From 820c75d483648a2208039a00580bdc257b22e5f6 Mon Sep 17 00:00:00 2001
From: Mungo Carstairs <gmungoc@gmail.com>
Date: Mon, 9 Apr 2018 17:07:09 +0100
Subject: [PATCH] JAL-2629 more error checking

---
 src/jalview/datamodel/HiddenMarkovModel.java |    5 ++++-
 src/jalview/hmmer/HMMBuild.java              |   17 +++++++++++++++--
 2 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/src/jalview/datamodel/HiddenMarkovModel.java b/src/jalview/datamodel/HiddenMarkovModel.java
index a4270cd..dd27fa6 100644
--- a/src/jalview/datamodel/HiddenMarkovModel.java
+++ b/src/jalview/datamodel/HiddenMarkovModel.java
@@ -606,7 +606,10 @@ public class HiddenMarkovModel
   public void setNodes(List<HMMNode> nodeList)
   {
     nodes = nodeList;
-    buildConsensusSequence();
+    if (nodes.size() > 1)
+    {
+      buildConsensusSequence();
+    }
   }
 }
 
diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index d95be48..c596cec 100644
--- a/src/jalview/hmmer/HMMBuild.java
+++ b/src/jalview/hmmer/HMMBuild.java
@@ -12,6 +12,7 @@ import jalview.gui.JvOptionPane;
 import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.io.HMMFile;
+import jalview.util.FileUtils;
 import jalview.util.MessageManager;
 import jalview.ws.params.ArgumentI;
 
@@ -147,8 +148,8 @@ public class HMMBuild extends HmmerCommand
     File alignmentFile = null;
     try
     {
-      hmmFile = createTempFile("hmm", ".hmm");
-      alignmentFile = createTempFile("output", ".sto");
+      hmmFile = FileUtils.createTempFile("hmm", ".hmm");
+      alignmentFile = FileUtils.createTempFile("output", ".sto");
 
       if (ac instanceof Alignment)
       {
@@ -330,10 +331,22 @@ public class HMMBuild extends HmmerCommand
   private void importData(File hmmFile, AnnotatedCollectionI ac)
           throws IOException
   {
+    if (hmmFile.length() == 0L)
+    {
+      Cache.log.error("Error: hmmbuild produced empty hmm file");
+      return;
+    }
+
     HMMFile file = new HMMFile(
             new FileParse(hmmFile.getAbsolutePath(), DataSourceType.FILE));
     SequenceI hmmSeq = file.getHMM().getConsensusSequence();
 
+    if (hmmSeq == null)
+    {
+      // hmmbuild failure not detected earlier
+      return;
+    }
+
     if (ac instanceof SequenceGroup)
     {
       SequenceGroup grp = (SequenceGroup) ac;
-- 
1.7.10.2