JAL-4392 Print annotations

Added colour by secondary structure conservation threshold to the output
file

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 7e4ee16..66c620b 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -569,6 +569,12 @@ public class AnnotationFile
           text.append("pidThreshold=");
           text.append(sg.cs.getThreshold());
         }
+        if (sg.cs.isConsensusSecondaryStructureColouring())
+        {
+          text.append("secondaryStructureConservationThreshold=");
+          text.append(sg.cs.getConsensusSecondaryStructureThreshold());
+          text.append("\t");
+        }
         if (sg.cs.conservationApplied())
         {
           text.append("consThreshold=");
@@ -1601,6 +1607,12 @@ public class AnnotationFile
         sg.cs.setThreshold(Integer.parseInt(value), true);
 
       }
+      else if(key.equalsIgnoreCase("secondaryStructureConservationThreshold")) 
+      {
+        sg.cs.setConsensusSecondaryStructureThreshold(Integer.parseInt(value));
+        sg.cs.setConsensusSecondaryStructureColouring(true);
+        
+      }
       else if (key.equalsIgnoreCase("consThreshold"))
       {
         sg.cs.setConservationInc(Integer.parseInt(value));