From 2bb0a2c4156ec75795c595df0c6300411557b066 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 21 Mar 2005 18:48:39 +0000
Subject: [PATCH] blc file reader modified

---
 src/jalview/io/BLCFile.java |   31 +++++++++++++------------------
 1 file changed, 13 insertions(+), 18 deletions(-)

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index 5f45aec..8db0a9a 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -65,31 +65,23 @@ public class BLCFile extends AlignFile {
         break;
       }
 
-      if (line.indexOf(">") > -1)
+      int abracket = line.indexOf(">");
+
+      if (abracket > -1)
       {
 
-        if(line.indexOf(" ")>-1 )
+        if(line.indexOf(" ")>-1)
         {
-          //>54402046         0             1   137   137: immunog
-          ids.addElement(line.substring(1, line.indexOf(" ")));
-
-          // remove p Value
-          line = line.substring(line.indexOf(" ") + 1);
-          line = line.trim();
-
-          line = line.substring(line.indexOf(" ") + 1);
-          line = line.trim();
-          starts.addElement(line.substring(0, line.indexOf(" ")));
-          line = line.substring(line.indexOf(" ") + 1);
-          line = line.trim();
-          ends.addElement(line.substring(0, line.indexOf(" ")));
+          ids.addElement(line.substring(abracket+1, line.indexOf(" ", abracket+1)));
+          starts.addElement("0");
+          ends.addElement("0");
         }
         else
         {
-          ids.addElement( line.substring(line.indexOf(">") + 1, line.indexOf("/")));
+          ids.addElement( line.substring(abracket + 1, line.indexOf("/")));
           line = line.substring(line.indexOf("/") + 1);
           starts.addElement(line.substring(0, line.indexOf("-")));
-          ends.addElement(line.substring(line.indexOf("-")+1));
+          ends.addElement(line.substring(line.indexOf("-") + 1));
         }
       }
     }while(!idsFound);
@@ -105,7 +97,10 @@ public class BLCFile extends AlignFile {
     while ((line = nextLine()).indexOf("*")==-1)
     {
       for(int i=0; i<ids.size(); i++)
-        seqstrings[i].append( line.charAt(i+starCol) );
+      {
+        if(line.length()>i+starCol)
+          seqstrings[i].append(line.charAt(i + starCol));
+      }
     }
 
     for(int i=0; i<ids.size(); i++)
-- 
1.7.10.2