * 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; - transparency = fr.transparency; - } - - BufferedImage offscreenImage; - boolean offscreenRender = false; - public Color findFeatureColour(Color initialCol, SequenceI seq, int res) - { - int seqindex = av.alignment.findIndex(seq); - - return new Color( findFeatureColour (initialCol.getRGB(), - seqindex, res )); - } - - /** - * This is used by the Molecule Viewer to get the accurate colour - * of the rendered sequence - */ - 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.getDatasetSequence().getSequenceFeatures(); - if(sequenceFeatures==null) - return initialCol; - - sfSize = sequenceFeatures.length; - } - - if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column))) - return Color.white.getRGB(); - - - //Only bother making an offscreen image if transparency is applied - if(transparency!=1.0f && offscreenImage==null) - { - offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB); - } - - currentColour = null; - - offscreenRender = true; - - if(offscreenImage!=null) - { - offscreenImage.setRGB(0,0,initialCol); - drawSequence(offscreenImage.getGraphics(), - lastSequence, - column,column,0); - - return offscreenImage.getRGB(0,0); - } - else - { - drawSequence(null, - lastSequence, - lastSequence.findPosition(column), - -1, -1); - - if (currentColour == null) - return initialCol; - else - 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.getDatasetSequence().getSequenceFeatures() == null - || seq.getDatasetSequence().getSequenceFeatures().length==0) - return; - - - if(g!=null) - fm = g.getFontMetrics(); - - - if (av.featuresDisplayed == null || renderOrder==null) - { - findAllFeatures(); - if(av.featuresDisplayed.size()<1) - return; - - sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures(); - sfSize = sequenceFeatures.length; - } - - if(lastSequence==null || seq!=lastSequence) - { - lastSequence = seq; - sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures(); - sfSize = sequenceFeatures.length; - } - - - if (transparency != 1 && g!=null) - { - Graphics2D g2 = (Graphics2D) g; - g2.setComposite( - AlphaComposite.getInstance( - AlphaComposite.SRC_OVER, transparency)); - } - - if(!offscreenRender) - { - spos = lastSequence.findPosition(start); - epos = lastSequence.findPosition(end); - } - - - String type; - for(int renderIndex=0; renderIndex epos - || sequenceFeatures[sfindex].getEnd() < spos)) - continue; - - if (offscreenRender && offscreenImage==null) - { - 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); - 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(transparency!=1.0f && g!=null) - { - Graphics2D g2 = (Graphics2D) g; - g2.setComposite( - AlphaComposite.getInstance( - AlphaComposite.SRC_OVER, 1.0f)); - } - } - - - 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 (fend >= end) - { - fend = end; - } - int pady = (y1 + av.charHeight) - av.charHeight / 5; - 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) * av.charWidth, y1, av.charWidth,av.charHeight); - - if(offscreenRender) - continue; - - g.setColor(Color.white); - charOffset = (av.charWidth - fm.charWidth(s)) / 2; - g.drawString(String.valueOf(s), - charOffset + (av.charWidth * (i - start)), - pady); - - } - } - } - - 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).getDatasetSequence().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, String group) - { - - setColour(name, col); - if(av.featuresDisplayed==null) - av.featuresDisplayed = new Hashtable(); - - if(group == null) - group = "NOGROUP"; - - av.featuresDisplayed.put(name, new Integer(col.getRGB())); - } - - 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 - if(av.featuresDisplayed!=null) - av.featuresDisplayed.clear(); - else - av.featuresDisplayed = new Hashtable(); - - 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(230,230,0)); - 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)); - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2006 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.gui; + +import jalview.datamodel.*; + +import java.awt.*; + +import java.util.*; + +import java.awt.image.*; + + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class FeatureRenderer +{ + AlignViewport av; + Color resBoxColour; + float transparency = 1.0f; + FontMetrics fm; + int charOffset; + + Hashtable featureColours = new Hashtable(); + + + // 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; + + /** + * Creates a new FeatureRenderer object. + * + * @param av DOCUMENT ME! + */ + public FeatureRenderer(AlignViewport av) + { + this.av = av; + } + + public void transferSettings(FeatureRenderer fr) + { + renderOrder = fr.renderOrder; + featureGroups = fr.featureGroups; + featureColours = fr.featureColours; + transparency = fr.transparency; + } + + BufferedImage offscreenImage; + boolean offscreenRender = false; + public Color findFeatureColour(Color initialCol, SequenceI seq, int res) + { + return new Color( findFeatureColour (initialCol.getRGB(), + seq, res )); + } + + /** + * This is used by the Molecule Viewer and Overview to + * get the accurate colourof the rendered sequence + */ + public int findFeatureColour(int initialCol, SequenceI seq, int column) + { + if(!av.showSequenceFeatures) + return initialCol; + + if(seq!