From 44b1e9ba73a6d6a321126e153aece11699eb1d2a Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 28 Sep 2017 14:25:12 +0100
Subject: [PATCH] JAL-2738 separate thread to load VCF; update FeatureSettings
 when done

---
 resources/lang/Messages.properties |    4 ++-
 src/jalview/io/vcf/VCFLoader.java  |   51 +++++++++++++++++++++++++++++-------
 2 files changed, 44 insertions(+), 11 deletions(-)

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 5620386..9ffe2ae 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -492,6 +492,8 @@ label.load_associated_tree = Load Associated Tree...
 label.load_features_annotations = Load Features/Annotations...
 label.load_vcf = Load SNP variants from plain text or indexed VCF data
 label.load_vcf_file = Load VCF File
+label.searching_vcf = Loading VCF variants...
+label.added_vcf = Added {0} VCF variants to {1} sequence(s)
 label.export_features = Export Features...
 label.export_annotations = Export Annotations...
 label.to_upper_case = To Upper Case
@@ -1321,4 +1323,4 @@ label.select_hidden_colour = Select hidden colour
 label.overview = Overview
 label.reset_to_defaults = Reset to defaults
 label.oview_calc = Recalculating overview...
-label.feature_details = Feature details
\ No newline at end of file
+label.feature_details = Feature details
diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index 78d2ad5..ddcecfe 100644
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -21,6 +21,7 @@ import jalview.io.gff.Gff3Helper;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
 
 import java.io.IOException;
 import java.util.HashMap;
@@ -66,19 +67,44 @@ public class VCFLoader
   }
 
   /**
-   * Loads VCF on to an alignment - provided it can be related to one or more
-   * sequence's chromosomal coordinates.
+   * Starts a new thread to query and load VCF variant data on to the alignment
    * <p>
    * This method is not thread safe - concurrent threads should use separate
    * instances of this class.
    * 
    * @param filePath
-   * @param status
+   * @param gui
    */
-  public void loadVCF(String filePath, AlignViewControllerGuiI status)
+  public void loadVCF(final String filePath,
+          final AlignViewControllerGuiI gui)
   {
-    VCFReader reader = null;
+    if (gui != null)
+    {
+      gui.setStatus(MessageManager.getString("label.searching_vcf"));
+    }
+
+    new Thread()
+    {
+
+      @Override
+      public void run()
+      {
+        VCFLoader.this.doLoad(filePath, gui);
+      }
+
+    }.start();
+  }
 
+  /**
+   * Loads VCF on to an alignment - provided it can be related to one or more
+   * sequence's chromosomal coordinates.
+   * 
+   * @param filePath
+   * @param gui
+   */
+  protected void doLoad(String filePath, AlignViewControllerGuiI gui)
+  {
+    VCFReader reader = null;
     try
     {
       // long start = System.currentTimeMillis();
@@ -108,17 +134,22 @@ public class VCFLoader
           transferAddedFeatures(seq);
         }
       }
-      // long elapsed = System.currentTimeMillis() - start;
-      String msg = String.format("Added %d VCF variants to %d sequence(s)",
-              varCount, seqCount);
-      if (status != null)
+      if (gui != null)
       {
-        status.setStatus(msg);
+        // long elapsed = System.currentTimeMillis() - start;
+        String msg = MessageManager.formatMessage("label.added_vcf",
+                varCount, seqCount);
+        gui.setStatus(msg);
+        gui.getFeatureSettingsUI().discoverAllFeatureData();
       }
     } catch (Throwable e)
     {
       System.err.println("Error processing VCF: " + e.getMessage());
       e.printStackTrace();
+      if (gui != null)
+      {
+        gui.setStatus("Error occurred - see console for details");
+      }
     } finally
     {
       if (reader != null)
-- 
1.7.10.2