X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=89e94c8ebfb2ae53588086470d7be50ab5c6a2c7;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=7c6032716287cee54db9b9818b34690d2d0628c2;hpb=ef36c8bbd6c5eef95e4d1a2cff57ea772af5110b;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java old mode 100755 new mode 100644 index 7c60327..89e94c8 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -1,466 +1,441 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 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 - * 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. - * - * 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 - */ -package jalview.gui; - -import jalview.datamodel.*; - -import java.awt.*; - -import java.util.*; - -import java.awt.image.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class FeatureRenderer -{ - 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 = null; - - // This is actually an Integer held in the hashtable, - // Retrieved using the key feature type - Object currentColour; - - String [] renderOrder; - - boolean newFeatureAdded = false; - - - /** - * Creates a new FeatureRenderer object. - * - * @param av DOCUMENT ME! - */ - public FeatureRenderer(AlignViewport av) - { - this.av = av; - } - - public void transferSettings(FeatureRenderer fr) - { - renderOrder = fr.renderOrder; - featureGroups = fr.featureGroups; - featureColours = fr.featureColours; - transparency = fr.transparency; - } - - 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) - { - lastSeq = seq; - sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures(); - if(sequenceFeatures==null) - return initialCol; - - sfSize = sequenceFeatures.length; - } - - 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; - - 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(); - sfSize = sequenceFeatures.length; - } - - if(lastSeq==null || seq!=lastSeq) - { - lastSeq = seq; - sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures(); - sfSize = sequenceFeatures.length; - } - - - 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); - } - - - String type; - for(int renderIndex=0; renderIndex epos - || sequenceFeatures[sfindex].getEnd() < spos)) - continue; - - if (offscreenRender && offscreenImage==null) - { - if (sequenceFeatures[sfindex].begin <= start && - sequenceFeatures[sfindex].end >= start) - { - 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, - 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.getSequence().charAt(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); - - } - } - } - - int count = 0; - synchronized public void featuresAdded() - { - newFeatureAdded = true; - findAllFeatures(); - newFeatureAdded = false; - } - - synchronized void findAllFeatures() - { - jalview.schemes.UserColourScheme ucs = new - jalview.schemes.UserColourScheme(); - - if(av.featuresDisplayed==null) - av.featuresDisplayed = new Hashtable(); - - av.featuresDisplayed.clear(); - - Vector allfeatures = new Vector(); - for (int i = 0; i < av.alignment.getHeight(); i++) - { - SequenceFeature [] features - = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures(); - - if (features == null) - continue; - - int index = 0; - while (index < features.length) - { - if (!av.featuresDisplayed.containsKey(features[index].getType())) - { - if(!(features[index].begin == 0 && features[index].end ==0)) - { - // If beginning and end are 0, the feature is for the whole sequence - // and we don't want to render the feature in the normal way - - if (getColour(features[index].getType()) == null) - { - featureColours.put(features[index].getType(), - ucs.createColourFromName(features[index]. - getType())); - } - - av.featuresDisplayed.put(features[index].getType(), - new Integer(getColour(features[index]. - getType()).getRGB())); - allfeatures.addElement(features[index].getType()); - } - } - index++; - } - } - - renderOrder = new String[allfeatures.size()]; - Enumeration en = allfeatures.elements(); - int i = allfeatures.size()-1; - while(en.hasMoreElements()) - { - renderOrder[i] = en.nextElement().toString(); - i--; - } - } - - public Color getColour(String featureType) - { - Color colour = (Color)featureColours.get(featureType); - return colour; - } - - - public void addNewFeature(String name, Color col, String group) - { - - setColour(name, col); - if(av.featuresDisplayed==null) - av.featuresDisplayed = new Hashtable(); - - if(group == null) - group = "NOGROUP"; - - av.featuresDisplayed.put(name, new Integer(col.getRGB())); - } - - public void setColour(String featureType, Color col) - { - featureColours.put(featureType, col); - } - - public void setTransparency(float value) - { - transparency = value; - } - - public float getTransparency() - { - return transparency; - } - - public void setFeaturePriority(Object [][] data) - { - // 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 - if(av.featuresDisplayed!