fix for JAL-686 - don't trim spaces before creating annotation

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 9cc3b55..f866928 100755 (executable)
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -76,14 +76,14 @@ public class FastaFile extends AlignFile
     StringBuffer sb = new StringBuffer();
     boolean firstLine = true;
 
-    String line;
+    String line,uline;
     Sequence seq = null;
 
     boolean annotation = false;
 
-    while ((line = nextLine()) != null)
+    while ((uline = nextLine()) != null)
     {
-      line = line.trim();
+      line = uline.trim();
       if (line.length() > 0)
       {
         if (line.charAt(0) == '>')
@@ -132,7 +132,7 @@ public class FastaFile extends AlignFile
         }
         else
         {
-          sb.append(line);
+          sb.append(annotation ? uline : line);
         }
       }
     }