last version stay many bugs ..

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 4948613..01227a6 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -52,6 +52,7 @@ import jalview.schemes.NucleotideColourScheme;
 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
@@ -92,6 +93,15 @@ import java.util.List;
 import java.util.StringTokenizer;\r
 import java.util.Vector;\r
 \r
+import javax.xml.parsers.ParserConfigurationException;\r
+\r
+import org.xml.sax.SAXException;\r
+\r
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;\r
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;\r
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;\r
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;\r
+\r
 public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemListener, KeyListener\r
 {\r
   public AlignmentPanel alignPanel;\r
@@ -203,6 +213,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
       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
@@ -1001,6 +1012,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     {\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
@@ -2775,6 +2790,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   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
@@ -2970,6 +2986,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     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
@@ -3188,6 +3206,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     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
@@ -3625,8 +3644,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
    * @param source File/URL/T-COFFEE score file contents\r
    * @throws IOException\r
    * @return true if alignment was annotated with data from source\r
+ * @throws SAXException \r
+ * @throws ParserConfigurationException \r
+ * @throws ExceptionFileFormatOrSyntax \r
+ * @throws ExceptionLoadingFailed \r
+ * @throws ExceptionPermissionDenied \r
+ * @throws InterruptedException \r
+ * @throws ExceptionUnmatchedClosingParentheses \r
    */\r
-  public boolean loadScoreFile( String source ) throws IOException {\r
+  public boolean loadScoreFile( String source ) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {\r
 \r
     TCoffeeScoreFile file = new TCoffeeScoreFile(source, AppletFormatAdapter.checkProtocol(source));\r
          if( !file.isValid()) {\r