=null) - av.featuresDisplayed.clear(); - else - av.featuresDisplayed = new Hashtable(); - - renderOrder = new String[data.length]; - - if (data.length > 0) - for (int i = 0; i < data.length; i++) - { - String type = data[i][0].toString(); - setColour(type, (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; - } - - } - - - - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 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. + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.gui; + +import jalview.datamodel.SearchResults; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.schemes.GraduatedColor; +import jalview.util.MessageManager; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.GridLayout; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; + +import javax.swing.JColorChooser; +import javax.swing.JComboBox; +import javax.swing.JLabel; +import javax.swing.JOptionPane; +import javax.swing.JPanel; +import javax.swing.JScrollPane; +import javax.swing.JSpinner; +import javax.swing.JTextArea; +import javax.swing.JTextField; +import javax.swing.SwingConstants; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class FeatureRenderer extends + jalview.renderer.seqfeatures.FeatureRenderer implements + jalview.api.FeatureRenderer +{ + Color resBoxColour; + + AlignmentPanel ap; + + /** + * Creates a new FeatureRenderer object. + * + * @param av + * DOCUMENT ME! + */ + public FeatureRenderer(AlignmentPanel ap) + { + super(); + 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); + } + } + + // // ///////////// + // // 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, + final SequenceFeature[] features, boolean newFeatures, + final AlignmentPanel ap) + { + + featureIndex = 0; + + 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; + + public void mousePressed(MouseEvent evt) + { + 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)); + + // ///////////////////////////////////// + // /MULTIPLE FEATURES AT SELECTED RESIDUE + if (!newFeatures && features.length > 1) + { + panel = new JPanel(new GridLayout(4, 1)); + tmp = new JPanel(); + tmp.add(new JLabel(MessageManager.getString("label.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() + ")"); + } + + tmp.add(overlaps); + + overlaps.addItemListener(new ItemListener() + { + 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.getSeqPanel().seqCanvas.highlightSearchResults(highlight); + + } + Object col = getFeatureStyle(name.getText()); + if (col == null) + { + col = new jalview.schemes.UserColourScheme() + .createColourFromName(name.getText()); + } + oldcol = fcol = col; + updateColourButton(bigPanel, colour, col); + } + }); + + panel.add(tmp); + } + // //////// + // //////////////////////////////////// + + tmp = new JPanel(); + panel.add(tmp); + tmp.add(new JLabel(MessageManager.getString("label.name"), JLabel.RIGHT)); + tmp.add(name); + + tmp = new JPanel(); + panel.add(tmp); + tmp.add(new JLabel(MessageManager.getString("label.group") + ":", + JLabel.RIGHT)); + tmp.add(source); + + tmp = new JPanel(); + panel.add(tmp); + 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(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(MessageManager.getString("label.start"), + JLabel.RIGHT)); + panel.add(start); + panel.add(new JLabel(MessageManager.getString("label.end"), + JLabel.RIGHT)); + panel.add(end); + bigPanel.add(panel, BorderLayout.CENTER); + } + else + { + bigPanel.add(panel, BorderLayout.CENTER); + } + + if (lastFeatureAdded == null) + { + 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"; + } + } + + if (newFeatures) + { + name.setText(lastFeatureAdded); + source.setText(lastFeatureGroupAdded); + } + else + { + name.setText(features[0].getType()); + source.setText(features[0].getFeatureGroup()); + } + + 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()))); + Object[] options; + if (!newFeatures) + { + options = new Object[] { "Amend", "Delete", "Cancel" }; + } + else + { + options = new Object[] { "OK", "Cancel" }; + } + + String title = newFeatures ? MessageManager + .getString("label.create_new_sequence_features") + : MessageManager.formatMessage("label.amend_delete_features", + new String[] { sequences[0].getName() }); + + int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop, + bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION, + JOptionPane.QUESTION_MESSAGE, null, options, + MessageManager.getString("action.ok")); + + jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile(); + + if (reply == JOptionPane.OK_OPTION && name.getText().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; + } + } + + if (!newFeatures) + { + SequenceFeature sf = features[featureIndex]; + + if (reply == JOptionPane.NO_OPTION) + { + sequences[0].getDatasetSequence().deleteFeature(sf); + } + else if (reply == JOptionPane.YES_OPTION) + { + sf.type = lastFeatureAdded; + sf.featureGroup = lastFeatureGroupAdded; + sf.description = lastDescriptionAdded; + + setColour(sf.type, fcol); + getFeaturesDisplayed().setVisible(sf.type); + + try + { + sf.begin = ((Integer) start.getValue()).intValue(); + sf.end = ((Integer) end.getValue()).intValue(); + } catch (NumberFormatException ex) + { + } + + ffile.parseDescriptionHTML(sf, false); + } + } + else + // NEW FEATURES ADDED + { + if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0) + { + for (int i = 0; i < sequences.length; i++) + { + features[i].type = lastFeatureAdded; + // 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 (lastFeatureGroupAdded != null) + { + setGroupVisibility(lastFeatureGroupAdded, true); + } + setColour(lastFeatureAdded, fcol); + setVisible(lastFeatureAdded); + + findAllFeatures(false); + + ap.paintAlignment(true); + + return true; + } + else + { + return false; + } + } + + ap.paintAlignment(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()); + } + } +}