From e96fc72825d181bbb0dede55a0bca7aa4e64232d Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 22 Mar 2005 12:17:29 +0000
Subject: [PATCH] read start end if available

---
 src/jalview/io/BLCFile.java |   34 ++++++++++++++++++++++++++++++----
 1 file changed, 30 insertions(+), 4 deletions(-)

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index 8db0a9a..920a12d 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -70,11 +70,37 @@ public class BLCFile extends AlignFile {
       if (abracket > -1)
       {
 
-        if(line.indexOf(" ")>-1)
+        if(line.indexOf(" ")>-1)//
         {
-          ids.addElement(line.substring(abracket+1, line.indexOf(" ", abracket+1)));
-          starts.addElement("0");
-          ends.addElement("0");
+          ///Colur it be this format?
+          //>54402046         0             1   137   137:
+          // or this??
+          //     1   >L1H14       30539  343
+          try{
+            ids.addElement(line.substring(abracket + 1,
+                                          line.indexOf(" ", abracket + 1)));
+
+
+            // remove p Value
+            line = line.substring(abracket + 1);
+            line = line.substring(line.indexOf(" ") + 1);
+            line = line.trim();
+            line = line.substring(line.indexOf(" ") + 1);
+            line = line.trim();
+            int value = Integer.parseInt(line.substring(0, line.indexOf(" ")));
+            starts.addElement(value+"");
+            line = line.substring(line.indexOf(" ") + 1);
+            line = line.trim();
+            value = Integer.parseInt(line.substring(0, line.indexOf(" ")));
+            ends.addElement(value+"");
+
+          }catch(Exception ex)
+          {
+            System.out.println("err");
+            starts.addElement("0");
+            ends.addElement("0");
+          }
+
         }
         else
         {
-- 
1.7.10.2