- // String type;
- // SequenceFeature sf;
- SequenceI lastSeq;
- SequenceFeature[] sequenceFeatures;
- int sfSize, sfindex, spos, epos;
-
- public void drawSequence(Graphics g, SequenceI seq,
- int start, int end, int y1)
- {
- if (seq.getDatasetSequence().getSequenceFeatures() == null
- || seq.getDatasetSequence().getSequenceFeatures().length == 0)
- {
- return;
- }
-
- if (g != null)
- {
- fm = g.getFontMetrics();
- }
-
- if (av.featuresDisplayed == null
- || renderOrder == null
- || newFeatureAdded)
- {
- findAllFeatures();
- if (av.featuresDisplayed.size() < 1)
- {
- return;
- }
-
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
- sfSize = sequenceFeatures.length;
- }
-
- if (lastSeq == null || seq != lastSeq)
- {
- lastSeq = seq;
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
- sfSize = sequenceFeatures.length;
- }
-
- if (transparency != 1 && g != null)
- {
- Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(
- AlphaComposite.getInstance(
- AlphaComposite.SRC_OVER, transparency));
- }
-
- if (!offscreenRender)
- {
- spos = lastSeq.findPosition(start);
- epos = lastSeq.findPosition(end);
- }
-
- String type;
- for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
- {
- type = renderOrder[renderIndex];
-
- if (type == null || !av.featuresDisplayed.containsKey(type))
- {
- continue;
- }
-
- // loop through all features in sequence to find
- // current feature to render
- for (sfindex = 0; sfindex < sfSize; sfindex++)
- {
- if (sequenceFeatures.length <= sfindex)
- {
- continue;
- }
- if (!sequenceFeatures[sfindex].type.equals(type))
- {
- continue;
- }
-
- if (featureGroups != null
- && sequenceFeatures[sfindex].featureGroup != null
- &&
- featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
- &&
- ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
- featureGroup)).
- booleanValue())
- {
- continue;
- }
-
- if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
- || sequenceFeatures[sfindex].getEnd() < spos))
- {
- continue;
- }
-
- if (offscreenRender && offscreenImage == null)
- {
- if (sequenceFeatures[sfindex].begin <= start &&
- sequenceFeatures[sfindex].end >= start)
- {
- currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
- type);
- }
- }
- else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
- {
-
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- new Color( ( (Integer) av.featuresDisplayed.get(
- sequenceFeatures[sfindex].type)).intValue()),
- start, end, y1);
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- new Color( ( (Integer) av.featuresDisplayed.get(
- sequenceFeatures[sfindex].type)).intValue()),
- start, end, y1);
-
- }
- else
- {
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex].type),
- start, end, y1);
- }
-
- }
-
- }
-
- if (transparency != 1.0f && g != null)
- {
- Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(
- AlphaComposite.getInstance(
- AlphaComposite.SRC_OVER, 1.0f));
- }
- }
-
- char s;
- int i;
- void renderFeature(Graphics g, SequenceI seq,
- int fstart, int fend, Color featureColour, int start,
- int end, int y1)
- {
-
- if ( ( (fstart <= end) && (fend >= start)))
- {
- if (fstart < start)
- { // fix for if the feature we have starts before the sequence start,
- fstart = start; // but the feature end is still valid!!
- }
-
- if (fend >= end)
- {
- fend = end;
- }
- int pady = (y1 + av.charHeight) - av.charHeight / 5;
- for (i = fstart; i <= fend; i++)
- {
- s = seq.getCharAt(i);
-
- if (jalview.util.Comparison.isGap(s))
- {
- continue;
- }
-
- g.setColor(featureColour);
-
- g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
-
- if (offscreenRender || !av.validCharWidth)
- {
- continue;
- }
-
- g.setColor(Color.white);
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- g.drawString(String.valueOf(s),
- charOffset + (av.charWidth * (i - start)),
- pady);
-
- }
- }
- }
-
- boolean newFeatureAdded = false;
-
- public void featuresAdded()
- {
- lastSeq=null;
- findAllFeatures();
- }
-
- boolean findingFeatures = false;
- synchronized void findAllFeatures()
- {
- newFeatureAdded = false;
-
- if (findingFeatures)
- {
- newFeatureAdded = true;
- return;
- }
-
- findingFeatures = true;
- jalview.schemes.UserColourScheme ucs = new
- jalview.schemes.UserColourScheme();
-
- if (av.featuresDisplayed == null)
- {
- av.featuresDisplayed = new Hashtable();
- }
-
- av.featuresDisplayed.clear();
-
- Vector allfeatures = new Vector();
- for (int i = 0; i < av.alignment.getHeight(); i++)
- {
- SequenceFeature[] features
- = av.alignment.getSequenceAt(i).getDatasetSequence().
