X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=75ce63acee4ad33ddebddde613bbdcd9c4169fc8;hb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;hp=69ecf14bb152662f1c54a80858ca0b0533cc53be;hpb=5825bd1ee04099b0c81e325cb5cf360c8977b07e;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index 69ecf14..75ce63a 100755 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -1,323 +1,1312 @@ -/* - * 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; - boolean drawText = true; - - // The following vector holds the features which are - // to be added, in the correct order or rendering - Vector featuresDisplayed = null; - - /** - * Creates a new FeatureRenderer object. - * - * @param av DOCUMENT ME! - */ - public FeatureRenderer(AlignViewport av) - { - this.av = av; - initColours(); - } - - /** - * This is used by the Molecule Viewer to get the accurate colour - * of the rendered sequence - */ - BufferedImage bi; - public Color findFeatureColour(Color initialCol, SequenceI seq, int i) - { - if(!av.showSequenceFeatures) - return initialCol; - - if (bi == null) - bi = new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB); - - bi.setRGB(0,0, initialCol.getRGB()); - - drawText = false; - - drawSequence(bi.getGraphics(), seq, i, i, 0, 0, 1, 1); - drawText = true; - - return new Color(bi.getRGB(0, 0)); - } - - - /** - * 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, - int start, int end, int x1, int y1, int width, int height) - { - -//System.out.println(start+" "+end+" "+x1+" "+y1); - if (seq.getDatasetSequence().getSequenceFeatures() == null - || seq.getDatasetSequence().getSequenceFeatures().size()==0) - return; - - fm = g.getFontMetrics(); - - if (transparency != 1) - { - Graphics2D g2 = (Graphics2D) g; - g2.setComposite( - AlphaComposite.getInstance( - AlphaComposite.SRC_OVER, transparency)); - } - - String type; - SequenceFeature sf; - if (featuresDisplayed == null) - findAllFeatures(); - - Enumeration e = featuresDisplayed.elements(), e2; - - // Loop through each visible feature - while (e.hasMoreElements()) - { - - type = e.nextElement().toString(); - e2 = seq.getDatasetSequence().getSequenceFeatures().elements(); - // loop through all features in sequence to find - // current feature to render - while (e2.hasMoreElements()) - { - - sf = (SequenceFeature) e2.nextElement(); - if (!type.equals(sf.getType())) - continue; - - if (sf.getBegin() > seq.getEnd()) - continue; - - if (type.equals("disulfide bond")) - { - - renderFeature(g, seq, - seq.findIndex(sf.getBegin()) - 1, - seq.findIndex(sf.getBegin()) - 1, - type, start, end, x1, y1, width, height); - renderFeature(g, seq, - seq.findIndex(sf.getEnd()) - 1, - seq.findIndex(sf.getEnd()) - 1, - type, start, end, x1, y1, width, height); - - } - else - renderFeature(g, seq, - seq.findIndex(sf.getBegin()) - 1, - seq.findIndex(sf.getEnd()) - 1, - type, start, end, x1, y1, width, height); - } - } - - if(transparency!=1.0f) - { - Graphics2D g2 = (Graphics2D) g; - g2.setComposite( - AlphaComposite.getInstance( - AlphaComposite.SRC_OVER, 1.0f)); - } - } - - - void renderFeature(Graphics g, SequenceI seq, - int fstart, int fend, String type, int start, int end, int x1, 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 (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); - - if(drawText) - { - g.setColor(Color.white); - charOffset = (width - fm.charWidth(s)) / 2; - g.drawString(String.valueOf(s), - charOffset + x1 + (width * (i - start)), - (y1 + height) - height / 5); //pady = height / 5; - } - } - } - } - - void findAllFeatures() - { - Vector features = new Vector(); - SequenceFeature sf; - featuresDisplayed = new Vector(); - Enumeration e; - for (int i = 0; i < av.alignment.getHeight(); i++) - { - features = av.alignment.getSequenceAt(i).getDatasetSequence(). - getSequenceFeatures(); - if (features == null) - continue; - - e = features.elements(); - while (e.hasMoreElements()) - { - sf = (SequenceFeature) e.nextElement(); - if (!featuresDisplayed.contains(sf.getType())) - { - featuresDisplayed.addElement(sf.getType()); - } - } - } - } - - public Color getColour(String featureType) - { - return (Color)featureColours.get(featureType); - } - - public void addNewFeature(String name, Color col) - { - setColour(name, col); - if(featuresDisplayed==null) - featuresDisplayed = new Vector(); - featuresDisplayed.insertElementAt(name, 0); - } - - 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.clear(); - 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(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 (Development Version 2.4.1) + * Copyright (C) 2009 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 java.util.