(JAL-885) RNA helix and purine pyrimidine colouring styles in applet

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 3ebc083..ea5ead8 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -131,7 +131,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }\r
 \r
     }\r
-\r
+    if (viewport.getAlignment().isNucleotide())\r
+    {\r
+      viewport.updateStrucConsensus(alignPanel);\r
+      if (viewport.getAlignment().hasRNAStructure())\r
+      {\r
+        RNAHelixColour.setEnabled(true);\r
+      }\r
+      else {\r
+        RNAHelixColour.setEnabled(false);\r
+      }\r
+    } else {\r
+      RNAHelixColour.setEnabled(false);\r
+      purinePyrimidineColour.setEnabled(false);\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
@@ -919,6 +932,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {\r
       changeColour(new NucleotideColourScheme());\r
     }\r
+    else if (source == purinePyrimidineColour)\r
+    {\r
+      changeColour(new PurinePyrimidineColourScheme());\r
+    }\r
+    else if (source == RNAHelixColour)\r
+    {\r
+      new RNAHelicesColourChooser(viewport, alignPanel);\r
+    }\r
     else if (source == modifyPID)\r
     {\r
       modifyPID_actionPerformed();\r
@@ -2774,6 +2795,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 \r
   MenuItem buriedColour = new MenuItem();\r
 \r
+  MenuItem purinePyrimidineColour = new MenuItem();\r
+  MenuItem RNAHelixColour = new MenuItem();\r
+  \r
   MenuItem userDefinedColour = new MenuItem();\r
 \r
   MenuItem PIDColour = new MenuItem();\r
@@ -2962,6 +2986,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     turnColour.addActionListener(this);\r
     buriedColour.setLabel("Buried Index");\r
     buriedColour.addActionListener(this);\r
+    purinePyrimidineColour.setLabel("Purine/Pyrimidine");\r
+    purinePyrimidineColour.addActionListener(this);\r
+    RNAHelixColour.setLabel("by RNA Helices");\r
+    RNAHelixColour.addActionListener(this);\r
     userDefinedColour.setLabel("User Defined...");\r
     userDefinedColour.addActionListener(this);\r
     PIDColour.setLabel("Percentage Identity");\r
@@ -3175,6 +3203,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     colourMenu.add(turnColour);\r
     colourMenu.add(buriedColour);\r
     colourMenu.add(nucleotideColour);\r
+    colourMenu.add(purinePyrimidineColour);\r
     colourMenu.add(userDefinedColour);\r
     colourMenu.addSeparator();\r
     colourMenu.add(conservationMenuItem);\r
@@ -3182,6 +3211,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     colourMenu.add(abovePIDThreshold);\r
     colourMenu.add(modifyPID);\r
     colourMenu.add(annotationColour);\r
+    colourMenu.add(RNAHelixColour);\r
     calculateMenu.add(sort);\r
     calculateMenu.add(calculate);\r
     calculateMenu.addSeparator();\r