From 2cc0663ace7adaa36478db77ca96daa736993890 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Mon, 9 Jul 2018 12:21:58 +0100 Subject: [PATCH] JAL-3060 extract FeatureEditor class --- src/jalview/gui/FeatureEditor.java | 556 ++++++++++++++++++++ src/jalview/gui/FeatureRenderer.java | 536 ------------------- src/jalview/gui/Finder.java | 7 +- src/jalview/gui/PopupMenu.java | 17 +- src/jalview/gui/SeqPanel.java | 15 +- .../seqfeatures/FeatureRendererModel.java | 29 +- 6 files changed, 604 insertions(+), 556 deletions(-) create mode 100644 src/jalview/gui/FeatureEditor.java diff --git a/src/jalview/gui/FeatureEditor.java b/src/jalview/gui/FeatureEditor.java new file mode 100644 index 0000000..a86725b --- /dev/null +++ b/src/jalview/gui/FeatureEditor.java @@ -0,0 +1,556 @@ +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.gui.JalviewColourChooser.ColourChooserListener; +import jalview.io.FeaturesFile; +import jalview.schemes.FeatureColour; +import jalview.util.ColorUtils; +import jalview.util.MessageManager; +import jalview.util.dialogrunner.RunResponse; + +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.List; + +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; + +/** + * Provides a dialog allowing the user to add new features, or amend or delete + * existing features + */ +public class FeatureEditor +{ + /* + * defaults for creating a new feature are the last created + * feature type and group + */ + static String lastFeatureAdded = "feature_1"; + + static String lastFeatureGroupAdded = "Jalview"; + + /* + * index into a list of features if more than one selected for editing + */ + int featureIndex; + + FeatureColourI oldColour; + + FeatureColourI featureColour; + + FeatureRenderer fr; + + AlignmentPanel ap; + + /** + * Constructor + * + * @param alignPanel + */ + public FeatureEditor(AlignmentPanel alignPanel) + { + ap = alignPanel; + fr = alignPanel.getSeqPanel().seqCanvas.fr; + } + + /** + * 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 + * @param responseHandler + * boolean true RunResponse is run if features are created + */ + public boolean amendFeatures(final List sequences, + final List features, boolean create, + final Runnable responseHandler) + { + 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 (featureColour.isSimpleColour()) + { + String title = MessageManager + .getString("label.select_feature_colour"); + ColourChooserListener listener = new ColourChooserListener() + { + @Override + public void colourSelected(Color c) + { + featureColour = new FeatureColour(c); + updateColourButton(mainPanel, colour, featureColour); + }; + }; + JalviewColourChooser.showColourChooser(Desktop.getDesktop(), + title, featureColour.getColour(), listener); + } + 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( + fr, type); + fcc.setRequestFocusEnabled(true); + fcc.requestFocus(); + fcc.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + featureColour = fr.getFeatureStyle(ft); + fr.setColour(type, featureColour); + updateColourButton(mainPanel, colour, featureColour); + } + }); + } + } + }); + 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(new Integer(sf.getBegin())); + end.setValue(new Integer(sf.getEnd())); + + SearchResultsI highlight = new SearchResults(); + highlight.addResult(sequences.get(0), sf.getBegin(), + sf.getEnd()); + + ap.getSeqPanel().seqCanvas + .highlightSearchResults(highlight, false); + } + FeatureColourI col = fr.getFeatureStyle(name.getText()); + if (col == null) + { + col = new FeatureColour( + ColorUtils.createColourFromName(name.getText())); + } + oldColour = featureColour = 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(new Integer(firstFeature.getBegin())); + end.setValue(new Integer(firstFeature.getEnd())); + description.setText(firstFeature.getDescription()); + featureColour = fr.getFeatureStyle(featureType); + oldColour = featureColour; + updateColourButton(mainPanel, colour, oldColour); + 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() }); + + /* + * register responses and show the dialog + */ + JvOptionPane.newOptionDialog(Desktop.desktop).response( + + new RunResponse(JvOptionPane.OK_OPTION) + { + public void run() + { + final String enteredType = name.getText().trim(); + final String enteredGroup = group.getText().trim(); + final String enteredDescription = description.getText() + .replaceAll("\n", " "); + if (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) + { + // NEW FEATURES ADDED + if (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); + new FeaturesFile().parseDescriptionHTML(sf2, false); + sequences.get(i).addSequenceFeature(sf2); + } + + fr.setColour(enteredType, featureColour); + + fr.featuresAdded(); + + responseHandler.run(); + } + } else { + SequenceFeature sf = features.get(featureIndex); + /* + * Feature amended - 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 |= (featureColour != oldColour); + fr.setColour(enteredType, featureColour); + 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); + new FeaturesFile().parseDescriptionHTML(newSf, false); + // amend features dialog only updates one sequence at a time + sequences.get(0).addSequenceFeature(newSf); + + if (refreshSettings) + { + fr.featuresAdded(); + } + } + ap.getSeqPanel().seqCanvas.highlightSearchResults(null, + false); + ap.paintAlignment(true, true); + } + }).response(new RunResponse(JvOptionPane.NO_OPTION) + { + public void run() + { + SequenceFeature sf = features.get(featureIndex); + /* + * NO_OPTION corresponds to the Delete button + */ + sequences.get(0).getDatasetSequence().deleteFeature(sf); + // update Feature Settings for removal of feature / group + fr.featuresAdded(); + ap.getSeqPanel().seqCanvas.highlightSearchResults(null, + false); + ap.paintAlignment(true, true); + } + }).defaultResponse(new Runnable() + { + public void run() + { + ap.getSeqPanel().seqCanvas.highlightSearchResults(null, + false); + ap.paintAlignment(true, true); + } + }).showInternalDialog(mainPanel, title, + JvOptionPane.YES_NO_CANCEL_OPTION, + JvOptionPane.QUESTION_MESSAGE, null, options, + MessageManager.getString("action.ok")); + return true; + } + + /** + * 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); + } + } + + /** + * 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 (!fr.isGroupVisible(group)) + { + String msg = MessageManager.formatMessage("label.warning_hidden", + MessageManager.getString("label.group"), group); + JvOptionPane.showMessageDialog(panel, msg, "", + JvOptionPane.OK_OPTION); + } + } + + /** + * 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 (fr.getRenderOrder().contains(type)) + { + if (!fr.showFeatureOfType(type)) + { + String msg = MessageManager.formatMessage("label.warning_hidden", + MessageManager.getString("label.feature_type"), type); + JvOptionPane.showMessageDialog(panel, msg, "", + JvOptionPane.OK_OPTION); + } + } + } + +} diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index 18c440e..0553fef 100644 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -20,46 +20,7 @@ */ 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.gui.JalviewColourChooser.ColourChooserListener; -import jalview.io.FeaturesFile; -import jalview.schemes.FeatureColour; -import jalview.util.ColorUtils; -import jalview.util.MessageManager; -import jalview.util.dialogrunner.RunResponse; - -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.JDialog; -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! @@ -70,14 +31,6 @@ import javax.swing.event.DocumentListener; 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; @@ -98,493 +51,4 @@ 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 - *
    - *
  • double-click on a sequence - Amend/Delete features at position
    • - *
  • Create sequence feature from pop-up menu on selected region
    • - *
  • Create features for pattern matches from Find
    • - *
- * 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 - * @param responseHandler - * boolean true RunResponse is run if features are created - */ - protected boolean amendFeatures(final List sequences, - final List features, boolean create, - final AlignmentPanel alignPanel, final Runnable responseHandler) - { - 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()) - { - String title = MessageManager - .getString("label.select_feature_colour"); - ColourChooserListener listener = new ColourChooserListener() - { - @Override - public void colourSelected(Color c) - { - fcol = new FeatureColour(c); - updateColourButton(mainPanel, colour, fcol); - }; - }; - JalviewColourChooser.showColourChooser(Desktop.getDesktop(), - title, fcol.getColour(), listener); - } - 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(new Integer(sf.getBegin())); - end.setValue(new Integer(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(new Integer(firstFeature.getBegin())); - end.setValue(new Integer(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() }); - - /* - * register responses and show the dialog - */ - JvOptionPane.newOptionDialog(Desktop.desktop).response( - - new RunResponse(JvOptionPane.OK_OPTION) - { - public void run() - { - final String enteredType = name.getText().trim(); - final String enteredGroup = group.getText().trim(); - final String enteredDescription = description.getText() - .replaceAll("\n", " "); - if (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) - { - // NEW FEATURES ADDED - if (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); - new FeaturesFile().parseDescriptionHTML(sf2, false); - sequences.get(i).addSequenceFeature(sf2); - } - - setColour(enteredType, fcol); - - featuresAdded(); - - responseHandler.run(); - } - } else { - SequenceFeature sf = features.get(featureIndex); - /* - * Feature amended - 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); - new