X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=89e94c8ebfb2ae53588086470d7be50ab5c6a2c7;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=cbdf2eff623e69f150ae02d7c018e6fc86bb167c;hpb=cca50cb3aee94f3ed1a5e504d45b8d8b665f8c5b;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index cbdf2ef..89e94c8 100644 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,59 +20,48 @@ */ package jalview.gui; -import java.util.*; -import java.util.concurrent.ConcurrentHashMap; - -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.datamodel.SearchResults; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; import jalview.schemes.GraduatedColor; import jalview.util.MessageManager; +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.GridLayout; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; + +import javax.swing.JColorChooser; +import javax.swing.JComboBox; +import javax.swing.JLabel; +import javax.swing.JOptionPane; +import javax.swing.JPanel; +import javax.swing.JScrollPane; +import javax.swing.JSpinner; +import javax.swing.JTextArea; +import javax.swing.JTextField; +import javax.swing.SwingConstants; + /** * DOCUMENT ME! * * @author $author$ * @version $Revision$ */ -public class FeatureRenderer implements jalview.api.FeatureRenderer +public class FeatureRenderer extends + jalview.renderer.seqfeatures.FeatureRenderer implements + jalview.api.FeatureRenderer { - AlignmentPanel ap; - - AlignViewport av; - Color resBoxColour; - /** - * global transparency for feature - */ - float transparency = 1.0f; - - FontMetrics fm; - - int charOffset; - - Map featureColours = new ConcurrentHashMap(); - - // A higher level for grouping features of a - // particular type - Map featureGroups = new ConcurrentHashMap(); - - // 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; + AlignmentPanel ap; /** * Creates a new FeatureRenderer object. @@ -82,904 +71,17 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer */ public FeatureRenderer(AlignmentPanel ap) { + super(); this.ap = ap; this.av = ap.av; - if (ap != null && ap.getSeqPanel() != null && ap.getSeqPanel().seqCanvas != null + if (ap != null && ap.getSeqPanel() != null + && ap.getSeqPanel().seqCanvas != null && ap.getSeqPanel().seqCanvas.fr != null) { transferSettings(ap.getSeqPanel().seqCanvas.fr); } } - public class FeatureRendererSettings implements Cloneable - { - String[] renderOrder; - - Map featureGroups; - - Map featureColours; - - float transparency; - - Map 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; - } - - /** - * create an independent instance of the feature renderer settings - * - * @param fr - */ - public FeatureRendererSettings(FeatureRenderer fr) - { - renderOrder = null; - featureGroups = new ConcurrentHashMap(); - featureColours = new ConcurrentHashMap(); - featureOrder = new ConcurrentHashMap(); - if (fr.renderOrder != null) - { - this.renderOrder = new String[fr.renderOrder.length]; - System.arraycopy(fr.renderOrder, 0, renderOrder, 0, - fr.renderOrder.length); - } - if (fr.featureGroups != null) - { - this.featureGroups = new ConcurrentHashMap(fr.featureGroups); - } - if (fr.featureColours != null) - { - this.featureColours = new ConcurrentHashMap(fr.featureColours); - } - Iterator en = fr.featureColours.keySet().iterator(); - while (en.hasNext()) - { - Object next = en.next(); - Object val = featureColours.get(next); - if (val instanceof GraduatedColor) - { - featureColours - .put(next, new GraduatedColor((GraduatedColor) val)); - } - } - this.transparency = fr.transparency; - if (fr.featureOrder != null) - { - this.featureOrder = new ConcurrentHashMap(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; - } - - /** - * update from another feature renderer - * - * @param fr - * settings to copy - */ - public void transferSettings(FeatureRenderer fr) - { - FeatureRendererSettings frs = new FeatureRendererSettings(fr); - this.renderOrder = frs.renderOrder; - this.featureGroups = frs.featureGroups; - this.featureColours = frs.featureColours; - this.transparency = frs.transparency; - this.featureOrder = frs.featureOrder; - if (av != null && av != fr.av) - { - // copy over the displayed feature settings - if (fr.av != null) - { - if (fr.av.featuresDisplayed != null) - { - // update display settings - if (av.featuresDisplayed == null) - { - av.featuresDisplayed = new Hashtable(fr.av.featuresDisplayed); - } - else - { - av.featuresDisplayed.clear(); - Enumeration en = fr.av.featuresDisplayed.keys(); - while (en.hasMoreElements()) - { - av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE); - } - - } - } - } - } - } - - 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 synchronized 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; - // TODO: non-threadsafe - each rendering thread needs its own instance of - // the feature renderer - or this should be synchronized. - 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(); - } - AlignmentI alignment = av.getAlignment(); - for (int i = 0; i < alignment.getHeight(); i++) - { - SequenceFeature[] features = 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); - } - - /** - * get a feature style object for the given type string. Creates a - * java.awt.Color for a featureType with no existing colourscheme. TODO: - * replace return type with object implementing standard abstract colour/style - * interface - * - * @param featureType - * @return java.awt.Color or GraduatedColor - */ - public Object getFeatureStyle(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, fc = col); - } - return fc; - } - - /** - * return a nominal colour for this feature - * - * @param featureType - * @return standard color, or maximum colour for graduated colourscheme - */ - public Color getColour(String featureType) - { - Object fc = getFeatureStyle(featureType); - - if (fc instanceof Color) - { - return (Color) fc; - } - else - { - if (fc instanceof GraduatedColor) - { - return ((GraduatedColor) fc).getMaxColor(); - } - } - throw new Error(MessageManager.formatMessage("error.implementation_error_unrecognised_render_object_for_features_type", new String[]{fc.getClass().toString(),featureType})); - } - - /** - * calculate the render colour for a specific feature using current feature - * settings. - * - * @param feature - * @return render colour for the given feature - */ - public Color getColour(SequenceFeature feature) - { - Object fc = getFeatureStyle(feature.getType()); - if (fc instanceof Color) - { - return (Color) fc; - } - else - { - if (fc instanceof GraduatedColor) - { - return ((GraduatedColor) fc).findColor(feature); - } - } - throw new Error(MessageManager.formatMessage("error.implementation_error_unrecognised_render_object_for_features_type", new String[]{fc.getClass().toString(),feature.getType()})); - } - - private boolean showFeature(SequenceFeature sequenceFeature) - { - Object fc = getFeatureStyle(sequenceFeature.type); - if (fc instanceof GraduatedColor) - { - return ((GraduatedColor) fc).isColored(sequenceFeature); - } - else - { - return true; - } - } - // // ///////////// // // Feature Editing Dialog // // Will be refactored in next release. @@ -1024,7 +126,8 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer if (fcol instanceof Color) { Color col = JColorChooser.showDialog(Desktop.desktop, - MessageManager.getString("label.select_feature_colour"), ((Color) fcol)); + MessageManager.getString("label.select_feature_colour"), + ((Color) fcol)); if (col != null) { fcol = col; @@ -1207,21 +310,22 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer Object[] options; if (!newFeatures) { - options = new Object[] - { "Amend", "Delete", "Cancel" }; + options = new Object[] { "Amend", "Delete", "Cancel" }; } else { - options = new Object[] - { "OK", "Cancel" }; + options = new Object[] { "OK", "Cancel" }; } - String title = newFeatures ? MessageManager.getString("label.create_new_sequence_features") - : MessageManager.formatMessage("label.amend_delete_features", new String[]{sequences[0].getName()}); + String title = newFeatures ? MessageManager + .getString("label.create_new_sequence_features") + : MessageManager.formatMessage("label.amend_delete_features", + new String[] { sequences[0].getName() }); int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop, bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION, - JOptionPane.QUESTION_MESSAGE, null, options, MessageManager.getString("action.ok")); + JOptionPane.QUESTION_MESSAGE, null, options, + MessageManager.getString("action.ok")); jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile(); @@ -1235,7 +339,9 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer lastDescriptionAdded = description.getText().replaceAll("\n", " "); // TODO: determine if the null feature group is valid if (lastFeatureGroupAdded.length() < 1) + { lastFeatureGroupAdded = null; + } } if (!newFeatures) @@ -1253,7 +359,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer sf.description = lastDescriptionAdded; setColour(sf.type, fcol); - av.featuresDisplayed.put(sf.type, getColour(sf.type)); + getFeaturesDisplayed().setVisible(sf.type); try { @@ -1274,27 +380,19 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer for (int i = 0; i < sequences.length; i++) { features[i].type = lastFeatureAdded; - if (lastFeatureGroupAdded != null) - features[i].featureGroup = lastFeatureGroupAdded; + // fix for JAL-1538 - always set feature group here + 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)); + setGroupVisibility(lastFeatureGroupAdded, true); } setColour(lastFeatureAdded, fcol); - av.featuresDisplayed.put(lastFeatureAdded, - getColour(lastFeatureAdded)); + setVisible(lastFeatureAdded); findAllFeatures(false); @@ -1340,145 +438,4 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer // colour.setForeground(colour.getBackground()); } } - - public void setColour(String featureType, Object col) - { - // overwrite - // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof - // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null; - // 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, data[i][1]); // todo : typesafety - feature color - // interface object - if (((Boolean) data[i][2]).booleanValue()) - { - av.featuresDisplayed.put(type, new Integer(getColour(type) - .getRGB())); - } - - renderOrder[data.length - i - 1] = type; - } - } - - } - - Map 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); - } }