X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=426ea32afb458c8215bcee53de0ca66d9b25e20f;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=a1de62e32e04b55c9a784222d380eaad92610fe4;hpb=97d6516fd717d0daddcbc8154c4de29a812982e5;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java old mode 100755 new mode 100644 index a1de62e..426ea32 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -1,706 +1,258 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 + * 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. - * - * 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 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.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.api.FeatureColourI; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.schemes.FeatureColour; +import jalview.schemes.UserColourScheme; +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.Arrays; +import java.util.Comparator; + +import javax.swing.JColorChooser; +import javax.swing.JComboBox; +import javax.swing.JLabel; +import javax.swing.JOptionPane; +import javax.swing.JPanel; +import javax.swing.JScrollPane; +import javax.swing.JSpinner; +import javax.swing.JTextArea; +import javax.swing.JTextField; +import javax.swing.SwingConstants; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ -public class FeatureRenderer +public class FeatureRenderer extends + jalview.renderer.seqfeatures.FeatureRenderer implements + jalview.api.FeatureRenderer { - AlignmentPanel ap; - AlignViewport av; Color resBoxColour; - float transparency = 1.0f; - FontMetrics fm; - int charOffset; - - Hashtable featureColours = new Hashtable(); - // A higher level for grouping features of a - // particular type - Hashtable featureGroups = new Hashtable(); - - // This is actually an Integer held in the hashtable, - // Retrieved using the key feature type - Object currentColour; - - String[] renderOrder; - PropertyChangeSupport changeSupport=new PropertyChangeSupport(this); - - Vector allfeatures; + AlignmentPanel ap; /** * Creates a new FeatureRenderer object. - * + * * @param av * DOCUMENT ME! */ public FeatureRenderer(AlignmentPanel ap) { + super(ap.av); this.ap = ap; - this.av = ap.av; - } - - - public void transferSettings(FeatureRenderer fr) - { - this.renderOrder = fr.renderOrder; - this.featureGroups = fr.featureGroups; - this.featureColours = fr.featureColours; - this.transparency = fr.transparency; - this.featureOrder = fr.featureOrder; - } - - BufferedImage offscreenImage; - boolean offscreenRender = false; - public Color findFeatureColour(Color initialCol, SequenceI seq, int res) - { - return new Color(findFeatureColour(initialCol.getRGB(), - seq, res)); - } - - /** - * This is used by the Molecule Viewer and Overview to get the accurate - * colourof the rendered sequence - */ - public int findFeatureColour(int initialCol, SequenceI seq, int column) - { - if (!av.showSequenceFeatures) - { - return initialCol; - } - - if (seq != lastSeq) + if (ap != null && ap.getSeqPanel() != null + && ap.getSeqPanel().seqCanvas != null + && ap.getSeqPanel().seqCanvas.fr != null) { - lastSeq = seq; - sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures(); - if (sequenceFeatures!=null) - { - sfSize = sequenceFeatures.length; - } + transferSettings(ap.getSeqPanel().seqCanvas.fr); } - - if (sequenceFeatures!=lastSeq.getDatasetSequence().getSequenceFeatures()) { - sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures(); - if (sequenceFeatures != null) - { - sfSize = sequenceFeatures.length; - } - } - - if (sequenceFeatures == null || sfSize==0) - { - return initialCol; - } - - - if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column))) - { - return Color.white.getRGB(); - } - - // Only bother making an offscreen image if transparency is applied - if (transparency != 1.0f && offscreenImage == null) - { - offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB); - } - - currentColour = null; - - offscreenRender = true; - - if (offscreenImage != null) - { - offscreenImage.setRGB(0, 0, initialCol); - drawSequence(offscreenImage.getGraphics(), - lastSeq, - column, column, 0); - - return offscreenImage.getRGB(0, 0); - } - else - { - drawSequence(null, - lastSeq, - lastSeq.findPosition(column), - -1, -1); - - if (currentColour == null) - { - return initialCol; - } - else - { - return ( (Integer) currentColour).intValue(); - } - } - } - /** - * DOCUMENT ME! - * - * @param g - * DOCUMENT ME! - * @param seq - * DOCUMENT ME! - * @param sg - * DOCUMENT ME! - * @param start - * DOCUMENT ME! - * @param end - * DOCUMENT ME! - * @param x1 - * DOCUMENT ME! - * @param y1 - * DOCUMENT ME! - * @param width - * DOCUMENT ME! - * @param height - * DOCUMENT ME! - */ - // String type; - // SequenceFeature sf; - SequenceI lastSeq; - SequenceFeature[] sequenceFeatures; - int sfSize, sfindex, spos, epos; - - synchronized public void drawSequence(Graphics g, SequenceI seq, - int start, int end, int y1) - { + // // ///////////// + // // Feature Editing Dialog + // // Will be refactored in next release. - if (seq.getDatasetSequence().getSequenceFeatures() == null - || seq.getDatasetSequence().getSequenceFeatures().length == 0) - { - return; - } + static String lastFeatureAdded; - if (g != null) - { - fm = g.getFontMetrics(); - } + static String lastFeatureGroupAdded; - if (av.featuresDisplayed == null - || renderOrder == null - || newFeatureAdded) - { - findAllFeatures(); - if (av.featuresDisplayed.size() < 1) - { - return; - } + static String lastDescriptionAdded; - sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures(); - } + FeatureColourI oldcol, fcol; - if (lastSeq == null || seq != lastSeq - || seq.getDatasetSequence().getSequenceFeatures()!