X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHMMERCommands.java;h=913eee8baad428dda856b67eab7e3edfd257c889;hb=d4db66b0d4d89405bc90aa999e15debc7bf85659;hp=4f1dbc6a7f6e1afe61215bb177211c0b5b93ccc7;hpb=c9a198a4eb76592ff9091cdba7d0299a0345ba09;p=jalview.git

diff --git a/src/jalview/hmmer/HMMERCommands.java b/src/jalview/hmmer/HMMERCommands.java
index 4f1dbc6..913eee8 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
@@ -24,17 +31,11 @@ public class HMMERCommands
   public String JALVIEWDIRECTORY = System.getProperty("user.dir")
           + "/";
 
-  public final String HMMALIGN = "/binaries/hmmalign ";
+  public final String HMMALIGN = "/hmmalign ";
 
-  public final String HMMBUILD = "/binaries/hmmbuild ";
+  public final String HMMBUILD = "/hmmbuild ";
 
-  public final String HMMSEARCH = "/binaries/hmmsearch ";
-
-  public String HMMBUFFER;
-
-  public String ALIGNMENTBUFFER;
-
-  public String ALIGNMENTINPUT;
+  public final String HMMSEARCH = "/hmmsearch ";
 
   public String OUTPUTALIGNMENT;
 
@@ -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
@@ -124,12 +136,7 @@ public class HMMERCommands
     if (seqs != null)
     {
       StockholmFile file = new StockholmFile(new Alignment(seqs));
-      boolean removeAnnots = false;
-      if (hmm == null)
-      {
-        removeAnnots = true;
-      }
-      String output = file.print(seqs, false, removeAnnots);
+      String output = file.print(seqs, false);
       PrintWriter writer = new PrintWriter(stoLocation);
       writer.println(output);
       writer.close();
@@ -138,13 +145,25 @@ public class HMMERCommands
     if (hmm != null)
     {
       HMMFile file = new HMMFile(hmm);
-      file.exportFile(hmmLocation);
+      PrintWriter writer = new PrintWriter(hmmLocation);
+      writer.print(file.print());
+      writer.close();
     }
   }
 
+  /**
+   * 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();
+    if (hmmSeqs == null || hmmSeqs.size() < 1)
+    {
+      return;
+    }
     for (SequenceI seq : hmmSeqs)
     {
       Integer position = seq.getPreviousPosition();
@@ -154,13 +173,24 @@ public class HMMERCommands
     af.alignPanel.adjustAnnotationHeight();
     af.getViewport().updateSequenceIdColours();
     af.buildSortByAnnotationScoresMenu();
+    af.getViewport().initInformation();
   }
 
+  /**
+   * 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;