FeaturesFile().parseDescriptionHTML(newSf, false); - // amend features dialog only updates one sequence at a time - sequences.get(0).addSequenceFeature(newSf); - - if (refreshSettings) - { - featuresAdded(); - } - } - alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null, false); - alignPanel.paintAlignment(true, true); - } - }).response(new RunResponse(JvOptionPane.NO_OPTION) - { - public void run() - { - SequenceFeature sf = features.get(featureIndex); - /* - * NO_OPTION corresponds to the Delete button - */ - sequences.get(0).getDatasetSequence().deleteFeature(sf); - // update Feature Settings for removal of feature / group - featuresAdded(); - alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null, false); - alignPanel.paintAlignment(true, true); - } - }).defaultResponse(new Runnable() - { - public void run() - { - alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null, false); - alignPanel.paintAlignment(true, true); - } - }).showInternalDialog(mainPanel, title, - JvOptionPane.YES_NO_CANCEL_OPTION, - JvOptionPane.QUESTION_MESSAGE, null, options, - MessageManager.getString("action.ok")); - 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); - } } diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index 8b5bbda..244e6df 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -227,10 +227,9 @@ public class Finder extends GFinder match.getEnd(), desc)); } - ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs, - features, true, ap, new Runnable() - { - @Override + new FeatureEditor(ap).amendFeatures(seqs, features, true, new Runnable() + { + @Override public void run() { diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 0a5224c..cb94409 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -46,7 +46,6 @@ import jalview.io.SequenceAnnotationReport; import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemes; -import jalview.schemes.FeatureColour; import jalview.schemes.PIDColourScheme; import jalview.util.GroupUrlLink; import jalview.util.GroupUrlLink.UrlStringTooLongException; @@ -71,8 +70,6 @@ import java.util.TreeMap; import java.util.Vector; import javax.swing.JCheckBoxMenuItem; -import javax.swing.JColorChooser; -import javax.swing.JDialog; import javax.swing.JMenu; import javax.swing.JMenuItem; import javax.swing.JPopupMenu; @@ -2041,12 +2038,14 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener */ if (!seqs.isEmpty()) { - ap.getSeqPanel().seqCanvas.getFeatureRenderer() - .amendFeatures(seqs, features, true, ap,new Runnable() { - public void run() { - ap.alignFrame.setShowSeqFeatures(true); - ap.av.setSearchResults(null); // clear highlighting - ap.repaint(); // draw new/amended features + new FeatureEditor(ap).amendFeatures(seqs, features, true, + new Runnable() + { + public void run() + { + ap.alignFrame.setShowSeqFeatures(true); + ap.av.setSearchResults(null); // clear highlighting + ap.repaint(); // draw new/amended features }}); } } diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 8f8e9a9..db0d902 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1680,13 +1680,16 @@ public class SeqPanel extends JPanel * whether changes were made or not */ List seqs = Collections.singletonList(sequence); - seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false, - ap, new Runnable() {@Override - public void run() + new FeatureEditor(ap).amendFeatures(seqs, features, false, + new Runnable() { - av.setSearchResults(null); // clear highlighting - seqCanvas.repaint(); // draw new/amended features - }}); + @Override + public void run() + { + av.setSearchResults(null); // clear highlighting + seqCanvas.repaint(); // draw new/amended features + } + }); } } } diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index 553f813..719cde4 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -37,6 +37,7 @@ import java.beans.PropertyChangeListener; import java.beans.PropertyChangeSupport; import java.util.ArrayList; import java.util.Arrays; +import java.util.Comparator; import java.util.HashMap; import java.util.HashSet; import java.util.Hashtable; @@ -612,7 +613,7 @@ public abstract class FeatureRendererModel * @param type * @return */ - protected boolean showFeatureOfType(String type) + public boolean showFeatureOfType(String type) { return type == null ? false : (av.getFeaturesDisplayed() == null ? true : av.getFeaturesDisplayed().isVisible(type)); @@ -1150,4 +1151,30 @@ public abstract class FeatureRendererModel return filter == null ? true : filter.matches(sf); } + /** + * Answers true unless the specified group is set to hidden. Defaults to true + * if group visibility is not set. + * + * @param group + * @return + */ + public boolean isGroupVisible(String group) + { + if (!featureGroups.containsKey(group)) + { + return true; + } + return featureGroups.get(group); + } + + /** + * 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); + } } -- 1.7.10.2