+ renderFeature(g, seq,\r
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
+ getColour(sequenceFeatures[sfindex].type),\r
+ start, end, y1);\r
+ }\r
+\r
+ }\r
+\r
+ }\r
+\r
+ if (transparency != 1.0f && g != null)\r
+ {\r
+ Graphics2D g2 = (Graphics2D) g;\r
+ g2.setComposite(\r
+ AlphaComposite.getInstance(\r
+ AlphaComposite.SRC_OVER, 1.0f));\r
+ }\r
+ }\r
+\r
+ char s;\r
+ int i;\r
+ void renderFeature(Graphics g, SequenceI seq,\r
+ int fstart, int fend, Color featureColour, int start,\r
+ int end, int y1)\r
+ {\r
+\r
+ if ( ( (fstart <= end) && (fend >= start)))\r
+ {\r
+ if (fstart < start)\r
+ { // fix for if the feature we have starts before the sequence start,\r
+ fstart = start; // but the feature end is still valid!!\r
+ }\r
+\r
+ if (fend >= end)\r
+ {\r
+ fend = end;\r
+ }\r
+ int pady = (y1 + av.charHeight) - av.charHeight / 5;\r
+ for (i = fstart; i <= fend; i++)\r
+ {\r
+ s = seq.getCharAt(i);\r
+\r
+ if (jalview.util.Comparison.isGap(s))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ g.setColor(featureColour);\r
+\r
+ g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);\r
+\r
+ if (offscreenRender || !av.validCharWidth)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ g.setColor(Color.white);\r
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
+ g.drawString(String.valueOf(s),\r
+ charOffset + (av.charWidth * (i - start)),\r
+ pady);\r
+\r
+ }\r
+ }\r
+ }\r
+\r
+ boolean newFeatureAdded = false;\r
+\r
+ public void featuresAdded()\r
+ {\r
+ findAllFeatures();\r
+ }\r
+\r
+ boolean findingFeatures = false;\r
+ synchronized void findAllFeatures()\r
+ {\r
+ newFeatureAdded = false;\r
+\r
+ if (findingFeatures)\r
+ {\r
+ newFeatureAdded = true;\r
+ return;\r
+ }\r
+\r
+ findingFeatures = true;\r
+ jalview.schemes.UserColourScheme ucs = new\r
+ jalview.schemes.UserColourScheme();\r
+\r
+ if (av.featuresDisplayed == null)\r
+ {\r
+ av.featuresDisplayed = new Hashtable();\r
+ }\r
+\r
+ av.featuresDisplayed.clear();\r
+\r
+ Vector allfeatures = new Vector();\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ {\r
+ SequenceFeature[] features\r
+ = av.alignment.getSequenceAt(i).getDatasetSequence().\r
+ getSequenceFeatures();\r
+\r
+ if (features == null)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ int index = 0;\r
+ while (index < features.length)\r
+ {\r
+ if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
+ {\r
+ if (! (features[index].begin == 0 && features[index].end == 0))\r
+ {\r
+ // If beginning and end are 0, the feature is for the whole sequence\r
+ // and we don't want to render the feature in the normal way\r
+\r
+ if (getColour(features[index].getType()) == null)\r
+ {\r
+ featureColours.put(features[index].getType(),\r
+ ucs.createColourFromName(features[index].\r
+ getType()));\r
+ }\r
+\r
+ av.featuresDisplayed.put(features[index].getType(),\r
+ new Integer(getColour(features[index].\r
+ getType()).getRGB()));\r
+ allfeatures.addElement(features[index].getType());\r
+ }\r
+ }\r
+ index++;\r
+ }\r
+ }\r
+\r
+ renderOrder = new String[allfeatures.size()];\r
+ Enumeration en = allfeatures.elements();\r
+ int i = allfeatures.size() - 1;\r
+ while (en.hasMoreElements())\r
+ {\r
+ renderOrder[i] = en.nextElement().toString();\r
+ i--;\r
+ }\r
+\r
+ findingFeatures = false;\r
+ }\r
+\r
+ public Color getColour(String featureType)\r
+ {\r
+ Color colour = (Color) featureColours.get(featureType);\r
+ return colour;\r
+ }\r
+\r
+ static String lastFeatureAdded;\r
+ static String lastFeatureGroupAdded;\r
+ static String lastDescriptionAdded;\r
+\r
+ public boolean createNewFeatures(SequenceI[] sequences,\r
+ SequenceFeature[] features)\r
+ {\r
+ return amendFeatures(sequences, features, true, null);\r
+ }\r
+\r
+ int featureIndex = 0;\r
+ boolean amendFeatures(final SequenceI[] sequences,\r
+ final SequenceFeature[] features,\r
