X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=61d32668fb0f91256ec03302a5cbf282857342fc;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=50a8689a587af6ccf87a8520087cbcf181edcb50;hpb=762dd65b19b26b7f6fb4583a476abfe173f37e49;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index 50a8689..61d3266 100644 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -20,40 +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.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.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; /** * DOCUMENT ME! @@ -61,8 +28,9 @@ import javax.swing.SwingConstants; * @author $author$ * @version $Revision$ */ -public class FeatureRenderer extends - jalview.renderer.seqfeatures.FeatureRenderer +public class FeatureRenderer + extends jalview.renderer.seqfeatures.FeatureRenderer + implements jalview.api.FeatureRenderer { Color resBoxColour; @@ -77,432 +45,10 @@ public class FeatureRenderer extends { super(alignPanel.av); this.ap = alignPanel; - if (alignPanel.getSeqPanel() != null - && alignPanel.getSeqPanel().seqCanvas != null - && alignPanel.getSeqPanel().seqCanvas.fr != null) - { - transferSettings(alignPanel.getSeqPanel().seqCanvas.fr); - } - } - - // // ///////////// - // // Feature Editing Dialog - // // Will be refactored in next release. - - static String lastFeatureAdded; - - static String lastFeatureGroupAdded; - - static String lastDescriptionAdded; - - 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 - * - * - * @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 features with start/end position set (if creating) - * @param create - * true to create features, false to amend or delete - * @param featureType - * the feature type to set on new features; if null, defaults to the - * type of the last new feature created if any, failing that to - * "feature_1" - * @param alignPanel - * @return - */ - protected boolean amendFeatures(final List sequences, - final List features, boolean create, - final AlignmentPanel alignPanel, String featureType) - { - - featureIndex = 0; - - final JPanel mainPanel = new JPanel(new BorderLayout()); - 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; - - @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, new FeatureColour(col)); - } - } - else - { - if (fcc == null) - { - final String ft = features.get(featureIndex).getType(); - final String type = ft == null ? lastFeatureAdded : ft; - fcc = new FeatureColourChooser(me, type); - fcc.setRequestFocusEnabled(true); - fcc.requestFocus(); - - fcc.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent e) - { - fcol = fcc.getLastColour(); - fcc = null; - 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 - */ - 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) - { - String text = sf.getType() + "/" + sf.getBegin() + "-" - + sf.getEnd() + " (" + sf.getFeatureGroup() + ")"; - overlaps.addItem(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()); - source.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); - - } - 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(source); - - 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); - } - - SequenceFeature firstFeature = features.get(0); - if (featureType != null) - { - lastFeatureAdded = featureType; - } - else - { - if (lastFeatureAdded == null) - { - if (firstFeature.type != null) - { - lastFeatureAdded = firstFeature.type; - } - else - { - lastFeatureAdded = "feature_1"; - } - } - } - - if (lastFeatureGroupAdded == null) + SeqPanel sp = alignPanel.getSeqPanel(); + if (sp != null && sp.seqCanvas != null && sp.seqCanvas.fr != null) { - if (firstFeature.featureGroup != null) - { - lastFeatureGroupAdded = firstFeature.featureGroup; - } - else - { - lastFeatureGroupAdded = "Jalview"; - } + transferSettings(sp.seqCanvas.fr); } - - if (create) - { - name.setText(lastFeatureAdded); - source.setText(lastFeatureGroupAdded); - } - else - { - name.setText(firstFeature.getType()); - source.setText(firstFeature.getFeatureGroup()); - } - - start.setValue(new Integer(firstFeature.getBegin())); - end.setValue(new Integer(firstFeature.getEnd())); - description.setText(firstFeature.getDescription()); - updateColourButton(mainPanel, colour, - (oldcol = fcol = getFeatureStyle(name.getText()))); - 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(); - - if (reply == JvOptionPane.OK_OPTION && name.getText().length() > 0) - { - 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 (!create) - { - SequenceFeature sf = features.get(featureIndex); - - if (reply == JvOptionPane.NO_OPTION) - { - /* - * NO_OPTION corresponds to the Delete button - */ - sequences.get(0).getDatasetSequence().deleteFeature(sf); - } - else if (reply == JvOptionPane.YES_OPTION) - { - /* - * YES_OPTION corresponds to the Amend button - */ - boolean typeChanged = !lastFeatureAdded.equals(sf.type); - 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); - if (typeChanged) - { - findAllFeatures(); - } - } - } - else - // NEW FEATURES ADDED - { - if (reply == JvOptionPane.OK_OPTION && lastFeatureAdded.length() > 0) - { - for (int i = 0; i < sequences.size(); i++) - { - SequenceFeature sf = features.get(i); - sf.type = lastFeatureAdded; - // fix for JAL-1538 - always set feature group here - sf.featureGroup = lastFeatureGroupAdded; - sf.description = lastDescriptionAdded; - sequences.get(i).addSequenceFeature(sf); - ffile.parseDescriptionHTML(sf, false); - } - - if (lastFeatureGroupAdded != null) - { - setGroupVisibility(lastFeatureGroupAdded, true); - } - setColour(lastFeatureAdded, fcol); - setVisible(lastFeatureAdded); - - findAllFeatures(false); - - alignPanel.paintAlignment(true); - - return true; - } - else - { - return false; - } - } - - alignPanel.paintAlignment(true); - - 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); - } - } - - /** - * 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); } }