Add support RNAML format

[jalview.git] / src / jalview / datamodel / SecondaryStructureAnnotation.java

diff --git a/src/jalview/datamodel/SecondaryStructureAnnotation.java b/src/jalview/datamodel/SecondaryStructureAnnotation.java
new file mode 100644 (file)
index 0000000..5c3eae9
--- /dev/null
+++ b/src/jalview/datamodel/SecondaryStructureAnnotation.java
@@ -0,0 +1,31 @@
+package jalview.datamodel;
+
+import fr.orsay.lri.varna.models.rna.RNA;
+
+public class SecondaryStructureAnnotation extends AlignmentAnnotation
+{
+       
+
+       private static RNA _rna = null;
+         public SecondaryStructureAnnotation (RNA rna) 
+         {
+                super("Secondary Structure", "Un truc trop cool",getAnnotation(rna));
+                
+           
+           _rna = rna;
+         }
+       
+         public RNA getRNA()
+        {
+                 return _rna;
+        }
+         public static Annotation[] getAnnotation(RNA rna) 
+         {
+                 Annotation[] ann =  new Annotation[rna.getSize()];
+                        for(int i=0;i<ann.length;i++)
+                        {      
+                                ann[i] = new Annotation(_rna.getStructDBN(true), "", ' ', 0f);; 
+                        }
+                 return ann;
+         }
+}