X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=ac56590446bbb586fd553c8bc3a512c32cffe75d;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=f7cc65edf84d1aa93ec5ff40ca9703b0ace5cd0d;hpb=25aaaa87042b3f507ad4348120df7dd073182759;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index f7cc65e..ac56590 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 2.8.2b1) - * 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. * @@ -20,10 +20,14 @@ */ 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.schemes.GraduatedColor; +import jalview.io.FeaturesFile; +import jalview.schemes.FeatureColour; +import jalview.util.ColorUtils; import jalview.util.MessageManager; import java.awt.BorderLayout; @@ -37,17 +41,21 @@ import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; +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.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; +import javax.swing.event.DocumentEvent; +import javax.swing.event.DocumentListener; /** * DOCUMENT ME! @@ -55,55 +63,117 @@ 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 { + /* + * 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; /** - * Creates a new FeatureRenderer object. + * Creates a new FeatureRenderer object * - * @param av - * DOCUMENT ME! + * @param alignPanel */ - public FeatureRenderer(AlignmentPanel ap) + public FeatureRenderer(AlignmentPanel alignPanel) { - super(); - this.ap = ap; - this.av = ap.av; - if (ap != null && ap.getSeqPanel() != null && ap.getSeqPanel().seqCanvas != null - && ap.getSeqPanel().seqCanvas.fr != null) + super(alignPanel.av); + this.ap = alignPanel; + if (alignPanel.getSeqPanel() != null + && alignPanel.getSeqPanel().seqCanvas != null + && alignPanel.getSeqPanel().seqCanvas.fr != null) { - transferSettings(ap.getSeqPanel().seqCanvas.fr); + transferSettings(alignPanel.getSeqPanel().seqCanvas.fr); } } - // // ///////////// - // // Feature Editing Dialog - // // Will be refactored in next release. + FeatureColourI oldcol, fcol; - static String lastFeatureAdded; + int featureIndex = 0; - static String lastFeatureGroupAdded; + /** + * 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; - static String lastDescriptionAdded; + final JPanel mainPanel = new JPanel(new BorderLayout()); - Object oldcol, fcol; + final JTextField name = new JTextField(25); + name.getDocument().addDocumentListener(new DocumentListener() + { + @Override + public void insertUpdate(DocumentEvent e) + { + warnIfTypeHidden(mainPanel, name.getText()); + } - int featureIndex = 0; + @Override + public void removeUpdate(DocumentEvent e) + { + warnIfTypeHidden(mainPanel, name.getText()); + } - boolean amendFeatures(final SequenceI[] sequences, - final SequenceFeature[] features, boolean newFeatures, - final AlignmentPanel ap) - { + @Override + public void changedUpdate(DocumentEvent e) + { + warnIfTypeHidden(mainPanel, name.getText()); + } + }); - featureIndex = 0; + 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 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(); @@ -118,24 +188,26 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere { FeatureColourChooser fcc = null; + @Override public void mousePressed(MouseEvent evt) { - if (fcol instanceof Color) + if (fcol.isSimpleColour()) { Color col = JColorChooser.showDialog(Desktop.desktop, - MessageManager.getString("label.select_feature_colour"), ((Color) fcol)); + MessageManager.getString("label.select_feature_colour"), + fcol.getColour()); if (col != null) { - fcol = col; - updateColourButton(bigPanel, colour, col); + fcol = new FeatureColour(col); + updateColourButton(mainPanel, colour, fcol); } } else { - if (fcc == null) { - final String type = features[featureIndex].getType(); + final String ft = features.get(featureIndex).getType(); + final String type = ft == null ? lastFeatureAdded : ft; fcc = new FeatureColourChooser(me, type); fcc.setRequestFocusEnabled(true); fcc.requestFocus(); @@ -143,12 +215,13 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere fcc.