*; + +import java.awt.*; +import java.awt.event.*; +import java.awt.image.*; +import java.beans.PropertyChangeListener; +import java.beans.PropertyChangeSupport; + +import javax.swing.*; + +import jalview.datamodel.*; +import jalview.schemes.GraduatedColor; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class FeatureRenderer +{ + AlignmentPanel ap; + + AlignViewport av; + + Color resBoxColour; + + /** + * global transparency for feature + */ + float transparency = 1.0f; + + FontMetrics fm; + + int charOffset; + + Hashtable featureColours = new Hashtable(); + + // A higher level for grouping features of a + // particular type + Hashtable featureGroups = new Hashtable(); + + // This is actually an Integer held in the hashtable, + // Retrieved using the key feature type + Object currentColour; + + String[] renderOrder; + + PropertyChangeSupport changeSupport = new PropertyChangeSupport(this); + + Vector allfeatures; + + /** + * Creates a new FeatureRenderer object. + * + * @param av + * DOCUMENT ME! + */ + public FeatureRenderer(AlignmentPanel ap) + { + this.ap = ap; + this.av = ap.av; + } + + public class FeatureRendererSettings implements Cloneable + { + String[] renderOrder; + + Hashtable featureGroups; + + Hashtable featureColours; + + float transparency; + + Hashtable featureOrder; + + public FeatureRendererSettings(String[] renderOrder, + Hashtable featureGroups, Hashtable featureColours, + float transparency, Hashtable featureOrder) + { + super(); + this.renderOrder = renderOrder; + this.featureGroups = featureGroups; + this.featureColours = featureColours; + this.transparency = transparency; + this.featureOrder = featureOrder; + } + + public FeatureRendererSettings(FeatureRenderer fr) + { + this.renderOrder = fr.renderOrder; + this.featureGroups = fr.featureGroups; + this.featureColours = fr.featureColours; + this.transparency = fr.transparency; + this.featureOrder = fr.featureOrder; + } + } + + public FeatureRendererSettings getSettings() + { + return new FeatureRendererSettings(this); + } + + public void transferSettings(FeatureRendererSettings fr) + { + this.renderOrder = fr.renderOrder; + this.featureGroups = fr.featureGroups; + this.featureColours = fr.featureColours; + this.transparency = fr.transparency; + this.featureOrder = fr.featureOrder; + } + + public void transferSettings(FeatureRenderer fr) + { + this.renderOrder = fr.renderOrder; + this.featureGroups = fr.featureGroups; + this.featureColours = fr.featureColours; + this.transparency = fr.transparency; + this.featureOrder = fr.featureOrder; + } + + 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) + { + sfSize = sequenceFeatures.length; + } + } + + if (sequenceFeatures != lastSeq.getDatasetSequence() + .getSequenceFeatures()) + { + sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures(); + if (sequenceFeatures != null) + { + sfSize = sequenceFeatures.length; + } + } + + if (sequenceFeatures == null || sfSize == 0) + { + return initialCol; + } + + 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; + + /** + * show scores as heights + */ + protected boolean varyHeight = false; + + synchronized 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(); + } + + if (lastSeq == null + || seq != lastSeq + || seq.getDatasetSequence().getSequenceFeatures() != sequenceFeatures) + { + lastSeq = seq; + sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures(); + } + + 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); + } + + sfSize = sequenceFeatures.length; + String type; + for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) + { + type = renderOrder[renderIndex]; + + if (type == null || !av.featuresDisplayed.containsKey(type)) + { + continue; + } + + // loop through all features in sequence to find + // current feature to render + for (sfindex = 0; sfindex < sfSize; sfindex++) + { + if (!sequenceFeatures[sfindex].type.equals(type)) + { + continue; + } + + if (featureGroups != null + && sequenceFeatures[sfindex].featureGroup != null + && sequenceFeatures[sfindex].featureGroup.length() != 0 + && featureGroups + .containsKey(sequenceFeatures[sfindex].featureGroup) + && !