From 9790722e2a94c8caa26ffd89378ee81a51867a47 Mon Sep 17 00:00:00 2001
From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Wed, 16 Aug 2017 11:07:48 +0100
Subject: [PATCH] JAL-2629 fix for hmmbuild not loading a HMM onto the current
 frame

---
 src/jalview/hmmer/HMMBuildThread.java |    3 ++-
 src/jalview/hmmer/HMMERCommands.java  |   44 +++++++++++++++++++++++++++------
 2 files changed, 38 insertions(+), 9 deletions(-)

diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java
index 656b6e5..a9ca8ce 100644
--- a/src/jalview/hmmer/HMMBuildThread.java
+++ b/src/jalview/hmmer/HMMBuildThread.java
@@ -61,7 +61,8 @@ public class HMMBuildThread implements Runnable
       group = af.getViewport().getSelectionGroup();
       forGroup = true;
     }
-    alignment = af.getViewport().getAlignment();
+    viewport = af.getViewport();
+    alignment = viewport.getAlignment();
 
   }
 
diff --git a/src/jalview/hmmer/HMMERCommands.java b/src/jalview/hmmer/HMMERCommands.java
index e3fcd69..281e1dc 100644
--- a/src/jalview/hmmer/HMMERCommands.java
+++ b/src/jalview/hmmer/HMMERCommands.java
@@ -16,6 +16,13 @@ import java.io.PrintWriter;
 import java.util.Hashtable;
 import java.util.List;
 
+/**
+ * Contains multiple commands and methods frequently used to run hmmbuild,
+ * hmmalign and hmmsearch
+ * 
+ * @author TZVanaalten
+ *
+ */
 public class HMMERCommands
 {
   // Path of hmmer binaries directory
@@ -30,12 +37,6 @@ public class HMMERCommands
 
   public final String HMMSEARCH = "/hmmsearch ";
 
-  public String HMMBUFFER;
-
-  public String ALIGNMENTBUFFER;
-
-  public String ALIGNMENTINPUT;
-
   public String OUTPUTALIGNMENT;
 
   public final String NAME = "-n ";
@@ -56,18 +57,29 @@ public class HMMERCommands
 
   List<SequenceI> hmmSeqs;
 
+  /**
+   * Uniquifies the sequences when exporting and stores their details in a
+   * hashtable.
+   * 
+   * @param seqs
+   */
   public void uniquifySequences(SequenceI[] seqs)
   {
     hash = jalview.analysis.SeqsetUtils.uniquify(seqs, true);
   }
 
+  /**
+   * Recover the sequence data lost by uniquifying.
+   * 
+   * @param seqs
+   */
   public void recoverSequenceNames(SequenceI[] seqs)
   {
     jalview.analysis.SeqsetUtils.deuniquify(hash, seqs);
   }
 
   /**
-   * Runs a command in the terminal.
+   * Runs a command in the command line.
    * 
    * @param command
    * @throws IOException
@@ -112,7 +124,7 @@ public class HMMERCommands
   }
 
   /**
-   * Exports an alignment to the buffer location in Jalview.
+   * Exports an alignment and/or HMM to the specified file.
    * 
    * @param alignment
    * @throws IOException
@@ -142,6 +154,12 @@ public class HMMERCommands
     }
   }
 
+  /**
+   * Adds any HMM sequences removed before submitting the alignment as a job
+   * back into the alignment.
+   * 
+   * @param af
+   */
   public void addHMMConsensusSequences(AlignFrame af)
   {
     AlignmentI al = af.getViewport().getAlignment();
@@ -156,11 +174,21 @@ public class HMMERCommands
     af.buildSortByAnnotationScoresMenu();
   }
 
+  /**
+   * Returns the list of HMM sequences removed
+   * 
+   * @return
+   */
   public List<SequenceI> getHmmSeqs()
   {
     return hmmSeqs;
   }
 
+  /**
+   * Sets the list of removed HMM sequences
+   * 
+   * @param hmmSeqs
+   */
   public void setHmmSeqs(List<SequenceI> hmmSeqs)
   {
     this.hmmSeqs = hmmSeqs;
-- 
1.7.10.2