=sequenceFeatures) - { - lastSeq = seq; - sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures(); - } + int featureIndex = 0; - if (transparency != 1 && g != null) - { - Graphics2D g2 = (Graphics2D) g; - g2.setComposite( - AlphaComposite.getInstance( - AlphaComposite.SRC_OVER, transparency)); - } + boolean amendFeatures(final SequenceI[] sequences, + final SequenceFeature[] features, boolean newFeatures, + final AlignmentPanel ap) + { - if (!offscreenRender) - { - spos = lastSeq.findPosition(start); - epos = lastSeq.findPosition(end); - } + featureIndex = 0; - sfSize = sequenceFeatures.length; - String type; - for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) + 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() { - type = renderOrder[renderIndex]; + FeatureColourChooser fcc = null; - 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++) + @Override + public void mousePressed(MouseEvent evt) { - 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)) + if (fcol.isSimpleColour()) { - continue; - } - - if (offscreenRender && offscreenImage == null) - { - if (sequenceFeatures[sfindex].begin <= start && - sequenceFeatures[sfindex].end >= start) + Color col = JColorChooser.showDialog(Desktop.desktop, + MessageManager.getString("label.select_feature_colour"), + fcol.getColour()); + if (col != null) { - currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex]. - type); + fcol = new FeatureColour(col); + updateColourButton(bigPanel, colour, new FeatureColour(col)); } } - else if (sequenceFeatures[sfindex].type.equals("disulfide bond")) - { - - 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, - 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); - - } else { - renderFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - getColour(sequenceFeatures[sfindex].type), - start, end, y1); - } - - } - - } - - if (transparency != 1.0f && g != null) - { - Graphics2D g2 = (Graphics2D) g; - g2.setComposite( - AlphaComposite.getInstance( - AlphaComposite.SRC_OVER, 1.0f)); - } - } - - 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; - } + if (fcc == null) + { + final String type = features[featureIndex].getType(); + fcc = new FeatureColourChooser(me, type); + fcc.setRequestFocusEnabled(true); + fcc.requestFocus(); - g.setColor(featureColour); + fcc.addActionListener(new ActionListener() + { - g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight); + @Override + public void actionPerformed(ActionEvent e) + { + fcol = fcc.getLastColour(); + fcc = null; + setColour(type, fcol); + updateColourButton(bigPanel, colour, fcol); + } + }); - 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); - } - } - } - - 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(); - } + }); + JPanel tmp = new JPanel(); + JPanel panel = new JPanel(new GridLayout(3, 1)); - allfeatures = new Vector(); - Vector oldfeatures = new Vector(); - if (renderOrder!=null) + // ///////////////////////////////////// + // /MULTIPLE FEATURES AT SELECTED RESIDUE + if (!newFeatures && features.length > 1) { - for (int i=0; i0) - { - for (int j=0; jsortOrder[i+1]; - } - i--; - } - if (iSize>1 && sort) - jalview.util.QuickSort.sort(sortOrder, newf); - sortOrder=null; - System.arraycopy(newf, 0, renderOrder, opos, newf.length); - } - public Color getColour(String featureType) - { - if (!featureColours.containsKey(featureType)) - { - jalview.schemes.UserColourScheme ucs = new - jalview.schemes.UserColourScheme(); - Color col = ucs.createColourFromName(featureType); - featureColours.put(featureType, col); - return col; - } - else - return (Color) featureColours.get(featureType); - } - - static String lastFeatureAdded; - static String lastFeatureGroupAdded; - static String lastDescriptionAdded; - - int featureIndex = 0; - boolean amendFeatures(final SequenceI[] sequences, - final SequenceFeature[] features, - boolean newFeatures, - final AlignmentPanel ap) - { - - featureIndex = 0; - - JPanel bigPanel = new JPanel(new BorderLayout()); - final JComboBox overlaps; - final JTextField name = new JTextField(25); - final JTextField source = new JTextField(25); - final JTextArea description = new JTextArea(3, 25); - final JSpinner start = new JSpinner(); - final JSpinner end = new JSpinner(); - start.setPreferredSize(new Dimension(80, 20)); - end.setPreferredSize(new Dimension(80, 20)); - - final JPanel colour = new JPanel(); - colour.setBorder(BorderFactory.createEtchedBorder()); - colour.setMaximumSize(new Dimension(40, 10)); - colour.addMouseListener(new MouseAdapter() - { - public void mousePressed(MouseEvent evt) - { - Color col = JColorChooser.showDialog(Desktop.desktop, - "Select Feature Colour", - colour.getBackground()); - if (col != null) - colour.setBackground(col); - - } - }); + }); - JPanel tmp = new JPanel(); - JPanel panel = new JPanel(new GridLayout(3, 1)); - - /////////////////////////////////////// - ///MULTIPLE FEATURES AT SELECTED RESIDUE - if(!newFeatures && features.length>1) - { - panel = new JPanel(new GridLayout(4, 1)); - tmp = new JPanel(); - tmp.add(new JLabel("Select Feature: ")); - overlaps = new JComboBox(); - for(int i=0; i0) + if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0) { // This ensures that the last sequence // is refreshed and new features are rendered @@ -797,9 +344,11 @@ public class FeatureRenderer lastFeatureAdded = name.getText().trim(); lastFeatureGroupAdded = source.getText().trim(); lastDescriptionAdded = description.getText().replaceAll("\n", " "); - - if(lastFeatureGroupAdded.length()<1) + // TODO: determine if the null feature group is valid + if (lastFeatureGroupAdded.length() < 1) + { lastFeatureGroupAdded = null; + } } if (!newFeatures) @@ -816,58 +365,46 @@ 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); + getFeaturesDisplayed().setVisible(sf.type); try { - sf.begin = ( (Integer) start.getValue()).intValue(); - sf.end = ( (Integer) end.getValue()).intValue(); + sf.begin = ((Integer) start.getValue()).intValue(); + sf.end = ((Integer) end.getValue()).intValue(); + } catch (NumberFormatException ex) + { } - catch (NumberFormatException ex) - {} ffile.parseDescriptionHTML(sf, false); } } - else //NEW FEATURES ADDED + else + // NEW FEATURES ADDED { - if (reply == JOptionPane.OK_OPTION - && lastFeatureAdded.length()>0) + if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0) { for (int i = 0; i < sequences.length; i++) { features[i].type = lastFeatureAdded; - if (lastFeatureGroupAdded!=null) - features[i].featureGroup = lastFeatureGroupAdded; + // fix for JAL-1538 - always set feature group here + features[i].featureGroup = lastFeatureGroupAdded; features[i].description = lastDescriptionAdded; sequences[i].addSequenceFeature(features[i]); ffile.parseDescriptionHTML(features[i], false); } - if (av.featuresDisplayed == null) - { - av.featuresDisplayed = new Hashtable(); - } - if (lastFeatureGroupAdded != null) { - if (featureGroups == null) - featureGroups = new Hashtable(); - featureGroups.put(lastFeatureGroupAdded, new Boolean(true)); + setGroupVisibility(lastFeatureGroupAdded, true); } - - Color col = colour.getBackground(); - setColour(lastFeatureAdded, colour.getBackground()); - av.featuresDisplayed.put(lastFeatureAdded, - new Integer(col.getRGB())); + setColour(lastFeatureAdded, fcol); + setVisible(lastFeatureAdded); findAllFeatures(false); ap.paintAlignment(true); - return true; } else @@ -881,124 +418,41 @@ public class FeatureRenderer return true; } - public void setColour(String featureType, Color col) - { - featureColours.put(featureType, col); - } - - public void setTransparency(float value) - { - transparency = value; - } - - public float getTransparency() - { - return transparency; - } /** - * Replace current ordering with new ordering - * @param data { String(Type), Colour(Type), Boolean(Displayed) } + * update the amend feature button dependent on the given style + * + * @param bigPanel + * @param col + * @param col */ - public void setFeaturePriority(Object[][] data) + protected void updateColourButton(JPanel bigPanel, JLabel colour, + FeatureColourI col) { - setFeaturePriority(data, true); - } - /** - * - * @param data { String(Type), Colour(Type), Boolean(Displayed) } - * @param visibleNew when true current featureDisplay list will be cleared - */ - public void setFeaturePriority(Object[][] data, boolean visibleNew) - { - if (visibleNew) - { - if (av.featuresDisplayed != null) - { - av.featuresDisplayed.clear(); - } - else - { - av.featuresDisplayed = new Hashtable(); - } - } - if (data==null) - { - return; - } + colour.removeAll(); + colour.setIcon(null); + colour.setToolTipText(null); + colour.setText(""); - // 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 (col.isSimpleColour()) { - for (int i = 0; i < data.length; i++) - { - String type = data[i][0].toString(); - setColour(type, (Color) data[i][1]); - if ( ( (Boolean) data[i][2]).booleanValue()) - { - av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB())); - } - - renderOrder[data.length - i - 1] = type; - } + colour.setBackground(col.getColour()); } - - } - Hashtable featureOrder=null; - /** - * analogous to colour - store a normalized ordering for all feature types in - * this rendering context. - * - * @param type - * Feature type string - * @param position - * normalized priority - 0 means always appears on top, 1 means - * always last. - */ - public float setOrder(String type, float position) - { - if (featureOrder==null) - { - featureOrder = new Hashtable(); - } - featureOrder.put(type, new Float(position)); - return position; - } - /** - * get the global priority (0 (top) to 1 (bottom)) - * - * @param type - * @return [0,1] or -1 for a type without a priority - */ - public float getOrder(String type) { - if (featureOrder!=null) + else { - if (featureOrder.containsKey(type)) - { - return ((Float)featureOrder.get(type)).floatValue(); - } + 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); } }