Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

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

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 50112c8..a850ff1 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -48,6 +48,7 @@ import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Vector;
 
@@ -88,7 +89,6 @@ public class StockholmFile extends AlignFile
   public static final int REGEX_STOCKHOLM = 0;
 
   public static final int REGEX_BRACKETS = 1;
-
   // use the following regex to decide an annotations (whole) line is NOT an RNA
   // SS (it contains only E,H,e,h and other non-brace/non-alpha chars)
   public static final int REGEX_NOT_RNASS = 2;
@@ -932,7 +932,6 @@ public class StockholmFile extends AlignFile
     type = id2type(type);
 
     boolean isrnass = false;
-
     if (type.equalsIgnoreCase("secondary structure"))
     {
       ss = true;
@@ -950,6 +949,7 @@ public class StockholmFile extends AlignFile
     for (int i = 0; i < annots.length(); i++)
     {
       String pos = annots.substring(i, i + 1);
+      // TODO 2.12 release: verify this Stockholm IO behaviour change in release notes
       if (UNDERSCORE == pos.charAt(0))
       {
         pos = " ";
@@ -1039,7 +1039,6 @@ public class StockholmFile extends AlignFile
     return ref.getSource().toString() + " ; "
             + ref.getAccessionId().toString();
   }
-
   @Override
   public String print(SequenceI[] s, boolean jvSuffix)
   {
@@ -1145,6 +1144,7 @@ public class StockholmFile extends AlignFile
         Annotation[] ann;
         for (int j = 0; j < alAnot.length; j++)
         {
+
           if (alAnot[j].annotations != null)
           {
             String key = type2id(alAnot[j].label);
@@ -1174,7 +1174,6 @@ public class StockholmFile extends AlignFile
             out.append(newline);
          }
         }
-
       }
 
       out.append(new Format("%-" + maxid + "s")
@@ -1239,7 +1238,6 @@ public class StockholmFile extends AlignFile
     return out.toString();
   }
 
-
   /**
    * add an annotation character to the output row
    * 
@@ -1364,6 +1362,7 @@ public class StockholmFile extends AlignFile
 
     }
   }
+
   
   protected static String id2type(String id)
   {