JAL-2629 manual curation of HMMs via reference annotation functional

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

diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java
index f940fbb..2fdc97b 100644 (file)
--- a/src/jalview/hmmer/HMMBuildThread.java
+++ b/src/jalview/hmmer/HMMBuildThread.java
@@ -234,7 +234,16 @@ public class HMMBuildThread implements Runnable
           }
 
           cmds.uniquifySequences(newArr);
-          cmds.exportData(newArr, stoTemp, null, null);
+
+        if (forGroup)
+        {
+          cmds.exportData(newArr, stoTemp, null, null, group);
+        }
+        else
+        {
+          cmds.exportData(newArr, stoTemp, null, null, alignment);
+        }
+
           jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, array);
 
       } catch (FileNotFoundException e)
@@ -330,8 +339,11 @@ public class HMMBuildThread implements Runnable
     {
         if (af != null)
         {
+        if (af.getTitle().length() < 15)
+        {
           name = af.getTitle();
         }
+        }
         if (name == null || "".equals(name))
         {
           name = "Alignment";
@@ -362,7 +374,8 @@ public class HMMBuildThread implements Runnable
    */
   private void importData() throws IOException, InterruptedException
   {
-      HMMFile file = new HMMFile(new FileParse(hmmTemp.getAbsolutePath(),
+    HMMFile file = new HMMFile(
+            new FileParse(hmmTemp.getAbsolutePath(),
               DataSourceType.FILE));
     SequenceI[] seqs = file.getSeqsAsArray();
     SequenceI seq = seqs[0];