Merge branch 'develop' into features/mchmmer

[jalview.git] / src / jalview / io / FileLoader.java

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index f26d6da..cabba00 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -26,6 +26,7 @@ import jalview.api.FeaturesDisplayedI;
 import jalview.api.FeaturesSourceI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
@@ -199,6 +200,32 @@ public class FileLoader implements Runnable
     return alignFrame;
   }
 
+  public void LoadFileOntoAlignmentWaitTillLoaded(AlignViewport viewport,
+          String file, DataSourceType sourceType, FileFormatI format)
+  {
+    this.viewport = viewport;
+    this.file = file;
+    this.protocol = sourceType;
+    this.format = format;
+    _LoadAlignmentFileWaitTillLoaded();
+  }
+
+  protected void _LoadAlignmentFileWaitTillLoaded()
+  {
+    Thread loader = new Thread(this);
+    loader.start();
+
+    while (loader.isAlive())
+    {
+      try
+      {
+        Thread.sleep(500);
+      } catch (Exception ex)
+      {
+      }
+    }
+  }
+
   public void updateRecentlyOpened()
   {
     Vector recent = new Vector();
@@ -394,6 +421,29 @@ public class FileLoader implements Runnable
             }
             // append to existing alignment
             viewport.addAlignment(al, title);
+            if (source instanceof HMMFile)
+            {
+              AlignmentI alignment = viewport.getAlignment();
+              SequenceI seq = alignment
+                      .getSequenceAt(alignment.getAbsoluteHeight() - 1);
+              seq.setIsHMMConsensusSequence(true);
+              AlignmentAnnotation[] annots = viewport.getAlignment()
+                      .getAlignmentAnnotation();
+              for (AlignmentAnnotation annot : annots)
+              {
+                if ("RF".equals(annot.label)
+                        || annot.label.contains("Reference"))
+                {
+                  seq.mapToReference(annot);
+                  break;
+                }
+              }
+              alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
+              alignment.insertSequenceAt(0, seq);
+              viewport.getAlignPanel().adjustAnnotationHeight();
+              viewport.updateSequenceIdColours();
+
+            }
           }
           else
           {