X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;fp=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=83badd0da33d0fa9ebbc71b6d8a4e6b00e32903b;hp=e22f506d662e1160d10dc0fceb1a7b5576f50b88;hb=65740880573a48adc758bec3939ece9d9ae104dd;hpb=71aa78b8a7d54e5aeb6b278310dfd735efb77477 diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index e22f506..83badd0 100644 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -20,63 +20,12 @@ */ package jalview.gui; -import jalview.api.FeatureColourI; -import jalview.datamodel.SearchResults; -import jalview.datamodel.SearchResultsI; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceI; -import jalview.io.FeaturesFile; -import jalview.schemes.FeatureColour; -import jalview.util.ColorUtils; -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.ArrayList; -import java.util.Arrays; -import java.util.Comparator; -import java.util.List; - -import javax.swing.JColorChooser; -import javax.swing.JComboBox; -import javax.swing.JLabel; -import javax.swing.JPanel; -import javax.swing.JScrollPane; -import javax.swing.JSpinner; -import javax.swing.JTextArea; -import javax.swing.JTextField; -import javax.swing.SwingConstants; -import javax.swing.event.DocumentEvent; -import javax.swing.event.DocumentListener; - /** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ + * A class that manages drawing of sequence features for the Swing gui */ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRenderer { - /* - * defaults for creating a new feature are the last created - * feature type and group - */ - static String lastFeatureAdded = "feature_1"; - - static String lastFeatureGroupAdded = "Jalview"; - - Color resBoxColour; - AlignmentPanel ap; /** @@ -95,483 +44,4 @@ public class FeatureRenderer transferSettings(alignPanel.getSeqPanel().seqCanvas.fr); } } - - FeatureColourI oldcol, fcol; - - int featureIndex = 0; - - /** - * Presents a dialog allowing the user to add new features, or amend or delete - * existing features. Currently this can be on - * - * If the supplied feature type is null, show (and update on confirm) the type - * and group of the last new feature created (with initial defaults of - * "feature_1" and "Jalview"). - * - * @param sequences - * the sequences features are to be created on (if creating - * features), or a single sequence (if amending features) - * @param features - * the current features at the position (if amending), or template - * new feature(s) with start/end position set (if creating) - * @param create - * true to create features, false to amend or delete - * @param alignPanel - * @return - */ - protected boolean amendFeatures(final List sequences, - final List features, boolean create, - final AlignmentPanel alignPanel) - { - featureIndex = 0; - - final JPanel mainPanel = new JPanel(new BorderLayout()); - - final JTextField name = new JTextField(25); - name.getDocument().addDocumentListener(new DocumentListener() - { - @Override - public void insertUpdate(DocumentEvent e) - { - warnIfTypeHidden(mainPanel, name.getText()); - } - - @Override - public void removeUpdate(DocumentEvent e) - { - warnIfTypeHidden(mainPanel, name.getText()); - } - - @Override - public void changedUpdate(DocumentEvent e) - { - warnIfTypeHidden(mainPanel, name.getText()); - } - }); - - final JTextField group = new JTextField(25); - group.getDocument().addDocumentListener(new DocumentListener() - { - @Override - public void insertUpdate(DocumentEvent e) - { - warnIfGroupHidden(mainPanel, group.getText()); - } - - @Override - public void removeUpdate(DocumentEvent e) - { - warnIfGroupHidden(mainPanel, group.getText()); - } - - @Override - public void changedUpdate(DocumentEvent e) - { - warnIfGroupHidden(mainPanel, group.getText()); - } - }); - - 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 JLabel colour = new JLabel(); - colour.setOpaque(true); - // colour.setBorder(BorderFactory.createEtchedBorder()); - colour.setMaximumSize(new Dimension(30, 16)); - colour.addMouseListener(new MouseAdapter() - { - /* - * open colour chooser on click in colour panel - */ - @Override - public void mousePressed(MouseEvent evt) - { - if (fcol.isSimpleColour()) - { - Color col = JColorChooser.showDialog(Desktop.desktop, - MessageManager.getString("label.select_feature_colour"), - fcol.getColour()); - if (col != null) - { - fcol = new FeatureColour(col); - updateColourButton(mainPanel, colour, fcol); - } - } - else - { - /* - * variable colour dialog - on OK, refetch the updated - * feature colour and update this display - */ - final String ft = features.get(featureIndex).getType(); - final String type = ft == null ? lastFeatureAdded : ft; - FeatureTypeSettings fcc = new FeatureTypeSettings( - FeatureRenderer.this, type); - fcc.setRequestFocusEnabled(true); - fcc.requestFocus(); - fcc.