use 1 & -1 if start/end not specified

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

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index a6c7a4f..9a6ca54 100755 (executable)
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -115,7 +115,7 @@ public class PfamFile
 \r
         String head = headers.elementAt(i).toString();\r
         int start = 1;\r
-        int end = seqhash.get(headers.elementAt(i)).toString().length();\r
+        int end = -1;\r
 \r
         if (head.indexOf("/") > 0)\r
         {\r
@@ -133,11 +133,6 @@ public class PfamFile
               start = Integer.valueOf(st.nextToken()).intValue();\r
               end = Integer.valueOf(st.nextToken()).intValue();\r
             }\r
-            else\r
-            {\r
-              start = -1;\r
-              end = -1;\r
-            }\r
           }\r
           else\r
           {\r
@@ -151,22 +146,11 @@ public class PfamFile
 \r
         Sequence newSeq = null;\r
 \r
-        if ( (start != -1) && (end != -1))\r
-        {\r
-          newSeq = new Sequence(ids.elementAt(i).toString(),\r
-                                seqhash.get(headers.elementAt(i).toString())\r
-                                .toString(), start, end);\r
-          seqs.addElement(newSeq);\r
-        }\r
-        else\r
-        {\r
-          newSeq = new Sequence(ids.elementAt(i).toString(),\r
-                                seqhash.get(headers.elementAt(i).toString())\r
-                                .toString(), 1,\r
-                                seqhash.get(headers.elementAt(i).toString())\r
-                                .toString().length());\r
-          seqs.addElement(newSeq);\r
-        }\r
+        newSeq = new Sequence(ids.elementAt(i).toString(),\r
+                              seqhash.get(headers.elementAt(i).toString())\r
+                              .toString(), start, end);\r
+        seqs.addElement(newSeq);\r
+\r
 \r
         if (!isValidProteinSequence(newSeq.getSequence()))\r
         {\r