X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=8a94a895aadded33776f94672513d8ec8d7cb52e;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=cd754c706a87aa38570ce6b9ebdd063b2ca6f0d2;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java old mode 100755 new mode 100644 index cd754c7..63d87af --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -1,85 +1,441 @@ -package jalview.gui; - -import jalview.datamodel.*; -import jalview.schemes.*; -import java.awt.*; -import java.util.*; - -public class FeatureRenderer implements RendererI { - - - public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) { - Color c = cs.findColour(seq,seq.getSequence(i,i+1),i,null); - return c; - } - - public void drawSequence(Graphics g,ColourSchemeI cs,SequenceI seq,int start, int end, int x1, int y1, double width, int height,boolean showScores, boolean displayBoxes, boolean displayText,Vector pid, int seqnum,AlignViewport av) { - - int i = start; - int length = seq.getLength(); - - Color currentColor = Color.black; - - - int prev = -1; - int fstart = 0; - char prevc = '-'; - - g.setColor(Color.magenta); - - while (i <= end && i < length) { - char c = seq.getCharAt(i); - if (c != '-') { - - if (prevc != c) { - - if (prevc == 'F') { - g.setColor(Color.green); - } else if (prevc == 'R') { - g.setColor(Color.cyan); - } else if (prevc == 'M') { - g.setColor(Color.magenta); - } else if (prevc == 'P') { - g.setColor(Color.yellow); - } - g.fillRect(x1+(int)(width*(i-fstart)),y1+height/4,(int)((prev-fstart+1)*width),height/2); - - prevc = c; - fstart = i; - } - } else if (prevc != '-') { - if (prevc == 'F') { - g.setColor(Color.green); - } else if (prevc == 'R') { - g.setColor(Color.cyan); - } else if (prevc == 'M') { - g.setColor(Color.magenta); - } else if (prevc == 'P') { - g.setColor(Color.yellow); - } - g.fillRect(x1+(int)(width*(fstart-start)),y1+height/4,(int)((i-fstart+1)*width),height/2); - - prevc = c; - } else { - fstart = -1; - } - i++; - } - - if (fstart != -1) { - if (prevc == 'F') { - g.setColor(Color.green); - } else if (prevc == 'R') { - g.setColor(Color.cyan); - } else if (prevc == 'M') { - g.setColor(Color.magenta); - } else if (prevc == 'P') { - g.setColor(Color.yellow); - } - - //g.fillRect(x1+(int)(width*(fstart-start)),y1+height/4,(int)((end-fstart+1)*width),height/2); - - } - } - -} +/* + * 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()); + } + } +}