JAL-2629 update spikes/mungo to latest

[jalview.git] / src / jalview / hmmer / HMMBuild.java

diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index d95be48..3c3bd40 100644 (file)
--- 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)
       {
@@ -187,6 +188,8 @@ public class HMMBuild extends HmmerCommand
       boolean ran = runCommand(alignmentFile, hmmFile, ac);
       if (!ran)
       {
+        JvOptionPane.showInternalMessageDialog(af, MessageManager
+                .formatMessage("warn.command_failed", "hmmbuild"));
         return;
       }
       importData(hmmFile, ac);
@@ -214,8 +217,8 @@ public class HMMBuild extends HmmerCommand
    */
   void deleteHmmSequences(AnnotatedCollectionI ac)
   {
-    SequenceI hmmSeq = ac.getHmmConsensus();
-    if (hmmSeq != null)
+    List<SequenceI> hmmSeqs = ac.getHmmSequences();
+    for (SequenceI hmmSeq : hmmSeqs)
     {
       if (ac instanceof SequenceGroup)
       {
@@ -311,8 +314,8 @@ public class HMMBuild extends HmmerCommand
       args.add(ARG_DNA);
     }
 
-    args.add(hmmFile.getAbsolutePath());
-    args.add(sequencesFile.getAbsolutePath());
+    args.add(getFilePath(hmmFile));
+    args.add(getFilePath(sequencesFile));
 
     return runCommand(args);
   }
@@ -330,10 +333,22 @@ 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;
@@ -346,17 +361,10 @@ public class HMMBuild extends HmmerCommand
       alignment.insertSequenceAt(topIndex, hmmSeq);
       ac.setSeqrep(hmmSeq);
       grp.addSequence(hmmSeq, false);
-      grp.setHmmConsensus(hmmSeq);
     }
     else
     {
       alignment.insertSequenceAt(0, hmmSeq);
-      alignment.setHmmConsensus(hmmSeq);
-    }
-
-    if (af.getSelectedHMM() == null)
-    {
-      af.setSelectedHMMSequence(hmmSeq);
     }
   }
 }