+ }\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
+ av.featuresDisplayed = new Hashtable();\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().getSequenceFeatures();\r
+\r
+ if (features == null)\r
+ continue;\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
+\r
+ static String lastFeatureAdded;\r
+ static String lastFeatureGroupAdded;\r
+ static String lastDescriptionAdded;\r
+\r
+ public boolean createNewFeatures(SequenceI[] sequences,\r
+ SequenceFeature [] features)\r
+ {\r
+\r
+ JPanel bigPanel = new JPanel(new BorderLayout());\r
+ JComboBox name = new JComboBox();\r
+ JComboBox source = new JComboBox();\r
+ JTextArea description = new JTextArea(3,25);\r
+\r
+ JPanel panel = new JPanel(new GridLayout(2, 2));\r
+ panel.add(new JLabel("New Sequence Feature Name: ",JLabel.RIGHT));\r
+ panel.add(name);\r
+ panel.add(new JLabel("Feature Group: ", JLabel.RIGHT));\r
+ panel.add(source);\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
+ bigPanel.add(panel, BorderLayout.CENTER);\r
+\r
+\r
+ Enumeration en;\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
+ if (featureGroups != null)\r
+ {\r
+ en = featureGroups.keys();\r
+ while (en.hasMoreElements())\r
+ {\r
+ source.addItem(en.nextElement().toString());\r
+ }\r
+ }\r
+\r
+ if (lastFeatureAdded == null)\r
+ if (features[0].type != null)\r
+ lastFeatureAdded = features[0].type;\r
+ else\r
+ lastFeatureAdded = "feature_1";\r
+\r
+ if (lastFeatureGroupAdded == null)\r
+ if (features[0].featureGroup != null)\r
+ lastFeatureGroupAdded = features[0].featureGroup;\r
+ else\r
+ lastFeatureAdded = "Jalview";\r
+\r
+\r
+ name.setSelectedItem(lastFeatureAdded);\r
+ source.setSelectedItem(lastFeatureGroupAdded);\r
+ description.setText(\r
+ lastDescriptionAdded == null ?\r
+ features[0].description : lastDescriptionAdded);\r
+\r
+\r
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
+ bigPanel, "Create New Sequence Feature(s)",\r
+ JOptionPane.OK_CANCEL_OPTION);\r
+\r
+\r
+ if(reply==JOptionPane.OK_OPTION\r
+ && name.getSelectedItem()!=null\r
+ && source.getSelectedItem()!=null)\r
+ {\r
+ lastFeatureAdded = name.getSelectedItem().toString();\r
+ lastFeatureGroupAdded = source.getSelectedItem().toString();\r
+ lastDescriptionAdded = description.getText().replaceAll("\n"," ");\r
+\r
+ jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();\r
+\r
+\r
+ for(int i=0; i<sequences.length; i++)\r
+ {\r
+ features[i].type = lastFeatureAdded;\r
+ features[i].featureGroup = lastFeatureGroupAdded;\r
+ features[i].description = lastDescriptionAdded;\r
+ sequences[i].addSequenceFeature(features[i]);\r
+ ffile.parseDescriptionHTML(features[i], false);\r