From a3bed79406073da41d03e8278733e4beae172e6e Mon Sep 17 00:00:00 2001
From: Thomas <170013569@dundee.ac.uk>
Date: Thu, 11 Jul 2019 15:11:52 +0100
Subject: [PATCH] JAL-2629 hmmer searches include seqs past inclusion
 threshold in output

---
 src/jalview/hmmer/Search.java |    9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/jalview/hmmer/Search.java b/src/jalview/hmmer/Search.java
index 24bd6b7..2fad426 100644
--- a/src/jalview/hmmer/Search.java
+++ b/src/jalview/hmmer/Search.java
@@ -69,9 +69,13 @@ public abstract class Search extends HmmerCommand
 
     int index = 0;
 
-    while (!"  ------ inclusion threshold ------".equals(line)
-            && !"".equals(line))
+    while (!"".equals(line) && line != null)
     {
+      if ("  ------ inclusion threshold ------".equals(line))
+      {
+        line = br.readLine();
+        continue;
+      }
 
       Scanner scanner = new Scanner(line);
       String evalue = scanner.next();
@@ -81,6 +85,7 @@ public abstract class Search extends HmmerCommand
         evalue = scanner.next();
       }
 
+
       String score = scanner.next();
       checkSequenceOrder(index, scanner);
       SequenceI seq = seqs[index];
-- 
1.7.10.2