X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=63d87af16d8d370c025e425e9e597d41fbd6460b;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=405fe9871999c467a6520e040d3a26affc52bf4b;hpb=391968dd70ca76090306df9b5852bbef10ab4ede;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java old mode 100755 new mode 100644 index 405fe98..63d87af --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -1,438 +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.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class FeatureRenderer -{ - AlignViewport av; - Color resBoxColour; - float transparency = 1.0f; - FontMetrics fm; - int charOffset; - - // 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; - - - /** - * Creates a new FeatureRenderer object. - * - * @param av DOCUMENT ME! - */ - public FeatureRenderer(AlignViewport av) - { - this.av = av; - initColours(); - } - - - public Color findFeatureColour(Color initialCol, SequenceI seq, int i) - { - if(!av.showSequenceFeatures) - return initialCol; - - lastSequence = seq; - sequenceFeatures = lastSequence.getDatasetSequence().getSequenceFeatures(); - if(sequenceFeatures==null) - return initialCol; - - sfSize = sequenceFeatures.length; - - if(jalview.util.Comparison.isGap(lastSequence.getCharAt(i))) - return Color.white; - - currentColour = null; - - drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1, -1, -1); - - if(currentColour==null) - return initialCol; - - return new Color( ((Integer)currentColour).intValue() ); - } - /** - * This is used by the Molecule Viewer to get the accurate colour - * of the rendered sequence - */ - - boolean overview = false; - - int white = Color.white.getRGB(); - public int findFeatureColour(int initialCol, int seqIndex, int column) - { - if(!av.showSequenceFeatures) - return initialCol; - - if(seqIndex!=lastSequenceIndex) - { - lastSequence = av.alignment.getSequenceAt(seqIndex); - lastSequenceIndex = seqIndex; - sequenceFeatures = lastSequence.getDatasetSequence().getSequenceFeatures(); - if(sequenceFeatures==null) - return initialCol; - - sfSize = sequenceFeatures.length; - } - - - if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column))) - return Color.white.getRGB(); - - currentColour = null; - - drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1, -1, -1); - - if(currentColour==null) - return initialCol; - - 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; - int lastSequenceIndex=-1; - SequenceI lastSequence; - SequenceFeature [] sequenceFeatures; - int sfSize, sfindex, spos, epos; - - public void drawSequence(Graphics g, SequenceI seq, - int start, int end, int y1, int width, int height) - { - if ( seq.getDatasetSequence().getSequenceFeatures() == null - || seq.getDatasetSequence().getSequenceFeatures().length==0) - return; - - - if(g!=null) - fm = g.getFontMetrics(); - - - if (av.featuresDisplayed == null || renderOrder==null) - { - findAllFeatures(); - sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures(); - sfSize = sequenceFeatures.length; - } - - if(lastSequence==null || seq!=lastSequence) - { - lastSequence = 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(!overview) - { - spos = lastSequence.findPosition(start); - epos = lastSequence.findPosition(end); - } - - String type; - for(int renderIndex=0; renderIndex epos - || sequenceFeatures[sfindex].getEnd() < spos)) - continue; - - if (overview) - { - - if (sequenceFeatures[sfindex].begin - 1 <= start && - sequenceFeatures[sfindex].end + 1 >= 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, width, height); - 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, width, height); - - } - else - renderFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - getColour(sequenceFeatures[sfindex].type), - start, end, y1, width, height); - - - } - - } - - 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, int width, int height) - { - - 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; - } - - 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) * width, y1, width, height); - - g.setColor(Color.white); - charOffset = (width - fm.charWidth(s)) / 2; - g.drawString(String.valueOf(s), - charOffset + (width * (i - start)), - (y1 + height) - height / 5); //pady = height / 5; - - } - } - } - - void findAllFeatures() - { - av.featuresDisplayed = new Hashtable(); - 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())) - { - av.featuresDisplayed.put(features[index].getType(), - new Integer( getColour(features[index].getType()).getRGB()) ); - } - index++; - } - } - - renderOrder = new String[av.featuresDisplayed.size()]; - Enumeration en = av.featuresDisplayed.keys(); - int i = 0; - while(en.hasMoreElements()) - { - renderOrder[i] = en.nextElement().toString(); - i++; - } - } - - public Color getColour(String featureType) - { - return (Color)featureColours.get(featureType); - } - - public void addNewFeature(String name, Color col) - { - - setColour(name, col); - if(av.featuresDisplayed==null) - av.featuresDisplayed = new Hashtable(); - - - av.featuresDisplayed.put(name, "NOGROUP"); - } - - 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 - av.featuresDisplayed.clear(); - - renderOrder = new String[data.length]; - - if(data.length>0) - for(int i=data.length-1; i>-1; 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[i] = type; - } - - } - - Hashtable featureColours = new Hashtable(); - void initColours() - { - featureColours.put("active site", new Color(255, 75, 0)); - featureColours.put("binding site", new Color(245, 85, 0)); - featureColours.put("calcium-binding region", new Color(235, 95, 0)); - featureColours.put("chain", new Color(225, 105, 0)); - featureColours.put("coiled-coil region", new Color(215, 115, 0)); - featureColours.put("compositionally biased region", new Color(205, 125, 0)); - featureColours.put("cross-link", new Color(195, 135, 0)); - featureColours.put("disulfide bond", new Color(230,230,0)); - featureColours.put("DNA-binding region", new Color(175, 155, 0)); - featureColours.put("domain", new Color(165, 165, 0)); - featureColours.put("glycosylation site", new Color(155, 175, 0)); - featureColours.put("helix", new Color(145, 185, 0)); - featureColours.put("initiator methionine", new Color(135, 195, 5)); - featureColours.put("lipid moiety-binding region", new Color(125, 205, 15)); - featureColours.put("metal ion-binding site", new Color(115, 215, 25)); - featureColours.put("modified residue", new Color(105, 225, 35)); - featureColours.put("mutagenesis site", new Color(95, 235, 45)); - featureColours.put("non-consecutive residues", new Color(85, 245, 55)); - featureColours.put("non-terminal residue", new Color(75, 255, 65)); - featureColours.put("nucleotide phosphate-binding region",new Color(65, 245, 75)); - featureColours.put("peptide", new Color(55, 235, 85)); - featureColours.put("propeptide", new Color(45, 225, 95)); - featureColours.put("region of interest", new Color(35, 215, 105)); - featureColours.put("repeat", new Color(25, 205, 115)); - featureColours.put("selenocysteine", new Color(15, 195, 125)); - featureColours.put("sequence conflict", new Color(5, 185, 135)); - featureColours.put("sequence variant", new Color(0, 175, 145)); - featureColours.put("short sequence motif", new Color(0, 165, 155)); - featureColours.put("signal peptide", new Color(0, 155, 165)); - featureColours.put("site", new Color(0, 145, 175)); - featureColours.put("splice variant", new Color(0, 135, 185)); - featureColours.put("strand", new Color(0, 125, 195)); - featureColours.put("topological domain", new Color(0, 115, 205)); - featureColours.put("transit peptide", new Color(0, 105, 215)); - featureColours.put("transmembrane region", new Color(0, 95, 225)); - featureColours.put("turn", new Color(0, 85, 235)); - featureColours.put("unsure residue", new Color(0, 75, 245)); - featureColours.put("zinc finger region", new Color(0, 65, 255)); - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * 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()); + } + } +}