use 1 & -1 if start/end not specified

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

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 74cb2d0..71e86b3 100755 (executable)
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -121,7 +121,7 @@ public class ClustalFile
       //Add sequences to the hash\r
       for (i = 0; i < headers.size(); i++)\r
       {\r
-        int start = -1;\r
+        int start = 1;\r
         int end = -1;\r
 \r
         if (seqhash.get(headers.elementAt(i)) != null)\r
@@ -134,8 +134,6 @@ public class ClustalFile
           }\r
 \r
           String head = headers.elementAt(i).toString();\r
-          start = 1;\r
-          end = seqhash.get(headers.elementAt(i)).toString().length();\r
 \r
           if (head.indexOf("/") > 0)\r
           {\r