((Boolean) featureGroups + .get(sequenceFeatures[sfindex].featureGroup)) + .booleanValue()) + { + continue; + } + + if (!offscreenRender + && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex] + .getEnd() < spos)) + { + continue; + } + + if (offscreenRender && offscreenImage == null) + { + if (sequenceFeatures[sfindex].begin <= start + && sequenceFeatures[sfindex].end >= start) + { + // this is passed out to the overview and other sequence renderers (e.g. molecule viewer) to get displayed colour for rendered sequence + currentColour = new Integer(getColour(sequenceFeatures[sfindex]).getRGB()); + // used to be retreived from av.featuresDisplayed + // 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, + getColour(sequenceFeatures[sfindex]) + //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, + getColour(sequenceFeatures[sfindex]) + //new Color(((Integer) av.featuresDisplayed + // .get(sequenceFeatures[sfindex].type)).intValue()) + , + start, end, y1); + + } + else + if (showFeature(sequenceFeatures[sfindex])) + { + if (av.showSeqFeaturesHeight + && sequenceFeatures[sfindex].score != Float.NaN) + { + renderScoreFeature(g, seq, seq + .findIndex(sequenceFeatures[sfindex].begin) - 1, + seq.findIndex(sequenceFeatures[sfindex].end) - 1, + getColour(sequenceFeatures[sfindex]), start, end, + y1, normaliseScore(sequenceFeatures[sfindex])); + } + else + { + renderFeature(g, seq, seq + .findIndex(sequenceFeatures[sfindex].begin) - 1, + seq.findIndex(sequenceFeatures[sfindex].end) - 1, + getColour(sequenceFeatures[sfindex]), start, end, + y1); + } + } + + } + + } + + if (transparency != 1.0f && g != null) + { + Graphics2D g2 = (Graphics2D) g; + g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, + 1.0f)); + } + } + + Hashtable minmax = new Hashtable(); + + /** + * normalise a score against the max/min bounds for the feature type. + * + * @param sequenceFeature + * @return byte[] { signed, normalised signed (-127 to 127) or unsigned + * (0-255) value. + */ + private final byte[] normaliseScore(SequenceFeature sequenceFeature) + { + float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0]; + final byte[] r = new byte[] + { 0, (byte) 255 }; + if (mm != null) + { + if (r[0] != 0 || mm[0] < 0.0) + { + r[0] = 1; + r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1])); + } + else + { + r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1])); + } + } + return r; + } + + 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.getCharAt(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); + + } + } + } + + void renderScoreFeature(Graphics g, SequenceI seq, int fstart, int fend, + Color featureColour, int start, int end, int y1, byte[] bs) + { + + 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; + int ystrt = 0, yend = av.charHeight; + if (bs[0] != 0) + { + // signed - zero is always middle of residue line. + if (bs[1] < 128) + { + yend = av.charHeight * (128 - bs[1]) / 512; + ystrt = av.charHeight - yend / 2; + } + else + { + ystrt = av.charHeight / 2; + yend = av.charHeight * (bs[1] - 128) / 512; + } + } + else + { + yend = av.charHeight * bs[1] / 255; + ystrt = av.charHeight - yend; + + } + for (i = fstart; i <= fend; i++) + { + s = seq.getCharAt(i); + + if (jalview.util.Comparison.isGap(s)) + { + continue; + } + + g.setColor(featureColour); + int x = (i - start) * av.charWidth; + g.drawRect(x, y1, av.charWidth, av.charHeight); + g.fillRect(x, y1 + ystrt, av.charWidth, yend); + + if (offscreenRender || !av.validCharWidth) + { + continue; + } + + g.setColor(Color.black); + charOffset = (av.charWidth - fm.charWidth(s)) / 2; + g.drawString(String.valueOf(s), charOffset + + (av.charWidth * (i - start)), pady); + + } + } + } + + boolean newFeatureAdded = false; + + /** + * Called when alignment in associated view has new/modified features to + * discover and display. + * + */ + public void featuresAdded() + { + lastSeq = null; + findAllFeatures(); + } + + boolean findingFeatures = false; + + /** + * search the alignment for all new features, give them a colour and display + * them. Then fires a PropertyChangeEvent on the changeSupport object. + * + */ + void findAllFeatures() + { + synchronized (firing) + { + if (firing.equals(Boolean.FALSE)) + { + firing = Boolean.TRUE; + findAllFeatures(true); // add all new features as visible + changeSupport.firePropertyChange("changeSupport", null, null); + firing = Boolean.FALSE; + } + } + } + + /** + * Searches alignment for all features and updates colours + * + * @param newMadeVisible + * if true newly added feature types will be rendered + * immediatly + */ + synchronized void findAllFeatures(boolean newMadeVisible) + { + newFeatureAdded = false; + + if (findingFeatures) + { + newFeatureAdded = true; + return; + } + + findingFeatures = true; + + if (av.featuresDisplayed == null) + { + av.featuresDisplayed = new Hashtable(); + } + + allfeatures = new Vector(); + Vector oldfeatures = new Vector(); + if (renderOrder != null) + { + for (int i = 0; i < renderOrder.length; i++) + { + if (renderOrder[i] != null) + { + oldfeatures.addElement(renderOrder[i]); + } + } + } + if (minmax == null) + { + minmax = new Hashtable(); + } + 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 (featureGroups.containsKey(features[index].getType())) + { + boolean visible = ((Boolean) featureGroups + .get(features[index].featureGroup)).booleanValue(); + + if (!visible) + { + index++; + continue; + } + } + + 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 (newMadeVisible + && !oldfeatures.contains(features[index].getType())) + { + // this is a new feature type on the alignment. Mark it for + // display. + av.featuresDisplayed.put(features[index].getType(), + new Integer(getColour(features[index].getType()) + .getRGB())); + setOrder(features[index].getType(), 0); + } + } + } + if (!allfeatures.contains(features[index].getType())) + { + allfeatures.addElement(features[index].getType()); + } + if (features[index].score != Float.NaN) + { + int nonpos= features[index].getBegin()>=1 ? 0 : 1; + float[][] mm = (float[][]) minmax.get(features[index].getType()); + if (mm == null) + { + mm = new float[][] {null, null }; + minmax.put(features[index].getType(), mm); + } + if (mm[nonpos]==null) + { + mm[nonpos] = new float[] { features[index].score, features[index].score }; + + } + else + { + if (mm[nonpos][0] > features[index].score) + { + mm[nonpos][0] = features[index].score; + } + if (mm[nonpos][1] < features[index].score) + { + mm[nonpos][1] = features[index].score; + } + } + } + index++; + } + } + updateRenderOrder(allfeatures); + findingFeatures = false; + } + + protected Boolean firing = Boolean.FALSE; + + /** + * replaces the current renderOrder with the unordered features in + * allfeatures. The ordering of any types in both renderOrder and allfeatures + * is preserved, and all new feature types are rendered on top of the existing + * types, in the order given by getOrder or the order given in allFeatures. + * Note. this operates directly on the featureOrder hash for efficiency. TODO: + * eliminate the float storage for computing/recalling the persistent ordering + * New Cability: updates min/max for colourscheme range if its dynamic + * @param allFeatures + */ + private void updateRenderOrder(Vector allFeatures) + { + Vector allfeatures = new Vector(allFeatures); + String[] oldRender = renderOrder; + renderOrder = new String[allfeatures.size()]; + Object mmrange,fc=null; + boolean initOrders = (featureOrder == null); + int opos = 0; + if (oldRender != null && oldRender.length > 0) + { + for (int j = 0; j < oldRender.length; j++) + { + if (oldRender[j] != null) + { + if (initOrders) + { + setOrder(oldRender[j], (1 - (1 + (float) j) + / (float) oldRender.length)); + } + if (allfeatures.contains(oldRender[j])) + { + renderOrder[opos++] = oldRender[j]; // existing features always + // appear below new features + allfeatures.removeElement(oldRender[j]); + if (minmax!=null) + { + mmrange = minmax.get(oldRender[j]); + if (mmrange!=null) + { + fc = featureColours.get(oldRender[j]); + if (fc!