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - fcol = FeatureRenderer.this.getFeatureStyle(ft); - setColour(type, fcol); - updateColourButton(mainPanel, colour, fcol); - } - }); - } - } - }); - JPanel gridPanel = new JPanel(new GridLayout(3, 1)); - - if (!create && features.size() > 1) - { - /* - * more than one feature at selected position - - * add a drop-down to choose the feature to amend - * space pad text if necessary to make entries distinct - */ - gridPanel = new JPanel(new GridLayout(4, 1)); - JPanel choosePanel = new JPanel(); - choosePanel.add(new JLabel( - MessageManager.getString("label.select_feature") + ":")); - final JComboBox overlaps = new JComboBox<>(); - List added = new ArrayList<>(); - for (SequenceFeature sf : features) - { - String text = String.format("%s/%d-%d (%s)", sf.getType(), - sf.getBegin(), sf.getEnd(), sf.getFeatureGroup()); - while (added.contains(text)) - { - text += " "; - } - overlaps.addItem(text); - added.add(text); - } - choosePanel.add(overlaps); - - overlaps.addItemListener(new ItemListener() - { - @Override - public void itemStateChanged(ItemEvent e) - { - int index = overlaps.getSelectedIndex(); - if (index != -1) - { - featureIndex = index; - SequenceFeature sf = features.get(index); - name.setText(sf.getType()); - description.setText(sf.getDescription()); - group.setText(sf.getFeatureGroup()); - start.setValue(Integer.valueOf(sf.getBegin())); - end.setValue(Integer.valueOf(sf.getEnd())); - - SearchResultsI highlight = new SearchResults(); - highlight.addResult(sequences.get(0), sf.getBegin(), - sf.getEnd()); - - alignPanel.getSeqPanel().seqCanvas.highlightSearchResults( - highlight, false); - } - FeatureColourI col = getFeatureStyle(name.getText()); - if (col == null) - { - col = new FeatureColour( - ColorUtils.createColourFromName(name.getText())); - } - oldcol = fcol = col; - updateColourButton(mainPanel, colour, col); - } - }); - - gridPanel.add(choosePanel); - } - - JPanel namePanel = new JPanel(); - gridPanel.add(namePanel); - namePanel.add(new JLabel(MessageManager.getString("label.name:"), - JLabel.RIGHT)); - namePanel.add(name); - - JPanel groupPanel = new JPanel(); - gridPanel.add(groupPanel); - groupPanel.add(new JLabel(MessageManager.getString("label.group:"), - JLabel.RIGHT)); - groupPanel.add(group); - - JPanel colourPanel = new JPanel(); - gridPanel.add(colourPanel); - colourPanel.add(new JLabel(MessageManager.getString("label.colour"), - JLabel.RIGHT)); - colourPanel.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); - mainPanel.add(gridPanel, BorderLayout.NORTH); - - JPanel descriptionPanel = new JPanel(); - descriptionPanel.add(new JLabel( - MessageManager.getString("label.description:"), JLabel.RIGHT)); - description.setFont(JvSwingUtils.getTextAreaFont()); - description.setLineWrap(true); - descriptionPanel.add(new JScrollPane(description)); - - if (!create) - { - mainPanel.add(descriptionPanel, BorderLayout.SOUTH); - - JPanel startEndPanel = new JPanel(); - startEndPanel.add(new JLabel(MessageManager.getString("label.start"), - JLabel.RIGHT)); - startEndPanel.add(start); - startEndPanel.add(new JLabel(MessageManager.getString("label.end"), - JLabel.RIGHT)); - startEndPanel.add(end); - mainPanel.add(startEndPanel, BorderLayout.CENTER); - } - else - { - mainPanel.add(descriptionPanel, BorderLayout.CENTER); - } - - /* - * default feature type and group to that of the first feature supplied, - * or to the last feature created if not supplied (null value) - */ - SequenceFeature firstFeature = features.get(0); - boolean useLastDefaults = firstFeature.getType() == null; - final String featureType = useLastDefaults ? lastFeatureAdded - : firstFeature.getType(); - final String featureGroup = useLastDefaults ? lastFeatureGroupAdded - : firstFeature.getFeatureGroup(); - name.setText(featureType); - group.setText(featureGroup); - - start.setValue(Integer.valueOf(firstFeature.getBegin())); - end.setValue(Integer.valueOf(firstFeature.getEnd())); - description.setText(firstFeature.getDescription()); - updateColourButton(mainPanel, colour, - (oldcol = fcol = getFeatureStyle(featureType))); - Object[] options; - if (!create) - { - options = new Object[] { MessageManager.getString("label.amend"), - MessageManager.getString("action.delete"), - MessageManager.getString("action.cancel") }; - } - else - { - options = new Object[] { MessageManager.getString("action.ok"), - MessageManager.getString("action.cancel") }; - } - - String title = create - ? MessageManager.getString("label.create_new_sequence_features") - : MessageManager.formatMessage("label.amend_delete_features", - new String[] - { sequences.get(0).getName() }); - - /* - * show the dialog - */ - int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop, - mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION, - JvOptionPane.QUESTION_MESSAGE, null, options, - MessageManager.getString("action.ok")); - - FeaturesFile ffile = new FeaturesFile(); - - final String enteredType = name.getText().trim(); - final String enteredGroup = group.getText().trim(); - final String enteredDescription = description.getText().replaceAll("\n", " "); - - if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0) - { - /* - * update default values only if creating using default values - */ - if (useLastDefaults) - { - lastFeatureAdded = enteredType; - lastFeatureGroupAdded = enteredGroup; - // TODO: determine if the null feature group is valid - if (lastFeatureGroupAdded.length() < 1) - { - lastFeatureGroupAdded = null; - } - } - } - - if (!create) - { - SequenceFeature sf = features.get(featureIndex); - - if (reply == JvOptionPane.NO_OPTION) - { - /* - * NO_OPTION corresponds to the Delete button - */ - sequences.get(0).getDatasetSequence().deleteFeature(sf); - // update Feature Settings for removal of feature / group - featuresAdded(); - } - else if (reply == JvOptionPane.YES_OPTION) - { - /* - * YES_OPTION corresponds to the Amend button - * need to refresh Feature Settings if type, group or colour changed; - * note we don't force the feature to be visible - the user has been - * warned if a hidden feature type or group was entered - */ - boolean refreshSettings = (!featureType.equals(enteredType) || !featureGroup - .equals(enteredGroup)); - refreshSettings |= (fcol != oldcol); - setColour(enteredType, fcol); - int newBegin = sf.begin; - int newEnd = sf.end; - try - { - newBegin = ((Integer) start.getValue()).intValue(); - newEnd = ((Integer) end.getValue()).intValue(); - } catch (NumberFormatException ex) - { - // JSpinner doesn't accept invalid format data :-) - } - - /* - * replace the feature by deleting it and adding a new one - * (to ensure integrity of SequenceFeatures data store) - */ - sequences.get(0).deleteFeature(sf); - SequenceFeature newSf = new SequenceFeature(sf, enteredType, - newBegin, newEnd, enteredGroup, sf.getScore()); - newSf.setDescription(enteredDescription); - ffile.parseDescriptionHTML(newSf, false); - // amend features dialog only updates one sequence at a time - sequences.get(0).addSequenceFeature(newSf); - - if (refreshSettings) - { - featuresAdded(); - } - } - } - else - // NEW FEATURES ADDED - { - if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0) - { - for (int i = 0; i < sequences.size(); i++) - { - SequenceFeature sf = features.get(i); - SequenceFeature sf2 = new SequenceFeature(enteredType, - enteredDescription, sf.getBegin(), sf.getEnd(), - enteredGroup); - ffile.parseDescriptionHTML(sf2, false); - sequences.get(i).addSequenceFeature(sf2); - } - - setColour(enteredType, fcol); - - featuresAdded(); - - alignPanel.paintAlignment(true, true); - - return true; - } - else - { - return false; - } - } - - alignPanel.paintAlignment(true, true); - - return true; - } - - /** - * Show a warning message if the entered type is one that is currently hidden - * - * @param panel - * @param type - */ - protected void warnIfTypeHidden(JPanel panel, String type) - { - if (getRenderOrder().contains(type)) - { - if (!showFeatureOfType(type)) - { - String msg = MessageManager.formatMessage("label.warning_hidden", - MessageManager.getString("label.feature_type"), type); - JvOptionPane.showMessageDialog(panel, msg, "", - JvOptionPane.OK_OPTION); - } - } - } - - /** - * Show a warning message if the entered group is one that is currently hidden - * - * @param panel - * @param group - */ - protected void warnIfGroupHidden(JPanel panel, String group) - { - if (featureGroups.containsKey(group) && !featureGroups.get(group)) - { - String msg = MessageManager.formatMessage("label.warning_hidden", - MessageManager.getString("label.group"), group); - JvOptionPane.showMessageDialog(panel, msg, "", - JvOptionPane.OK_OPTION); - } - } - - /** - * update the amend feature button dependent on the given style - * - * @param bigPanel - * @param col - * @param col - */ - protected void updateColourButton(JPanel bigPanel, JLabel colour, - FeatureColourI col) - { - colour.removeAll(); - colour.setIcon(null); - colour.setToolTipText(null); - colour.setText(""); - - if (col.isSimpleColour()) - { - colour.setBackground(col.getColour()); - } - else - { - colour.setBackground(bigPanel.getBackground()); - colour.setForeground(Color.black); - FeatureSettings.renderGraduatedColor(colour, col); - } - } - - /** - * Orders features in render precedence (last in order is last to render, so - * displayed on top of other features) - * - * @param order - */ - public void orderFeatures(Comparator order) - { - Arrays.sort(renderOrder, order); - } }