X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=cbdf2eff623e69f150ae02d7c018e6fc86bb167c;hb=cca50cb3aee94f3ed1a5e504d45b8d8b665f8c5b;hp=b6806e72a10b6bc6b76517aff28523ebfe007b85;hpb=79912985d2d21c7d456bbd2281ed84fdfe2e99e7;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java old mode 100755 new mode 100644 index b6806e7..cbdf2ef --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -1,24 +1,27 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 The Jalview Authors * - * 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 file is part of Jalview. * - * 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. + * 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. + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; import java.util.*; +import java.util.concurrent.ConcurrentHashMap; import java.awt.*; import java.awt.event.*; @@ -29,6 +32,8 @@ import java.beans.PropertyChangeSupport; import javax.swing.*; import jalview.datamodel.*; +import jalview.schemes.GraduatedColor; +import jalview.util.MessageManager; /** * DOCUMENT ME! @@ -36,13 +41,14 @@ import jalview.datamodel.*; * @author $author$ * @version $Revision$ */ -public class FeatureRenderer +public class FeatureRenderer implements jalview.api.FeatureRenderer { AlignmentPanel ap; AlignViewport av; Color resBoxColour; + /** * global transparency for feature */ @@ -52,11 +58,11 @@ public class FeatureRenderer int charOffset; - Hashtable featureColours = new Hashtable(); + Map featureColours = new ConcurrentHashMap(); // A higher level for grouping features of a // particular type - Hashtable featureGroups = new Hashtable(); + Map featureGroups = new ConcurrentHashMap(); // This is actually an Integer held in the hashtable, // Retrieved using the key feature type @@ -72,25 +78,30 @@ public class FeatureRenderer * Creates a new FeatureRenderer object. * * @param av - * DOCUMENT ME! + * DOCUMENT ME! */ public FeatureRenderer(AlignmentPanel ap) { this.ap = ap; this.av = ap.av; + 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; - Hashtable featureGroups; + Map featureGroups; - Hashtable featureColours; + Map featureColours; float transparency; - Hashtable featureOrder; + Map featureOrder; public FeatureRendererSettings(String[] renderOrder, Hashtable featureGroups, Hashtable featureColours, @@ -104,13 +115,47 @@ public class FeatureRenderer this.featureOrder = featureOrder; } + /** + * create an independent instance of the feature renderer settings + * + * @param fr + */ public FeatureRendererSettings(FeatureRenderer fr) { - this.renderOrder = fr.renderOrder; - this.featureGroups = fr.featureGroups; - this.featureColours = fr.featureColours; + 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; - this.featureOrder = fr.featureOrder; + if (fr.featureOrder != null) + { + this.featureOrder = new ConcurrentHashMap(fr.featureOrder); + } } } @@ -128,13 +173,45 @@ public class FeatureRenderer this.featureOrder = fr.featureOrder; } + /** + * update from another feature renderer + * + * @param fr + * settings to copy + */ 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; + 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; @@ -150,7 +227,8 @@ public class FeatureRenderer * 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) + public synchronized int findFeatureColour(int initialCol, SequenceI seq, + int column) { if (!av.showSequenceFeatures) { @@ -194,7 +272,8 @@ public class FeatureRenderer } 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) @@ -224,23 +303,23 @@ public class FeatureRenderer * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! * @param seq - * DOCUMENT ME! + * DOCUMENT ME! * @param sg - * DOCUMENT ME! + * DOCUMENT ME! * @param start - * DOCUMENT ME! + * DOCUMENT ME! * @param end - * DOCUMENT ME! + * DOCUMENT ME! * @param x1 - * DOCUMENT ME! + * DOCUMENT ME! * @param y1 - * DOCUMENT ME! + * DOCUMENT ME! * @param width - * DOCUMENT ME! + * DOCUMENT ME! * @param height - * DOCUMENT ME! + * DOCUMENT ME! */ // String type; // SequenceFeature sf; @@ -253,7 +332,7 @@ public class FeatureRenderer /** * show scores as heights */ - protected boolean varyHeight=false; + protected boolean varyHeight = false; synchronized public void