From fd6ec6e0265ccdeebe7ecd29f6a615553f3878c2 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 30 Mar 2018 10:36:16 +0100
Subject: [PATCH] JAL-2629 add title to output alignment window

---
 src/jalview/hmmer/HMMAlign.java |   34 +++++++++++++++-------------------
 1 file changed, 15 insertions(+), 19 deletions(-)

diff --git a/src/jalview/hmmer/HMMAlign.java b/src/jalview/hmmer/HMMAlign.java
index 942342c..6255e9f 100644
--- a/src/jalview/hmmer/HMMAlign.java
+++ b/src/jalview/hmmer/HMMAlign.java
@@ -34,8 +34,6 @@ public class HMMAlign extends HmmerCommand
 
   private final AlignmentI dataset;
 
-  private AlignmentView msa;
-
   /**
    * Constructor for the HMMAlignThread
    * 
@@ -75,8 +73,9 @@ public class HMMAlign extends HmmerCommand
     long msgId = System.currentTimeMillis();
     af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
             msgId);
-    prepareAlignment();
-    SequenceI[][] subAlignments = msa.getVisibleContigs('-');
+
+    AlignmentView msa = af.gatherSequencesForAlignment();
+    SequenceI[][] subAlignments = msa.getVisibleContigs(alignment.getGapCharacter());
 
     List<AlignmentOrder> allOrders = new ArrayList<>();
 
@@ -115,7 +114,8 @@ public class HMMAlign extends HmmerCommand
       job++;
     }
 
-    displayResults(allResults, allOrders);
+    String title = "hmmalign to " + hmm.getConsensusSequence().getName();
+    displayResults(allResults, allOrders, msa, title);
 
     af.setProgressBar("", msgId);
   }
@@ -134,8 +134,7 @@ public class HMMAlign extends HmmerCommand
    * @throws IOException
    */
   private boolean runCommand(File modelFile, File alignmentFile,
-          File resultFile)
-          throws IOException
+          File resultFile) throws IOException
   {
     String command = getCommandPath(HMMALIGN);
     if (command == null)
@@ -188,26 +187,21 @@ public class HMMAlign extends HmmerCommand
   }
 
   /**
-   * Gathers the sequences in preparation for the alignment.
-   */
-  private void prepareAlignment()
-  {
-    msa = af.gatherSequencesForAlignment();
-  }
-
-  /**
    * Displays the results of all 'jobs' in a new frame
    * 
    * @param allResults
    * 
    * @param allOrders
+   * @param msa
+   * @param title
    */
   private void displayResults(SequenceI[][] allResults,
-          List<AlignmentOrder> allOrders)
+          List<AlignmentOrder> allOrders, AlignmentView msa, String title)
   {
     AlignmentOrder[] arrOrders = allOrders
             .toArray(new AlignmentOrder[allOrders.size()]);
-    Object[] newview = msa.getUpdatedView(allResults, arrOrders, '-');
+    Object[] newview = msa.getUpdatedView(allResults, arrOrders,
+            alignment.getGapCharacter());
     SequenceI[] seqs = (SequenceI[]) newview[0];
     HiddenColumns hidden = (HiddenColumns) newview[1];
     Alignment al = new Alignment(seqs);
@@ -217,7 +211,7 @@ public class HMMAlign extends HmmerCommand
       al.setDataset(dataset);
     }
 
-    displayInNewFrame(al, allOrders, hidden);
+    displayInNewFrame(al, allOrders, hidden, title);
   }
 
   /**
@@ -230,12 +224,14 @@ public class HMMAlign extends HmmerCommand
    *          run
    * @param hidden
    *          Hidden columns in the previous alignment
+   * @param title
    */
   private void displayInNewFrame(AlignmentI al,
-          List<AlignmentOrder> alorders, HiddenColumns hidden)
+          List<AlignmentOrder> alorders, HiddenColumns hidden, String title)
   {
     AlignFrame alignFrame = new AlignFrame(al, hidden, AlignFrame.DEFAULT_WIDTH,
             AlignFrame.DEFAULT_HEIGHT);
+    alignFrame.setTitle(title);
 
     FeatureRendererSettings featureSettings = af.getFeatureRenderer()
             .getSettings();
-- 
1.7.10.2