- getSequenceFeatures();
-
- if (features == null)
- {
- continue;
- }
-
- int index = 0;
- while (index < features.length)
- {
- if (!av.featuresDisplayed.containsKey(features[index].getType()))
- {
- if (! (features[index].begin == 0 && features[index].end == 0))
- {
- // If beginning and end are 0, the feature is for the whole sequence
- // and we don't want to render the feature in the normal way
-
- if (getColour(features[index].getType()) == null)
- {
- featureColours.put(features[index].getType(),
- ucs.createColourFromName(features[index].
- getType()));
- }
-
- av.featuresDisplayed.put(features[index].getType(),
- new Integer(getColour(features[index].
- getType()).getRGB()));
- allfeatures.addElement(features[index].getType());
- }
- }
- index++;
- }
- }
-
- renderOrder = new String[allfeatures.size()];
- Enumeration en = allfeatures.elements();
- int i = allfeatures.size() - 1;
- while (en.hasMoreElements())
- {
- renderOrder[i] = en.nextElement().toString();
- i--;
- }
-
- findingFeatures = false;
- }
-
- public Color getColour(String featureType)
- {
- Color colour = (Color) featureColours.get(featureType);
- return colour;
- }
-
- static String lastFeatureAdded;
- static String lastFeatureGroupAdded;
- static String lastDescriptionAdded;
-
- public boolean createNewFeatures(SequenceI[] sequences,
- SequenceFeature[] features)
- {
- return amendFeatures(sequences, features, true, null);
- }
-
- int featureIndex = 0;
- boolean amendFeatures(final SequenceI[] sequences,
- final SequenceFeature[] features,
- boolean newFeatures,
- final AlignmentPanel ap)
- {
- JPanel bigPanel = new JPanel(new BorderLayout());
- final JComboBox name = new JComboBox();
- final JComboBox source = new JComboBox();
- 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 JPanel colour = new JPanel();
- colour.setBorder(BorderFactory.createEtchedBorder());
- colour.setMaximumSize(new Dimension(40, 10));
- colour.addMouseListener(new MouseAdapter()
- {
- public void mousePressed(MouseEvent evt)
- {
- colour.setBackground(
- JColorChooser.showDialog(Desktop.desktop,
- "Select Feature Colour",
- colour.getBackground()));
- }
- });
-
- JPanel panel = new JPanel(new GridLayout(3, 2));
- panel.add(new JLabel("Sequence Feature Name: ", JLabel.RIGHT));
- panel.add(name);
- panel.add(new JLabel("Feature Group: ", JLabel.RIGHT));
- panel.add(source);
- panel.add(new JLabel("Feature Colour: ", JLabel.RIGHT));
- JPanel tmp = new JPanel();
- tmp.add(colour);
- colour.setPreferredSize(new Dimension(150, 15));
- panel.add(tmp);
- name.setEditable(true);
- source.setEditable(true);
-
- bigPanel.add(panel, BorderLayout.NORTH);
- panel = new JPanel();
- panel.add(new JLabel("Description: ", JLabel.RIGHT));
- description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- description.setLineWrap(true);
- panel.add(new JScrollPane(description));
-
- if (!newFeatures)
- {
- bigPanel.add(panel, BorderLayout.SOUTH);
-
- panel = new JPanel();
- panel.add(new JLabel(" Start:", JLabel.RIGHT));
- panel.add(start);
- panel.add(new JLabel(" 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
- {
- lastFeatureAdded = "Jalview";
- }
- }
-
- Enumeration en;
- if (featureGroups != null)
- {
- en = featureGroups.keys();
- while (en.hasMoreElements())
- {
- source.addItem(en.nextElement().toString());
- }
- }
-
- if (newFeatures)
- {
- if (av.featuresDisplayed != null)
- {
- en = av.featuresDisplayed.keys();
- while (en.hasMoreElements())
- {
- name.addItem(en.nextElement().toString());
- }
- }
-
- name.setSelectedItem(lastFeatureAdded);
- source.setSelectedItem(lastFeatureGroupAdded);
- description.setText(
- lastDescriptionAdded == null ?
