From 45ae91e9bc0b3a9046d2f587d7810f5d27c04890 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 10 May 2018 15:17:53 +0100
Subject: [PATCH] JAL-2629 default HMMBuild to alignment if not specified by
 args

---
 src/jalview/hmmer/HMMBuild.java |   12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index 3c3bd40..6de7029 100644
--- a/src/jalview/hmmer/HMMBuild.java
+++ b/src/jalview/hmmer/HMMBuild.java
@@ -96,11 +96,14 @@ public class HMMBuild extends HmmerCommand
           AlignViewportI viewport)
   {
     List<AnnotatedCollectionI> runBuildFor = new ArrayList<>();
+    boolean foundArg = false;
+
     for (ArgumentI arg : params)
     {
       String name = arg.getName();
       if (MessageManager.getString("label.hmmbuild_for").equals(name))
       {
+        foundArg = true;
         String value = arg.getValue();
         if (MessageManager.getString("label.alignment").equals(value))
         {
@@ -134,6 +137,15 @@ public class HMMBuild extends HmmerCommand
         }
       }
     }
+
+    /*
+     * default is to build for the whole alignment
+     */
+    if (!foundArg)
+    {
+      runBuildFor.add(alignment);
+    }
+
     return runBuildFor;
   }
 
-- 
1.7.10.2