drawSequence(Graphics g, SequenceI seq, int start, int end, int y1) @@ -347,44 +426,54 @@ public class FeatureRenderer if (sequenceFeatures[sfindex].begin <= start && sequenceFeatures[sfindex].end >= start) { - currentColour = av.featuresDisplayed - .get(sequenceFeatures[sfindex].type); + // 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, + renderFeature(g, seq, seq.findIndex(sequenceFeatures[sfindex].begin) - 1, seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - new Color(((Integer) av.featuresDisplayed - .get(sequenceFeatures[sfindex].type)).intValue()), - start, end, y1); - renderFeature( - g, - seq, + 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, - new Color(((Integer) av.featuresDisplayed - .get(sequenceFeatures[sfindex].type)).intValue()), - start, end, y1); + getColour(sequenceFeatures[sfindex]) + // new Color(((Integer) av.featuresDisplayed + // .get(sequenceFeatures[sfindex].type)).intValue()) + , start, end, y1); } - else - 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].type), start, end, y1, normaliseScore(sequenceFeatures[sfindex])); - } else + else if (showFeature(sequenceFeatures[sfindex])) { - renderFeature(g, seq, seq - .findIndex(sequenceFeatures[sfindex].begin) - 1, seq - .findIndex(sequenceFeatures[sfindex].end) - 1, - getColour(sequenceFeatures[sfindex].type), start, end, y1); + 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); + } } } @@ -398,24 +487,31 @@ public class FeatureRenderer 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. + * @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); - final byte[] r=new byte[] { 0, (byte) 255}; - if (mm!=null) + 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) + 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])); + 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; @@ -468,6 +564,7 @@ public class FeatureRenderer } } } + void renderScoreFeature(Graphics g, SequenceI seq, int fstart, int fend, Color featureColour, int start, int end, int y1, byte[] bs) { @@ -484,21 +581,25 @@ public class FeatureRenderer fend = end; } int pady = (y1 + av.charHeight) - av.charHeight / 5; - int ystrt = 0,yend=av.charHeight; - if (bs[0]!=0) + int ystrt = 0, yend = av.charHeight; + if (bs[0] != 0) { // signed - zero is always middle of residue line. - if (bs[1]<128) + 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; + yend = av.charHeight * (128 - bs[1]) / 512; + ystrt = av.charHeight - yend / 2; } - } else { - yend = av.charHeight*bs[1]/255; - ystrt = av.charHeight-yend; + 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++) @@ -511,10 +612,9 @@ public class FeatureRenderer } g.setColor(featureColour); - int x=(i-start)*av.charWidth; + int x = (i - start) * av.charWidth; g.drawRect(x, y1, av.charWidth, av.charHeight); - g.fillRect(x, y1+ystrt, av.charWidth, - yend); + g.fillRect(x, y1 + ystrt, av.charWidth, yend); if (offscreenRender || !av.validCharWidth) { @@ -568,8 +668,7 @@ public class FeatureRenderer * Searches alignment for all features and updates colours * * @param newMadeVisible - * if true newly added feature types will be rendered - * immediatly + * if true newly added feature types will be rendered immediatly */ synchronized void findAllFeatures(boolean newMadeVisible) { @@ -600,13 +699,14 @@ public class FeatureRenderer } } } - if (minmax==null) + if (minmax == null) { minmax = new Hashtable(); } - for (int i = 0; i < av.alignment.getHeight(); i++) + AlignmentI alignment = av.getAlignment(); + for (int i = 0; i < alignment.getHeight(); i++) { - SequenceFeature[] features = av.alignment.getSequenceAt(i) + SequenceFeature[] features = alignment.getSequenceAt(i) .getDatasetSequence().getSequenceFeatures(); if (features == null) @@ -653,21 +753,31 @@ public class FeatureRenderer { allfeatures.addElement(features[index].getType()); } - if (features[index].score!