import jalview.schemes.PIDColourScheme;\r
import jalview.schemes.PurinePyrimidineColourScheme;\r
import jalview.schemes.RNAHelicesColourChooser;\r
+import jalview.schemes.RNAInteractionColourScheme;\r
import jalview.schemes.ResidueProperties;\r
import jalview.schemes.StrandColourScheme;\r
import jalview.schemes.TCoffeeColourScheme;\r
RNAHelixColour.setEnabled(false);\r
purinePyrimidineColour.setEnabled(false);\r
}\r
+ \r
// Some JVMS send keyevents to Top frame or lowest panel,\r
// Havent worked out why yet. So add to both this frame and seqCanvas for\r
// now\r
{\r
changeColour(new PurinePyrimidineColourScheme());\r
}\r
+ else if (source == RNAInteractionColour)\r
+ {\r
+ changeColour(new RNAInteractionColourScheme());\r
+ }\r
else if (source == RNAHelixColour)\r
{\r
new RNAHelicesColourChooser(viewport, alignPanel);\r
MenuItem buriedColour = new MenuItem();\r
\r
MenuItem purinePyrimidineColour = new MenuItem();\r
+ MenuItem RNAInteractionColour = new MenuItem();\r
MenuItem RNAHelixColour = new MenuItem();\r
\r
MenuItem userDefinedColour = new MenuItem();\r
buriedColour.addActionListener(this);\r
purinePyrimidineColour.setLabel("Purine/Pyrimidine");\r
purinePyrimidineColour.addActionListener(this);\r
+ RNAInteractionColour.setLabel("Purine/Pyrimidine");\r
+ RNAInteractionColour.addActionListener(this);\r
RNAHelixColour.setLabel("by RNA Helices");\r
RNAHelixColour.addActionListener(this);\r
userDefinedColour.setLabel("User Defined...");\r
colourMenu.add(buriedColour);\r
colourMenu.add(nucleotideColour);\r
colourMenu.add(purinePyrimidineColour);\r
+ colourMenu.add(RNAInteractionColour);\r
colourMenu.add(tcoffeeColour);\r
colourMenu.add(userDefinedColour);\r
colourMenu.addSeparator();\r
* @throws ExceptionFileFormatOrSyntax \r
* @throws ExceptionLoadingFailed \r
* @throws ExceptionPermissionDenied \r
+ * @throws InterruptedException \r
*/\r
- public boolean loadScoreFile( String source ) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed {\r
+ public boolean loadScoreFile( String source ) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException {\r
\r
TCoffeeScoreFile file = new TCoffeeScoreFile(source, AppletFormatAdapter.checkProtocol(source));\r
if( !file.isValid()) {\r