X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=b33ada2c6320ea03b34dc1d32940f1ec79b65c32;hb=9c007fa50a82b3ae0f987e6454ae17c941b63563;hp=89e94c8ebfb2ae53588086470d7be50ab5c6a2c7;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index 89e94c8..b33ada2 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 2.9) - * Copyright (C) 2015 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; @@ -37,11 +41,14 @@ 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.HashMap; +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; @@ -56,29 +63,26 @@ import javax.swing.SwingConstants; * @version $Revision$ */ public class FeatureRenderer extends - jalview.renderer.seqfeatures.FeatureRenderer implements - jalview.api.FeatureRenderer + jalview.renderer.seqfeatures.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) + 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); } } @@ -92,19 +96,42 @@ public class FeatureRenderer extends static String lastDescriptionAdded; - Object oldcol, fcol; + FeatureColourI oldcol, fcol; int featureIndex = 0; - boolean amendFeatures(final SequenceI[] sequences, - final SequenceFeature[] features, boolean newFeatures, - final AlignmentPanel ap) + /** + * 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 bigPanel = new JPanel(new BorderLayout()); - final JComboBox overlaps; + 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); @@ -121,25 +148,26 @@ public class FeatureRenderer extends { 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)); + fcol.getColour()); if (col != null) { - fcol = col; - updateColourButton(bigPanel, colour, col); + fcol = new FeatureColour(col); + updateColourButton(mainPanel, colour, new FeatureColour(col)); } } 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(); @@ -147,12 +175,13 @@ public class FeatureRenderer extends 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); } }); @@ -160,79 +189,84 @@ public class FeatureRenderer extends } } }); - 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()); + source.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(source); - 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); @@ -240,50 +274,59 @@ public class FeatureRenderer extends 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); + startEndPanel.add(end); + mainPanel.add(startEndPanel, BorderLayout.CENTER); } else { - bigPanel.add(panel, BorderLayout.CENTER); + mainPanel.add(descriptionPanel, BorderLayout.CENTER); } - if (lastFeatureAdded == null) + SequenceFeature firstFeature = features.get(0); + if (featureType != null) { - if (features[0].type != null) - { - lastFeatureAdded = features[0].type; - } - else + lastFeatureAdded = featureType; + } + else + { + if (lastFeatureAdded == null) { - lastFeatureAdded = "feature_1"; + if (firstFeature.type != null) + { + lastFeatureAdded = firstFeature.type; + } + else + { + lastFeatureAdded = "feature_1"; + } } } if (lastFeatureGroupAdded == null) { - if (features[0].featureGroup != null) + if (firstFeature.featureGroup != null) { - lastFeatureGroupAdded = features[0].featureGroup; + lastFeatureGroupAdded = firstFeature.featureGroup; } else { @@ -291,49 +334,52 @@ public class FeatureRenderer extends } } - if (newFeatures) + if (create) { name.setText(lastFeatureAdded); source.setText(lastFeatureGroupAdded); } else { - name.setText(features[0].getType()); - source.setText(features[0].getFeatureGroup()); + name.setText(firstFeature.getType()); + source.setText(firstFeature.getFeatureGroup()); } - start.setValue(new Integer(features[0].getBegin())); - end.setValue(new Integer(features[0].getEnd())); - description.setText(features[0].getDescription()); - updateColourButton(bigPanel, colour, + 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 (!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 + String title = create ? 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, + 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")); - jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile(); + FeaturesFile ffile = new FeaturesFile(); - if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0) + if (reply == JvOptionPane.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", " "); @@ -344,47 +390,85 @@ public class FeatureRenderer extends } } - 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); } - 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 + */ + boolean typeChanged = !lastFeatureAdded.equals(sf.type); + String newType = lastFeatureAdded; + String newFeatureGroup = lastFeatureGroupAdded; + String newDescription = lastDescriptionAdded; + + setColour(newType, fcol); + getFeaturesDisplayed().setVisible(newType); + 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 :-) + } + + /* + * 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(newType, + newDescription, newBegin, newEnd, sf.getScore(), + newFeatureGroup); + // ensure any additional properties are copied + if (sf.otherDetails != null) + { + newSf.otherDetails = new HashMap(sf.otherDetails); + } + ffile.parseDescriptionHTML(newSf, false); + // add any additional links not parsed from description + if (sf.links != null) + { + for (String link : sf.links) + { + newSf.addLink(link); + } } + // amend features only gets one sequence to act on + sequences.get(0).addSequenceFeature(newSf); - ffile.parseDescriptionHTML(sf, false); + if (typeChanged) + { + findAllFeatures(); + } } } else // NEW FEATURES ADDED { - if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0) + if (reply == JvOptionPane.OK_OPTION && lastFeatureAdded.length() > 0) { - for (int i = 0; i < sequences.length; i++) + for (int i = 0; i < sequences.size(); i++) { - features[i].type = lastFeatureAdded; + SequenceFeature sf = features.get(i); + sf.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); + sf.featureGroup = lastFeatureGroupAdded; + sf.description = lastDescriptionAdded; + sequences.get(i).addSequenceFeature(sf); + ffile.parseDescriptionHTML(sf, false); } if (lastFeatureGroupAdded != null) @@ -396,7 +480,7 @@ public class FeatureRenderer extends findAllFeatures(false); - ap.paintAlignment(true); + alignPanel.paintAlignment(true); return true; } @@ -406,7 +490,7 @@ public class FeatureRenderer extends } } - ap.paintAlignment(true); + alignPanel.paintAlignment(true); return true; } @@ -416,26 +500,36 @@ public class FeatureRenderer extends * * @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); + } }