=null && fc instanceof GraduatedColor && ((GraduatedColor)fc).isAutoScale()) + { + ((GraduatedColor) fc).updateBounds(((float[][])mmrange)[0][0],((float[][])mmrange)[0][1]); + } + } + } + } + } + } + } + if (allfeatures.size() == 0) + { + // no new features - leave order unchanged. + return; + } + int i = allfeatures.size() - 1; + int iSize = i; + boolean sort = false; + String[] newf = new String[allfeatures.size()]; + float[] sortOrder = new float[allfeatures.size()]; + Enumeration en = allfeatures.elements(); + // sort remaining elements + while (en.hasMoreElements()) + { + newf[i] = en.nextElement().toString(); + if (minmax!=null) + { + // update from new features minmax if necessary + mmrange = minmax.get(newf[i]); + if (mmrange!=null) + { + fc = featureColours.get(newf[i]); + if (fc!=null && fc instanceof GraduatedColor && ((GraduatedColor)fc).isAutoScale()) + { + ((GraduatedColor) fc).updateBounds(((float[][])mmrange)[0][0],((float[][])mmrange)[0][1]); + } + } + } + if (initOrders || !featureOrder.containsKey(newf[i])) + { + int denom = initOrders ? allfeatures.size() : featureOrder.size(); + // new unordered feature - compute persistent ordering at head of + // existing features. + setOrder(newf[i], i / (float) denom); + } + // set order from newly found feature from persisted ordering. + sortOrder[i] = 2 - ((Float) featureOrder.get(newf[i])).floatValue(); + if (i < iSize) + { + // only sort if we need to + sort = sort || sortOrder[i] > sortOrder[i + 1]; + } + i--; + } + if (iSize > 1 && sort) + { + jalview.util.QuickSort.sort(sortOrder, newf); + } + sortOrder = null; + System.arraycopy(newf, 0, renderOrder, opos, newf.length); + } + + public Color getColour(String featureType) + { + Object fc = featureColours.get(featureType); + if (fc == null) + { + jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(); + Color col = ucs.createColourFromName(featureType); + featureColours.put(featureType, col); + return col; + } + else if (fc instanceof Color) + { + return (Color) fc; + } + else + { + if (fc instanceof GraduatedColor) + { + return ((GraduatedColor) fc).getMaxColor(); + } + // TODO: raise an implementation error here. + return null; // Color.white; + } + } + + /** + * implement graduated colouring for features with scores + * + * @param feature + * @return render colour for the given feature + */ + public Color getColour(SequenceFeature feature) + { + Object fc = featureColours.get(feature.type); + if (fc == null) + { + jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(); + Color col = ucs.createColourFromName(feature.type); + featureColours.put(feature.type, col); + return col; + } + else if (fc instanceof Color) + { + return (Color) fc; + } + else + { + if (fc instanceof GraduatedColor) + { + return ((GraduatedColor) fc).findColor(feature); + } + // TODO: raise an implementation error here. + return null; // Color.white; + } + } + private boolean showFeature(SequenceFeature sequenceFeature) + { + Object fc = featureColours.get(sequenceFeature.type); + if (fc instanceof GraduatedColor) + { + return ((GraduatedColor) fc).isColored(sequenceFeature); + } else { return true; } + } + + + static String lastFeatureAdded; + + static String lastFeatureGroupAdded; + + static String lastDescriptionAdded; + + int featureIndex = 0; + + boolean amendFeatures(final SequenceI[] sequences, + final SequenceFeature[] features, boolean newFeatures, + final AlignmentPanel ap) + { + + featureIndex = 0; + + JPanel bigPanel = new JPanel(new BorderLayout()); + final JComboBox overlaps; + final JTextField name = new JTextField(25); + final JTextField source = new JTextField(25); + final JTextArea description = new JTextArea(3, 25); + final JSpinner start = new JSpinner(); + final JSpinner end = new JSpinner(); + start.setPreferredSize(new Dimension(80, 20)); + end.setPreferredSize(new Dimension(80, 20)); + + final JPanel colour = new JPanel(); + colour.setBorder(BorderFactory.createEtchedBorder()); + colour.setMaximumSize(new Dimension(40, 10)); + colour.addMouseListener(new MouseAdapter() + { + public void mousePressed(MouseEvent evt) + { + // TODO: use featurecolourchooser here + Color col = JColorChooser.showDialog(Desktop.desktop, + "Select Feature Colour", colour.getBackground()); + if (col != null) + colour.setBackground(col); + + } + }); + + JPanel tmp = new JPanel(); + JPanel panel = new JPanel(new GridLayout(3, 1)); + + // ///////////////////////////////////// + // /MULTIPLE FEATURES AT SELECTED RESIDUE + if (!newFeatures && features.length > 1) + { + panel = new JPanel(new GridLayout(4, 1)); + tmp = new JPanel(); + tmp.add(new JLabel("Select Feature: ")); + overlaps = new JComboBox(); + for (int i = 0; i < features.length; i++) + { + overlaps.addItem(features[i].getType() + "/" + + features[i].getBegin() + "-" + features[i].getEnd() + + " (" + features[i].getFeatureGroup() + ")"); + } + + tmp.add(overlaps); + + overlaps.