From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Fri, 25 Aug 2017 16:11:17 +0000 (+0100)
Subject: JAL-2629 hmmbuild runs on the alignment by default
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=23c49d515996d8b0dac0bf0c4a50827d247fdf8b;p=jalview.git

JAL-2629 hmmbuild runs on the alignment by default
---

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 5e17deb..be20995 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1330,7 +1330,7 @@ warn.no_selected_hmm = Please select a hidden Markov model sequence.
 label.select_hmm = Select HMM
 warn.no_sequence_data = No sequence data found.
 warn.empty_grp_or_alignment = An empty group or alignment was found.
-label.no_sequences_found = No matching sequences were found.
+label.no_sequences_found = No matching sequences, or an error occurred.
 label.hmmer = HMMER
 label.trim_termini = Trim Non-Matching Termini
 label.trim_termini_desc = If true, non-matching regions on either end of the resulting alignment are removed.
diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java
index dc24d9e..b0e9d70 100644
--- a/src/jalview/hmmer/HMMBuildThread.java
+++ b/src/jalview/hmmer/HMMBuildThread.java
@@ -128,6 +128,10 @@ public class HMMBuildThread implements Runnable
         }
       }
     }
+    else
+    {
+      alignment = viewport.getAlignment();
+    }
 
     if (alignment != null)
     {