X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=61d32668fb0f91256ec03302a5cbf282857342fc;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=3ce831e4e6ac3d0792dce774436702723640635a;hpb=30133ea9afab31009432eb013c299eb6c36ae75e;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index 3ce831e..61d3266 100644 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,34 +20,7 @@ */ 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! @@ -55,383 +28,27 @@ import javax.swing.SwingConstants; * @author $author$ * @version $Revision$ */ -public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRenderer implements jalview.api.FeatureRenderer +public class FeatureRenderer + extends jalview.renderer.seqfeatures.FeatureRenderer + implements jalview.api.FeatureRenderer { Color resBoxColour; AlignmentPanel ap; /** - * Creates a new FeatureRenderer object. + * Creates a new FeatureRenderer object * - * @param av - * DOCUMENT ME! + * @param alignPanel */ - 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) + public FeatureRenderer(AlignmentPanel alignPanel) { - - 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 + super(alignPanel.av); + this.ap = alignPanel; + SeqPanel sp = alignPanel.getSeqPanel(); + if (sp != null && sp.seqCanvas != null && sp.seqCanvas.fr != null) { - colour.setBackground(bigPanel.getBackground()); - colour.setForeground(Color.black); - FeatureSettings.renderGraduatedColor(colour, (GraduatedColor) col2); - // colour.setForeground(colour.getBackground()); + transferSettings(sp.seqCanvas.fr); } } }