Merge branch 'develop' into merged_2_11_2_0_to_2_12

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

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index a850ff1..a4bc631 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -58,8 +58,6 @@ import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
 import fr.orsay.lri.varna.factories.RNAFactory;
 import fr.orsay.lri.varna.models.rna.RNA;
 
-// import org.apache.log4j.*;
-
 /**
  * This class is supposed to parse a Stockholm format file into Jalview There
  * are TODOs in this class: we do not know what the database source and version
@@ -138,7 +136,7 @@ public class StockholmFile extends AlignFile
         pat = "(<|>|\\[|\\]|\\(|\\)|\\{|\\})";
         break;
       case REGEX_NOT_RNASS:
-        pat = "^[^<>[\\](){}A-DF-Za-df-z]*$";
+        pat = "^[^<>[\\](){}ADFJ-RUVWYZadfj-ruvwyz]*$"; // update 2.11.2
         break;
       case REGEX_ANNOTATION:
         pat = "(\\w+)\\s*(.*)";
@@ -332,7 +330,7 @@ public class StockholmFile extends AlignFile
     Regex closeparen = getRegex(REGEX_CLOSE_PAREN);//"(>|\\])", ")");
 
 //    // Detect if file is RNA by looking for bracket types
-    // Regex detectbrackets = getRegex("(<|>|\\[|\\]|\\(|\\))");
+//    Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
 
     rend.optimize();
     p.optimize();
@@ -1204,7 +1202,7 @@ public class StockholmFile extends AlignFile
         }
         else
         {
-          key = type2id(aa.label.toLowerCase());
+          key = type2id(aa.label.toLowerCase(Locale.ROOT));
           if (key == null)
           {
             label = aa.label;