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { fcol = fcc.getLastColour(); fcc = null; setColour(type, fcol); - updateColourButton(bigPanel, colour, fcol); + updateColourButton(mainPanel, colour, fcol); } }); @@ -156,79 +229,82 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere } } }); - JPanel tmp = new JPanel(); - JPanel panel = new JPanel(new GridLayout(3, 1)); + JPanel gridPanel = new JPanel(new GridLayout(3, 1)); - // ///////////////////////////////////// - // /MULTIPLE FEATURES AT SELECTED RESIDUE - if (!newFeatures && features.length > 1) + if (!create && features.size() > 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++) + /* + * more than one feature at selected position - add a drop-down + * to choose the feature to amend + */ + 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(); + for (SequenceFeature sf : features) { - overlaps.addItem(features[i].getType() + "/" - + features[i].getBegin() + "-" + features[i].getEnd() - + " (" + features[i].getFeatureGroup() + ")"); + String text = sf.getType() + "/" + sf.getBegin() + "-" + + sf.getEnd() + " (" + sf.getFeatureGroup() + ")"; + overlaps.addItem(text); } - - tmp.add(overlaps); + choosePanel.add(overlaps); overlaps.addItemListener(new ItemListener() { + @Override 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())); + 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())); - SearchResults highlight = new SearchResults(); - highlight.addResult(sequences[0], features[index].getBegin(), - features[index].getEnd()); + SearchResultsI highlight = new SearchResults(); + highlight.addResult(sequences.get(0), sf.getBegin(), + sf.getEnd()); - ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight); + alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(highlight); } - Object col = getFeatureStyle(name.getText()); + FeatureColourI col = getFeatureStyle(name.getText()); if (col == null) { - col = new jalview.schemes.UserColourScheme() - .createColourFromName(name.getText()); + col = new FeatureColour(ColorUtils + .createColourFromName(name.getText())); } oldcol = fcol = col; - updateColourButton(bigPanel, colour, col); + updateColourButton(mainPanel, colour, col); } }); - panel.add(tmp); + gridPanel.add(choosePanel); } - // //////// - // //////////////////////////////////// - tmp = new JPanel(); - panel.add(tmp); - tmp.add(new JLabel(MessageManager.getString("label.name"), JLabel.RIGHT)); - tmp.add(name); + JPanel namePanel = new JPanel(); + gridPanel.add(namePanel); + namePanel.add(new JLabel(MessageManager.getString("label.name:"), + JLabel.RIGHT)); + namePanel.add(name); - tmp = new JPanel(); - panel.add(tmp); - tmp.add(new JLabel(MessageManager.getString("label.group") + ":", + JPanel groupPanel = new JPanel(); + gridPanel.add(groupPanel); + groupPanel.add(new JLabel(MessageManager.getString("label.group:"), JLabel.RIGHT)); - tmp.add(source); + groupPanel.add(group); - tmp = new JPanel(); - panel.add(tmp); - tmp.add(new JLabel(MessageManager.getString("label.colour"), + JPanel colourPanel = new JPanel(); + gridPanel.add(colourPanel); + colourPanel.add(new JLabel(MessageManager.getString("label.colour"), JLabel.RIGHT)); - tmp.add(colour); + colourPanel.add(colour); colour.setPreferredSize(new Dimension(150, 15)); colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9)); colour.setForeground(Color.black); @@ -236,162 +312,175 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere colour.setVerticalAlignment(SwingConstants.CENTER); colour.setHorizontalTextPosition(SwingConstants.CENTER); colour.setVerticalTextPosition(SwingConstants.CENTER); - bigPanel.add(panel, BorderLayout.NORTH); + mainPanel.add(gridPanel, BorderLayout.NORTH); - panel = new JPanel(); - panel.add(new JLabel(MessageManager.getString("label.description"), + JPanel descriptionPanel = new JPanel(); + descriptionPanel.add(new JLabel(MessageManager + .getString("label.description:"), JLabel.RIGHT)); description.setFont(JvSwingUtils.getTextAreaFont()); description.setLineWrap(true); - panel.add(new JScrollPane(description)); + descriptionPanel.add(new JScrollPane(description)); - if (!newFeatures) + if (!create) { - bigPanel.add(panel, BorderLayout.SOUTH); + mainPanel.add(descriptionPanel, BorderLayout.SOUTH); - panel = new JPanel(); - panel.add(new JLabel(MessageManager.getString("label.start"), + JPanel startEndPanel = new JPanel(); + startEndPanel.add(new JLabel(MessageManager.getString("label.start"), JLabel.RIGHT)); - panel.add(start); - panel.add(new JLabel(MessageManager.getString("label.end"), + startEndPanel.add(start); + startEndPanel.