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent e) + { + int index = overlaps.getSelectedIndex(); + if (index != -1) + { + featureIndex = index; + name.setText(features[index].getType()); + description.setText(features[index].getDescription()); + source.setText(features[index].getFeatureGroup()); + start.setValue(new Integer(features[index].getBegin())); + end.setValue(new Integer(features[index].getEnd())); + + SearchResults highlight = new SearchResults(); + highlight.addResult(sequences[0], features[index].getBegin(), + features[index].getEnd()); + + ap.seqPanel.seqCanvas.highlightSearchResults(highlight); + + } + Color col = getColour(name.getText()); + if (col == null) + { + col = new jalview.schemes.UserColourScheme() + .createColourFromName(name.getText()); + } + + colour.setBackground(col); + } + }); + + panel.add(tmp); + } + // //////// + // //////////////////////////////////// + + tmp = new JPanel(); + panel.add(tmp); + tmp.add(new JLabel("Name: ", JLabel.RIGHT)); + tmp.add(name); + + tmp = new JPanel(); + panel.add(tmp); + tmp.add(new JLabel("Group: ", JLabel.RIGHT)); + tmp.add(source); + + tmp = new JPanel(); + panel.add(tmp); + tmp.add(new JLabel("Colour: ", JLabel.RIGHT)); + tmp.add(colour); + colour.setPreferredSize(new Dimension(150, 15)); + + bigPanel.add(panel, BorderLayout.NORTH); + + panel = new JPanel(); + panel.add(new JLabel("Description: ", JLabel.RIGHT)); + description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + description.setLineWrap(true); + panel.add(new JScrollPane(description)); + + if (!newFeatures) + { + bigPanel.add(panel, BorderLayout.SOUTH); + + panel = new JPanel(); + panel.add(new JLabel(" Start:", JLabel.RIGHT)); + panel.add(start); + panel.add(new JLabel(" End:", JLabel.RIGHT)); + panel.add(end); + bigPanel.add(panel, BorderLayout.CENTER); + } + else + { + bigPanel.add(panel, BorderLayout.CENTER); + } + + if (lastFeatureAdded == null) + { + if (features[0].type != null) + { + lastFeatureAdded = features[0].type; + } + else + { + lastFeatureAdded = "feature_1"; + } + } + + if (lastFeatureGroupAdded == null) + { + if (features[0].featureGroup != null) + { + lastFeatureGroupAdded = features[0].featureGroup; + } + else + { + lastFeatureGroupAdded = "Jalview"; + } + } + + if (newFeatures) + { + name.setText(lastFeatureAdded); + source.setText(lastFeatureGroupAdded); + } + else + { + name.setText(features[0].getType()); + source.setText(features[0].getFeatureGroup()); + } + + start.setValue(new Integer(features[0].getBegin())); + end.setValue(new Integer(features[0].getEnd())); + description.setText(features[0].getDescription()); + colour.setBackground(getColour(name.getText())); + + Object[] options; + if (!newFeatures) + { + options = new Object[] + { "Amend", "Delete", "Cancel" }; + } + else + { + options = new Object[] + { "OK", "Cancel" }; + } + + String title = newFeatures ? "Create New Sequence Feature(s)" + : "Amend/Delete Features for " + sequences[0].getName(); + + int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop, + bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION, + JOptionPane.QUESTION_MESSAGE, null, options, "OK"); + + jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile(); + + if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0) + { + // This ensures that the last sequence + // is refreshed and new features are rendered + lastSeq = null; + lastFeatureAdded = name.getText().trim(); + lastFeatureGroupAdded = source.getText().trim(); + lastDescriptionAdded = description.getText().replaceAll("\n", " "); + + if (lastFeatureGroupAdded.length() < 