JAL-2507 capitalisation for annotation lines generated from stockholm annotation

[jalview.git] / src / jalview / io / StockholmFile.java

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 7f3f93b..c2f3683 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -820,7 +820,7 @@ public class StockholmFile extends AlignFile
     }
     boolean ss = false, posterior = false;
     type = id2type(type);
-    if (type.equals("secondary structure"))
+    if (type.equalsIgnoreCase("secondary structure"))
     {
       ss = true;
     }
@@ -1163,10 +1163,10 @@ public class StockholmFile extends AlignFile
     if (typeIds == null)
     {
       typeIds = new Hashtable();
-      typeIds.put("SS", "secondary structure");
-      typeIds.put("SA", "surface accessibility");
+      typeIds.put("SS", "Secondary Structure");
+      typeIds.put("SA", "Surface Accessibility");
       typeIds.put("TM", "transmembrane");
-      typeIds.put("PP", "posterior probability");
+      typeIds.put("PP", "Posterior Probability");
       typeIds.put("LI", "ligand binding");
       typeIds.put("AS", "active site");
       typeIds.put("IN", "intron");
@@ -1177,7 +1177,7 @@ public class StockholmFile extends AlignFile
       typeIds.put("DE", "description");
       typeIds.put("DR", "reference");
       typeIds.put("LO", "look");
-      typeIds.put("RF", "reference positions");
+      typeIds.put("RF", "Reference Positions");
 
     }
   }
@@ -1200,7 +1200,7 @@ public class StockholmFile extends AlignFile
     while (e.hasMoreElements())
     {
       Object ll = e.nextElement();
-      if (typeIds.get(ll).toString().equals(type))
+      if (typeIds.get(ll).toString().equalsIgnoreCase(type))
       {
         key = (String) ll;
         break;