Make a new FeatureRenderer

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

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index f933961..1dafb91 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -48,24 +48,6 @@ public abstract class AlignFile extends FileParse
     {\r
     }\r
 \r
-    /**\r
-     * Creates a new AlignFile object.\r
-     *\r
-     * @param inStr DOCUMENT ME!\r
-     */\r
-    public AlignFile(String inStr)\r
-    {\r
-        initData();\r
-        System.out.println("is this ever called??");\r
-\r
-        try\r
-        {\r
-            parse();\r
-        }\r
-        catch (Exception ex)\r
-        {\r
-        }\r
-    }\r
 \r
     /**\r
      * Constructor which parses the data from a file of some specified type.\r
@@ -135,12 +117,15 @@ public abstract class AlignFile extends FileParse
             if (!jalview.schemes.ResidueProperties.aaHash.containsKey(\r
                         String.valueOf(sequence.charAt(i))))\r
             {\r
+                invalidCharacter = sequence.charAt(i);\r
                 return false;\r
             }\r
 \r
         return true;\r
     }\r
 \r
+    char invalidCharacter;\r
+\r
     /**\r
      * This method must be implemented to parse the contents of the file.\r
      */\r