JAL-3026 srcjar files for VARNA and log4j

[jalview.git] / srcjar / fr / orsay / lri / varna / models / templates / RNANodeValueTemplateBrokenBasePair.java

diff --git a/srcjar/fr/orsay/lri/varna/models/templates/RNANodeValueTemplateBrokenBasePair.java b/srcjar/fr/orsay/lri/varna/models/templates/RNANodeValueTemplateBrokenBasePair.java
new file mode 100644 (file)
index 0000000..efa1679
--- /dev/null
+++ b/srcjar/fr/orsay/lri/varna/models/templates/RNANodeValueTemplateBrokenBasePair.java
@@ -0,0 +1,47 @@
+package fr.orsay.lri.varna.models.templates;
+
+import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix;
+
+/**
+ * See RNANodeValueTemplate.
+ * 
+ * @author Raphael Champeimont
+ */
+public class RNANodeValueTemplateBrokenBasePair extends RNANodeValueTemplate {
+       
+       /**
+        * The original template element this node came from.
+        */
+       private RNATemplateHelix helix;
+
+       /**
+        * The position (in the 5' to 3' order)
+        * of this base in the original helix.
+        */
+       private int positionInHelix;
+       
+       
+       
+       public String toGraphvizNodeName() {
+               return "BH[" + positionInHelix + "]";
+       }
+       
+       
+       
+       public RNATemplateHelix getHelix() {
+               return helix;
+       }
+
+       public void setHelix(RNATemplateHelix helix) {
+               this.helix = helix;
+       }
+
+       public int getPositionInHelix() {
+               return positionInHelix;
+       }
+
+       public void setPositionInHelix(int positionInHelix) {
+               this.positionInHelix = positionInHelix;
+       }
+       
+}