- features[0].description : lastDescriptionAdded);
-
- if (getColour(lastFeatureAdded) != null)
- {
- colour.setBackground(getColour(lastFeatureAdded));
- }
- else
- {
- colour.setBackground(new Color(60, 160, 115));
- }
-
- }
- else if (!newFeatures)
- {
- featureIndex = 0;
- for (int f = 0; f < features.length; f++)
- {
- name.addItem(features[f].getType().toString());
- }
-
- description.setText(features[0].getDescription());
- source.setSelectedItem(features[0].getFeatureGroup());
- start.setValue(new Integer(features[0].getBegin()));
- end.setValue(new Integer(features[0].getEnd()));
- colour.setBackground(
- getColour(name.getSelectedItem().toString()));
- name.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent e)
- {
- int index = name.getSelectedIndex();
- if (index != -1)
- {
- featureIndex = index;
- description.setText(features[index].getDescription());
- source.setSelectedItem(features[index].getFeatureGroup());
- start.setValue(new Integer(features[index].getBegin()));
- end.setValue(new Integer(features[index].getEnd()));
- colour.setBackground(
- getColour(name.getSelectedItem().toString()));
-
- SearchResults highlight = new SearchResults();
- highlight.addResult(sequences[0],
- features[index].getBegin(),
- features[index].getEnd());
-
- ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
-
- }
- Color col = getColour(name.getSelectedItem().toString());
- if (col == null)
- {
- col = new
- jalview.schemes.UserColourScheme()
- .createColourFromName(name.getSelectedItem().toString());
- }
-
- colour.setBackground(col);
- }
- });
-
- }
-
- Object[] options;
- if (!newFeatures)
- {
- options = new Object[]
- {
- "Amend", "Delete", "Cancel"};
- }
- else
- {
- options = new Object[]
- {
- "OK", "Cancel"};
- }
-
- String title = newFeatures ? "Create New Sequence Feature(s)" :
- "Amend/Delete Features for "
- + sequences[0].getName();
-
- int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
- bigPanel,
- title,
- JOptionPane.YES_NO_CANCEL_OPTION,
- JOptionPane.QUESTION_MESSAGE,
- null,
- options, "OK");
-
- jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
-
- if (reply == JOptionPane.OK_OPTION
- && name.getSelectedItem() != null
- && source.getSelectedItem() != null)
- {
- //This ensures that the last sequence
- //is refreshed and new features are rendered
- lastSeq = null;
- lastFeatureAdded = name.getSelectedItem().toString();
- lastFeatureGroupAdded = source.getSelectedItem().toString();
- lastDescriptionAdded = description.getText().replaceAll("\n", " ");
- }
-
- if (!newFeatures)
- {
- SequenceFeature sf = features[featureIndex];
-
- if (reply == JOptionPane.NO_OPTION)
- {
- sequences[0].getDatasetSequence().deleteFeature(sf);
- }
- else if (reply == JOptionPane.YES_OPTION)
- {
- sf.type = lastFeatureAdded;
- sf.featureGroup = lastFeatureGroupAdded;
- sf.description = lastDescriptionAdded;
- setColour(sf.type, colour.getBackground());
- try
- {
- sf.begin = ( (Integer) start.getValue()).intValue();
- sf.end = ( (Integer) end.getValue()).intValue();
- }
- catch (NumberFormatException ex)
- {}
-
- ffile.parseDescriptionHTML(sf, false);
- }
- }
- else
- {
- if (reply == JOptionPane.OK_OPTION
- && name.getSelectedItem() != null
- && source.getSelectedItem() != null)
- {
- for (int i = 0; i < sequences.length; i++)
- {
- features[i].type = lastFeatureAdded;
- features[i].featureGroup = lastFeatureGroupAdded;
- features[i].description = lastDescriptionAdded;
- sequences[i].addSequenceFeature(features[i]);
- ffile.parseDescriptionHTML(features[i], false);
- }
-
- if (av.featuresDisplayed == null)
- {
- av.featuresDisplayed = new Hashtable();
- }
-
- if (featureGroups == null)
- {
- featureGroups = new Hashtable();
- }
-
- featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
-
- Color col = colour.getBackground();
- setColour(lastFeatureAdded, colour.getBackground());
-
- av.featuresDisplayed.put(lastFeatureGroupAdded,
- new Integer(col.getRGB()));
-
- findAllFeatures();
-
- return true;
- }
- else
- {
- return false;
- }
- }
-
- if (name.getSelectedIndex() == -1)
- {
- findAllFeatures();
- }
-
- return true;
- }
-
- public void setColour(String featureType, Color col)
- {
- featureColours.put(featureType, col);
- }
-
- public void setTransparency(float value)
- {
- transparency = value;
- }
-
- public float getTransparency()
- {
- return transparency;
- }
-
- public void setFeaturePriority(Object[][] data)