X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=46f574e03ec4d9f4c3b9f8183582c6aa80079767;hb=e16e9699b56f3db4e42dc694aaafad76dae66c4b;hp=3c89d43e7e8d829f58817296271eeee1a7fe011b;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java old mode 100755 new mode 100644 index 3c89d43..46f574e --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -1,1120 +1,315 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview 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 3 of the License, or (at your option) any later version. - * + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * * Jalview 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 Jalview. If not, see . - */ -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.schemes.GraduatedColor; - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class 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; - - /** - * 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; - - 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; - } - - 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(); + * 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 Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.gui; - if (!visible) - { - index++; - continue; - } - } +import jalview.api.FeatureColourI; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SearchResultsI; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.io.FeaturesFile; +import jalview.schemes.FeatureColour; +import jalview.util.ColorUtils; +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 java.util.ArrayList; +import java.util.Arrays; +import java.util.Comparator; +import java.util.List; + +import javax.swing.JColorChooser; +import javax.swing.JComboBox; +import javax.swing.JLabel; +import javax.swing.JPanel; +import javax.swing.JScrollPane; +import javax.swing.JSpinner; +import javax.swing.JTextArea; +import javax.swing.JTextField; +import javax.swing.SwingConstants; +import javax.swing.event.DocumentEvent; +import javax.swing.event.DocumentListener; - 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 +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class FeatureRenderer + extends jalview.renderer.seqfeatures.FeatureRenderer +{ + /* + * defaults for creating a new feature are the last created + * feature type and group + */ + static String lastFeatureAdded = "feature_1"; - 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 }; + static String lastFeatureGroupAdded = "Jalview"; - } - 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; - } + Color resBoxColour; - protected Boolean firing = Boolean.FALSE; + AlignmentPanel ap; /** - * 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 + * Creates a new FeatureRenderer object * - * @param allFeatures + * @param alignPanel */ - private void updateRenderOrder(Vector allFeatures) + public FeatureRenderer(AlignmentPanel alignPanel) { - 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) + super(alignPanel.av); + this.ap = alignPanel; + if (alignPanel.getSeqPanel() != null + && alignPanel.getSeqPanel().seqCanvas != null + && alignPanel.getSeqPanel().seqCanvas.fr != null) { - jalview.util.QuickSort.sort(sortOrder, newf); + transferSettings(alignPanel.getSeqPanel().seqCanvas.fr); } - 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; - } + FeatureColourI oldcol, fcol; + + int featureIndex = 0; /** - * return a nominal colour for this feature + * Presents a dialog allowing the user to add new features, or amend or delete + * existing features. Currently this can be on + * + * If the supplied feature type is null, show (and update on confirm) the type + * and group of the last new feature created (with initial defaults of + * "feature_1" and "Jalview"). * - * @param featureType - * @return standard color, or maximum colour for graduated colourscheme + * @param sequences + * the sequences features are to be created on (if creating + * features), or a single sequence (if amending features) + * @param features + * the current features at the position (if amending), or template + * new feature(s) with start/end position set (if creating) + * @param create + * true to create features, false to amend or delete + * @param alignPanel + * @return */ - public Color getColour(String featureType) + protected boolean amendFeatures(final List sequences, + final List features, boolean create, + final AlignmentPanel alignPanel) { - Object fc = getFeatureStyle(featureType); + featureIndex = 0; - if (fc instanceof Color) - { - return (Color) fc; - } - else + final JPanel mainPanel = new JPanel(new BorderLayout()); + + final JTextField name = new JTextField(25); + name.getDocument().addDocumentListener(new DocumentListener() { - if (fc instanceof GraduatedColor) + @Override + public void insertUpdate(DocumentEvent e) { - return ((GraduatedColor) fc).getMaxColor(); + warnIfTypeHidden(mainPanel, name.getText()); } - } - throw new Error("Implementation Error: Unrecognised render object " - + fc.getClass() + " for features of type " + 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) + @Override + public void removeUpdate(DocumentEvent e) { - return ((GraduatedColor) fc).findColor(feature); + warnIfTypeHidden(mainPanel, name.getText()); } - } - throw new Error("Implementation Error: Unrecognised render object " - + fc.getClass() + " for features of type " + 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. - - static String lastFeatureAdded; - static String lastFeatureGroupAdded; - - static String lastDescriptionAdded; - - Object oldcol, fcol; + @Override + public void changedUpdate(DocumentEvent e) + { + warnIfTypeHidden(mainPanel, name.getText()); + } + }); - int featureIndex = 0; + final JTextField group = new JTextField(25); + group.getDocument().addDocumentListener(new DocumentListener() + { + @Override + public void insertUpdate(DocumentEvent e) + { + warnIfGroupHidden(mainPanel, group.getText()); + } - boolean amendFeatures(final SequenceI[] sequences, - final SequenceFeature[] features, boolean newFeatures, - final AlignmentPanel ap) - { + @Override + public void removeUpdate(DocumentEvent e) + { + warnIfGroupHidden(mainPanel, group.getText()); + } - featureIndex = 0; + @Override + public void changedUpdate(DocumentEvent e) + { + warnIfGroupHidden(mainPanel, group.getText()); + } + }); - final 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 FeatureRenderer me = this; final JLabel colour = new JLabel(); colour.setOpaque(true); // colour.setBorder(BorderFactory.createEtchedBorder()); colour.setMaximumSize(new Dimension(30, 16)); colour.addMouseListener(new MouseAdapter() { - FeatureColourChooser fcc = null; - + /* + * open colour chooser on click in colour panel + */ + @Override public void mousePressed(MouseEvent evt) { - if (fcol instanceof Color) + if (fcol.isSimpleColour()) { Color col = JColorChooser.showDialog(Desktop.desktop, - "Select Feature Colour", ((Color) fcol)); + MessageManager.getString("label.select_feature_colour"), + fcol.getColour()); if (col != null) { - fcol = col; - updateColourButton(bigPanel, colour, col); + fcol = new FeatureColour(col); + updateColourButton(mainPanel, colour, fcol); } } else { - - if (fcc == null) + /* + * variable colour dialog - on OK, refetch the updated + * feature colour and update this display + */ + final String ft = features.get(featureIndex).getType(); + final String type = ft == null ? lastFeatureAdded : ft; + FeatureTypeSettings fcc = new FeatureTypeSettings( + FeatureRenderer.this, type); + fcc.setRequestFocusEnabled(true); + fcc.requestFocus(); + fcc.addActionListener(new ActionListener() { - final String type = features[featureIndex].getType(); - fcc = new FeatureColourChooser(me, type); - fcc.setRequestFocusEnabled(true); - fcc.requestFocus(); - - fcc.addActionListener(new ActionListener() + @Override + public void actionPerformed(ActionEvent e) { - - public void actionPerformed(ActionEvent e) - { - fcol = fcc.getLastColour(); - fcc = null; - setColour(type, fcol); - updateColourButton(bigPanel, colour, fcol); - } - }); - - } + fcol = FeatureRenderer.this.getFeatureStyle(ft); + setColour(type, fcol); + updateColourButton(mainPanel, colour, fcol); + } + }); } } }); - 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() + ")"); + JPanel gridPanel = new JPanel(new GridLayout(3, 1)); + + if (!create && features.size() > 1) + { + /* + * more than one feature at selected position - + * add a drop-down to choose the feature to amend + * space pad text if necessary to make entries distinct + */ + gridPanel = new JPanel(new GridLayout(4, 1)); + JPanel choosePanel = new JPanel(); + choosePanel.add(new JLabel( + MessageManager.getString("label.select_feature") + ":")); + final JComboBox overlaps = new JComboBox<>(); + List added = new ArrayList<>(); + for (SequenceFeature sf : features) + { + String text = String.format("%s/%d-%d (%s)", sf.getType(), + sf.getBegin(), sf.getEnd(), sf.getFeatureGroup()); + while (added.contains(text)) + { + text += " "; + } + overlaps.addItem(text); + added.add(text); } - - tmp.add(overlaps); + choosePanel.add(overlaps); overlaps.addItemListener(new ItemListener() { + @Override 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); - + SequenceFeature sf = features.get(index); + name.setText(sf.getType()); + description.setText(sf.getDescription()); + group.setText(sf.getFeatureGroup()); + start.setValue(new Integer(sf.getBegin())); + end.setValue(new Integer(sf.getEnd())); + + SearchResultsI highlight = new SearchResults(); + highlight.addResult(sequences.get(0), sf.getBegin(), + sf.getEnd()); + + alignPanel.getSeqPanel().seqCanvas.highlightSearchResults( + highlight, false); } - Object col = getFeatureStyle(name.getText()); + FeatureColourI col = getFeatureStyle(name.getText()); if (col == null) { - col = new jalview.schemes.UserColourScheme() - .createColourFromName(name.getText()); + col = new FeatureColour( + ColorUtils.createColourFromName(name.getText())); } oldcol = fcol = col; - updateColourButton(bigPanel, colour, col); + updateColourButton(mainPanel, colour, col); } }); - panel.add(tmp); + gridPanel.add(choosePanel); } - // //////// - // //////////////////////////////////// - tmp = new JPanel(); - panel.add(tmp); - tmp.add(new JLabel("Name: ", JLabel.RIGHT)); - tmp.add(name); + JPanel namePanel = new JPanel(); + gridPanel.add(namePanel); + namePanel.add(new JLabel(MessageManager.getString("label.name:"), + JLabel.RIGHT)); + namePanel.add(name); - tmp = new JPanel(); - panel.add(tmp); - tmp.add(new JLabel("Group: ", JLabel.RIGHT)); - tmp.add(source); + JPanel groupPanel = new JPanel(); + gridPanel.add(groupPanel); + groupPanel.add(new JLabel(MessageManager.getString("label.group:"), + JLabel.RIGHT)); + groupPanel.add(group); - tmp = new JPanel(); - panel.add(tmp); - tmp.add(new JLabel("Colour: ", JLabel.RIGHT)); - tmp.add(colour); + JPanel colourPanel = new JPanel(); + gridPanel.add(colourPanel); + colourPanel.add(new JLabel(MessageManager.getString("label.colour"), + JLabel.RIGHT)); + colourPanel.add(colour); colour.setPreferredSize(new Dimension(150, 15)); colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9)); colour.setForeground(Color.black); @@ -1122,165 +317,175 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer colour.setVerticalAlignment(SwingConstants.CENTER); colour.setHorizontalTextPosition(SwingConstants.CENTER); colour.setVerticalTextPosition(SwingConstants.CENTER); - bigPanel.add(panel, BorderLayout.NORTH); + mainPanel.add(gridPanel, BorderLayout.NORTH); - panel = new JPanel(); - panel.add(new JLabel("Description: ", JLabel.RIGHT)); + JPanel descriptionPanel = new JPanel(); + descriptionPanel.add(new JLabel( + MessageManager.getString("label.description:"), JLabel.RIGHT)); description.setFont(JvSwingUtils.getTextAreaFont()); 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); - } + descriptionPanel.add(new JScrollPane(description)); - if (lastFeatureAdded == null) + if (!create) { - 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"; - } - } + mainPanel.add(descriptionPanel, BorderLayout.SOUTH); - if (newFeatures) - { - name.setText(lastFeatureAdded); - source.setText(lastFeatureGroupAdded); + JPanel startEndPanel = new JPanel(); + startEndPanel.add(new JLabel(MessageManager.getString("label.start"), + JLabel.RIGHT)); + startEndPanel.add(start); + startEndPanel.add(new JLabel(MessageManager.getString("label.end"), + JLabel.RIGHT)); + startEndPanel.add(end); + mainPanel.add(startEndPanel, BorderLayout.CENTER); } else { - name.setText(features[0].getType()); - source.setText(features[0].getFeatureGroup()); + mainPanel.add(descriptionPanel, BorderLayout.CENTER); } - start.setValue(new Integer(features[0].getBegin())); - end.setValue(new Integer(features[0].getEnd())); - description.setText(features[0].getDescription()); - updateColourButton(bigPanel, colour, - (oldcol = fcol = getFeatureStyle(name.getText()))); + /* + * default feature type and group to that of the first feature supplied, + * or to the last feature created if not supplied (null value) + */ + SequenceFeature firstFeature = features.get(0); + boolean useLastDefaults = firstFeature.getType() == null; + final String featureType = useLastDefaults ? lastFeatureAdded + : firstFeature.getType(); + final String featureGroup = useLastDefaults ? lastFeatureGroupAdded + : firstFeature.getFeatureGroup(); + name.setText(featureType); + group.setText(featureGroup); + + start.setValue(new Integer(firstFeature.getBegin())); + end.setValue(new Integer(firstFeature.getEnd())); + description.setText(firstFeature.getDescription()); + updateColourButton(mainPanel, colour, + (oldcol = fcol = getFeatureStyle(featureType))); Object[] options; - if (!newFeatures) + if (!create) { - options = new Object[] - { "Amend", "Delete", "Cancel" }; + options = new Object[] { MessageManager.getString("label.amend"), + MessageManager.getString("action.delete"), + MessageManager.getString("action.cancel") }; } else { - options = new Object[] - { "OK", "Cancel" }; + options = new Object[] { MessageManager.getString("action.ok"), + MessageManager.getString("action.cancel") }; } - String title = newFeatures ? "Create New Sequence Feature(s)" - : "Amend/Delete Features for " + sequences[0].getName(); + String title = create + ? MessageManager.getString("label.create_new_sequence_features") + : MessageManager.formatMessage("label.amend_delete_features", + new String[] + { sequences.get(0).getName() }); - int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop, - bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION, - JOptionPane.QUESTION_MESSAGE, null, options, "OK"); + /* + * show the dialog + */ + int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop, + mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION, + JvOptionPane.QUESTION_MESSAGE, null, options, + MessageManager.getString("action.ok")); + + FeaturesFile ffile = new FeaturesFile(); - jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile(); + final String enteredType = name.getText().trim(); + final String enteredGroup = group.getText().trim(); + final String enteredDescription = description.getText().replaceAll("\n", " "); - if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0) + if (reply == JvOptionPane.OK_OPTION && enteredType.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", " "); - // TODO: determine if the null feature group is valid - if (lastFeatureGroupAdded.length() < 1) - lastFeatureGroupAdded = null; + /* + * update default values only if creating using default values + */ + if (useLastDefaults) + { + lastFeatureAdded = enteredType; + lastFeatureGroupAdded = enteredGroup; + // TODO: determine if the null feature group is valid + if (lastFeatureGroupAdded.length() < 1) + { + lastFeatureGroupAdded = null; + } + } } - if (!newFeatures) + if (!create) { - SequenceFeature sf = features[featureIndex]; + SequenceFeature sf = features.get(featureIndex); - if (reply == JOptionPane.NO_OPTION) + if (reply == JvOptionPane.NO_OPTION) { - sequences[0].getDatasetSequence().deleteFeature(sf); + /* + * NO_OPTION corresponds to the Delete button + */ + sequences.get(0).getDatasetSequence().deleteFeature(sf); + // update Feature Settings for removal of feature / group + featuresAdded(); } - else if (reply == JOptionPane.YES_OPTION) + else if (reply == JvOptionPane.YES_OPTION) { - sf.type = lastFeatureAdded; - sf.featureGroup = lastFeatureGroupAdded; - sf.description = lastDescriptionAdded; - - setColour(sf.type, fcol); - av.featuresDisplayed.put(sf.type, getColour(sf.type)); - + /* + * YES_OPTION corresponds to the Amend button + * need to refresh Feature Settings if type, group or colour changed; + * note we don't force the feature to be visible - the user has been + * warned if a hidden feature type or group was entered + */ + boolean refreshSettings = (!featureType.equals(enteredType) || !featureGroup + .equals(enteredGroup)); + refreshSettings |= (fcol != oldcol); + setColour(enteredType, fcol); + int newBegin = sf.begin; + int newEnd = sf.end; try { - sf.begin = ((Integer) start.getValue()).intValue(); - sf.end = ((Integer) end.getValue()).intValue(); + newBegin = ((Integer) start.getValue()).intValue(); + newEnd = ((Integer) end.getValue()).intValue(); } catch (NumberFormatException ex) { + // JSpinner doesn't accept invalid format data :-) } - ffile.parseDescriptionHTML(sf, false); + /* + * replace the feature by deleting it and adding a new one + * (to ensure integrity of SequenceFeatures data store) + */ + sequences.get(0).deleteFeature(sf); + SequenceFeature newSf = new SequenceFeature(sf, enteredType, + newBegin, newEnd, enteredGroup, sf.getScore()); + newSf.setDescription(enteredDescription); + ffile.parseDescriptionHTML(newSf, false); + // amend features dialog only updates one sequence at a time + sequences.get(0).addSequenceFeature(newSf); + + if (refreshSettings) + { + featuresAdded(); + } } } else // NEW FEATURES ADDED { - if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0) + if (reply == JvOptionPane.OK_OPTION && enteredType.