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); + startEndPanel.add(end); + mainPanel.add(startEndPanel, BorderLayout.CENTER); } else { - name.setText(features[0].getType()); - source.setText(features[0].getFeatureGroup()); + mainPanel.add(descriptionPanel, BorderLayout.CENTER); } - 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()))); + /* + * 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 (!newFeatures) + if (!create) { - options = new Object[] - { "Amend", "Delete", "Cancel" }; + options = new Object[] { MessageManager.getString("label.amend"), + MessageManager.getString("action.delete"), + MessageManager.getString("action.cancel") }; } else { - options = new Object[] - { "OK", "Cancel" }; + options = new Object[] { MessageManager.getString("action.ok"), + MessageManager.getString("action.cancel") }; } - String title = newFeatures ? MessageManager.getString("label.create_new_sequence_features") - : MessageManager.formatMessage("label.amend_delete_features", new String[]{sequences[0].getName()}); + String title = create ? MessageManager + .getString("label.create_new_sequence_features") + : MessageManager.formatMessage("label.amend_delete_features", + new String[] { sequences.get(0).getName() }); - int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop, - bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION, - JOptionPane.QUESTION_MESSAGE, null, options, MessageManager.getString("action.ok")); + /* + * 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")); - jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile(); + FeaturesFile ffile = new FeaturesFile(); - if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0) + 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) { - // 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) + /* + * update default values only if creating using default values + */ + if (useLastDefaults) { - lastFeatureGroupAdded = null; + lastFeatureAdded = enteredType; + lastFeatureGroupAdded = enteredGroup; + // TODO: determine if the null feature group is valid + if (lastFeatureGroupAdded.length() < 1) + { + lastFeatureGroupAdded = null; + } } } - if (!newFeatures) + if (!create) { - SequenceFeature sf = features[featureIndex]; + SequenceFeature sf = features.get(featureIndex); - if (reply == JOptionPane.NO_OPTION) + if (reply == JvOptionPane.NO_OPTION) { - sequences[0].getDatasetSequence().deleteFeature(sf); + /* + * 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 == JOptionPane.YES_OPTION) + else if (reply == JvOptionPane.YES_OPTION) { - sf.type = lastFeatureAdded; - sf.featureGroup = lastFeatureGroupAdded; - sf.description = lastDescriptionAdded; - - setColour(sf.type, fcol); - getFeaturesDisplayed().setVisible(sf.type); - + /* + * 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 { - sf.begin = ((Integer) start.getValue()).intValue(); - sf.end = ((Integer) end.getValue()).intValue(); + newBegin = ((Integer) start.getValue()).intValue(); + newEnd = ((Integer) end.getValue()).intValue(); } catch (NumberFormatException ex) { + // JSpinner doesn't accept invalid format data :-) } - ffile.parseDescriptionHTML(sf, false); + /* + * 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, newBegin, newEnd, + enteredGroup, sf.getScore()); + sf.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 == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0) + if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0) { - for (int i = 0; i < sequences.length; i++) + for (int i = 0; i < sequences.size(); 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); + 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); } - if (lastFeatureGroupAdded != null) - { - setGroupVisibility(lastFeatureGroupAdded, true); - } - setColour(lastFeatureAdded, fcol); - setVisible(lastFeatureAdded); + setColour(enteredType, fcol); - findAllFeatures(false); + featuresAdded(); - ap.paintAlignment(true); + alignPanel.paintAlignment(true); return true; } @@ -401,37 +490,82 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere } } - ap.paintAlignment(true); + alignPanel.paintAlignment(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 col2 + * @param col */ protected void updateColourButton(JPanel bigPanel, JLabel colour, - Object col2) + FeatureColourI col) { colour.removeAll(); colour.setIcon(null); colour.setToolTipText(null); colour.setText(""); - if (col2 instanceof Color) + if (col.isSimpleColour()) { - colour.setBackground((Color) col2); + colour.setBackground(col.getColour()); } else { colour.setBackground(bigPanel.getBackground()); colour.setForeground(Color.black); - FeatureSettings.renderGraduatedColor(colour, (GraduatedColor) col2); - // colour.setForeground(colour.getBackground()); + 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); + } }