=Float.NaN) - { - float[] mm = (float[]) minmax.get(features[index].getType()); - if (mm==null) + 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[] { features[index].score,features[index].score}; + mm = new float[][] + { null, null }; minmax.put(features[index].getType(), mm); - } else { - if (mm[0]>features[index].score) + } + if (mm[nonpos] == null) + { + mm[nonpos] = new float[] + { features[index].score, features[index].score }; + + } + else + { + if (mm[nonpos][0] > features[index].score) { - mm[0] = features[index].score; + mm[nonpos][0] = features[index].score; } - if (mm[1] 0) @@ -713,6 +825,21 @@ public class FeatureRenderer 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]); + } + } + } } } } @@ -732,6 +859,21 @@ public class FeatureRenderer 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(); @@ -749,30 +891,107 @@ public class FeatureRenderer 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) + /** + * 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) { - if (!featureColours.containsKey(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; + 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 - return (Color) featureColours.get(featureType); + { + 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. + static String lastFeatureAdded; static String lastFeatureGroupAdded; static String lastDescriptionAdded; + Object oldcol, fcol; + int featureIndex = 0; boolean amendFeatures(final SequenceI[] sequences, @@ -782,7 +1001,7 @@ public class FeatureRenderer featureIndex = 0; - JPanel bigPanel = new JPanel(new BorderLayout()); + final JPanel bigPanel = new JPanel(new BorderLayout()); final JComboBox overlaps; final JTextField name = new JTextField(25); final JTextField source = new JTextField(25); @@ -791,22 +1010,53 @@ public class FeatureRenderer 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)); + 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; + public void mousePressed(MouseEvent evt) { - Color col = JColorChooser.showDialog(Desktop.desktop, - "Select Feature Colour", colour.getBackground()); - if (col != null) - colour.setBackground(col); + if (fcol instanceof Color) + { + Color col = JColorChooser.showDialog(Desktop.desktop, + MessageManager.getString("label.select_feature_colour"), ((Color) fcol)); + if (col != null) + { + fcol = col; + updateColourButton(bigPanel, colour, col); + } + } + else + { + if (fcc == null) + { + final String type = features[featureIndex].getType(); + fcc = new FeatureColourChooser(me, type); + fcc.setRequestFocusEnabled(true); + fcc.requestFocus(); + + fcc.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + fcol = fcc.getLastColour(); + fcc = null; + setColour(type, fcol); + updateColourButton(bigPanel, colour, fcol); + } + }); + + } + } } }); - JPanel tmp = new JPanel(); JPanel panel = new JPanel(new GridLayout(3, 1)); @@ -816,7 +1066,7 @@ public class FeatureRenderer { panel = new JPanel(new GridLayout(4, 1)); tmp = new JPanel(); - tmp.add(new JLabel("Select Feature: ")); + tmp.add(new JLabel(MessageManager.getString("label.select_feature"))); overlaps = new JComboBox(); for (int i = 0; i < features.length; i++) { @@ -845,17 +1095,17 @@ public class FeatureRenderer highlight.addResult(sequences[0], features[index].getBegin(), features[index].getEnd()); - ap.seqPanel.seqCanvas.highlightSearchResults(highlight); + ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight); } - Color col = getColour(name.getText()); + Object col = getFeatureStyle(name.getText()); if (col == null) { col = new jalview.schemes.UserColourScheme() .createColourFromName(name.getText()); } - - colour.setBackground(col); + oldcol = fcol = col; + updateColourButton(bigPanel, colour, col); } }); @@ -866,25 +1116,33 @@ public class FeatureRenderer tmp = new JPanel(); panel.add(tmp); - tmp.add(new JLabel("Name: ", JLabel.RIGHT)); + tmp.add(new JLabel(MessageManager.getString("label.name"), JLabel.RIGHT)); tmp.add(name); tmp = new JPanel(); panel.add(tmp); - tmp.add(new JLabel("Group: ", JLabel.RIGHT)); + tmp.add(new JLabel(MessageManager.getString("label.group") + ":", + JLabel.RIGHT)); tmp.add(source); tmp = new JPanel(); panel.add(tmp); - tmp.add(new JLabel("Colour: ", JLabel.RIGHT)); + tmp.add(new JLabel(MessageManager.getString("label.colour"), + JLabel.RIGHT)); tmp.add(colour); colour.setPreferredSize(new Dimension(150, 15)); - + colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9)); + colour.setForeground(Color.black); + colour.setHorizontalAlignment(SwingConstants.CENTER); + colour.setVerticalAlignment(SwingConstants.CENTER); + colour.setHorizontalTextPosition(SwingConstants.CENTER); + colour.setVerticalTextPosition(SwingConstants.CENTER); 