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) + for (int i = 0; i < sequences.size(); i++) { - av.featuresDisplayed = new Hashtable(); + SequenceFeature sf = features.get(i); + SequenceFeature sf2 = new SequenceFeature(enteredType, + enteredDescription, sf.getBegin(), sf.getEnd(), + enteredGroup); + ffile.parseDescriptionHTML(sf2, false); + sequences.get(i).addSequenceFeature(sf2); } - if (lastFeatureGroupAdded != null) - { - if (featureGroups == null) - featureGroups = new Hashtable(); - featureGroups.put(lastFeatureGroupAdded, new Boolean(true)); - } - setColour(lastFeatureAdded, fcol); - av.featuresDisplayed.put(lastFeatureAdded, - getColour(lastFeatureAdded)); + setColour(enteredType, fcol); - findAllFeatures(false); + featuresAdded(); - ap.paintAlignment(true); + alignPanel.paintAlignment(true, true); return true; } @@ -1290,177 +495,83 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer } } - ap.paintAlignment(true); + alignPanel.paintAlignment(true, true); return true; } /** - * update the amend feature button dependent on the given style - * - * @param bigPanel - * @param col - * @param col2 - */ - protected void updateColourButton(JPanel bigPanel, JLabel colour, - Object col2) - { - colour.removeAll(); - colour.setIcon(null); - colour.setToolTipText(null); - colour.setText(""); - - if (col2 instanceof Color) - { - colour.setBackground((Color) col2); - } - else - { - colour.setBackground(bigPanel.getBackground()); - colour.setForeground(Color.black); - FeatureSettings.renderGraduatedColor(colour, (GraduatedColor) col2); - // 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 + * Show a warning message if the entered type is one that is currently hidden * - * @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 + * @param panel + * @param type */ - public void setFeaturePriority(Object[][] data, boolean visibleNew) + protected void warnIfTypeHidden(JPanel panel, String type) { - 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) + if (getRenderOrder().contains(type)) { - for (int i = 0; i < data.length; i++) + if (!showFeatureOfType(type)) { - 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; + String msg = MessageManager.formatMessage("label.warning_hidden", + MessageManager.getString("label.feature_type"), type); + JvOptionPane.showMessageDialog(panel, msg, "", + JvOptionPane.OK_OPTION); } } - } - Map featureOrder = null; - /** - * analogous to colour - store a normalized ordering for all feature types in - * this rendering context. + * Show a warning message if the entered group is one that is currently hidden * - * @param type - * Feature type string - * @param position - * normalized priority - 0 means always appears on top, 1 means - * always last. + * @param panel + * @param group */ - public float setOrder(String type, float position) + protected void warnIfGroupHidden(JPanel panel, String group) { - if (featureOrder == null) + if (featureGroups.containsKey(group) && !featureGroups.get(group)) { - featureOrder = new Hashtable(); + String msg = MessageManager.formatMessage("label.warning_hidden", + MessageManager.getString("label.group"), group); + JvOptionPane.showMessageDialog(panel, msg, "", + JvOptionPane.OK_OPTION); } - featureOrder.put(type, new Float(position)); - return position; } /** - * get the global priority (0 (top) to 1 (bottom)) + * update the amend feature button dependent on the given style * - * @param type - * @return [0,1] or -1 for a type without a priority + * @param bigPanel + * @param col + * @param col */ - public float getOrder(String type) + protected void updateColourButton(JPanel bigPanel, JLabel colour, + FeatureColourI col) { - if (featureOrder != null) + colour.removeAll(); + colour.setIcon(null); + colour.setToolTipText(null); + colour.setText(""); + + if (col.isSimpleColour()) { - if (featureOrder.containsKey(type)) - { - return ((Float) featureOrder.get(type)).floatValue(); - } + colour.setBackground(col.getColour()); + } + else + { + colour.setBackground(bigPanel.getBackground()); + colour.setForeground(Color.black); + FeatureSettings.renderGraduatedColor(colour, col); } - 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) + * Orders features in render precedence (last in order is last to render, so + * displayed on top of other features) + * + * @param order */ - public void removePropertyChangeListener(PropertyChangeListener listener) + public void orderFeatures(Comparator order) { - changeSupport.removePropertyChangeListener(listener); + Arrays.sort(renderOrder, order); } }