+ boolean newFeatures,\r
+ final AlignmentPanel ap)\r
+ {\r
+ JPanel bigPanel = new JPanel(new BorderLayout());\r
+ final JComboBox name = new JComboBox();\r
+ final JComboBox source = new JComboBox();\r
+ final JTextArea description = new JTextArea(3, 25);\r
+ final JSpinner start = new JSpinner();\r
+ final JSpinner end = new JSpinner();\r
+ start.setPreferredSize(new Dimension(80, 20));\r
+ end.setPreferredSize(new Dimension(80, 20));\r
+ final JPanel colour = new JPanel();\r
+ colour.setBorder(BorderFactory.createEtchedBorder());\r
+ colour.setMaximumSize(new Dimension(40, 10));\r
+ colour.addMouseListener(new MouseAdapter()\r
+ {\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ colour.setBackground(\r
+ JColorChooser.showDialog(Desktop.desktop,\r
+ "Select Feature Colour",\r
+ colour.getBackground()));\r
+ }\r
+ });\r
+\r
+ JPanel panel = new JPanel(new GridLayout(3, 2));\r
+ panel.add(new JLabel("Sequence Feature Name: ", JLabel.RIGHT));\r
+ panel.add(name);\r
+ panel.add(new JLabel("Feature Group: ", JLabel.RIGHT));\r
+ panel.add(source);\r
+ panel.add(new JLabel("Feature Colour: ", JLabel.RIGHT));\r
+ JPanel tmp = new JPanel();\r
+ tmp.add(colour);\r
+ colour.setPreferredSize(new Dimension(150, 15));\r
+ panel.add(tmp);\r
+ name.setEditable(true);\r
+ source.setEditable(true);\r
+\r
+ bigPanel.add(panel, BorderLayout.NORTH);\r
+ panel = new JPanel();\r
+ panel.add(new JLabel("Description: ", JLabel.RIGHT));\r
+ description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ description.setLineWrap(true);\r
+ panel.add(new JScrollPane(description));\r
+\r
+ if (!newFeatures)\r
+ {\r
+ bigPanel.add(panel, BorderLayout.SOUTH);\r
+\r
+ panel = new JPanel();\r
+ panel.add(new JLabel(" Start:", JLabel.RIGHT));\r
+ panel.add(start);\r
+ panel.add(new JLabel(" End:", JLabel.RIGHT));\r
+ panel.add(end);\r
+ bigPanel.add(panel, BorderLayout.CENTER);\r
+ }\r
+ else\r
+ {\r
+ bigPanel.add(panel, BorderLayout.CENTER);\r
+ }\r
+\r
+ if (lastFeatureAdded == null)\r
+ {\r
+ if (features[0].type != null)\r
+ {\r
+ lastFeatureAdded = features[0].type;\r
+ }\r
+ else\r
+ {\r
+ lastFeatureAdded = "feature_1";\r
+ }\r
+ }\r
+\r
+ if (lastFeatureGroupAdded == null)\r
+ {\r
+ if (features[0].featureGroup != null)\r
+ {\r
+ lastFeatureGroupAdded = features[0].featureGroup;\r
+ }\r
+ else\r
+ {\r
+ lastFeatureAdded = "Jalview";\r
+ }\r
+ }\r
+\r
+ Enumeration en;\r
+ if (featureGroups != null)\r
+ {\r
+ en = featureGroups.keys();\r
+ while (en.hasMoreElements())\r
+ {\r
+ source.addItem(en.nextElement().toString());\r
+ }\r
+ }\r
+\r
+ if (newFeatures)\r
+ {\r
+ if (av.featuresDisplayed != null)\r
+ {\r
+ en = av.featuresDisplayed.keys();\r
+ while (en.hasMoreElements())\r
+ {\r
+ name.addItem(en.nextElement().toString());\r
+ }\r
+ }\r
+\r
+ name.setSelectedItem(lastFeatureAdded);\r
+ source.setSelectedItem(lastFeatureGroupAdded);\r
+ description.setText(\r
+ lastDescriptionAdded == null ?\r
+ features[0].description : lastDescriptionAdded);\r
+\r
+ if (getColour(lastFeatureAdded) != null)\r
+ {\r
+ colour.setBackground(getColour(lastFeatureAdded));\r
+ }\r
+ else\r
+ {\r
+ colour.setBackground(new Color(60, 160, 115));\r
+ }\r
+\r
+ }\r
+ else if (!newFeatures)\r
+ {\r
+ featureIndex = 0;\r
+ for (int f = 0; f < features.length; f++)\r
+ {\r
+ name.addItem(features[f].getType().toString());\r
+ }\r
+\r
+ description.setText(features[0].getDescription());\r
+ source.setSelectedItem(features[0].getFeatureGroup());\r
+ start.setValue(new Integer(features[0].getBegin()));\r
+ end.setValue(new Integer(features[0].getEnd()));\r
+ colour.setBackground(\r
+ getColour(name.getSelectedItem().toString()));\r
+ name.addItemListener(new ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent e)\r
+ {\r
+ int index = name.getSelectedIndex();\r
+ if (index != -1)\r