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)); + panel.add(new JLabel(MessageManager.getString("label.description"), + JLabel.RIGHT)); + description.setFont(JvSwingUtils.getTextAreaFont()); description.setLineWrap(true); panel.add(new JScrollPane(description)); @@ -893,9 +1151,11 @@ public class FeatureRenderer bigPanel.add(panel, BorderLayout.SOUTH); panel = new JPanel(); - panel.add(new JLabel(" Start:", JLabel.RIGHT)); + panel.add(new JLabel(MessageManager.getString("label.start"), + JLabel.RIGHT)); panel.add(start); - panel.add(new JLabel(" End:", JLabel.RIGHT)); + panel.add(new JLabel(MessageManager.getString("label.end"), + JLabel.RIGHT)); panel.add(end); bigPanel.add(panel, BorderLayout.CENTER); } @@ -942,8 +1202,8 @@ public class FeatureRenderer start.setValue(new Integer(features[0].getBegin())); end.setValue(new Integer(features[0].getEnd())); description.setText(features[0].getDescription()); - colour.setBackground(getColour(name.getText())); - + updateColourButton(bigPanel, colour, + (oldcol = fcol = getFeatureStyle(name.getText()))); Object[] options; if (!newFeatures) { @@ -956,12 +1216,12 @@ public class FeatureRenderer { "OK", "Cancel" }; } - String title = newFeatures ? "Create New Sequence Feature(s)" - : "Amend/Delete Features for " + 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, "OK"); + JOptionPane.QUESTION_MESSAGE, null, options, MessageManager.getString("action.ok")); jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile(); @@ -973,7 +1233,7 @@ public class FeatureRenderer 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; } @@ -992,9 +1252,8 @@ public class FeatureRenderer sf.featureGroup = lastFeatureGroupAdded; sf.description = lastDescriptionAdded; - setColour(sf.type, colour.getBackground()); - av.featuresDisplayed.put(sf.type, new Integer(colour - .getBackground().getRGB())); + setColour(sf.type, fcol); + av.featuresDisplayed.put(sf.type, getColour(sf.type)); try { @@ -1033,11 +1292,9 @@ public class FeatureRenderer featureGroups = new Hashtable(); featureGroups.put(lastFeatureGroupAdded, new Boolean(true)); } - - Color col = colour.getBackground(); - setColour(lastFeatureAdded, colour.getBackground()); + setColour(lastFeatureAdded, fcol); av.featuresDisplayed.put(lastFeatureAdded, - new Integer(col.getRGB())); + getColour(lastFeatureAdded)); findAllFeatures(false); @@ -1056,9 +1313,45 @@ public class FeatureRenderer return true; } - public void setColour(String featureType, Color col) + /** + * 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) { - featureColours.put(featureType, col); + 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) @@ -1074,8 +1367,8 @@ public class FeatureRenderer /** * Replace current ordering with new ordering * - * @param data { - * String(Type), Colour(Type), Boolean(Displayed) } + * @param data + * { String(Type), Colour(Type), Boolean(Displayed) } */ public void setFeaturePriority(Object[][] data) { @@ -1084,10 +1377,10 @@ public class FeatureRenderer /** * - * @param data { - * String(Type), Colour(Type), Boolean(Displayed) } + * @param data + * { String(Type), Colour(Type), Boolean(Displayed) } * @param visibleNew - * when true current featureDisplay list will be cleared + * when true current featureDisplay list will be cleared */ public void setFeaturePriority(Object[][] data, boolean visibleNew) { @@ -1117,7 +1410,8 @@ public class FeatureRenderer for (int i = 0; i < data.length; i++) { String type = data[i][0].toString(); - setColour(type, (Color) data[i][1]); + 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) @@ -1130,17 +1424,17 @@ public class FeatureRenderer } - Hashtable featureOrder = null; + Map featureOrder = null; /** * analogous to colour - store a normalized ordering for all feature types in * this rendering context. * * @param type - * Feature type string + * Feature type string * @param position - * normalized priority - 0 means always appears on top, 1 means - * always last. + * normalized priority - 0 means always appears on top, 1 means + * always last. */ public float setOrder(String type, float position) {