1) + lastFeatureGroupAdded = null; + } + + if (!newFeatures) + { + SequenceFeature sf = features[featureIndex]; + + if (reply == JOptionPane.NO_OPTION) + { + sequences[0].getDatasetSequence().deleteFeature(sf); + } + else if (reply == JOptionPane.YES_OPTION) + { + sf.type = lastFeatureAdded; + sf.featureGroup = lastFeatureGroupAdded; + sf.description = lastDescriptionAdded; + + setColour(sf.type, colour.getBackground()); + av.featuresDisplayed.put(sf.type, new Integer(colour + .getBackground().getRGB())); + + try + { + sf.begin = ((Integer) start.getValue()).intValue(); + sf.end = ((Integer) end.getValue()).intValue(); + } catch (NumberFormatException ex) + { + } + + ffile.parseDescriptionHTML(sf, false); + } + } + else + // NEW FEATURES ADDED + { + if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0) + { + for (int i = 0; i < sequences.length; i++) + { + features[i].type = lastFeatureAdded; + if (lastFeatureGroupAdded != null) + features[i].featureGroup = lastFeatureGroupAdded; + features[i].description = lastDescriptionAdded; + sequences[i].addSequenceFeature(features[i]); + ffile.parseDescriptionHTML(features[i], false); + } + + if (av.featuresDisplayed == null) + { + av.featuresDisplayed = new Hashtable(); + } + + if (lastFeatureGroupAdded != null) + { + if (featureGroups == null) + featureGroups = new Hashtable(); + featureGroups.put(lastFeatureGroupAdded, new Boolean(true)); + } + + Color col = colour.getBackground(); + setColour(lastFeatureAdded, colour.getBackground()); + av.featuresDisplayed.put(lastFeatureAdded, + new Integer(col.getRGB())); + + findAllFeatures(false); + + ap.paintAlignment(true); + + return true; + } + else + { + return false; + } + } + + ap.paintAlignment(true); + + return true; + } + + public void setColour(String featureType, Color col) + { + Object c = featureColours.get(featureType); + if (c == null || c instanceof Color || (c instanceof GraduatedColor && !((GraduatedColor)c).getMaxColor().equals(col))) + { + featureColours.put(featureType, col); + } + } + + public void setTransparency(float value) + { + transparency = value; + } + + public float getTransparency() + { + return transparency; + } + + /** + * Replace current ordering with new ordering + * + * @param data { + * String(Type), Colour(Type), Boolean(Displayed) } + */ + public void setFeaturePriority(Object[][] data) + { + setFeaturePriority(data, true); + } + + /** + * + * @param data { + * String(Type), Colour(Type), Boolean(Displayed) } + * @param visibleNew + * when true current featureDisplay list will be cleared + */ + public void setFeaturePriority(Object[][] data, boolean visibleNew) + { + if (visibleNew) + { + if (av.featuresDisplayed != null) + { + av.featuresDisplayed.clear(); + } + else + { + av.featuresDisplayed = new Hashtable(); + } + } + if (data == null) + { + return; + } + + // 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 + 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 featureOrder = null; + + /** + * analogous to colour - store a normalized ordering for all feature types in + * this rendering context. + * + * @param type + * Feature type string + * @param position + * normalized priority - 0 means always appears on top, 1 means + * always last. + */ + public float setOrder(String type, float position) + { + if (featureOrder == null) + { + featureOrder = new Hashtable(); + } + featureOrder.put(type, new Float(position)); + return position; + } + + /** + * get the global priority (0 (top) to 1 (bottom)) + * + * @param type + * @return [0,1] or -1 for a type without a priority + */ + public float getOrder(String type) + { + if (featureOrder != null) + { + if (featureOrder.containsKey(type)) + { + return ((Float) featureOrder.get(type)).floatValue(); + } + } + return -1; + } + + /** + * @param listener + * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener) + */ + public void addPropertyChangeListener(PropertyChangeListener listener) + { + changeSupport.addPropertyChangeListener(listener); + } + + /** + * @param listener + * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener) + */ + public void removePropertyChangeListener(PropertyChangeListener listener) + { + changeSupport.removePropertyChangeListener(listener); + } +}