=lastSeq) + { + lastSeq = seq; + sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures(); + if(sequenceFeatures==null) + return initialCol; + + sfSize = sequenceFeatures.length; + } + + if(jalview.util.Comparison.isGap(lastSeq.getCharAt(column))) + return Color.white.getRGB(); + + + //Only bother making an offscreen image if transparency is applied + if(transparency!=1.0f && offscreenImage==null) + { + offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB); + } + + currentColour = null; + + offscreenRender = true; + + if(offscreenImage!=null) + { + offscreenImage.setRGB(0,0,initialCol); + drawSequence(offscreenImage.getGraphics(), + lastSeq, + column,column,0); + + return offscreenImage.getRGB(0,0); + } + else + { + drawSequence(null, + lastSeq, + lastSeq.findPosition(column), + -1, -1); + + if (currentColour == null) + return initialCol; + else + 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; + SequenceI lastSeq; + SequenceFeature [] sequenceFeatures; + int sfSize, sfindex, spos, epos; + + public void drawSequence(Graphics g, SequenceI seq, + int start, int end, int y1) + { + if ( seq.getDatasetSequence().getSequenceFeatures() == null + || seq.getDatasetSequence().getSequenceFeatures().length==0) + return; + + if(g!=null) + fm = g.getFontMetrics(); + + + if (av.featuresDisplayed == null + || renderOrder==null + || newFeatureAdded) + { + findAllFeatures(); + if(av.featuresDisplayed.size()<1) + return; + + sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures(); + sfSize = sequenceFeatures.length; + } + + if(lastSeq==null || seq!=lastSeq) + { + lastSeq = seq; + sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures(); + sfSize = sequenceFeatures.length; + } + + + if (transparency != 1 && g!=null) + { + Graphics2D g2 = (Graphics2D) g; + g2.setComposite( + AlphaComposite.getInstance( + AlphaComposite.SRC_OVER, transparency)); + } + + if(!offscreenRender) + { + spos = lastSeq.findPosition(start); + epos = lastSeq.findPosition(end); + } + + + String type; + for(int renderIndex=0; renderIndex epos + || sequenceFeatures[sfindex].getEnd() < spos)) + continue; + + if (offscreenRender && offscreenImage==null) + { + 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); + 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(transparency!=1.0f && g!=null) + { + Graphics2D g2 = (Graphics2D) g; + g2.setComposite( + AlphaComposite.getInstance( + AlphaComposite.SRC_OVER, 1.0f)); + } + } + + + 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 (fend >= end) + { + fend = end; + } + int pady = (y1 + av.charHeight) - av.charHeight / 5; + 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) * av.charWidth, y1, av.charWidth,av.charHeight); + + if(offscreenRender || !av.validCharWidth) + continue; + + g.setColor(Color.white); + charOffset = (av.charWidth - fm.charWidth(s)) / 2; + g.drawString(String.valueOf(s), + charOffset + (av.charWidth * (i - start)), + pady); + + } + } + } + + + boolean newFeatureAdded = false; + + public void featuresAdded() + { + findAllFeatures(); + } + + boolean findingFeatures = false; + synchronized void findAllFeatures() + { + newFeatureAdded = false; + + if(findingFeatures) + { + newFeatureAdded = true; + return; + } + + findingFeatures = true; + jalview.schemes.UserColourScheme ucs = new + jalview.schemes.UserColourScheme(); + + if(av.featuresDisplayed==null) + av.featuresDisplayed = new Hashtable(); + + av.featuresDisplayed.clear(); + + Vector allfeatures = new Vector(); + for (int i = 0; i < av.alignment.getHeight(); i++) + { + SequenceFeature [] features + = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures(); + + if (features == null) + continue; + + int index = 0; + while (index < features.length) + { + if (!av.featuresDisplayed.containsKey(features[index].getType())) + { + if(!(features[index].begin == 0 && features[index].end ==0)) + { + // If beginning and end are 0, the feature is for the whole sequence + // and we don't want to render the feature in the normal way + + if (getColour(features[index].getType()) == null) + { + featureColours.put(features[index].getType(), + ucs.createColourFromName(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--; + } + + findingFeatures = false; + } + + public Color getColour(String featureType) + { + Color colour = (Color)featureColours.get(featureType); + return colour; + } + + + public void addNewFeature(String name, Color col, String group) + { + + setColour(name, col); + if(av.featuresDisplayed==null) + av.featuresDisplayed = new Hashtable(); + + if(group == null) + group = "NOGROUP"; + + av.featuresDisplayed.put(name, new Integer(col.getRGB())); + } + + 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 + if(av.featuresDisplayed!=null) + av.featuresDisplayed.clear(); + else + av.featuresDisplayed = new Hashtable(); + + 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; + } + + } + + + + +}