-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import java.awt.*;\r
-import java.util.*;\r
-\r
-public class FeatureRenderer implements RendererI\r
-{\r
- AlignViewport av;\r
-\r
- SequenceGroup currentSequenceGroup = null;\r
- SequenceGroup [] allGroups = null;\r
- Color resBoxColour;\r
- Graphics graphics;\r
-\r
- public FeatureRenderer(AlignViewport av)\r
- {\r
- this.av = av;\r
- }\r
-\r
-\r
- public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height, Vector pid, int seqnum)\r
- {\r
- Vector features = seq.getSequenceFeatures();\r
- Enumeration e = features.elements();\r
- while( e.hasMoreElements() )\r
- {\r
- SequenceFeature sf = (SequenceFeature)e.nextElement();\r
- int fstart = seq.findIndex(sf.getStart())-1;\r
- int fend = seq.findIndex(sf.getEnd())-1;\r
-\r
- if( (fstart<=end && fend>=start) )\r
- {\r
- if(fstart<0) // fix for if the feature we have starts before the sequence start,\r
- fstart = 0;// but the feature end is still valid!!\r
-\r
- if(fstart==fend)\r
- {\r
- g.setColor(Color.red);\r
- g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4);\r
- g.setColor(Color.white);\r
-\r
- char s = seq.getSequence().charAt(fstart);\r
- FontMetrics fm = g.getFontMetrics();\r
- int charOffset = (width - fm.charWidth(s))/2;\r
- int pady = height/5;\r
- g.drawString(String.valueOf(s), charOffset + x1 + width * (fstart - start), y1 + height - pady);\r
-\r
- }\r
- else\r
- {\r
- for (int i = fstart; i <= fend; i++)\r
- {\r
- g.setColor(Color.blue);\r
- g.fillRect( (i-start) * width, y1, width, height);\r
-\r
- g.setColor(Color.white);\r
- char s = seq.getSequence().charAt(i);\r
- FontMetrics fm = g.getFontMetrics();\r
- int charOffset = (width - fm.charWidth(s)) / 2;\r
- int pady = height / 5;\r
- g.drawString(String.valueOf(s),\r
- charOffset + x1 + width * (i-start),\r
- y1 + height - pady);\r
- }\r
- }\r
- }\r
-\r
- }\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+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 $Revision$
+ */
+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
+ *
+ * @param alignPanel
+ */
+ public FeatureRenderer(AlignmentPanel alignPanel)
+ {
+ super(alignPanel.av);
+ this.ap = alignPanel;
+ if (alignPanel.getSeqPanel() != null
+ && alignPanel.getSeqPanel().seqCanvas != null
+ && alignPanel.getSeqPanel().seqCanvas.fr != null)
+ {
+ 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
+ * <ul>
+ * <li>double-click on a sequence - Amend/Delete features at position</li>
+ * <li>Create sequence feature from pop-up menu on selected region</li>
+ * <li>Create features for pattern matches from Find</li>
+ * </ul>
+ * 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<SequenceI> sequences,
+ final List<SequenceFeature> 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<String> overlaps = new JComboBox<>();
+ List<String> 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() });
+
+ /*
+ * 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<String> order)
+ {
+ Arrays.sort(renderOrder, order);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff