X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=585e0a268bf3de7c0d7de13bd355a09630be7548;hb=a10a465359de7b8c0baff4925d4b267a28eb0071;hp=75ce63acee4ad33ddebddde613bbdcd9c4169fc8;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index 75ce63a..585e0a2 100755 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This 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. * - * 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 + * 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; @@ -74,7 +73,7 @@ public class FeatureRenderer * Creates a new FeatureRenderer object. * * @param av - * DOCUMENT ME! + * DOCUMENT ME! */ public FeatureRenderer(AlignmentPanel ap) { @@ -106,13 +105,47 @@ 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 Hashtable(); + featureColours = new Hashtable(); + featureOrder = new Hashtable(); + if (fr.renderOrder != null) + { + this.renderOrder = new String[fr.renderOrder.length]; + System.arraycopy(fr.renderOrder, 0, renderOrder, 0, + renderOrder.length); + } + if (fr.featureGroups != null) + { + this.featureGroups = new Hashtable(fr.featureGroups); + } + if (fr.featureColours != null) + { + this.featureColours = new Hashtable(fr.featureColours); + } + Enumeration en = fr.featureColours.keys(); + while (en.hasMoreElements()) + { + Object next = en.nextElement(); + 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 Hashtable(fr.featureOrder); + } } } @@ -226,23 +259,23 @@ 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; @@ -349,61 +382,55 @@ public class FeatureRenderer 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 + // 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); - - + // .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, + 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, + // 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); + // new Color(((Integer) av.featuresDisplayed + // .get(sequenceFeatures[sfindex].type)).intValue()) + , start, end, y1); } - else - if (showFeature(sequenceFeatures[sfindex])) + else if (showFeature(sequenceFeatures[sfindex])) + { + if (av.showSeqFeaturesHeight + && sequenceFeatures[sfindex].score != Float.NaN) { - 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); - } + 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); } + } } @@ -597,8 +624,7 @@ 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) { @@ -684,17 +710,19 @@ public class FeatureRenderer } if (features[index].score != Float.NaN) { - int nonpos= features[index].getBegin()>=1 ? 0 : 1; + int nonpos = features[index].getBegin() >= 1 ? 0 : 1; float[][] mm = (float[][]) minmax.get(features[index].getType()); if (mm == null) { - mm = new float[][] {null, 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 }; - + if (mm[nonpos] == null) + { + mm[nonpos] = new float[] + { features[index].score, features[index].score }; + } else { @@ -725,6 +753,7 @@ public class FeatureRenderer * 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) @@ -732,7 +761,7 @@ public class FeatureRenderer Vector allfeatures = new Vector(allFeatures); String[] oldRender = renderOrder; renderOrder = new String[allfeatures.size()]; - Object mmrange,fc=null; + Object mmrange, fc = null; boolean initOrders = (featureOrder == null); int opos = 0; if (oldRender != null && oldRender.length > 0) @@ -751,21 +780,24 @@ public class FeatureRenderer renderOrder[opos++] = oldRender[j]; // existing features always // appear below new features allfeatures.removeElement(oldRender[j]); - if (minmax!=null) + if (minmax != null) { mmrange = minmax.get(oldRender[j]); - if (mmrange!=null) + if (mmrange != null) { fc = featureColours.get(oldRender[j]); - if (fc!=null && fc instanceof GraduatedColor && ((GraduatedColor)fc).isAutoScale()) + if (fc != null && fc instanceof GraduatedColor + && ((GraduatedColor) fc).isAutoScale()) { - ((GraduatedColor) fc).updateBounds(((float[][])mmrange)[0][0],((float[][])mmrange)[0][1]); + ((GraduatedColor) fc).updateBounds( + ((float[][]) mmrange)[0][0], + ((float[][]) mmrange)[0][1]); } + } } } } } - } } if (allfeatures.size() == 0) { @@ -782,16 +814,18 @@ public class FeatureRenderer while (en.hasMoreElements()) { newf[i] = en.nextElement().toString(); - if (minmax!=null) + if (minmax != null) { // update from new features minmax if necessary mmrange = minmax.get(newf[i]); - if (mmrange!=null) + if (mmrange != null) { fc = featureColours.get(newf[i]); - if (fc!=null && fc instanceof GraduatedColor && ((GraduatedColor)fc).isAutoScale()) + if (fc != null && fc instanceof GraduatedColor + && ((GraduatedColor) fc).isAutoScale()) { - ((GraduatedColor) fc).updateBounds(((float[][])mmrange)[0][0],((float[][])mmrange)[0][1]); + ((GraduatedColor) fc).updateBounds(((float[][]) mmrange)[0][0], + ((float[][]) mmrange)[0][1]); } } } @@ -819,17 +853,38 @@ public class FeatureRenderer 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) { 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); } - else if (fc instanceof Color) + 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; } @@ -839,28 +894,22 @@ public class FeatureRenderer { return ((GraduatedColor) fc).getMaxColor(); } - // TODO: raise an implementation error here. - return null; // Color.white; } + throw new Error("Implementation Error: Unrecognised render object " + + fc.getClass() + " for features of type " + featureType); } /** - * implement graduated colouring for features with scores + * 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 = featureColours.get(feature.type); - if (fc == null) - { - jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(); - Color col = ucs.createColourFromName(feature.type); - featureColours.put(feature.type, col); - return col; - } - else if (fc instanceof Color) + Object fc = getFeatureStyle(feature.getType()); + if (fc instanceof Color) { return (Color) fc; } @@ -870,19 +919,27 @@ public class FeatureRenderer { return ((GraduatedColor) fc).findColor(feature); } - // TODO: raise an implementation error here. - return null; // Color.white; } + throw new Error("Implementation Error: Unrecognised render object " + + fc.getClass() + " for features of type " + feature.getType()); } + private boolean showFeature(SequenceFeature sequenceFeature) { - Object fc = featureColours.get(sequenceFeature.type); + Object fc = getFeatureStyle(sequenceFeature.type); if (fc instanceof GraduatedColor) { return ((GraduatedColor) fc).isColored(sequenceFeature); - } else { return true; } + } + else + { + return true; + } } + // // ///////////// + // // Feature Editing Dialog + // // Will be refactored in next release. static String lastFeatureAdded; @@ -890,6 +947,8 @@ public class FeatureRenderer static String lastDescriptionAdded; + Object oldcol, fcol; + int featureIndex = 0; boolean amendFeatures(final SequenceI[] sequences, @@ -899,7 +958,7 @@ 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); @@ -908,23 +967,53 @@ 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) { - // TODO: use featurecolourchooser here - 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, + "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)); @@ -966,14 +1055,14 @@ public class FeatureRenderer ap.seqPanel.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); } }); @@ -997,7 +1086,12 @@ public class FeatureRenderer tmp.add(new JLabel("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(); @@ -1060,8 +1154,8 @@ 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) { @@ -1091,7 +1185,7 @@ 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; } @@ -1110,9 +1204,8 @@ 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 { @@ -1151,11 +1244,9 @@ 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); @@ -1174,10 +1265,42 @@ 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) + { + 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) { - Object c = featureColours.get(featureType); - if (c == null || c instanceof Color || (c instanceof GraduatedColor && !((GraduatedColor)c).getMaxColor().equals(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); } @@ -1196,8 +1319,8 @@ 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) { @@ -1206,10 +1329,10 @@ 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) { @@ -1239,7 +1362,8 @@ 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) @@ -1259,10 +1383,10 @@ public class FeatureRenderer * 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) {